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Sharma NK, Dwivedi P, Bhushan R, Maurya PK, Kumar A, Dakal TC. Engineering circular RNA for molecular and metabolic reprogramming. Funct Integr Genomics 2024; 24:117. [PMID: 38918231 DOI: 10.1007/s10142-024-01394-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
The role of messenger RNA (mRNA) in biological systems is extremely versatile. However, it's extremely short half-life poses a fundamental restriction on its application. Moreover, the translation efficiency of mRNA is also limited. On the contrary, circular RNAs, also known as circRNAs, are a common and stable form of RNA found in eukaryotic cells. These molecules are synthesized via back-splicing. Both synthetic circRNAs and certain endogenous circRNAs have the potential to encode proteins, hence suggesting the potential of circRNA as a gene expression machinery. Herein, we aim to summarize all engineering aspects that allow exogenous circular RNA (circRNA) to prolong the time that proteins are expressed from full-length RNA signals. This review presents a systematic engineering approach that have been devised to efficiently assemble circRNAs and evaluate several aspects that have an impact on protein production derived from. We have also reviewed how optimization of the key components of circRNAs, including the topology of vector, 5' and 3' untranslated sections, entrance site of the internal ribosome, and engineered aptamers could be efficiently impacting the translation machinery for molecular and metabolic reprogramming. Collectively, molecular and metabolic reprogramming present a novel way of regulating distinctive cellular features, for instance growth traits to neoplastic cells, and offer new possibilities for therapeutic inventions.
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Affiliation(s)
- Narendra Kumar Sharma
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India.
| | - Pragya Dwivedi
- Department of Bioscience and Biotechnology, Banasthali Vidyapith (Deemed University), P.O. Banasthali Vidyapith Distt. Tonk, Rajasthan, 304 022, India
| | - Ravi Bhushan
- Department of Zoology, M.S. College, Motihari, Bihar, India
| | - Pawan Kumar Maurya
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
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2
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Choi SW, Nam JW. Optimal design of synthetic circular RNAs. Exp Mol Med 2024:10.1038/s12276-024-01251-w. [PMID: 38871815 DOI: 10.1038/s12276-024-01251-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs are an unusual class of single-stranded RNAs whose ends are covalently linked via back-splicing. Due to their versatility, the need to express circular RNAs in vivo and in vitro has increased. Efforts have been made to efficiently and precisely synthesize circular RNAs. However, a review on the optimization of the processes of circular RNA design, synthesis, and delivery is lacking. Our review highlights the multifaceted aspects considered when producing optimal circular RNAs and summarizes the available options for each step of exogenous circular RNA design and synthesis, including circularization strategies. Additionally, this review describes several potential applications of circular RNAs.
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Affiliation(s)
- Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seoul, 04763, Republic of Korea.
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3
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Zhang L, Wang Y, Gao J, Zhou X, Huang M, Wang X, He Z. Non‑coding RNA: A promising diagnostic biomarker and therapeutic target for esophageal squamous cell carcinoma (Review). Oncol Lett 2024; 27:255. [PMID: 38646493 PMCID: PMC11027111 DOI: 10.3892/ol.2024.14388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
Esophageal cancer (EC) is a common form of malignant tumor in the digestive system that is classified into two types: Esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinoma. ESCC is known for its early onset of symptoms, which can be difficult to identify, as well as its rapid progression and tendency to develop drug resistance to chemotherapy and radiotherapy. These factors contribute to the high incidence of disease and low cure rate. Therefore, a diagnostic biomarker and therapeutic target need to be identified for ESCC. Non-coding RNAs (ncRNAs) are a class of molecules that are transcribed from DNA but do not encode proteins. Initially, ncRNAs were considered to be non-functional segments generated during transcription. However, with advancements in high-throughput sequencing technologies in recent years, ncRNAs have been associated with poor prognosis, drug resistance and progression of ESCC. The present study provides a comprehensive overview of the biogenesis, characteristics and functions of ncRNAs, particularly focusing on microRNA, long ncRNAs and circular RNAs. Furthermore, the ncRNAs that could potentially be used as diagnostic biomarkers and therapeutic targets for ESCC are summarized to highlight their application value and prospects in ESCC.
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Affiliation(s)
- Longze Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Yanyang Wang
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Cell Engineering Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Jianmei Gao
- School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xue Zhou
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Minglei Huang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xianyao Wang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Zhixu He
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Cell Engineering Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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4
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Liao C, He ZW, Yu R, Yu YJ, Liu XR, Kong DL, Wang Y. CircRNA: a rising therapeutic strategy for lung injury induced by pulmonary toxicants. Arch Toxicol 2024; 98:1297-1310. [PMID: 38498160 DOI: 10.1007/s00204-024-03706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/14/2024] [Indexed: 03/20/2024]
Abstract
Lung injury has been a serious medical problem that requires new therapeutic approaches and biomarkers. Circular RNAs (circRNAs) are non-coding RNAs (ncRNAs) that exist widely in eukaryotes. CircRNAs are single-stranded RNAs that form covalently closed loops. CircRNAs are significant gene regulators that have a role in the development, progression, and therapy of lung injury by controlling transcription, translating into protein, and sponging microRNAs (miRNAs) and proteins. Although the study of circRNAs in lung injury caused by pulmonary toxicants is just beginning, several studies have revealed their expression patterns. The function that circRNAs perform in relation to pulmonary toxicants (severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2), drug abuse, PM2.5, and cigarette smoke) is the main topic of this review. A variety of circRNAs can serve as potential biomarkers of lung injury. In this review, the biogenesis, properties, and biological functions of circRNAs were concluded, and the relationship between circRNAs and pulmonary toxicants was discussed. It is expected that the new ideas and potential treatment targets that circRNAs provide would be beneficial to research into the molecular mechanisms behind lung injury.
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Affiliation(s)
- Cai Liao
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Zhen-Wei He
- Department of Neurology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Rui Yu
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Ya-Jie Yu
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - Xiao-Ru Liu
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China
| | - De-Lei Kong
- Department of Respiratory and Critical Care Medicine, The First Hospital of China Medical University, No. 155, Nanjing Street, Heping District, Shenyang, 110000, Liaoning, China.
| | - Yun Wang
- Department of Clinical Pharmacology, School of Pharmacy, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, 110122, Liaoning, China.
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5
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Guo SK, Liu CX, Xu YF, Wang X, Nan F, Huang Y, Li S, Nan S, Li L, Kon E, Li C, Wei MY, Su R, Wei J, Peng S, Ad-El N, Liu J, Peer D, Chen T, Yang L, Chen LL. Therapeutic application of circular RNA aptamers in a mouse model of psoriasis. Nat Biotechnol 2024:10.1038/s41587-024-02204-4. [PMID: 38653797 DOI: 10.1038/s41587-024-02204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/25/2024]
Abstract
Efforts to advance RNA aptamers as a new therapeutic modality have been limited by their susceptibility to degradation and immunogenicity. In a previous study, we demonstrated synthesized short double-stranded region-containing circular RNAs (ds-cRNAs) with minimal immunogenicity targeted to dsRNA-activated protein kinase R (PKR). Here we test the therapeutic potential of ds-cRNAs in a mouse model of imiquimod-induced psoriasis. We find that genetic supplementation of ds-cRNAs leads to inhibition of PKR, resulting in alleviation of downstream interferon-α and dsRNA signals and attenuation of psoriasis phenotypes. Delivery of ds-cRNAs by lipid nanoparticles to the spleen attenuates PKR activity in examined splenocytes, resulting in reduced epidermal thickness. These findings suggest that ds-cRNAs represent a promising approach to mitigate excessive PKR activation for therapeutic purposes.
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Affiliation(s)
- Si-Kun Guo
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chu-Xiao Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Feng Xu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao Wang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fang Nan
- Center for Molecular Medicine, Children's Hospital of 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, Shanghai, China
| | - Youkui Huang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Siqi Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shan Nan
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Edo Kon
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Chen Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meng-Yuan Wei
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rina Su
- Department of Dermatology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Jia Wei
- Center for Molecular Medicine, Children's Hospital of 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, Shanghai, China
| | - Shiguang Peng
- Department of Dermatology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Nitay Ad-El
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Jiaquan Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dan Peer
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Center for Nanoscience and Nanotechnology, Cancer Biology Research Center, Tel Aviv University, Tel Aviv, Israel
| | - Ting Chen
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital of 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, Shanghai, China
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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6
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Luan X, Wang L, Song G, Zhou W. Innate immune responses to RNA: sensing and signaling. Front Immunol 2024; 15:1287940. [PMID: 38343534 PMCID: PMC10854198 DOI: 10.3389/fimmu.2024.1287940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Nucleic acids are among the most essential PAMPs (pathogen-associated molecular patterns). Animals have evolved numerous sensors to recognize nucleic acids and trigger immune signaling against pathogen replication, cellular stress and cancer. Many sensor proteins (e.g., cGAS, AIM2, and TLR9) recognize the molecular signature of infection or stress and are responsible for the innate immune response to DNA. Remarkably, recent evidence demonstrates that cGAS-like receptors acquire the ability to sense RNA in some forms of life. Compared with the nucleic-acid sensing by cGAS, innate immune responses to RNA are based on various RNA sensors, including RIG-I, MDA5, ADAR1, TLR3/7/8, OAS1, PKR, NLRP1/6, and ZBP1, via a broad-spectrum signaling axis. Importantly, new advances have brought to light the potential clinical application of targeting these signaling pathways. Here, we highlight the latest discoveries in the field. We also summarize the activation and regulatory mechanisms of RNA-sensing signaling. In addition, we discuss how RNA sensing is tightly controlled in cells and why the disruption of immune homeostasis is linked to disease.
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Affiliation(s)
- Xiaohan Luan
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lei Wang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Guangji Song
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wen Zhou
- Shenzhen Key Laboratory of Biomolecular Assembling and Regulation, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
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7
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Xie C, Hao X, Yuan H, Wang C, Sharif R, Yu H. Crosstalk Between circRNA and Tumor Microenvironment of Hepatocellular Carcinoma: Mechanism, Function and Applications. Onco Targets Ther 2024; 17:7-26. [PMID: 38283733 PMCID: PMC10812140 DOI: 10.2147/ott.s437536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common aggressive tumors in the world. Despite the availability of various treatments, its prognosis remains poor due to the lack of specific diagnostic indicators and the high heterogeneity of HCC cases. CircRNAs are noncoding RNAs with stable and highly specific expression. Extensive research evidence suggests that circRNAs mediate the pathogenesis and progression of HCC through acting as miRNA sponges, protein modulators, and translation templates. Tumor microenvironment (TME) has become a hotspot of immune-related research in recent years due to its effects on metabolism, secretion and immunity of HCC. Accordingly, understanding the role played by circRNAs in TME is important for the study of HCC. This review will discuss the crosstalk between circRNAs and TME in HCC. In addition, we will discuss the current deficiencies and controversies in research on circRNAs and predict future research directions.
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Affiliation(s)
- Chenxi Xie
- Hepatobiliary Center, Department of Hepatobiliary Surgery, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Xiaopei Hao
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, People’s Republic of China
| | - Hao Yuan
- Hepatobiliary Center, Department of Hepatobiliary Surgery, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Chongyu Wang
- The First Clinical Medical College of Xuzhou Medical University, Xuzhou, People’s Republic of China
| | - Razinah Sharif
- Center for Healthy Ageing & Wellness, Faculty of Health Sciences, University Kebangsaan Malaysia, Kuala Lumpur, 50300, Malaysia
- Biocompatibility Laboratory, Centre for Research and Instrumentation, University Kebangsaan Malaysia, UKM, Bangi, Selangor Darul Ehsan, 43600, Malaysia
| | - Haibo Yu
- Hepatobiliary Center, Department of Hepatobiliary Surgery, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
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Ma XK, Gao X, Cao M, Yang L. Base-Editor-Mediated circRNA Knockout by Targeting Predominantly Back-Splice Sites. Methods Mol Biol 2024; 2765:193-208. [PMID: 38381341 DOI: 10.1007/978-1-0716-3678-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Back-splicing of eukaryotic exon(s) leads to the production of covalently closed circular RNAs (circRNAs). Generally, most circRNAs contain overlapping sequences to their cognate linear RNAs from the same gene loci, leading to difficulties in distinguishing them from each other. A recent study has shown that some circRNAs can be specifically depleted by using base editing systems to target their predominantly back-splice sites for circularization, suggesting an efficient approach for circRNA knockout (KO). Here, we describe the detailed protocol for applying base editors to disrupt back-splice sites of predominantly circularized exons for circRNA KO at the genomic DNA level.
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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, China
| | - Xiang Gao
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mei Cao
- 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, 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, China.
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9
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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] [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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10
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Perenkov AD, Sergeeva AD, Vedunova MV, Krysko DV. In Vitro Transcribed RNA-Based Platform Vaccines: Past, Present, and Future. Vaccines (Basel) 2023; 11:1600. [PMID: 37897003 PMCID: PMC10610676 DOI: 10.3390/vaccines11101600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
mRNA was discovered in 1961, but it was not used as a vaccine until after three decades. Recently, the development of mRNA vaccine technology gained great impetus from the pursuit of vaccines against COVID-19. To improve the properties of RNA vaccines, and primarily their circulation time, self-amplifying mRNA and trans-amplifying mRNA were developed. A separate branch of mRNA technology is circular RNA vaccines, which were developed with the discovery of the possibility of translation on their protein matrix. Circular RNA has several advantages over mRNA vaccines and is considered a fairly promising platform, as is trans-amplifying mRNA. This review presents an overview of the mRNA platform and a critical discussion of the more modern self-amplifying mRNA, trans-amplifying mRNA, and circular RNA platforms created on its basis. Finally, the main features, advantages, and disadvantages of each of the presented mRNA platforms are discussed. This discussion will facilitate the decision-making process in selecting the most appropriate platform for creating RNA vaccines against cancer or viral diseases.
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Affiliation(s)
- Alexey D Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Alena D Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Maria V Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
| | - Dmitri V Krysko
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, 603022 Nizhny Novgorod, Russia
- Cell Death Investigation and Therapy (CDIT) Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Science, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
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11
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Feng XY, Zhu SX, Pu KJ, Huang HJ, Chen YQ, Wang WT. New insight into circRNAs: characterization, strategies, and biomedical applications. Exp Hematol Oncol 2023; 12:91. [PMID: 37828589 PMCID: PMC10568798 DOI: 10.1186/s40164-023-00451-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed, endogenous ncRNAs. Most circRNAs are derived from exonic or intronic sequences by precursor RNA back-splicing. Advanced high-throughput RNA sequencing and experimental technologies have enabled the extensive identification and characterization of circRNAs, such as novel types of biogenesis, tissue-specific and cell-specific expression patterns, epigenetic regulation, translation potential, localization and metabolism. Increasing evidence has revealed that circRNAs participate in diverse cellular processes, and their dysregulation is involved in the pathogenesis of various diseases, particularly cancer. In this review, we systematically discuss the characterization of circRNAs, databases, challenges for circRNA discovery, new insight into strategies used in circRNA studies and biomedical applications. Although recent studies have advanced the understanding of circRNAs, advanced knowledge and approaches for circRNA annotation, functional characterization and biomedical applications are continuously needed to provide new insights into circRNAs. The emergence of circRNA-based protein translation strategy will be a promising direction in the field of biomedicine.
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Affiliation(s)
- Xin-Yi Feng
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shun-Xin Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ke-Jia Pu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Heng-Jing Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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12
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Kim YS, Kim DH, An D, Lim Y, Seo YJ, Kim HK, Kang HY. The RNA ligation method using modified splint DNAs significantly improves the efficiency of circular RNA synthesis. Anim Cells Syst (Seoul) 2023; 27:208-218. [PMID: 37808549 PMCID: PMC10552601 DOI: 10.1080/19768354.2023.2265165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
Circular RNA (circRNA) is a non-coding RNA with a covalently closed loop structure and usually more stable than messenger RNA (mRNA). However, coding sequences (CDSs) following an internal ribosome entry site (IRES) in circRNAs can be translated, and this property has been recently utilized to produce proteins as novel therapeutic tools. However, it is difficult to produce large proteins from circRNAs because of the low circularization efficiency of lengthy RNAs. In this study, we report that we successfully synthesized circRNAs with the splint DNA ligation method using RNA ligase 1 and the splint DNAs, which contain complementary sequences to both ends of precursor linear RNAs. This method results in more efficient circularization than the conventional enzymatic method that does not use the splint DNAs, easily generating circRNAs that express relatively large proteins, including IgG heavy and light chains. Longer splint DNA (42 nucleotide) is more effective in circularization. Also, the use of splint DNAs with an adenine analog, 2,6-diaminopurine (DAP), increase the circularization efficiency presumably by strengthening the interaction between the splint DNAs and the precursor RNAs. The splint DNA ligation method requires 5 times more splint DNA than the precursor RNA to efficiently produce circRNAs, but our modified splint DNA ligation method can produce circRNAs using the amount of splint DNA which is equal to that of the precursor RNA. Our modified splint DNA ligation method will help develop novel therapeutic tools using circRNAs, to treat various diseases and to develop human and veterinary vaccines.
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Affiliation(s)
- Yoon-Seob Kim
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
| | - Do-Hyung Kim
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
| | - Daegi An
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Younghyun Lim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ho-Young Kang
- Drug Discovery Center, NuclixBio, Seoul, Republic of Korea
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13
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Dolgin E. Why rings of RNA could be the next blockbuster drug. Nature 2023; 622:22-24. [PMID: 37794271 DOI: 10.1038/d41586-023-03058-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
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14
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Lee KH, Kim S, Song J, Han SR, Kim JH, Lee SW. Efficient circular RNA engineering by end-to-end self-targeting and splicing reaction using Tetrahymena group I intron ribozyme. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:587-598. [PMID: 37637208 PMCID: PMC10457212 DOI: 10.1016/j.omtn.2023.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023]
Abstract
Circular RNA (circRNA) has various advantages over linear mRNA that is gaining success as a new vaccine and therapeutic agent. Thus, circRNA and its engineering methods have attracted attention recently. In this study, we developed a new in vitro circRNA engineering method by end-to-end self-targeting and splicing (STS) reaction using Tetrahymena group I intron ribozyme. We found that only the P1 helix structure of the group I intron was enough to generate circRNA by STS reaction. The efficacy of circRNA generation by STS reaction was comparable to the method using a permuted intron-exon (PIE) reaction. However, an end-to-end STS reaction does not introduce any extraneous fragments, such as an intronic scar that can be generated by PIE reaction and might trigger unwanted innate immune responses in cells, into circRNA sequences. Moreover, generated circRNA was efficiently purified by ion pair-reversed phase high-pressure liquid chromatography and used for cell-based analysis. Of note, efficient protein expression and stability with least innate immune induction by the circRNA with coxsackievirus B3 IRES were observed in cells. In conclusion, our new in vitro circRNA strategy can effectively generate highly useful circRNAs in vitro as an alternative circRNA engineering method.
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Affiliation(s)
- Kyung Hyun Lee
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seongcheol Kim
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Jaehwi Song
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seung Ryul Han
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Ji Hyun Kim
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
| | - Seong-Wook Lee
- R&D Center, Rznomics Inc, Seongnam 13486, Republic of Korea
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin 16890, Republic of Korea
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15
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Niu D, Wu Y, Lian J. Circular RNA vaccine in disease prevention and treatment. Signal Transduct Target Ther 2023; 8:341. [PMID: 37691066 PMCID: PMC10493228 DOI: 10.1038/s41392-023-01561-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/02/2023] [Accepted: 07/09/2023] [Indexed: 09/12/2023] Open
Abstract
CircRNAs are a class of single-stranded RNAs with covalently linked head-to-tail topology. In the decades since its initial discovery, their biogenesis, regulation, and function have rapidly disclosed, permitting a better understanding and adoption of them as new tools for medical applications. With the development of biotechnology and molecular medicine, artificial circRNAs have been engineered as a novel class of vaccines for disease treatment and prevention. Unlike the linear mRNA vaccine which applications were limited by its instability, inefficiency, and innate immunogenicity, circRNA vaccine which incorporate internal ribosome entry sites (IRESs) and open reading frame (ORF) provides an improved approach to RNA-based vaccination with safety, stability, simplicity of manufacture, and scalability. However, circRNA vaccines are at an early stage, and their optimization, delivery and applications require further development and evaluation. In this review, we comprehensively describe circRNA vaccine, including their history and superiority. We also summarize and discuss the current methodological research for circRNA vaccine preparation, including their design, synthesis, and purification. Finally, we highlight the delivery options of circRNA vaccine and its potential applications in diseases treatment and prevention. Considering their unique high stability, low immunogenicity, protein/peptide-coding capacity and special closed-loop construction, circRNA vaccine, and circRNA-based therapeutic platforms may have superior application prospects in a broad range of diseases.
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Affiliation(s)
- Dun Niu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Yaran Wu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China
| | - Jiqin Lian
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
- Department of Clinical Biochemistry, Army Medical University (Third Military Medical University), 400038, Chongqing, China.
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16
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Wei HH, Zheng L, Wang Z. mRNA therapeutics: New vaccination and beyond. FUNDAMENTAL RESEARCH 2023; 3:749-759. [PMID: 38933291 PMCID: PMC10017382 DOI: 10.1016/j.fmre.2023.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
The idea of mRNA therapy had been conceived for decades before it came into reality during the Covid-19 pandemic. The mRNA vaccine emerges as a powerful and general tool against new viral infections, largely due to its versatility and rapid development. In addition to prophylactic vaccines, mRNA technology also offers great promise for new applications as a versatile drug modality. However, realizing the conceptual potential faces considerable challenges, such as minimal immune stimulation, high and long-term expression, and efficient delivery to target cells and tissues. Here we review the applications of mRNA-based therapeutics, with emphasis on the innovative design and future challenges/solutions. In addition, we also discuss the next generation of mRNA therapy, including circular mRNA and self-amplifying RNAs. We aim to provide a conceptual overview and outlook on mRNA therapeutics beyond prophylactic vaccines.
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Affiliation(s)
- Huan-Huan Wei
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Shanghai Institute of Nutrition and Health, Shanghai 200032, China
| | | | - Zefeng Wang
- Bio-med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Shanghai Institute of Nutrition and Health, Shanghai 200032, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Beijing 100049, China
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17
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Liu J, Zhao F, Chen LL, Su S. Dysregulation of circular RNAs in inflammation and cancers. FUNDAMENTAL RESEARCH 2023; 3:683-691. [PMID: 38933304 PMCID: PMC11197579 DOI: 10.1016/j.fmre.2023.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/24/2023] [Accepted: 04/19/2023] [Indexed: 06/28/2024] Open
Abstract
Emerging lines of evidence have shown that the production of the covalently closed single-stranded circular RNAs is not splicing errors, but rather a regulated process with distinct biogenesis and turnover. Circular RNAs are expressed in a cell type- and tissue-specific manner and often localize to specific subcellular regions or organelles for functions. The dysregulation of circular RNAs from birth to death is linked to the pathogenesis and progression of diverse diseases. This review outlines how aberrant circular RNA biogenesis, subcellular location, and degradation are linked to disease progression, focusing on metaflammation and cancers. We also discuss potential therapeutic strategies and obstacles in targeting such disease-related circular RNAs.
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Affiliation(s)
- Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310003, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200092, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310003, China
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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18
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Cui J, Zhang L, Zhang Z, Luo X, Liu Y, Li C, Huang W, Zou L, Yu X, Xiao F. A precise and efficient circular RNA synthesis system based on a ribozyme derived from Tetrahymena thermophila. Nucleic Acids Res 2023; 51:e78. [PMID: 37378451 PMCID: PMC10415121 DOI: 10.1093/nar/gkad554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 05/17/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Classic strategies for circular RNA (circRNA) preparation always introduce large numbers of linear transcripts or extra nucleotides to the circularized product. In this study, we aimed to develop an efficient system for circRNA preparation based on a self-splicing ribozyme derived from an optimized Tetrahymena thermophila group Ⅰ intron. The target RNA sequence was inserted downstream of the ribozyme and a complementary antisense region was added upstream of the ribozyme to assist cyclization. Then, we compared the circularization efficiency of ribozyme or flanking intronic complementary sequence (ICS)-mediated methods through the DNMT1, CDR1as, FOXO3, and HIPK3 genes and found that the efficiency of our system was remarkably higher than that of flanking ICS-mediated method. Consequently, the circularized products mediated by ribozyme are not introduced with additional nucleotides. Meanwhile, the overexpressed circFOXO3 maintained its biological functions in regulating cell proliferation, migration, and apoptosis. Finally, a ribozyme-based circular mRNA expression system was demonstrated with a split green fluorescent protein (GFP) using an optimized Coxsackievirus B3 (CVB3) internal ribosome entry site (IRES) sequence, and this system achieved successful translation of circularized mRNA. Therefore, this novel, convenient, and rapid engineering RNA circularization system can be applied for the functional study and large-scale preparation of circular RNA in the future.
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Affiliation(s)
- Jingyi Cui
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
- Graduate School of Peking Union Medical College, Beijing 100730, PR China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Lanxin Zhang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Zaifeng Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
- Graduate School of Peking Union Medical College, Beijing 100730, PR China
| | - Xuanmei Luo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
| | - Ye Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
| | - Chang Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
| | - Wei Huang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
| | - Lihui Zou
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
| | - Xue Yu
- Department of Cardiology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
| | - Fei Xiao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, PR China
- Graduate School of Peking Union Medical College, Beijing 100730, PR China
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China
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Maarouf M, Wang L, Wang Y, Rai KR, Chen Y, Fang M, Chen JL. Functional Involvement of circRNAs in the Innate Immune Responses to Viral Infection. Viruses 2023; 15:1697. [PMID: 37632040 PMCID: PMC10458642 DOI: 10.3390/v15081697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Effective viral clearance requires fine-tuned immune responses to minimize undesirable inflammatory responses. Circular RNAs (circRNAs) are a class of non-coding RNAs that are abundant and highly stable, formed by backsplicing pre-mRNAs, and expressed ubiquitously in eukaryotic cells, emerging as critical regulators of a plethora of signaling pathways. Recent progress in high-throughput sequencing has enabled a better understanding of the physiological and pathophysiological functions of circRNAs, overcoming the obstacle of the sequence overlap between circRNAs and their linear cognate mRNAs. Some viruses also encode circRNAs implicated in viral replication or disease progression. There is increasing evidence that viral infections dysregulate circRNA expression and that the altered expression of circRNAs is critical in regulating viral infection and replication. circRNAs were shown to regulate gene expression via microRNA and protein sponging or via encoding small polypeptides. Recent studies have also highlighted the potential role of circRNAs as promising diagnostic and prognostic biomarkers, RNA vaccines and antiviral therapy candidates due to their higher stability and lower immunogenicity. This review presents an up-to-date summary of the mechanistic involvement of circRNAs in innate immunity against viral infections, the current understanding of their regulatory roles, and the suggested applications.
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Affiliation(s)
- Mohamed Maarouf
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Lulu Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiming Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kul Raj Rai
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Microbiology, ShiGan International College of Science and Technology/ShiGan Health Foundation, Narayangopal Chowk, Kathmandu 44600, Nepal
| | - Yuhai Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Ji-Long Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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20
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Gu A, Jaijyan DK, Yang S, Zeng M, Pei S, Zhu H. Functions of Circular RNA in Human Diseases and Illnesses. Noncoding RNA 2023; 9:38. [PMID: 37489458 PMCID: PMC10366867 DOI: 10.3390/ncrna9040038] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/26/2023] Open
Abstract
Circular RNAs (circRNAs) represent single-stranded RNA species that contain covalently closed 3' and 5' ends that provide them more stability than linear RNA, which has free ends. Emerging evidence indicates that circRNAs perform essential functions in many DNA viruses, including coronaviruses, Epstein-Barr viruses, cytomegalovirus, and Kaposi sarcoma viruses. Recent studies have confirmed that circRNAs are present in viruses, including DNA and RNA viruses, and play various important functions such as evading host immune response, disease pathogenesis, protein translation, miRNA sponges, regulating cell proliferation, and virus replication. Studies have confirmed that circRNAs can be biological signatures or pathological markers for autoimmune diseases, neurological diseases, and cancers. However, our understanding of circRNAs in DNA and RNA viruses is still limited, and functional evaluation of viral and host circRNAs is essential to completely understand their biological functions. In the present review, we describe the metabolism and cellular roles of circRNA, including its roles in various diseases and viral and cellular circRNA functions. Circular RNAs are found to interact with RNA, proteins, and DNA, and thus can modulate cellular processes, including translation, transcription, splicing, and other functions. Circular RNAs interfere with various signaling pathways and take part in vital functions in various biological, physiological, cellular, and pathophysiological processes. We also summarize recent evidence demonstrating cellular and viral circRNA's roles in DNA and RNA viruses in this growing field of research.
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Affiliation(s)
- Alison Gu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Dabbu Kumar Jaijyan
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Shaomin Yang
- Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen 518052, China
| | - Mulan Zeng
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Shaokai Pei
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ 070101, USA
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21
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Zhang F, Jiang J, Qian H, Yan Y, Xu W. Exosomal circRNA: emerging insights into cancer progression and clinical application potential. J Hematol Oncol 2023; 16:67. [PMID: 37365670 DOI: 10.1186/s13045-023-01452-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/10/2023] [Indexed: 06/28/2023] Open
Abstract
Exosomal circRNA serves a novel genetic information molecule, facilitating communication between tumor cells and microenvironmental cells, such as immune cells, fibroblasts, and other components, thereby regulating critical aspects of cancer progression including immune escape, tumor angiogenesis, metabolism, drug resistance, proliferation and metastasis. Interestingly, microenvironment cells have new findings in influencing tumor progression and immune escape mediated by the release of exosomal circRNA. Given the intrinsic stability, abundance, and broad distribution of exosomal circRNAs, they represent excellent diagnostic and prognostic biomarkers for liquid biopsy. Moreover, artificially synthesized circRNAs may open up new possibilities for cancer therapy, potentially bolstered by nanoparticles or plant exosome delivery strategies. In this review, we summarize the functions and underlying mechanisms of tumor cell and non-tumor cell-derived exosomal circRNAs in cancer progression, with a special focus on their roles in tumor immunity and metabolism. Finally, we examine the potential application of exosomal circRNAs as diagnostic biomarkers and therapeutic targets, highlighting their promise for clinical use.
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Affiliation(s)
- Fan Zhang
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, 279 Jingang Road, Zhangjiagang, Suzhou, 215600, Jiangsu, People's Republic of China
- Zhenjiang Key Laboratory of High Technology Research on sEVs Foundation and Transformation Application, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Jiajia Jiang
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, 279 Jingang Road, Zhangjiagang, Suzhou, 215600, Jiangsu, People's Republic of China
- Zhenjiang Key Laboratory of High Technology Research on sEVs Foundation and Transformation Application, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Hui Qian
- Zhenjiang Key Laboratory of High Technology Research on sEVs Foundation and Transformation Application, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Yongmin Yan
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, 279 Jingang Road, Zhangjiagang, Suzhou, 215600, Jiangsu, People's Republic of China.
- Department of Laboratory Medicine, Wujin Hospital Affiliated with Jiangsu University, No. 2 North Yongning Road, Changzhou, 213017, Jiangsu, People's Republic of China.
| | - Wenrong Xu
- Aoyang Institute of Cancer, Affiliated Aoyang Hospital of Jiangsu University, 279 Jingang Road, Zhangjiagang, Suzhou, 215600, Jiangsu, People's Republic of China.
- Zhenjiang Key Laboratory of High Technology Research on sEVs Foundation and Transformation Application, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
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22
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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] [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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23
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Wu C, Wang S, Cao T, Huang T, Xu L, Wang J, Li Q, Wang Y, Qian L, Xu L, Xia Y, Huang X. Newly discovered mechanisms that mediate tumorigenesis and tumour progression: circRNA-encoded proteins. J Cell Mol Med 2023; 27:1609-1620. [PMID: 37070530 PMCID: PMC10273065 DOI: 10.1111/jcmm.17751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/18/2023] [Accepted: 04/08/2023] [Indexed: 04/19/2023] Open
Abstract
Proteins produced by cap-independent translation mediated by an internal ribosome entry site (IRES) in circular RNAs (circRNAs) play important roles in tumour progression. To date, numerous studies have been performed on circRNAs and the proteins they encode. In this review, we summarize the biogenesis of circRNAs and the mechanisms regulating circRNA-encoded proteins expression. We also describe relevant research methods and their applications to biological processes such as tumour cell proliferation, metastasis, epithelial-mesenchymal transition (EMT), apoptosis, autophagy and chemoresistance. This paper offers deeper insights into the roles that circRNA-encoded proteins play in tumours. It also provides a theoretical basis for the use of circRNA-encoded proteins as biomarkers of tumorigenesis and for the development of new targets for tumour therapy.
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Affiliation(s)
- Chengwei Wu
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Song Wang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Tingting Cao
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Tao Huang
- Department of Thoracic SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
| | - Lishuai Xu
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Jiawei Wang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Qian Li
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Ye Wang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Long Qian
- The Second Affiliated Hospital of Wannan Medical CollegeWuhuChina
| | - Li Xu
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Yabin Xia
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
| | - Xiaoxu Huang
- Department of Gastrointestinal SurgeryThe First Affiliated Yijishan Hospital of Wannan Medical CollegeWuhuChina
- Key Laboratory of Non‐coding RNA Transformation Research of Anhui Higher Education InstitutionWannan Medical CollegeWuhuChina
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24
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Tai J, Chen YG. Differences in the immunogenicity of engineered circular RNAs. J Mol Cell Biol 2023; 15:mjad002. [PMID: 36787893 PMCID: PMC10257478 DOI: 10.1093/jmcb/mjad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 01/11/2023] [Indexed: 02/16/2023] Open
Affiliation(s)
- Justin Tai
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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25
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Li Z, Lu J. CircRNAs in osteoarthritis: research status and prospect. Front Genet 2023; 14:1173812. [PMID: 37229197 PMCID: PMC10203419 DOI: 10.3389/fgene.2023.1173812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/18/2023] [Indexed: 05/27/2023] Open
Abstract
Osteoarthritis (OA) is the most common joint disease globally, and its progression is irreversible. The mechanism of osteoarthritis is not fully understood. Research on the molecular biological mechanism of OA is deepening, among which epigenetics, especially noncoding RNA, is an emerging hotspot. CircRNA is a unique circular noncoding RNA not degraded by RNase R, so it is a possible clinical target and biomarker. Many studies have found that circRNAs play an essential role in the progression of OA, including extracellular matrix metabolism, autophagy, apoptosis, the proliferation of chondrocytes, inflammation, oxidative stress, cartilage development, and chondrogenic differentiation. Differential expression of circRNAs was also observed in the synovium and subchondral bone in the OA joint. In terms of mechanism, existing studies have mainly found that circRNA adsorbs miRNA through the ceRNA mechanism, and a few studies have found that circRNA can serve as a scaffold for protein reactions. In terms of clinical transformation, circRNAs are considered promising biomarkers, but no large cohort has tested their diagnostic value. Meanwhile, some studies have used circRNAs loaded in extracellular vesicles for OA precision medicine. However, there are still many problems to be solved in the research, such as the role of circRNA in different OA stages or OA subtypes, the construction of animal models of circRNA knockout, and more research on the mechanism of circRNA. In general, circRNAs have a regulatory role in OA and have particular clinical potential, but further studies are needed in the future.
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Affiliation(s)
- Zhuang Li
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Jun Lu
- Department of Orthopaedics, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
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26
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Loan Young T, Chang Wang K, James Varley A, Li B. Clinical Delivery of Circular RNA: Lessons Learned from RNA Drug Development. Adv Drug Deliv Rev 2023; 197:114826. [PMID: 37088404 DOI: 10.1016/j.addr.2023.114826] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Circular RNAs (circRNA) represent a distinct class of covalently closed-loop RNA molecules, which play diverse roles in regulating biological processes and disease states. The enhanced stability of synthetic circRNAs compared to their linear counterparts has recently garnered considerable research interest, paving the way for new therapeutic applications. While clinical circRNA technology is still in its early stages, significant advancements in mRNA technology offer valuable insights into its potential future applications. Two primary obstacles that must be addressed are the development of efficient production methods and the optimization of delivery systems. To expedite progress in this area, this review aims to provide an overview of the current state of knowledge on circRNA structure and function, outline recent techniques for synthesizing circRNAs, highlight key delivery strategies and applications, and discuss the current challenges and future prospects in the field of circRNA-based therapeutics.
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Affiliation(s)
- Tiana Loan Young
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Kevin Chang Wang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Andrew James Varley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Bowen Li
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3M2, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada.
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27
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Hou L, Zhang J, Zhao F. Full-length circular RNA profiling by nanopore sequencing with CIRI-long. Nat Protoc 2023:10.1038/s41596-023-00815-w. [PMID: 37045995 DOI: 10.1038/s41596-023-00815-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/17/2023] [Indexed: 04/14/2023]
Abstract
Circular RNAs (circRNAs) have important roles in regulating developmental processes and disease progression. As most circRNA sequences are highly similar to their cognate linear transcripts, the current short-read sequencing-based methods rely on the back-spliced junction signal for distinguishing circular and linear reads, which does not allow circRNAs' full-length structure to be effectively reconstructed. Here we describe a long-read sequencing-based protocol, CIRI-long, for the detection of full-length circular RNAs. The CIRI-long protocol combines rolling circular reverse transcription and nanopore sequencing to capture full-length circRNA sequences. After poly(A) tailing, RNase R treatment, and size selection of polymerase chain reaction products, CIRI-long achieves an increased percentage (6%) of circular reads in the constructed library, which is 20-fold higher compared with previous Illumina-based strategies. This method can be applied in cell lines or tissue samples, enabling accurate detection of full-length circRNAs in the range of 100-3,000 bp. The entire protocol can be completed in 1 d, and can be scaled up for large-scale analysis using the nanopore barcoding kit and PromethION sequencing device. CIRI-long can serve as an effective and user-friendly protocol for characterizing full-length circRNAs, generating direct and convincing evidence for the existence of detected circRNAs. The analytical pipeline offers convenient functions for identification of full-length circRNA isoforms and integration of multiple datasets. The assembled full-length transcripts and their splicing patterns provide indispensable information to explore the biological function of circRNAs.
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Affiliation(s)
- Lingling Hou
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 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.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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28
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Zhang ZH, Wang Y, Zhang Y, Zheng SF, Feng T, Tian X, Abudurexiti M, Wang ZD, Zhu WK, Su JQ, Zhang HL, Shi GH, Wang ZL, Cao DL, Ye DW. The function and mechanisms of action of circular RNAs in Urologic Cancer. Mol Cancer 2023; 22:61. [PMID: 36966306 PMCID: PMC10039696 DOI: 10.1186/s12943-023-01766-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/17/2023] [Indexed: 03/27/2023] Open
Abstract
Kidney, bladder, and prostate cancer are the three major tumor types of the urologic system that seriously threaten human health. Circular RNAs (CircRNAs), special non-coding RNAs with a stabile structure and a unique back-splicing loop-forming ability, have received recent scientific attention. CircRNAs are widely distributed within the body, with important biologic functions such as sponges for microRNAs, as RNA binding proteins, and as templates for regulation of transcription and protein translation. The abnormal expression of circRNAs in vivo is significantly associated with the development of urologic tumors. CircRNAs have now emerged as potential biomarkers for the diagnosis and prognosis of urologic tumors, as well as targets for the development of new therapies. Although we have gained a better understanding of circRNA, there are still many questions to be answered. In this review, we summarize the properties of circRNAs and detail their function, focusing on the effects of circRNA on proliferation, metastasis, apoptosis, metabolism, and drug resistance in kidney, bladder, and prostate cancers.
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Affiliation(s)
- Zi-Hao Zhang
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Yue Wang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Ya Zhang
- Department of Nephrology, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Sheng-Feng Zheng
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Tao Feng
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Xi Tian
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Mierxiati Abudurexiti
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
- Shanghai Pudong New Area Gongli Hospital, Shanghai, 200135, China
| | - Zhen-Da Wang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Wen-Kai Zhu
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Jia-Qi Su
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Hai-Liang Zhang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Guo-Hai Shi
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Zi-Liang Wang
- Institute of Cancer Research, Department of Gynecology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, P. R. China
| | - Da-Long Cao
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Ding-Wei Ye
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China.
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China.
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29
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Peña-Paladines JJ, Wong CH, Chen Y. Circularized RNA as novel therapeutics in cancer. Int J Biochem Cell Biol 2023; 156:106364. [PMID: 36639095 DOI: 10.1016/j.biocel.2023.106364] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/22/2022] [Accepted: 01/07/2023] [Indexed: 01/12/2023]
Abstract
Circular RNAs (CircRNAs) regulate gene expression by functioning as microRNA sponges, regulating protein stability, and gilding proteins for gene transcription and translation. Also, limited circRNAs harbour protein-coding ability through cap-independent pathways. These molecular mechanisms of circRNAs contribute to their importance in several cellular processes. Particularly, the dysregulation of circRNAs also plays a critical role in disease development. Targeting disease-causing circRNAs by restoring their normal expression by gain-of-function or loss-of-function approach and regulating their molecular activities could be potential direction for the development of anti-cancer therapies. Furthermore, due to unique covalently closed circular structure, the superior stability of circRNAs also grants them as novel therapeutic tools replacing the therapeutic small interfering RNAs and messenger RNAs. Here, we will review the functional and molecular mechanisms of circRNAs in pathogenesis, the current methods for targeting the dysregulated circRNAs, and the potential of using synthetic circRNAs in disease treatment and prevention.
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Affiliation(s)
| | - Chi Hin Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518087, China
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518087, China.
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30
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Kameda S, Ohno H, Saito H. Synthetic circular RNA switches and circuits that control protein expression in mammalian cells. Nucleic Acids Res 2023; 51:e24. [PMID: 36642090 PMCID: PMC9976894 DOI: 10.1093/nar/gkac1252] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
Synthetic messenger RNA (mRNA) has been focused on as an emerging application for mRNA-based therapies and vaccinations. Recently, synthetic circular RNAs (circRNAs) have shown promise as a new class of synthetic mRNA that enables superior stability and persistent gene expression in cells. However, translational control of circRNA remained challenging. Here, we develop 'circRNA switches' capable of controlling protein expression from circRNA by sensing intracellular RNA or proteins. We designed microRNA (miRNA) and protein-responsive circRNA switches by inserting miRNA-binding or protein-binding sequences into untranslated regions (UTRs), or Coxsackievirus B3 Internal Ribosome Entry Site (CVB3 IRES), respectively. Engineered circRNAs efficiently expressed reporter proteins without inducing severe cell cytotoxicity and immunogenicity, and responded to target miRNAs or proteins, controlling translation levels from circRNA in a cell type-specific manner. Moreover, we constructed circRNA-based gene circuits that selectively activated translation by detecting endogenous miRNA, by connecting miRNA and protein-responsive circRNAs. The designed circRNA circuits performed better than the linear mRNA-based circuits in terms of persistent expression levels. Synthetic circRNA devices provide new insights into RNA engineering and have a potential for RNA synthetic biology and therapies.
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Affiliation(s)
- Shigetoshi Kameda
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan.,Graduate School of Medicine, Kyoto University,Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirohisa Ohno
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyoku, Kyoto, 606-8507, Japan
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31
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Bai Y, Liu D, He Q, Liu J, Mao Q, Liang Z. Research progress on circular RNA vaccines. Front Immunol 2023; 13:1091797. [PMID: 36713460 PMCID: PMC9878156 DOI: 10.3389/fimmu.2022.1091797] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Owing to the success of linear mRNA coronavirus disease 2019 (COVID-19) vaccines, biopharmaceutical companies and research teams worldwide have attempted to develop more stable circular RNA (circRNA) vaccines and have achieved some preliminary results. This review aims to summarize key findings and important progress made in circRNA research, the in vivo metabolism and biological functions of circRNAs, and research progress and production process of circRNA vaccines. Further, considerations regarding the quality control of circRNA vaccines are highlighted herein, and the main challenges and problem-solving strategies in circRNA vaccine development and quality control are outlined to provide a reference for circRNA vaccine-related research.
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Affiliation(s)
- Yu Bai
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Dong Liu
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Qian He
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Jianyang Liu
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China
| | - Qunying Mao
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China,*Correspondence: Zhenglun Liang, ; Qunying Mao,
| | - Zhenglun Liang
- Division of Hepatitis and Enterovirus Vaccines, National Institutes for Food and Drug Control, Beijing, China,NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, China,NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute of Biological Products, National Institutes for Food and Drug Control, Beijing, China,*Correspondence: Zhenglun Liang, ; Qunying Mao,
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32
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Liu C, Wu X, Gokulnath P, Li G, Xiao J. The Functions and Mechanisms of Translatable Circular RNAs. J Pharmacol Exp Ther 2023; 384:52-60. [PMID: 35609922 DOI: 10.1124/jpet.122.001085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 04/03/2022] [Accepted: 04/29/2022] [Indexed: 12/27/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA produced by back-splicing. CircRNAs have been considered as a type of noncoding RNAs for a long time. However, recent studies have shown that circRNAs can be translated into functional proteins. Proteins specifically encoded by circRNAs have been proved to play important roles in cancer pathology. In this review, we introduce the methods commonly used to identify and validate circRNA translation in detail. We also describe the major mechanisms driving the translation of these circRNAs. In addition, we summarize the main functions of the circRNA-encoded proteins in both physiologic and pathologic conditions. Finally, we discuss the therapeutic potential and challenges in the usage of synthetic translatable circRNAs. This brief review highlights recent discoveries made in this field and the progress of therapy based on translatable circRNAs. SIGNIFICANCE STATEMENT: Understanding the translation of circRNA could facilitate the identification of novel drug targets in various diseases. Moreover, some circRNA encoded proteins were demonstrated to have therapeutic functions in cancer. The application of synthetic circRNAs as carriers to achieve stable protein expression in vitro and in vivo has tremendous therapeutic potential.
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Affiliation(s)
- Chang Liu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - Xinying Wu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - Priyanka Gokulnath
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - Guoping Li
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
| | - 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, China (C.L., X.W., J.X.); Cardiac Regeneration and Ageing Laboratory, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai, China (C.L., X.W., J.X.); and Cardiovascular Division of the Massachusetts General Hospitaland Harvard Medical School, Boston, Massachusetts (P.G., G.L.)
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33
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Lee KH, Kim S, Lee SW. Pros and Cons of In Vitro Methods for Circular RNA Preparation. Int J Mol Sci 2022; 23:13247. [PMID: 36362032 PMCID: PMC9654983 DOI: 10.3390/ijms232113247] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 08/29/2023] Open
Abstract
mRNA is gaining success as a new therapeutic agent and vaccine. However, mRNA has limitations in stability. To overcome the shortcomings of mRNA, circular RNA is emerging as a new modality. In this review, several current methods of manufacturing circular RNA in vitro are introduced and their advantages and disadvantages are reviewed. Furthermore, this study discusses which fields and directions of research and development are needed for the increase in the efficacy and productivity of circular RNA as a therapeutic agent and vaccine formulation.
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Affiliation(s)
| | | | - Seong-Wook Lee
- R&D Center, Rznomics Inc., Seongnam 13486, Korea
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin 16890, Korea
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Abstract
Covalently closed, single-stranded circular RNAs can be produced from viral RNA genomes as well as from the processing of cellular housekeeping noncoding RNAs and precursor messenger RNAs. Recent transcriptomic studies have surprisingly uncovered that many protein-coding genes can be subjected to backsplicing, leading to widespread expression of a specific type of circular RNAs (circRNAs) in eukaryotic cells. Here, we discuss experimental strategies used to discover and characterize diverse circRNAs at both the genome and individual gene scales. We further highlight the current understanding of how circRNAs are generated and how the mature transcripts function. Some circRNAs act as noncoding RNAs to impact gene regulation by serving as decoys or competitors for microRNAs and proteins. Others form extensive networks of ribonucleoprotein complexes or encode functional peptides that are translated in response to certain cellular stresses. Overall, circRNAs have emerged as an important class of RNAmolecules in gene expression regulation that impact many physiological processes, including early development, immune responses, neurogenesis, and tumorigenesis.
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Affiliation(s)
- 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, Shanghai, China;
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, Texas, USA;
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China;
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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35
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Huang N, Dong H, Shao B. Phase separation in immune regulation and immune-related diseases. J Mol Med (Berl) 2022; 100:1427-1440. [PMID: 36085373 PMCID: PMC9462646 DOI: 10.1007/s00109-022-02253-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/28/2022]
Abstract
Phase separation is an emerging paradigm for understanding the biochemical interactions between proteins, DNA, and RNA. Research over the past decade has provided mounting evidence that phase separation modulates a great variety of cellular activities. Particularly, phase separation is directly relevant to immune signaling, immune cells, and immune-related diseases like cancer, neurodegenerative diseases, and even SARS-CoV-2. In this review, we summarized current knowledge of phase separation in immunology and emerging findings related to immune responses as they enable possible treatment approaches.
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Affiliation(s)
- Ning Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases and State Key Laboratory of Biotherapy, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Hao Dong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases and State Key Laboratory of Biotherapy, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Bin Shao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases and State Key Laboratory of Biotherapy, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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36
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Huang Y, Li Y, Lin W, Fan S, Chen H, Xia J, Pi J, Xu JF. Promising Roles of Circular RNAs as Biomarkers and Targets for Potential Diagnosis and Therapy of Tuberculosis. Biomolecules 2022; 12:biom12091235. [PMID: 36139074 PMCID: PMC9496049 DOI: 10.3390/biom12091235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) infection, remains one of the most threatening infectious diseases worldwide. A series of challenges still exist for TB prevention, diagnosis and treatment, which therefore require more attempts to clarify the pathological and immunological mechanisms in the development and progression of TB. Circular RNAs (circRNAs) are a large class of non-coding RNA, mostly expressed in eukaryotic cells, which are generated by the spliceosome through the back-splicing of linear RNAs. Accumulating studies have identified that circRNAs are widely involved in a variety of physiological and pathological processes, acting as the sponges or decoys for microRNAs and proteins, scaffold platforms for proteins, modulators for transcription and special templates for translation. Due to the stable and widely spread characteristics of circRNAs, they are expected to serve as promising prognostic/diagnostic biomarkers and therapeutic targets for diseases. In this review, we briefly describe the biogenesis, classification, detection technology and functions of circRNAs, and, in particular, outline the dynamic, and sometimes aberrant changes of circRNAs in TB. Moreover, we further summarize the recent progress of research linking circRNAs to TB-related pathogenetic processes, as well as the potential roles of circRNAs as diagnostic biomarkers and miRNAs sponges in the case of Mtb infection, which is expected to enhance our understanding of TB and provide some novel ideas about how to overcome the challenges associated TB in the future.
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Affiliation(s)
- Yifan Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Wensen Lin
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Shuhao Fan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Haorong Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Jiaojiao Xia
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Jiang Pi
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
- Correspondence: (J.P.); (J.-F.X.)
| | - Jun-Fa Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- Institute of Laboratory Medicine, School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
- Correspondence: (J.P.); (J.-F.X.)
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37
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Rahmani-Kukia N, Abbasi A. New insights on circular RNAs and their potential applications as biomarkers, therapeutic agents, and preventive vaccines in viral infections: with a glance at SARS-CoV-2. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:705-717. [PMID: 35992045 PMCID: PMC9375856 DOI: 10.1016/j.omtn.2022.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The occurrence of viral infections and approaches to handling them are very challenging and require prompt diagnosis and timely treatment. Recently, genomic medicine approaches have come up with the discovery of the competing endogenous RNA (ceRNA) network, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) on the basis of gene silencing. CircRNAs, as a group of non-encoded RNAs, make a loop-like structure by back-splicing through 3′ and 5′ ends. They are stable, abundant, specific, and highly conserved and can be quickly generated at large scales in vitro. CircRNAs have the potential to contribute in several cellular processes in a way that some serve as microRNA sponges, cellular transporters, protein-binding RNAs, transcriptional regulators, and immune system modulators. CircRNAs can even play an important role in modulating antiviral immune responses. In the present review, circRNAs’ biogenesis, function, and biomarker and therapeutic potential as well as their prospective applications as vaccines against viral infections such as SARS-CoV-2 are explained. By considering their unique properties, their potential to be used as novel vaccines, biomarkers, and a therapeutic approach appears possible.
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38
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Liu X, Zhang Y, Zhou S, Dain L, Mei L, Zhu G. Circular RNA: An emerging frontier in RNA therapeutic targets, RNA therapeutics, and mRNA vaccines. J Control Release 2022; 348:84-94. [PMID: 35649485 PMCID: PMC9644292 DOI: 10.1016/j.jconrel.2022.05.043] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
Circular RNAs (circRNA) is a class of natural (biogenic) or synthetic closed RNA without 5' or 3' ends. Meanwhile, their unique covalently-closed structures of circRNA prevent RNA degradation by exonucleases, thereby empowering them with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNA. Natural circRNA can be non-coding RNAs as well as protein-coding RNA, the latter of which was recently discovered. The physiological functions of biogenic circRNAs, which largely remain elusive, include protein and gene sponges, cell activity modulators, and protein translation. The discovery that the circRNA levels can be correlated with some human diseases empowers circRNA with the potential as a novel type of disease biomarkers and a noncanonical class of therapeutic targets. Recently, synthetic circRNA have been engineered to explore their applications as a novel class of mRNA therapeutics and vaccines. In this review, we will discuss the current understanding of the biogenesis and physiological functions of natural circRNAs, the approaches to circRNA synthesis, and current research in the exploration of endogenous circRNAs as novel therapeutic targets and testing circRNAs as an emerging class of RNA therapeutics and vaccines.
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Affiliation(s)
- Xiang Liu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Yu Zhang
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Shurong Zhou
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lauren Dain
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lei Mei
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Guizhi Zhu
- Department of Pharmaceutics and Center for Pharmaceutical Engineering and Sciences, School of Pharmacy, Institute for Structural Biology and Drug Discovery, The Developmental Therapeutics Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.
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39
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Zhu Y, Zhu L, Wang X, Jin H. RNA-based therapeutics: an overview and prospectus. Cell Death Dis 2022; 13:644. [PMID: 35871216 PMCID: PMC9308039 DOI: 10.1038/s41419-022-05075-2] [Citation(s) in RCA: 145] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
The growing understanding of RNA functions and their crucial roles in diseases promotes the application of various RNAs to selectively function on hitherto "undruggable" proteins, transcripts and genes, thus potentially broadening the therapeutic targets. Several RNA-based medications have been approved for clinical use, while others are still under investigation or preclinical trials. Various techniques have been explored to promote RNA intracellular trafficking and metabolic stability, despite significant challenges in developing RNA-based therapeutics. In this review, the mechanisms of action, challenges, solutions, and clinical application of RNA-based therapeutics have been comprehensively summarized.
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Affiliation(s)
- Yiran Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
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40
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Yao X, Zhang Q. Function and Clinical Significance of Circular RNAs in Thyroid Cancer. Front Mol Biosci 2022; 9:925389. [PMID: 35936780 PMCID: PMC9353217 DOI: 10.3389/fmolb.2022.925389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/22/2022] [Indexed: 12/28/2022] Open
Abstract
Thyroid cancer (TC) is the leading cause and mortality of endocrine malignancies worldwide. Tumourigenesis involves multiple molecules including circular RNAs (circRNAs). circRNAs with covalently closed single-stranded structures have been identified as a type of regulatory RNA because of their high stability, abundance, and tissue/developmental stage-specific expression. Accumulating evidence has demonstrated that various circRNAs are aberrantly expressed in thyroid tissues, cells, exosomes, and body fluids in patients with TC. CircRNAs have been identified as either oncogenic or tumour suppressor roles in regulating tumourigenesis, tumour metabolism, metastasis, ferroptosis, and chemoradiation resistance in TC. Importantly, circRNAs exert pivotal effects on TC through various mechanisms, including acting as miRNA sponges or decoys, interacting with RNA-binding proteins, and translating functional peptides. Recent studies have suggested that many different circRNAs are associated with certain clinicopathological features, implying that the altered expression of circRNAs may be characteristic of TC. The purpose of this review is to provide an overview of recent advances on the dysregulation, functions, molecular mechanisms and potential clinical applications of circRNAs in TC. This review also aimes to improve our understanding of the functions of circRNAs in the initiation and progression of cancer, and to discuss the future perspectives on strategies targeting circRNAs in TC.
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41
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Liu CX, Chen LL. Circular RNAs: Characterization, cellular roles, and applications. Cell 2022; 185:2016-2034. [PMID: 35584701 DOI: 10.1016/j.cell.2022.04.021] [Citation(s) in RCA: 297] [Impact Index Per Article: 148.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 02/07/2023]
Abstract
Most circular RNAs are produced from the back-splicing of exons of precursor mRNAs. Recent technological advances have in part overcome problems with their circular conformation and sequence overlap with linear cognate mRNAs, allowing a better understanding of their cellular roles. Depending on their localization and specific interactions with DNA, RNA, and proteins, circular RNAs can modulate transcription and splicing, regulate stability and translation of cytoplasmic mRNAs, interfere with signaling pathways, and serve as templates for translation in different biological and pathophysiological contexts. Emerging applications of RNA circles to interfere with cellular processes, modulate immune responses, and direct translation into proteins shed new light on biomedical research. In this review, we discuss approaches used in circular RNA studies and the current understanding of their regulatory roles and potential applications.
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Affiliation(s)
- Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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42
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Awan FM. The HOPE for Pandora’s Box of artificial circular RNA immunogenicity. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:640-642. [PMID: 35614995 PMCID: PMC9112057 DOI: 10.1016/j.omtn.2022.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Faryal Mehwish Awan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, 22620 Khyber Pakhtunkhwa, Pakistan
- Corresponding author Faryal Mehwish Awan, Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, 22620 Khyber Pakhtunkhwa, Pakistan.
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43
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Qu L, Yi Z, Shen Y, Lin L, Chen F, Xu Y, Wu Z, Tang H, Zhang X, Tian F, Wang C, Xiao X, Dong X, Guo L, Lu S, Yang C, Tang C, Yang Y, Yu W, Wang J, Zhou Y, Huang Q, Yisimayi A, Liu S, Huang W, Cao Y, Wang Y, Zhou Z, Peng X, Wang J, Xie XS, Wei W. Circular RNA vaccines against SARS-CoV-2 and emerging variants. Cell 2022; 185:1728-1744.e16. [PMID: 35460644 PMCID: PMC8971115 DOI: 10.1016/j.cell.2022.03.044] [Citation(s) in RCA: 203] [Impact Index Per Article: 101.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/11/2022] [Accepted: 03/30/2022] [Indexed: 02/08/2023]
Abstract
As the emerging variants of SARS-CoV-2 continue to drive the worldwide pandemic, there is a constant demand for vaccines that offer more effective and broad-spectrum protection. Here, we report a circular RNA (circRNA) vaccine that elicited potent neutralizing antibodies and T cell responses by expressing the trimeric RBD of the spike protein, providing robust protection against SARS-CoV-2 in both mice and rhesus macaques. Notably, the circRNA vaccine enabled higher and more durable antigen production than the 1mΨ-modified mRNA vaccine and elicited a higher proportion of neutralizing antibodies and distinct Th1-skewed immune responses. Importantly, we found that the circRNARBD-Omicron vaccine induced effective neutralizing antibodies against the Omicron but not the Delta variant. In contrast, the circRNARBD-Delta vaccine protected against both Delta and Omicron or functioned as a booster after two doses of either native- or Delta-specific vaccination, making it a favorable choice against the current variants of concern (VOCs) of SARS-CoV-2.
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Affiliation(s)
- Liang Qu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zongyi Yi
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yong Shen
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Liangru Lin
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Feng Chen
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yiyuan Xu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Huixian Tang
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoxue Zhang
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Feng Tian
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chunhui Wang
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xia Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaojing Dong
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Li Guo
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Shuaiyao Lu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Chengyun Yang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Cong Tang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Yun Yang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Wenhai Yu
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Junbin Wang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Yanan Zhou
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Qing Huang
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Ayijiang Yisimayi
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shuo Liu
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing 102629, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing 102629, China
| | - Yunlong Cao
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing 102629, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaozhong Peng
- National Kunming High-level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China; State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaoliang Sunney Xie
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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Wen SY, Qadir J, Yang BB. Circular RNA translation: novel protein isoforms and clinical significance. Trends Mol Med 2022; 28:405-420. [DOI: 10.1016/j.molmed.2022.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
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Abe BT, Wesselhoeft RA, Chen R, Anderson DG, Chang HY. Circular RNA migration in agarose gel electrophoresis. Mol Cell 2022; 82:1768-1777.e3. [PMID: 35358469 PMCID: PMC9081248 DOI: 10.1016/j.molcel.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/24/2022] [Accepted: 03/02/2022] [Indexed: 12/18/2022]
Abstract
Circular RNAs are garnering increasing interest as potential regulatory RNAs and a format for gene expression. The characterization of circular RNA using analytical techniques commonly employed in the literature, such as gel electrophoresis, can, under differing conditions, yield different results when attempting to distinguish circular RNA from linear RNA of similar molecular weights. Here, we describe circular RNA migration in different conditions, analyzed by gel electrophoresis and high-performance liquid chromatography (HPLC). We characterize key parameters that affect the migration pattern of circular RNA in gel electrophoresis systems, which include gel type, electrophoresis time, sample buffer composition, and voltage. Finally, we demonstrate the utility of orthogonal analytical tests for circular RNA that take advantage of its covalently closed structure to further distinguish circular RNA from linear RNA following in vitro synthesis.
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Affiliation(s)
- Brian T Abe
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Robert Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Institute for Medical Engineering and Science, and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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Wu N, Qadir J, Yang BB. CircRNA perspective: new strategies for RNA therapy. Trends Mol Med 2022; 28:343-344. [DOI: 10.1016/j.molmed.2022.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/24/2022]
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