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Song W, Fu J, Wu J, Ren J, Xiang R, Kong C, Fu T. CircFBXW4 Suppresses Colorectal Cancer Progression by Regulating the MiR-338-5p/SLC5A7 Axis. Adv Sci (Weinh) 2024; 11:e2300129. [PMID: 38461489 DOI: 10.1002/advs.202300129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/04/2024] [Indexed: 03/12/2024]
Abstract
Dysregulated circular RNAs (circRNAs) contribute to tumourigenesis and cancer progression. However, the expression patterns and biological functions of circRNAs in colorectal cancer (CRC) remain elusive. Here, RNA sequencing and bioinformatics analyses are applied to screen for aberrantly expressed circRNAs. The expression of circFBXW4 in CRC tissues and cell lines is determined by quantitative real-time PCR. A series of in vitro and in vivo biological function assays are implemented to assess the functions of circFBXW4. The regulatory mechanisms linking circFBXW4, miR-338-5p, and SLC5A7 are explored by western blotting, dual luciferase reporter assays, and RNA pull-down assays. CircFBXW4 is dramatically downregulated in CRC tissues and cell lines. circFBXW4 downregulation is clearly correlated with malignant features and patient overall survival in CRC. Functionally, ectopic expression of circFBXW4 strikingly impairs the proliferation, migration, and invasion capacities of CRC cells in vitro and in vivo, whereas circFBXW4 knockdown has the opposite effects. Mechanistically, circFBXW4 competitively binds to miR-338-5p and prevents it from interacting with and repressing its target SLC5A7, thus suppressing the progression of CRC. This study reveals the specific critical role of circFBXW4 in inhibiting CRC progression via the miR-338-5p/SLC5A7 axis and provides an additional target for eradicating CRC.
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Affiliation(s)
- Wei Song
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, 430060, P. R. China
| | - Jincheng Fu
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, 430060, P. R. China
- Department of General Surgery, Qingdao Municipal Hospital, Qingdao, 266071, P. R. China
| | - Jing Wu
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, 430060, P. R. China
| | - Jun Ren
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, 430060, P. R. China
| | - Rensheng Xiang
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, 430060, P. R. China
| | - Can Kong
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, 430060, P. R. China
| | - Tao Fu
- Department of General Surgery, Qingdao Municipal Hospital, Qingdao, 266071, P. R. China
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2
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Drula R, Braicu C, Neagoe IB. Current advances in circular RNA detection and investigation methods: Are we running in circles? Wiley Interdiscip Rev RNA 2024; 15:e1850. [PMID: 38702943 DOI: 10.1002/wrna.1850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 05/06/2024]
Abstract
Circular RNAs (circRNAs), characterized by their closed-loop structure, have emerged as significant transcriptomic regulators, with roles spanning from microRNA sponging to modulation of gene expression and potential peptide coding. The discovery and functional analysis of circRNAs have been propelled by advancements in both experimental and bioinformatics tools, yet the field grapples with challenges related to their detection, isoform diversity, and accurate quantification. This review navigates through the evolution of circRNA research methodologies, from early detection techniques to current state-of-the-art approaches that offer comprehensive insights into circRNA biology. We examine the limitations of existing methods, particularly the difficulty in differentiating circRNA isoforms and distinguishing circRNAs from their linear counterparts. A critical evaluation of various bioinformatics tools and novel experimental strategies is presented, emphasizing the need for integrated approaches to enhance our understanding and interpretation of circRNA functions. Our insights underscore the dynamic and rapidly advancing nature of circRNA research, highlighting the ongoing development of analytical frameworks designed to address the complexity of circRNAs and facilitate the assessment of their clinical utility. As such, this comprehensive overview aims to catalyze further advancements in circRNA study, fostering a deeper understanding of their roles in cellular processes and potential implications in disease. This article is categorized under: RNA Methods > RNA Nanotechnology RNA Methods > RNA Analyses in Cells RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Rareș Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana-Berindan Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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3
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Liu Q, Li S. Exosomal circRNAs: Novel biomarkers and therapeutic targets for urinary tumors. Cancer Lett 2024; 588:216759. [PMID: 38417667 DOI: 10.1016/j.canlet.2024.216759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Exosomal circRNAs have emerged as promising biomarkers and therapeutic targets for urinary tumors. In this review, we explored the intricate role of exosomal circRNAs in urological cancers, focusing on their biological functions, dysregulation in tumors, and potential clinical applications. The review delves into the mechanisms by which exosomal circRNAs contribute to tumor progression and highlights their diagnostic and therapeutic implications. By synthesizing current research findings, we present a compelling case for the significance of exosomal circRNAs in the context of urinary tumors. Furthermore, the review discusses the challenges and opportunities associated with utilizing exosomal circRNAs as diagnostic tools and targeted therapeutic agents. There is a need for further research to elucidate the specific mechanisms of exosomal circRNA secretion and delivery, as well as to enhance the detection methods for clinical translational applications. Overall, this comprehensive review underscores the pivotal role of exosomal circRNAs in urinary tumors and underscores their potential as valuable biomarkers and therapeutic tools in the management of urological cancers.
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Affiliation(s)
- Qiang Liu
- Department of Urology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital and Institute, Shenyang, 110042, Liaoning, China
| | - Shenglong Li
- Second Ward of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province, 110042, China; The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang, Liaoning Province, 110042, China.
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4
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Xu C, Xu P, Zhang J, He S, Hua T, Huang A. Exosomal noncoding RNAs in gynecological cancers: implications for therapy resistance and biomarkers. Front Oncol 2024; 14:1349474. [PMID: 38737906 PMCID: PMC11082286 DOI: 10.3389/fonc.2024.1349474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Gynecologic cancers, including ovarian cancer (OC), cervical cancer (CC), and endometrial cancer (EC), pose a serious threat to women's health and quality of life due to their high incidence and lethality. Therapeutic resistance in tumors refers to reduced sensitivity of tumor cells to therapeutic drugs or radiation, which compromises the efficacy of treatment or renders it ineffective. Therapeutic resistance significantly contributes to treatment failure in gynecologic tumors, although the specific molecular mechanisms remain unclear. Exosomes are nanoscale vesicles released and received by distinct kinds of cells. Exosomes contain proteins, lipids, and RNAs closely linked to their origins and functions. Recent studies have demonstrated that exosomal ncRNAs may be involved in intercellular communication and can modulate the progression of tumorigenesis, aggravation and metastasis, tumor microenvironment (TME), and drug resistance. Besides, exosomal ncRNAs also have the potential to become significant diagnostic and prognostic biomarkers in various of diseases. In this paper, we reviewed the biological roles and mechanisms of exosomal ncRNAs in the drug resistance of gynecologic tumors, as well as explored the potential of exosomal ncRNAs acting as the liquid biopsy molecular markers in gynecologic cancers.
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Affiliation(s)
| | | | | | | | | | - Aiwu Huang
- Department of Gynecology and Obstetrics , Hangzhou Lin'an Traditional Chinese Medicine Hospital, Hangzhou, Zhejiang, China
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Fuchs Wightman F, Lukin J, Giusti S, Soutschek M, Bragado L, Pozzi B, Pierelli M, González P, Fededa J, Schratt G, Fujiwara R, Wilusz J, Refojo D, de la Mata M. Influence of RNA circularity on Target RNA-Directed MicroRNA Degradation. Nucleic Acids Res 2024; 52:3358-3374. [PMID: 38381063 PMCID: PMC11014252 DOI: 10.1093/nar/gkae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
A subset of circular RNAs (circRNAs) and linear RNAs have been proposed to 'sponge' or block microRNA activity. Additionally, certain RNAs induce microRNA destruction through the process of Target RNA-Directed MicroRNA Degradation (TDMD), but whether both linear and circular transcripts are equivalent in driving TDMD is unknown. Here, we studied whether circular/linear topology of endogenous and artificial RNA targets affects TDMD. Consistent with previous knowledge that Cdr1as (ciRS-7) circular RNA protects miR-7 from Cyrano-mediated TDMD, we demonstrate that depletion of Cdr1as reduces miR-7 abundance. In contrast, overexpression of an artificial linear version of Cdr1as drives miR-7 degradation. Using plasmids that express a circRNA with minimal co-expressed cognate linear RNA, we show differential effects on TDMD that cannot be attributed to the nucleotide sequence, as the TDMD properties of a sequence often differ when in a circular versus linear form. By analysing RNA sequencing data of a neuron differentiation system, we further detect potential effects of circRNAs on microRNA stability. Our results support the view that RNA circularity influences TDMD, either enhancing or inhibiting it on specific microRNAs.
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Affiliation(s)
- Federico Fuchs Wightman
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
| | - Jerónimo Lukin
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Buenos Aires 1425, Argentina
| | - Sebastián A Giusti
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Buenos Aires 1425, Argentina
| | - Michael Soutschek
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich 8092, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, ETH Zürich 8092, Switzerland
| | - Laureano Bragado
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
| | - Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | - María L Pierelli
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires 1428, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
| | - Paula González
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, Buenos Aires 1650, Argentina
| | - Juan P Fededa
- Instituto de Investigaciones Biotecnológicas “Dr. Rodolfo A. Ugalde”, IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de San Martín, Buenos Aires 1650, Argentina
| | - Gerhard Schratt
- Lab of Systems Neuroscience, D-HEST Institute for Neuroscience, ETH Zürich 8092, Switzerland
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, ETH Zürich 8092, Switzerland
| | - Rina Fujiwara
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX77030, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX77030, USA
| | - Damián Refojo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Godoy Cruz 2390, C1425FQD Buenos Aires 1425, Argentina
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Manuel de la Mata
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires 1428, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires 1428, Argentina
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6
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Zhou Z, Zhang J, Zheng X, Pan Z, Zhao F, Gao Y. CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning. Adv Sci (Weinh) 2024; 11:e2308115. [PMID: 38308181 PMCID: PMC11005702 DOI: 10.1002/advs.202308115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Circular RNAs (circRNAs) are a crucial yet relatively unexplored class of transcripts known for their tissue- and cell-type-specific expression patterns. Despite the advances in single-cell and spatial transcriptomics, these technologies face difficulties in effectively profiling circRNAs due to inherent limitations in circRNA sequencing efficiency. To address this gap, a deep learning model, CIRI-deep, is presented for comprehensive prediction of circRNA regulation on diverse types of RNA-seq data. CIRI-deep is trained on an extensive dataset of 25 million high-confidence circRNA regulation events and achieved high performances on both test and leave-out data, ensuring its accuracy in inferring differential events from RNA-seq data. It is demonstrated that CIRI-deep and its adapted version enable various circRNA analyses, including cluster- or region-specific circRNA detection, BSJ ratio map visualization, and trans and cis feature importance evaluation. Collectively, CIRI-deep's adaptability extends to all major types of RNA-seq datasets including single-cell and spatial transcriptomic data, which will undoubtedly broaden the horizons of circRNA research.
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Affiliation(s)
- Zihan Zhou
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Jinyang Zhang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Xin Zheng
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Zhicheng Pan
- Center for Computational Biology Flatiron InstituteNew York10010USA
| | - Fangqing Zhao
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
| | - Yuan Gao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing100101China
- University of Chinese Academy of SciencesBeijing100101China
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7
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Wu M, Yuan H, Zou W, Xu S, Liu S, Gao Q, Guo Q, Han Y, An X. Circular RNAs: characteristics, functions, mechanisms, and potential applications in thyroid cancer. Clin Transl Oncol 2024; 26:808-824. [PMID: 37864677 DOI: 10.1007/s12094-023-03324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/08/2023] [Indexed: 10/23/2023]
Abstract
Thyroid cancer (TC) is one of the most common endocrine malignancies, and its incidence has increased globally. Despite extensive research, the underlying molecular mechanisms of TC remain partially understood, warranting continued exploration of molecular markers for diagnostic and prognostic applications. Circular RNAs (circRNAs) have recently garnered significant attention owing to their distinct roles in cancers. This review article introduced the classification and biological functions of circRNAs and summarized their potential as diagnostic and prognostic markers in TC. Further, the interplay of circRNAs with PI3K/Akt/mTOR, Wnt/β-catenin, MAPK/ERK, Notch, JAK/STAT, and AMPK pathways is elaborated upon. The article culminates with an examination of circRNA's role in drug resistance of TC and highlights the challenges in circRNA research in TC.
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Affiliation(s)
- Mengmeng Wu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Haibin Yuan
- Department of Health Management, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Weiwei Zou
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Shujian Xu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Song Liu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Qiang Gao
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Qingqun Guo
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Yong Han
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China.
| | - Xingguo An
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China.
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8
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Wang Y, Wang B, Cao W, Xu X. TGF-β-activated circRYK drives glioblastoma progression by increasing VLDLR mRNA expression and stability in a ceRNA- and RBP-dependent manner. J Exp Clin Cancer Res 2024; 43:73. [PMID: 38454465 PMCID: PMC10921701 DOI: 10.1186/s13046-024-03000-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND The TGF-β signalling pathway is intricately associated with the progression of glioblastoma (GBM). The objective of this study was to examine the role of circRNAs in the TGF-β signalling pathway. METHODS In our research, we used transcriptome analysis to search for circRNAs that were activated by TGF-β. After confirming the expression pattern of the selected circRYK, we carried out in vitro and in vivo cell function assays. The underlying mechanisms were analysed via RNA pull-down, luciferase reporter, and RNA immunoprecipitation assays. RESULTS CircRYK expression was markedly elevated in GBM, and this phenotype was strongly associated with a poor prognosis. Functionally, circRYK promotes epithelial-mesenchymal transition and GSC maintenance in GBM. Mechanistically, circRYK sponges miR-330-5p and promotes the expression of the oncogene VLDLR. In addition, circRYK could enhance the stability of VLDLR mRNA via the RNA-binding protein HuR. CONCLUSION Our findings show that TGF-β promotes epithelial-mesenchymal transition and GSC maintenance in GBM through the circRYK-VLDLR axis, which may provide a new therapeutic target for the treatment of GBM.
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Affiliation(s)
- Yuhang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, 210000, China
| | - Binbin Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, 210000, China
| | - Wenping Cao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, 210000, China.
| | - Xiupeng Xu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, 210000, China.
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Zhu J, Li Q, Wu Z, Xu W, Jiang R. Circular RNA-mediated miRNA sponge & RNA binding protein in biological modulation of breast cancer. Noncoding RNA Res 2024; 9:262-276. [PMID: 38282696 PMCID: PMC10818160 DOI: 10.1016/j.ncrna.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
Circular RNAs (circRNAs) and small non-coding RNAs of the head-to-junction circle in the construct play critical roles in gene regulation and are significantly associated with breast cancer (BC). Numerous circRNAs are potential cancer biomarkers that may be used for diagnosis and prognosis. Widespread expression of circRNAs is regarded as a feature of gene expression in highly diverged eukaryotes. Recent studies show that circRNAs have two main biological modulation models: sponging and RNA-binding. This review explained the biogenesis of circRNAs and assessed emerging findings on their sponge function and role as RNA-binding proteins (RBPs) to better understand how their interaction alters cellular function in BC. We focused on how sponges significantly affect the phenotype and progression of BC. We described how circRNAs exercise the translation functions in ribosomes. Furthermore, we reviewed recent studies on RBPs, and post-protein modifications influencing BC and provided a perspective on future research directions for treating BC.
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Affiliation(s)
- Jing Zhu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Qian Li
- Medical Department, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Zhongping Wu
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Wei Xu
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Rilei Jiang
- School of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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10
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Pathmendra P, Park Y, Enguita FJ, Byrne JA. Verification of nucleotide sequence reagent identities in original publications in high impact factor cancer research journals. Naunyn Schmiedebergs Arch Pharmacol 2024:10.1007/s00210-023-02846-2. [PMID: 38194106 DOI: 10.1007/s00210-023-02846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024]
Abstract
Human gene research studies that describe wrongly identified nucleotide sequence reagents have been mostly identified in journals of low to moderate impact factor, where unreliable findings could be considered to have limited influence on future research. This study examined whether papers describing wrongly identified nucleotide sequences are also published in high-impact-factor cancer research journals. We manually verified nucleotide sequence identities in original Molecular Cancer articles published in 2014, 2016, 2018, and 2020, including nucleotide sequence reagents that were claimed to target circRNAs. Using keywords identified in some 2018 and 2020 Molecular Cancer papers, we also verified nucleotide sequence identities in 2020 Oncogene papers that studied miRNA(s) and/or circRNA(s). Overall, 3.8% (251/6647) and 4.0% (47/1165) nucleotide sequences that were verified in Molecular Cancer and Oncogene papers, respectively, were found to be wrongly identified. Wrongly identified nucleotide sequences were distributed across 18% (91/500) original Molecular Cancer papers, including 38% (31/82) Molecular Cancer papers from 2020, and 40% (21/52) selected Oncogene papers from 2020. Original papers with wrongly identified nucleotide sequences were therefore unexpectedly frequent in two high-impact-factor cancer research journals, highlighting the risks of employing journal impact factors or citations as proxies for research quality.
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Affiliation(s)
- Pranujan Pathmendra
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Yasunori Park
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Jennifer A Byrne
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.
- NSW Health Statewide Biobank, NSW Health Pathology, Camperdown, NSW, 2050, Australia.
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11
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Masante L, Susin G, Baudet ML. Droplet Digital PCR for the Detection and Quantification of Bona Fide CircRNAs. Methods Mol Biol 2024; 2765:107-126. [PMID: 38381336 DOI: 10.1007/978-1-0716-3678-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
CircRNAs are covalently closed RNA molecules gaining increasing attention over the years. Initially considered mere splicing errors, circRNAs are now recognized as a novel class of endogenous, conserved RNAs, expressed in many different species. The unique structure, the low levels of expression, and the almost complete sequence overlap with the cognate linear RNA make their detection and quantification challenging. Moreover, it has become crucial to prove the circular nature of the targeted transcript and unequivocally distinguish the circRNA from its linear counterpart. Nowadays, the most widely used technique to quantify circRNA expression is real-time quantitative PCR (qPCR). However, in the particular case of quantification of circles, it shows several technical shortcomings which affect the accuracy of the quantification. To precisely assess circRNA expression level, droplet digital PCR (ddPCR) is rapidly taking over for the more popular qPCR. In this chapter, we describe the detailed procedure based on droplets partitioning to quantify both linear and circRNA abundancy and demonstrate the circularity of the transcript under study with high precision, in a single experiment.
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Affiliation(s)
- Linda Masante
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Giorgia Susin
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Marie-Laure Baudet
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.
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12
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Kelly D, Schratt G. Screening and Characterization of Functional circRNAs in Neuronal Cultures. Methods Mol Biol 2024; 2765:311-324. [PMID: 38381347 DOI: 10.1007/978-1-0716-3678-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
This chapter describes a methodology for the screening and characterization of functional circRNAs, particularly in the context of neural circuit development. Taking advantage of a primary rat neuron culture model of synaptogenesis, we propose a means of selecting from the plethora of circRNA species based on their expression levels, dendritic localization, conservation, and activity regulation. These candidates are then knocked down with RNAi approaches in a functional screen for their potential role in the formation and maturation of excitatory synapses.Upon identification of top candidates regulating synaptogenesis, we tie together different "Omics" approaches to explore the molecular mechanisms underlying the phenotypes observed upon circRNA knockdown. We utilized our EnrichMir algorithm to identify overrepresented miRNA binding sites in differentially expressed genes from polyA-RNA-seq following circRNA knockdown. Furthermore, our ScanMiR web tool allows for the miRNA binding prediction of reconstructed internal circular RNA sequences. Small-RNA sequencing is used to monitor changes in miRNA levels in the circRNA knockdown to complement results obtained from EnrichMiR. Finally, the experimental validation of promising miRNA-circRNA pairs sets the stage for in-depth biochemical exploration of the circRNA interactome and mechanism of action.
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Affiliation(s)
- Darren Kelly
- Lab of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Gerhard Schratt
- Lab of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.
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13
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Venø MT, Su J, Yan Y, Kjems J. Nanopore-Mediated Sequencing of Circular RNA. Methods Mol Biol 2024; 2765:143-157. [PMID: 38381338 DOI: 10.1007/978-1-0716-3678-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Circular RNAs (circRNAs) constitute a group of RNAs defined by a covalent bond between the 5' and 3' end formed by a unique back-splicing event. Most circRNAs are composed of more than one exon, which are spliced together in a linear fashion. This protocol describes methods to sequence full-length circRNA across the back-splicing junction, allowing unambiguous characterization of circRNA-specific exon-intron structures by long-read sequencing (LRS). Two different sequencing approaches are provided: (1) Global circRNA sequencing (the circNick-LRS strategy) relying on circRNA enrichment from total RNA followed by total circRNA long-read sequencing, and (2) targeted circRNA sequencing (the circPanel-LRS strategy) where a preselected panel of circRNA are sequenced without prior circRNA enrichment. Both methods were originally described in Karim et al. (Rahimi et al., Nat Commun 12: 4825, 2021) where they were applied to characterize the exon-intron structure of >10.000 circRNAs in mouse and human brains.
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Affiliation(s)
| | - Junyi Su
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | | | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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14
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Di Timoteo G, Dattilo D, Bozzoni I. Characterizing Post-transcriptional Modifications of circRNAs to Investigate Biogenesis and Translation. Methods Mol Biol 2024; 2765:263-296. [PMID: 38381345 DOI: 10.1007/978-1-0716-3678-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Recent studies have shown that circular RNAs (circRNAs) are decorated with N6-methyladenosine (m6A), a co-transcriptional modification known to participate in the regulation of many processes governing linear RNA metabolism. Nevertheless, the activity of this mark on circRNAs is still poorly understood. In order to facilitate the study of m6A-dependent regulation of these molecules, we provide protocols that enable circOme-wide detection of m6A as well as the perturbation of several components of the m6A machinery followed by assays useful to evaluate the impact of their depletion on the production and, when applicable, on the translation of circRNAs. Other modifications exist and can be explored following the same principles.
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Affiliation(s)
- Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Dario Dattilo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy.
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy.
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, Italy.
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15
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Patop IL, Canori M, Kadener S. In Vivo Tissue-Specific Knockdown of circRNAs Using shRNAs in Drosophila melanogaster. Methods Mol Biol 2024; 2765:161-172. [PMID: 38381339 DOI: 10.1007/978-1-0716-3678-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Studying circular RNAs' function in vivo has been challenging due to the lack of generic tools to manipulate their levels without affecting their linear counterparts. This is particularly challenging as the back-splice junction is the only sequence not shared between the linear and circular version. In this chapter, we describe a method to study circRNA function in vivo targeting shRNAs against the desired back-splice junction to achieve knockdown with tissue-specific resolution in flies.
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16
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Srinivas T, Siqueira E, Guil S. Techniques for investigating lncRNA transcript functions in neurodevelopment. Mol Psychiatry 2023:10.1038/s41380-023-02377-5. [PMID: 38145986 DOI: 10.1038/s41380-023-02377-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.
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Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain.
- Germans Trias i Pujol Health Science Research Institute, 08916, Badalona, Barcelona, Catalonia, Spain.
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17
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Hoque P, Romero B, Akins RE, Batish M. Exploring the Multifaceted Biologically Relevant Roles of circRNAs: From Regulation, Translation to Biomarkers. Cells 2023; 12:2813. [PMID: 38132133 PMCID: PMC10741722 DOI: 10.3390/cells12242813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
CircRNAs are a category of regulatory RNAs that have garnered significant attention in the field of regulatory RNA research due to their structural stability and tissue-specific expression. Their circular configuration, formed via back-splicing, results in a covalently closed structure that exhibits greater resistance to exonucleases compared to linear RNAs. The distinctive regulation of circRNAs is closely associated with several physiological processes, as well as the advancement of pathophysiological processes in several human diseases. Despite a good understanding of the biogenesis of circular RNA, details of their biological roles are still being explored. With the steady rise in the number of investigations being carried out regarding the involvement of circRNAs in various regulatory pathways, understanding the biological and clinical relevance of circRNA-mediated regulation has become challenging. Given the vast landscape of circRNA research in the development of the heart and vasculature, we evaluated cardiovascular system research as a model to critically review the state-of-the-art understanding of the biologically relevant functions of circRNAs. We conclude the review with a discussion of the limitations of current functional studies and provide potential solutions by which these limitations can be addressed to identify and validate the meaningful and impactful functions of circRNAs in different physiological processes and diseases.
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Affiliation(s)
- Parsa Hoque
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Robert E Akins
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA;
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
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18
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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19
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Ma XK, Zhai SN, Yang L. Approaches and challenges in genome-wide circular RNA identification and quantification. Trends Genet 2023; 39:897-907. [PMID: 37839990 DOI: 10.1016/j.tig.2023.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
Numerous circular RNAs (circRNAs) produced from back-splicing of exon(s) have been recently revealed on a genome-wide scale across species. Although generally expressed at a low level, some relatively abundant circRNAs can play regulatory roles in various biological processes, prompting continuous profiling of circRNA in broader conditions. Over the past decade, distinct strategies have been applied in both transcriptome enrichment and bioinformatic tools for detecting and quantifying circRNAs. Understanding the scope and limitations of these strategies is crucial for the subsequent annotation and characterization of circRNAs, especially those with functional potential. Here, we provide an overview of different transcriptome enrichment, deep sequencing and computational approaches for genome-wide circRNA identification, and discuss strategies for accurate quantification and characterization of circRNA.
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Affiliation(s)
- Xu-Kai Ma
- 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.
| | - Si-Nan Zhai
- 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; Shanghai Institute of Nutrition and Health, 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.
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20
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Stringer BW, Gabryelska M, Marri S, Clark L, Lin H, Gantley L, Liu R, Wilusz JE, Conn VM, Conn SJ. Versatile toolkit for highly-efficient and scarless overexpression of circular RNAs. bioRxiv 2023:2023.11.21.568171. [PMID: 38045421 PMCID: PMC10690289 DOI: 10.1101/2023.11.21.568171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded, covalently closed RNA that contain a unique back-splice junction (bsj) sequence created by the ligation of their 5' and 3' ends via spliceosome-catalyzed back-splicing. A key step in illuminating the cellular roles of specific circRNAs is via increasing their expression. This is frequently done by transfecting cells with plasmid DNA containing cloned exons from which the circRNA is transcribed, flanked by sequences that promote back-splicing. We observed that commonly used plasmids lead to the production of circRNAs with molecular scars at the circRNA bsj. Stepwise redesign of the cloning vector corrected this problem, ensuring bona fide circRNAs are produced with their natural bsj at high efficiency. The fidelity of circRNAs produced from this new construct was validated by RNA sequencing and also functionally validated. To increase the utility of this modified resource for expressing circRNA, we developed an expanded set of vectors incorporating this design that (i) enables selection with a variety of antibiotics and fluorescent proteins, (ii) employs a range of promoters varying in promoter strength and (iii) generated a complementary set of lentiviral plasmids for difficult-to-transfect cells. These resources provide a novel and versatile toolkit for high-efficiency and scarless overexpression of circular RNAs that fulfill a critical need for the investigation of circRNA function.
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21
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Huang P, Deng H, Wang C, Zhou Y, Chen X. Cellular Trafficking of Nanotechnology-Mediated mRNA Delivery. Adv Mater 2023:e2307822. [PMID: 37929780 DOI: 10.1002/adma.202307822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Messenger RNA (mRNA)-based therapy has emerged as a powerful, safe, and rapidly scalable therapeutic approach that involves technologies for both mRNA itself and the delivery vehicle. Although there are some unique challenges for different applications of mRNA therapy, a common challenge for all mRNA therapeutics is the transport of mRNA into the target cell cytoplasm for sufficient protein expression. This review is focused on the behaviors at the cellular level of nanotechnology-mediated mRNA delivery systems, which have not been comprehensively reviewed yet. First, the four main therapeutic applications of mRNA are introduced, including immunotherapy, protein replacement therapy, genome editing, and cellular reprogramming. Second, common types of mRNA cargos and mRNA delivery systems are summarized. Third, strategies to enhance mRNA delivery efficiency during the cellular trafficking process are highlighted, including accumulation to the cell, internalization into the cell, endosomal escape, release of mRNA from the nanocarrier, and translation of mRNA into protein. Finally, the challenges and opportunities for the development of nanotechnology-mediated mRNA delivery systems are presented. This review can provide new insights into the future fabrication of mRNA nanocarriers with desirable cellular trafficking performance.
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Affiliation(s)
- Pei Huang
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongzhang Deng
- School of Life Science and Technology and Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Changrong Wang
- School of Life Science and Technology and Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, Xidian University, Xi'an, Shaanxi, 710126, China
| | - Yongfeng Zhou
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive Proteos, Singapore, 138673, Singapore
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22
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Wang L, Cui X, Jiang F, Hu Y, Wan W, Li G, Lin Y, Xiao J. Circular RNA Translation in Cardiovascular Diseases. Curr Genomics 2023; 24:66-71. [PMID: 37994328 PMCID: PMC10662380 DOI: 10.2174/1389202924666230911121358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 11/24/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of endogenous functional RNA generated by back-splicing. Recently, circRNAs have been found to have certain coding potential. Proteins/peptides translated from circRNAs play essential roles in various diseases. Here, we briefly summarize the basic knowledge and technologies that are usually applied to study circRNA translation. Then, we focus on the research progress of circRNA translation in cardiovascular diseases and discuss the perspective and future direction of translatable circRNA study in cardiovascular diseases.
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Affiliation(s)
- Lijun Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Xinxin Cui
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Fei Jiang
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Yuxue Hu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Wensi Wan
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Yanjuan Lin
- Department of Nursing, Union Hospital, Fujian Medical University Union Hospital, Fuzhou, 350001, China
- Fujian Provincial Special Reserve Talents Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong, 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, 200444, China
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23
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Orba Y, Abu YE, Chambaro HM, Lundu T, Muleya W, Eshita Y, Qiu Y, Harima H, Kajihara M, Mori-Kajihara A, Matsuno K, Sasaki M, Hall WW, Hang'ombe BM, Sawa H. Expanding diversity of bunyaviruses identified in mosquitoes. Sci Rep 2023; 13:18165. [PMID: 37875565 PMCID: PMC10598057 DOI: 10.1038/s41598-023-45443-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/19/2023] [Indexed: 10/26/2023] Open
Abstract
Mosquitoes interact with various organisms in the environment, and female mosquitoes in particular serve as vectors that directly transmit a number of microorganisms to humans and animals by blood-sucking. Comprehensive analysis of mosquito-borne viruses has led to the understanding of the existence of diverse viral species and to the identification of zoonotic arboviruses responsible for significant outbreaks and epidemics. In the present study on mosquito-borne bunyaviruses we employed a broad-spectrum RT-PCR approach and identified eighteen different additional species in the Phenuiviridae family and also a number of related but unclassified bunyaviruses in mosquitoes collected in Zambia. The entire RNA genome segments of the newly identified viruses were further analyzed by RNA sequencing with a ribonuclease R (RNase R) treatment to reduce host-derived RNAs and enrich viral RNAs, taking advantage of the dsRNA panhandle structure of the bunyavirus genome. All three or four genome segments were identified in eight bunyavirus species. Furthermore, L segments of three different novel viruses related to the Leishbunyaviridae were found in mosquitoes together with genes from the suspected host, the Crithidia parasite. In summary, our virus detection approach using a combination of broad-spectrum RT-PCR and RNA sequencing analysis with a simple virus enrichment method allowed the discovery of novel bunyaviruses. The diversity of bunyaviruses is still expanding and studies on this will allow a better understanding of the ecology of hematophagous mosquitoes.
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Affiliation(s)
- Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
| | - Yusuf Eshimutu Abu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, 10101, Lusaka, Zambia
| | - Herman M Chambaro
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan
- Virology Unit, Central Veterinary Research Institute, Lusaka, Zambia
| | - Tapiwa Lundu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, 10101, Lusaka, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, 10101, Lusaka, Zambia
| | - Yuki Eshita
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hayato Harima
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Akina Mori-Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Keita Matsuno
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
- Global Virus Network, Baltimore, MD, USA
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, Lusaka, Zambia
| | - Hirofumi Sawa
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan.
- One Health Research Center, Hokkaido University, Sapporo, Japan.
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland.
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24
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García-Rodríguez JL, Korsgaard U, Ahmadov U, Jarlstad Olesen MT, Dietrich KG, Hansen EB, Vissing SM, Ulhøi BP, Dyrskjøt L, Sørensen KD, Kjems J, Hager H, Kristensen LS. Spatial Profiling of Circular RNAs in Cancer Reveals High Expression in Muscle and Stromal Cells. Cancer Res 2023; 83:3340-3353. [PMID: 37477923 PMCID: PMC10570686 DOI: 10.1158/0008-5472.can-23-0748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/05/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
Circular RNAs (circRNA) are covalently closed molecules that can play important roles in cancer development and progression. Hundreds of differentially expressed circRNAs between tumors and adjacent normal tissues have been identified in studies using RNA sequencing or microarrays, emphasizing a strong translational potential. Most previous studies have been performed using RNA from bulk tissues and lack information on the spatial expression patterns of circRNAs. Here, we showed that the majority of differentially expressed circRNAs from bulk tissue analyses of colon tumors relative to adjacent normal tissues were surprisingly not differentially expressed when comparing cancer cells directly with normal epithelial cells. Manipulating the proliferation rates of cells grown in culture revealed that these discrepancies were explained by circRNAs accumulating to high levels in quiescent muscle cells due to their high stability; on the contrary, circRNAs were diluted to low levels in the fast-proliferating cancer cells due to their slow biogenesis rates. Thus, different subcompartments of colon tumors and adjacent normal tissues exhibited striking differences in circRNA expression patterns. Likewise, the high circRNA content in muscle cells was also a strong confounding factor in bulk analyses of circRNAs in bladder and prostate cancers. Together, these findings emphasize the limitations of using bulk tissues for studying differential circRNA expression in cancer and highlight a particular need for spatial analysis in this field of research. SIGNIFICANCE The abundance of circRNAs varies systematically between subcompartments of solid tumors and adjacent tissues, implying that differentially expressed circRNAs discovered in bulk tissue analyses may reflect differences in cell type composition between samples.
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Affiliation(s)
| | - Ulrik Korsgaard
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark
- Danish Colorectal Cancer Center South, Vejle Hospital, Vejle, Denmark
| | - Ulvi Ahmadov
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | | | - Emma B. Hansen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karina D. Sørensen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Henrik Hager
- Department of Clinical Pathology, Vejle Hospital, Vejle, Denmark
- Danish Colorectal Cancer Center South, Vejle Hospital, Vejle, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
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25
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Singh S, Sinha T, Panda AC. Regulation of microRNA by circular RNA. Wiley Interdiscip Rev RNA 2023:e1820. [PMID: 37783567 DOI: 10.1002/wrna.1820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Ning J, Luo Y, Chen L, Xiao G, Tanzhu G, Zhou R. CircRNAs and lung cancer: Insight into their roles in metastasis. Biomed Pharmacother 2023; 166:115260. [PMID: 37633056 DOI: 10.1016/j.biopha.2023.115260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. A major contributing factor to the poor survival rates in lung cancer is the high prevalence of metastasis at the time of diagnosis. To address this critical issue, it is imperative to investigate the mechanisms underlying lung cancer metastasis. Circular RNAs (circRNAs), a distinct type of ribonucleic acid characterized by their unique circular structure, have been implicated in the progression of various diseases. Recent studies have highlighted the close association between circRNAs and the occurrence and development of lung cancer, particularly in relation to metastasis. In this review, we provide a concise overview of the expression patterns and prognostic significance of circRNAs in lung cancer. Additionally, we summarized the current understanding of the clinical relevance of circRNAs in lung cancer metastasis. Furthermore, we systematically focused on the roles of circRNAs in each step of lung cancer metastasis, reflecting the sequential progression of this process. Notably, circRNAs exhibit dual functionality in lung cancer metastasis, acting both as facilitators and inhibitors of metastatic processes. Given their potential, circRNAs hold promise as novel biomarkers and therapeutic targets for lung cancer metastasis, warranting further investigation.
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Affiliation(s)
- Jiaoyang Ning
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yi Luo
- Department of Geriatric Medicine, Center of Coronary Circulation, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
| | - Liu Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Gang Xiao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Guilong Tanzhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Rongrong Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China.
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27
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Abdollahi E, Mozdarani H. Role of The circ-HIPK3, circ-PVT1, miR-25, and miR-149 in Response of Breast Cancer Cells to Ionizing Radiation. Cell J 2023; 25:688-695. [PMID: 37865877 PMCID: PMC10591259 DOI: 10.22074/cellj.2023.1995943.1255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/18/2023] [Accepted: 07/16/2023] [Indexed: 10/23/2023]
Abstract
OBJECTIVE Determining cellular radiosensitivity of breast cancer (BC) patients through molecular markers before radiation therapy (RT) allows accurate prediction of individual's response to radiation. The aim of this study was therefore to investigate the potential role of epigenetic biomarkers in breast cancer cellular radiosensitivity. MATERIALS AND METHODS In this experimental study, we treated two BC cell lines, MDA-MB 231 and MCF-7, with doses of 2, 4, and 8Gy of irradiation for 24 and 48 hours. Expression levels of circ-HIPK3, circ-PVT1, miR-25, and miR- 149 were quantified using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Significance of the observations was statistically verified using one-way ANOVA with a significance level of P<0.05. Annexin V-FITC/PI binding assay was utilized to measure cellular apoptosis. RESULTS The rate of cell apoptosis was significantly higher in MCF-7 cells compared to MDA-MB-231 cells at doses of 4Gy and 8Gy (P=0.013 and P=0.004, respectively). RNA expression analysis showed that circ-HIPK3 was increased in the MDA-MB-231 cell line compared to the MCF-7 cell line after exposure to 8Gy for 48 hours. Expression of circ-PVT1 was found to be higher in MDA-MB-231 cells compared to MCF-7 cells after exposure to 8Gy for 24 hours, likewise after exposure to 4Gy and 8Gy for 48 hours. After exposing 8Gy, expression of miR-25 was increased in MDA-MB-231 cells compared to MCF-7 cells at 24 and 48 hours. After exposing 8Gy dose, expression of miR-149 was increased in MCF-7 cells compared to MDA-MB-231 cells at 24 and 48 hours. CONCLUSION circ-HIPK3, circ-PVT1, and miR-25 played crucial roles in the mechanisms of radioresistance in breast cancer. Additionally, miR-149 was involved in regulating cellular radiosensitivity. Therefore, these factors provided predictive information about a tumor's radiosensitivity or its response to treatment, which could be valuable in personalizing radiation dosage.
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Affiliation(s)
- Elahe Abdollahi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Mozdarani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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28
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Kong Y, Luo Y, Zheng S, Yang J, Zhang D, Zhao Y, Zheng H, An M, Lin Y, Ai L, Diao X, Lin Q, Chen C, Chen R. Mutant KRAS Mediates circARFGEF2 Biogenesis to Promote Lymphatic Metastasis of Pancreatic Ductal Adenocarcinoma. Cancer Res 2023; 83:3077-3094. [PMID: 37363990 PMCID: PMC10502454 DOI: 10.1158/0008-5472.can-22-3997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/05/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Circular RNAs (circRNA) contribute to cancer stemness, proliferation, and metastasis. The biogenesis of circRNAs can be impacted by the genetic landscape of tumors. Herein, we identified a novel circRNA, circARFGEF2 (hsa_circ_0060665), which was upregulated in KRASG12D pancreatic ductal adenocarcinoma (PDAC) and positively associated with KRASG12D PDAC lymph node (LN) metastasis. CircARFGEF2 overexpression significantly facilitated KRASG12D PDAC LN metastasis in vitro and in vivo. Mechanistically, circARFGEF2 biogenesis in KRASG12D PDAC was significantly activated by the alternative splicing factor QKI-5, which recruited U2AF35 to facilitate spliceosome assembly. QKI-5 bound the QKI binding motifs and neighboring reverse complement sequence in intron 3 and 6 of ARFGEF2 pre-mRNA to facilitate circARFGEF2 biogenesis. CircARFGEF2 sponged miR-1205 and promoted the activation of JAK2, which phosphorylated STAT3 to trigger KRASG12D PDAC lymphangiogenesis and LN metastasis. Importantly, circARFGEF2 silencing significantly inhibited LN metastasis in the KrasG12D/+Trp53R172H/+Pdx-1-Cre (KPC) mouse PDAC model. These findings provide insight into the mechanism and metastasis-promoting function of mutant KRAS-mediated circRNA biogenesis. SIGNIFICANCE Increased splicing-mediated biogenesis of circARFGEF2 in KRAS-mutant pancreatic ductal adenocarcinoma activates JAK2-STAT3 signaling and triggers lymph node metastasis, suggesting circARFGEF2 could be a therapeutic target to inhibit pancreatic cancer progression.
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Affiliation(s)
- Yao Kong
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, P.R. China
| | - Yuming Luo
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Shangyou Zheng
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jiabin Yang
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
| | - Dingwen Zhang
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
| | - Yue Zhao
- Department of Tumor Intervention, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, P.R. China
| | - Hanhao Zheng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Mingjie An
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Yan Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Le Ai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiayao Diao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Qing Lin
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Changhao Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Rufu Chen
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
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29
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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: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Liu J, Xie J, Xu E, Xu B, Zhou J, Zhou J, Yang Q. CircRNA hsa_circ_0000043 acts as a miR-4492 sponge to promote lung cancer progression via BDNF and STAT3 expression regulation in anti-benzo[a]pyrene-trans-7,8-dihydrodiol-9,10-epoxide-transformed 16HBE cells. Toxicol Sci 2023; 195:87-102. [PMID: 37326964 DOI: 10.1093/toxsci/kfad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
Increasing evidence shows that circular RNA (circRNA) plays an important role in the progression of lung cancer. In this study, we found that has_circ_0000043 was highly expressed in 16HBE-T human bronchial epithelial cells that were malignantly transformed by benzo[a]pyrene-trans-7,8-diol-9,10-epoxide via circRNA microarray. We verified that hsa_circ_0000043 was also significantly overexpressed in lung cancer cell lines and tissues. Moreover, hsa_circ_0000043 overexpression was positively correlated with poor clinicopathological parameters, such as tumor-node metastasis stage, distant metastasis, lymph-node metastasis, and overall survival. In vitro assays revealed that hsa_circ_0000043 inhibition suppressed 16HBE-T cell proliferation, migration, and invasion. Furthermore, hsa_circ_0000043 inhibition suppressed tumor growth in a mouse xenograft model. We discovered that hsa_circ_0000043 binds with miR-4492, acting as a miR-4492 sponge. Decreased miR-4492 expression was also associated with poor clinicopathological parameters. Thus, hsa_circ_0000043 was shown to contribute to the proliferation, malignant transformation ability, migration, and invasion of 16HBE-T cells via miR-4492 sponging and BDNF and STAT3 involvement.
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Affiliation(s)
- Jiayu Liu
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Guangzhou 511436, China
| | - Jiaying Xie
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Guangzhou 511436, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, Guangzhou 510010, China
| | - Binhe Xu
- Basic Medicine College, Zunyi Medical University, Zunyi 563000, China
| | - Jiaxin Zhou
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Guangzhou 511436, China
| | - Jiazhen Zhou
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Guangzhou 511436, China
| | - Qiaoyuan Yang
- The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Guangzhou 511436, China
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31
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Kang DD, Li H, Dong Y. Advancements of in vitro transcribed mRNA (IVT mRNA) to enable translation into the clinics. Adv Drug Deliv Rev 2023; 199:114961. [PMID: 37321375 PMCID: PMC10264168 DOI: 10.1016/j.addr.2023.114961] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/02/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
The accelerated progress and approval of two mRNA-based vaccines to address the SARS-CoV-2 virus were unprecedented. This record-setting feat was made possible through the solid foundation of research on in vitro transcribed mRNA (IVT mRNA) which could be utilized as a therapeutic modality. Through decades of thorough research to overcome barriers to implementation, mRNA-based vaccines or therapeutics offer many advantages to rapidly address a broad range of applications including infectious diseases, cancers, and gene editing. Here, we describe the advances that have supported the adoption of IVT mRNA in the clinics, including optimization of the IVT mRNA structural components, synthesis, and lastly concluding with different classes of IVT RNA. Continuing interest in driving IVT mRNA technology will enable a safer and more efficacious therapeutic modality to address emerging and existing diseases.
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Affiliation(s)
- Diana D Kang
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Haoyuan Li
- Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Yizhou Dong
- Division of Pharmaceutics & Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Biomedical Engineering, The Center for Clinical and Translational Science, The Comprehensive Cancer Center; Dorothy M. Davis Heart & Lung Research Institute, Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, United States; Genomics Institute, Precision Immunology Institute, Department of Oncological Sciences, Tisch Cancer Institute, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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32
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Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen CY, Chu Q, Chuang TJ, Dehghannasiri R, Dieterich C, Dong X, Flicek P, Gaffo E, Gu W, He C, Hoffmann S, Izuogu O, Jackson MS, Jakobi T, Lai EC, Nuytens J, Salzman J, Santibanez-Koref M, Stadler P, Thas O, Vanden Eynde E, Verniers K, Wen G, Westholm J, Yang L, Ye CY, Yigit N, Yuan GH, Zhang J, Zhao F, Vandesompele J, Volders PJ. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nat Methods 2023; 20:1159-1169. [PMID: 37443337 PMCID: PMC10870000 DOI: 10.1038/s41592-023-01944-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/12/2023] [Indexed: 07/15/2023]
Abstract
The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected more than 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were validated using three orthogonal methods. Generally, tool-specific precision is high and similar (median of 98.8%, 96.3% and 95.5% for qPCR, RNase R and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant differentiators. Of note, precision values are lower when evaluating low-abundance circRNAs. We also show that the tools can be used complementarily to increase detection sensitivity. Finally, we offer recommendations for future circRNA detection and validation.
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Affiliation(s)
- Marieke Vromman
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jasper Anckaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan
| | - Qinjie Chu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Zhejiang, China
| | | | - Roozbeh Dehghannasiri
- Department of Biomedical Data Science and of Biochemistry, Stanford University, Stanford, CA, USA
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, University Hospital Heidelberg, German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Xin Dong
- School of Basic Medical Science, Department of Medical Genetics, Wuhan University, Wuhan, China
| | | | - Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Wanjun Gu
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunjiang He
- School of Basic Medical Science, Department of Medical Genetics, Wuhan University, Wuhan, China
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Michael S Jackson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Tobias Jakobi
- Translational Cardiovascular Research Center, University of Arizona - College of Medicine Phoenix, Phoenix, AZ, USA
| | - Eric C Lai
- Sloan Kettering Institute, New York, NY, USA
| | - Justine Nuytens
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Julia Salzman
- Department of Biomedical Data Science and of Biochemistry, Stanford University, Stanford, CA, USA
| | | | - Peter Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Olivier Thas
- Data Science Institute, I-Biostat, Hasselt University, Hasselt, Belgium
| | - Eveline Vanden Eynde
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kimberly Verniers
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Jakub Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - 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, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Fudan, China
| | - Chu-Yu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Zhejiang, China
| | - Nurten Yigit
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Guo-Hua Yuan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinyang Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
| | - Pieter-Jan Volders
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Blandino G, Dinami R, Marcia M, Anastasiadou E, Ryan BM, Palcau AC, Fattore L, Regazzo G, Sestito R, Loria R, Díaz Méndez AB, Cappelletto MC, Pulito C, Monteonofrio L, Calin GA, Sozzi G, Cheong JK, Aharonov R, Ciliberto G. The new world of RNA diagnostics and therapeutics. J Exp Clin Cancer Res 2023; 42:189. [PMID: 37507791 PMCID: PMC10386627 DOI: 10.1186/s13046-023-02752-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The 5th Workshop IRE on Translational Oncology was held in Rome (Italy) on 27-28 March at the IRCCS Regina Elena National Cancer Institute. This meeting entitled "The New World of RNA diagnostics and therapeutics" highlightes the significant progress in the RNA field made over the last years. Research moved from pure discovery towards the development of diagnostic biomarkers or RNA-base targeted therapies seeking validation in several clinical trials. Non-coding RNAs in particular have been the focus of this workshop due to their unique properties that make them attractive tools for the diagnosis and therapy of cancer.This report collected the presentations of many scientists from different institutions that discussed recent oncology research providing an excellent overview and representative examples for each possible application of RNA as biomarker, for therapy or to increase the number of patients that can benefit from precision oncology treatment.In particular, the meeting specifically emphasized two key features of RNA applications: RNA diagnostic (Blandino, Palcau, Sestito, Díaz Méndez, Cappelletto, Pulito, Monteonofrio, Calin, Sozzi, Cheong) and RNA therapeutics (Dinami, Marcia, Anastasiadou, Ryan, Fattore, Regazzo, Loria, Aharonov).
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Affiliation(s)
- Giovanni Blandino
- Translational Oncology Research Unit, IRCCS, Regina Elena National Cancer Institute, Rome, Italy.
| | - Roberto Dinami
- Translational Oncology Research Unit, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | | | - Eleni Anastasiadou
- Department of Clinical and Molecular Medicine, Sapienza University, Rome, Italy
| | | | - Alina Catalina Palcau
- Translational Oncology Research Unit, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Luigi Fattore
- SAFU Laboratory, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Regazzo
- Translational Oncology Research Unit, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Rosanna Sestito
- Preclinical models and new therapeutic agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Rossella Loria
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Ana Belén Díaz Méndez
- Translational Oncology Research Unit, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Maria Chiara Cappelletto
- Translational Oncology Research Unit, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Claudio Pulito
- Translational Oncology Research Unit, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Laura Monteonofrio
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | | | - Jit Kong Cheong
- National University of Singapore Yong Loo Lin School of Medicine, NUS Centre for Cancer Research and Mirxes Lab Pte Ltd, Singapore, Singapore
| | | | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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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: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth PA, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. Bioinform Adv 2023; 3:vbad093. [PMID: 37485422 PMCID: PMC10359604 DOI: 10.1093/bioadv/vbad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
Motivation Circular RNAs (circRNAs) are long noncoding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. Results We developed circRNA-sponging, a nextflow pipeline that (i) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (ii) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (iii) performs differential expression analysis, (iv) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (v) predicts miRNA binding sites on circRNAs, (vi) systematically investigates potential circRNA-miRNA sponging events, (vii) creates a network of competing endogenous RNAs and (viii) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. Availability and implementation https://github.com/biomedbigdata/circRNA-sponging. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | | | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Jakub Jankowski
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jan Baumbach
- Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A Furth
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study, Technical University of Munich, Garching D-85748, Germany
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Markus List
- To whom correspondence should be addressed. or
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Rao G, Peng X, Tian Y, Fu X, Zhang Y. Circular RNAs in hepatocellular carcinoma: biogenesis, function, and pathology. Front Genet 2023; 14:1106665. [PMID: 37485335 PMCID: PMC10361733 DOI: 10.3389/fgene.2023.1106665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. Both genetic and environmental factors through a multitude of underlying molecular mechanisms participate in the pathogenesis of HCC. Recently, numerous studies have shown that circular RNAs (circRNAs), an emerging class of non-coding RNAs characterized by the presence of covalent bonds linking 3' and 5' ends, play an important role in the initiation and progression of cancers, including HCC. In this review, we outline the current status of the field of circRNAs, with an emphasis on the functions and mechanisms of circRNAs in HCC and its microenvironment. We also summarize and discuss recent advances of circRNAs as biomarkers and therapeutic targets. These efforts are anticipated to throw new insights into future perspectives about circRNAs in basic, translational and clinical research, eventually advancing the diagnosis, prevention and treatment of HCC.
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Affiliation(s)
- Guocheng Rao
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Xi Peng
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yan Tian
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yuwei Zhang
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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Qin M, Zhang C, Li Y. Circular RNAs in gynecologic cancers: mechanisms and implications for chemotherapy resistance. Front Pharmacol 2023; 14:1194719. [PMID: 37361215 PMCID: PMC10285541 DOI: 10.3389/fphar.2023.1194719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Chemotherapy resistance remains a major challenge in the treatment of gynecologic malignancies. Increasing evidence suggests that circular RNAs (circRNAs) play a significant role in conferring chemoresistance in these cancers. In this review, we summarize the current understanding of the mechanisms by which circRNAs regulate chemotherapy sensitivity and resistance in gynecologic malignancies. We also discuss the potential clinical implications of these findings and highlight areas for future research. CircRNAs are a novel class of RNA molecules that are characterized by their unique circular structure, which confers increased stability and resistance to degradation by exonucleases. Recent studies have shown that circRNAs can act as miRNA sponges, sequestering miRNAs and preventing them from binding to their target mRNAs. This can lead to upregulation of genes involved in drug resistance pathways, ultimately resulting in decreased sensitivity to chemotherapy. We discuss several specific examples of circRNAs that have been implicated in chemoresistance in gynecologic cancers, including cervical cancer, ovarian cancer, and endometrial cancer. We also highlight the potential clinical applications of circRNA-based biomarkers for predicting chemotherapy response and guiding treatment decisions. Overall, this review provides a comprehensive overview of the current state of knowledge regarding the role of circRNAs in chemotherapy resistance in gynecologic malignancies. By elucidating the underlying mechanisms by which circRNAs regulate drug sensitivity, this work has important implications for improving patient outcomes and developing more effective therapeutic strategies for these challenging cancers.
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Nuthalapati SS, Ulshöfer CJ, Bindereif A. CircRNP complexes: from nature to design. J Mol Cell Biol 2023; 15:mjad006. [PMID: 36722152 PMCID: PMC10234438 DOI: 10.1093/jmcb/mjad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/18/2022] [Accepted: 01/30/2023] [Indexed: 02/02/2023] Open
Affiliation(s)
| | | | - Albrecht Bindereif
- Institute of Biochemistry, Justus Liebig University of Giessen, 35392 Giessen, Germany
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39
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Sillivan SE, Gillespie A. Circular RNA regulation and function in drug seeking phenotypes. Mol Cell Neurosci 2023; 125:103841. [PMID: 36935046 PMCID: PMC10247439 DOI: 10.1016/j.mcn.2023.103841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Drug overdoses have increased dramatically in the United States over the last decade where they are now the leading cause of accidental death. To develop efficient therapeutic options for decreasing drug consumption and overdose risk, it is critical to understand the neurobiological changes induced by drug exposure. Chronic systemic exposure to all drug classes, including opioids, psychostimulants, nicotine, cannabis, and alcohol, induces profound molecular neuroadaptations within the central nervous system that may reveal crucial information about the lasting effects that these substances impart on brain cells. Transcriptome analyses of messenger RNAs (mRNAs) have identified gene patterns in the brain that result from exposure to various classes of drugs. However, mRNAs represent only a small fraction of the RNA within the cell, and drug exposure also impacts other classes of RNA that are largely understudied, especially circular RNAs. Circular RNAs (circRNAs) are a naturally occurring RNA species formed from back-splicing events during mRNA processing and are enriched in the nervous system. circRNAs are a pleiotropic class of RNAs and have a diverse impact on cellular function, with putative functions including regulation of mRNA transcription, protein translation, microRNA sponging, and sequestration of RNA-binding proteins. Recent studies have demonstrated that circRNAs can modulate cognition and are regulated in the brain in response to drug exposure, yet very few studies have explored the contribution of circRNAs to drug seeking phenotypes. In this review, we will provide an overview of the mechanisms of circRNA function in the cell to highlight how drug-induced circRNA dysregulation may impact the molecular substrates that mediate drug seeking behavior and the current studies that have reported drug-induced dysregulation of circRNAs in the brain. Furthermore, we will discuss how principles of circRNA biology can be adapted to study circRNAs in models of drug exposure and seek to provide further insight into the neurobiology of addiction.
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Affiliation(s)
- Stephanie E Sillivan
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA; Department of Neural Sciences, Temple University, Philadelphia, PA, USA.
| | - Aria Gillespie
- Center for Substance Abuse Research, Temple University, Philadelphia, PA, USA; Department of Neural Sciences, Temple University, Philadelphia, PA, USA
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40
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Wang G, Cheng T, Yuan H, Zou F, Miao P, Jiao J. Tracing cellular interaction of circRNA-miRNA axis with Cu metal-organic framework supported DNA cascade assembly. Biosens Bioelectron 2023; 228:115226. [PMID: 36934606 DOI: 10.1016/j.bios.2023.115226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
Circular RNAs (circRNAs) can act as molecular sponges of microRNA (miRNA) to form circRNA-miRNA axis, which regulates the expressions of downstream proteins. Although the mechanism has been widely reported in various bioprocesses, there is still a lack of reliable and facile way to intuitively monitor and locate the interaction between circRNA and miRNA inside living cells. In this study, multiple DNA probes are designed and loaded onto two-dimensional Cu metal-organic framework (2D Cu-MOF) nanosheets for one-step analysis of circRNA-miRNA axis. The nanosheets serve as not only powerful fluorescence quenchers but also excellent nanocarriers of abundant DNA probes for further assembly. The Probes@Cu-MOF complex can be applied to track the circRNA-miRNA axis in living cells with high sensitivity and co-localization analysis. This platform combines the transmembrane advantage of nanosheets and the signal amplification ability of localized DNA cascade assembly, so it holds great potential for understanding the biological functions of circRNA-miRNAs in cancer pathogenesis and for therapeutic applications.
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Affiliation(s)
- Gang Wang
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Tao Cheng
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Hongxiu Yuan
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Fangbo Zou
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, PR China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, PR China; Jinan Guoke Medical Technology Development Co, Ltd, Jinan, 250103, PR China.
| | - Jin Jiao
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, PR China.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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42
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Huang Y, Xue Q, Cheng C, Wang Y, Wang X, Chang J, Miao C. Circular RNA in autoimmune diseases: special emphasis on regulation mechanism in RA and SLE. J Pharm Pharmacol 2023; 75:370-384. [PMID: 36583516 DOI: 10.1093/jpp/rgac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/26/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Autoimmune diseases are diseases caused by tissue damage caused by the body's immune response to autoantibodies. Circular RNAs (CircRNAs) are a kind of special endogenous non-coding RNA that play a biological role by regulating gene transcription. METHODS In this work, we searched the PubMed, Web of Science (SCIE), National Science and Technology Library (NSTL), and ScienceDirect Online (SDOL) databases to summarize the impact of circRNAs on autoimmune diseases, especially the results of circRNAs in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). RESULTS The study on the function of circRNAs and autoimmune diseases further deepened our understanding of the development and pathogenesis of autoimmune diseases. CircRNAs may act as miRNA sponges to regulate biological processes and affect the occurrence and development of autoimmune diseases. CircRNAs are closely related to the pathogenesis of RA and SLE and may become potential biomarkers for the diagnosis and treatment of RA and SLE. CONCLUSION CircRNAs play an important role in the pathogenesis of RA, SLE and other autoimmune diseases, and are expected to provide new biomarkers for the diagnosis and treatment of autoimmune diseases. However, the function and mechanism of circRNAs in autoimmune diseases need more comprehensive research.
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Affiliation(s)
- Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Qiuyun Xue
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Yuting Wang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, China
| | - Jun Chang
- Department of Orthopaedics, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, China.,Anhui Public Health Clinical Center, Hefei, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
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43
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Guo X, Gao C, Yang DH, Li S. Exosomal circular RNAs: A chief culprit in cancer chemotherapy resistance. Drug Resist Updat 2023; 67:100937. [PMID: 36753923 DOI: 10.1016/j.drup.2023.100937] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/03/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Chemotherapy is one of the primary treatments for malignant tumors. However, the acquired drug resistance hinders clinical efficacy and leads to treatment failure in most patients. Exosomes are cell-derived vesicles with a diameter of 30-150 nm carrying and delivering substances such as DNAs, RNAs, lipids, and proteins for cellular communication in tumor development. Circular RNAs (circRNAs) present covalently closed-loop RNA structures, which regulate tumor cell proliferation, apoptosis, and metastasis by controlling different genes and signaling pathways. CircRNAs are abundant and stably expressed in exosomes. Recent studies have shown that they play critical roles in chemotherapy resistance in various cancers. In this review, we summarized the origin of exosomes and discussed the regulation mechanism of exosomal circRNAs in cancer drug resistance.
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Affiliation(s)
- Xu Guo
- Department of Neurosurgery, Cancer Hospital of Dalian University of Technology,Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning Province 110042, China
| | - Congying Gao
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Dong-Hua Yang
- New York College of Traditional Chinese Medicine, Mineola, NY, USA.
| | - Shenglong Li
- Department of Bone and Soft Tissue Tumor Surgery, Cancer Hospital of Dalian University of Technology,Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang Liaoning Province 110042, China.
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44
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Seeler S, Andersen MS, Sztanka-Toth T, Rybiczka-Tešulov M, van den Munkhof MH, Chang CC, Maimaitili M, Venø MT, Hansen TB, Pasterkamp RJ, Rybak-Wolf A, Denham M, Rajewsky N, Kristensen LS, Kjems J. A Circular RNA Expressed from the FAT3 Locus Regulates Neural Development. Mol Neurobiol 2023; 60:3239-3260. [PMID: 36840844 PMCID: PMC10122638 DOI: 10.1007/s12035-023-03253-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/28/2023] [Indexed: 02/26/2023]
Abstract
Circular RNAs (circRNAs) are key regulators of cellular processes, are abundant in the nervous system, and have putative regulatory roles during neural differentiation. However, the knowledge about circRNA functions in brain development is limited. Here, using RNA-sequencing, we show that circRNA levels increased substantially over the course of differentiation of human embryonic stem cells into rostral and caudal neural progenitor cells (NPCs), including three of the most abundant circRNAs, ciRS-7, circRMST, and circFAT3. Knockdown of circFAT3 during early neural differentiation resulted in minor transcriptional alterations in bulk RNA analysis. However, single-cell transcriptomics of 30 and 90 days differentiated cerebral organoids deficient in circFAT3 showed a loss of telencephalic radial glial cells and mature cortical neurons, respectively. Furthermore, non-telencephalic NPCs in cerebral organoids showed changes in the expression of genes involved in neural differentiation and migration, including FAT4, ERBB4, UNC5C, and DCC. In vivo depletion of circFat3 in mouse prefrontal cortex using in utero electroporation led to alterations in the positioning of the electroporated cells within the neocortex. Overall, these findings suggest a conserved role for circFAT3 in neural development involving the formation of anterior cell types, neuronal differentiation, or migration.
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Affiliation(s)
- Sabine Seeler
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Maria Schertz Andersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Tamas Sztanka-Toth
- Berlin Institute for Medical Systems Biology (BIMSB), MDC Berlin-Mitte, 10115, Berlin, Germany
| | - Mateja Rybiczka-Tešulov
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, 3584 CG, Utrecht, Netherlands
| | - Marleen H van den Munkhof
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, 3584 CG, Utrecht, Netherlands
| | - Chi-Chih Chang
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Muyesier Maimaitili
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Danish Research Institute of Translational Neuroscience, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Morten Trillingsgaard Venø
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Omiics ApS, 8200 Aarhus N, Aarhus, Denmark
| | - Thomas Birkballe Hansen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, 3584 CG, Utrecht, Netherlands
| | - Agnieszka Rybak-Wolf
- Berlin Institute for Medical Systems Biology (BIMSB), MDC Berlin-Mitte, 10115, Berlin, Germany
| | - Mark Denham
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
- Danish Research Institute of Translational Neuroscience, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, 8000 Aarhus C, Aarhus, Denmark
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), MDC Berlin-Mitte, 10115, Berlin, Germany
| | - Lasse Sommer Kristensen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark.
- Department of Biomedicine, The Skou Building, Aarhus University, 8000 Aarhus C, Aarhus, Denmark.
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Aarhus, Denmark.
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth P, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. bioRxiv 2023:2023.01.19.524495. [PMID: 36789427 PMCID: PMC9928029 DOI: 10.1101/2023.01.19.524495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Motivation Circular RNAs (circRNAs) are long non-coding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. Results We developed circRNA-sponging, a nextflow pipeline that (1) identifies circRNAs via back-splicing junctions detected in RNA-seq data, (2) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (3) performs differential expression analysis, (4) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (5) predicts miRNA binding sites on circRNAs, (6) systematically investigates potential circRNA-miRNA sponging events, (7) creates a network of competing endogenous RNAs, and (8) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues where we identified two distinct types of circRNAs characterized by a distinct ratio of the binding site length. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. Availability https://github.com/biomedbigdata/circRNA-sponging. Contact markus.daniel.hoffmann@tum.de ; markus.list@tum.de. Supplementary Material Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America,corresponding authors Contact:;
| | - Leon Schwartz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Octavia-Andreea Ciora
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jakub Jankowski
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany,Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,corresponding authors Contact:;
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Abstract
Currently, bone defect repair is still an intractable clinical problem. Numerous treatments have been performed, but their clinical results are unsatisfactory. As a key element of cell-free therapy, exosome is becoming a promising tool of bone regeneration in recent decades, because of its promoting osteogenesis and osteogenic differentiation function in vivo and in vitro. However, low yield, weak activity, inefficient targeting ability, and unpredictable side effects of natural exosomes have limited the clinical application. To overcome the weakness, various approaches have been applied to produce engineering exosomes by regulating their production and function at present. In this review, we will focus on the engineering exosomes for bone defect repair. By summarizing the exosomal cargos affecting osteogenesis, the strategies of engineering exosomes and properties of exosome-integrated biomaterials, this work will provide novel insights into exploring advanced engineering exosome-based cell-free therapy for bone defect repair.
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Affiliation(s)
| | | | | | | | - Ye Li
- *Correspondence: Ye Li, ; Dandan Pei,
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Qiu Y, Chen Y, Agbede O, Eshaghi E, Peng C. Circular RNAs in Epithelial Ovarian Cancer: From Biomarkers to Therapeutic Targets. Cancers (Basel) 2022; 14. [PMID: 36428803 DOI: 10.3390/cancers14225711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecological cancer, and more than 70% of patients are diagnosed at advanced stages. Despite the application of surgery and chemotherapy, the prognosis remains poor due to the high relapse rate. It is urgent to identify novel biomarkers and develop novel therapeutic strategies for EOC. Circular RNAs (circRNAs) are a class of noncoding RNAs generated from the "back-splicing" of precursor mRNA. CircRNAs exert their functions via several mechanisms, including acting as miRNA sponges, interacting with proteins, regulating transcription, and encoding functional proteins. Recent studies have identified many circRNAs that are dysregulated in EOC and may be used as diagnostic and prognostic markers. Increasing evidence has revealed that circRNAs play a critical role in ovarian cancer progression by regulating various cellular processes, including proliferation, apoptosis, metastasis, and chemosensitivity. The circRNA-based therapy may be a novel strategy that is worth exploring in the future. Here, we provide an overview of EOC and circRNA biogenesis and functions. We then discuss the dysregulations of circRNAs in EOC and the possibility of using them as diagnostic/prognostic markers. We also summarize the role of circRNAs in regulating ovarian cancer development and speculate their potential as therapeutic targets.
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48
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Lin Z, Ma Y, Zhu X, Dai S, Sun W, Li W, Niu S, Chu M, Zhang J. Potential predictive and therapeutic applications of small extracellular vesicles-derived circPARD3B in osteoarthritis. Front Pharmacol 2022; 13:968776. [DOI: 10.3389/fphar.2022.968776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Heterogeneous phenotypes that display distinct common characteristics of osteoarthritis (OA) are not well defined and will be helpful in identifying more customized therapeutic options for OA. Circular RNAs (circRNAs) have attracted more and more attention due to their role in the progression of OA. Investigating the role of circRNAs in the pathogenesis of OA will contribute to the phenotyping of OA and to individualized treatment.Methods: Small extracellular vesicles (sEV) were isolated from serum samples from patients with OA of different stages and sEV-derived circPARD3B was determined using RT-qPCR analysis. CircPARD3B expression in a stimulated coculture that included OA fibroblast-like synoviocytes (OA-FLS) as well as human dermal microvascular endothelial cells (HDMECs), plus the effects of circPARD3B on the expression of vascular endothelial growth factor (VEGF) long with angiogenic activity, were evaluated in vitro. Based on bioinformatics analysis and luciferase reporter assay (LRA), MiR-326 and sirtuin 1 (SIRT1) were found to be interactive partners of circPARD3B. Mesenchymal stem cells (SMSCs) overexpressing circPARD3B were constructed and SMSCs-derived sEV with overexpressed circPARD3B (OE-circPARD3B-SMSCs-sEV) were obtained to explore the effect of the intervention of circPARD3B combined with SMSCs-sEV-based therapy in vitro and in a OA model induced by collagenase in vivo.Results: Serum sEV-linked circPARD3B was indentified to be significantly decreased in the inflammatory phenotype of OA. Overexpression of circPARD3B was found to inhibit the expression of VEGF, as well as the angiogenesis induced by VEGF in a IL-1β stimulated the co-culture of OA-FLS as well as HDMECs. CircPARD3B is directly bound to miR-326. SIRT1 was considered a novel miR-326 target gene. OE-circPARD3B-SMSCs-sEV significantly reduced VEGF expression in coculture of OA-FLS and HDMECs. Injection of OE-circPARD3B-SMSCs-sEV could also reduce synovial VEGF; additionally, it could further ameliorate OA in the mouse model of OA in vivo.Conclusion: Serum sEV circPARD3B is a potential biomarker that enables the identification of the inflammatory phenotype of patients with OA. Correspondingly, intracellular transfer of circPARD3B through OE-circPARD3B-SMSCs-sEV could postpone disease progression through a functional module regulated angiogenesis of circPARD3B-miR-326-SIRT1, providing a novel therapeutic strategy for OA.
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Marx V. Some roads ahead for noncoding RNAs. Nat Methods 2022; 19:1171-1174. [PMID: 36203022 DOI: 10.1038/s41592-022-01628-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Toraih EA, Hussein MH, Fawzy MS, Kandil E. A Review and In Silico Analysis of Tissue and Exosomal Circular RNAs: Opportunities and Challenges in Thyroid Cancer. Cancers (Basel) 2022; 14:4728. [PMID: 36230649 PMCID: PMC9564022 DOI: 10.3390/cancers14194728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Thyroid cancer is the most common endocrine neoplasm. Recently, knowledge of the molecular genetic changes of thyroid cancer has dramatically improved. Understanding the roles of these molecular changes in thyroid cancer tumorigenesis and progression is essential in developing a successful treatment strategy and improving disease outcomes. As a family of non-coding RNAs, circular RNAs (circRNAs) have been involved in several aspects of the physiological and pathological processes of the cells. The roles of circRNAs in cancer development and progress are evident. In the current review, we aimed to explore the clinical potential of circRNAs as potential diagnostic, prognostic, and therapeutic targets in thyroid cancer. Furthermore, screening the genome-wide circRNAs and performing functional enrichment analyses for all associated dysregulated circRNAs in thyroid cancer have been done. Given the unique advantages circRNAs have, such as superior stability, higher abundance, and presence in different body fluids, this family of non-coding RNAs could be promising diagnostic and prognostic biomarkers and potential therapeutic targets for thyroid cancer. Abstract Thyroid cancer (TC) is the most common endocrine tumor. The genetic and epigenetic molecular alterations of TC have become more evident in recent years. However, a deeper understanding of the roles these molecular changes play in TC tumorigenesis and progression is essential in developing a successful treatment strategy and improving patients’ prognoses. Circular RNAs (circRNAs), a family of non-coding RNAs, have been implicated in several aspects of carcinogenesis in multiple cancers, including TC. In the current review, we aimed to explore the clinical potential of circRNAs as putative diagnostic, prognostic, and therapeutic targets in TC. The current analyses, including genome-wide circRNA screening and functional enrichment for all deregulated circRNA expression signatures, show that circRNAs display atypical contributions, such as sponging for microRNAs, regulating transcription and translation processes, and decoying for proteins. Given their exceptional clinical advantages, such as higher stability, wider abundance, and occurrence in several body fluids, circRNAs are promising prognostic and theranostic biomarkers for TC.
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