51
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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: 26] [Impact Index Per Article: 26.0] [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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52
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Tassinari V, La Rosa P, Guida E, Colopi A, Caratelli S, De Paolis F, Gallo A, Cenciarelli C, Sconocchia G, Dolci S, Cesarini V. Contribution of A-to-I RNA editing, M6A RNA Methylation, and Alternative Splicing to physiological brain aging and neurodegenerative diseases. Mech Ageing Dev 2023; 212:111807. [PMID: 37023929 DOI: 10.1016/j.mad.2023.111807] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Aging is a physiological and progressive phenomenon in all organisms' life cycle, characterized by the accumulation of degenerative processes triggered by several alterations within molecular pathways. These changes compromise cell fate, resulting in the loss of functions in tissues throughout the body, including the brain. Physiological brain aging has been linked to structural and functional alterations, as well as to an increased risk of neurodegenerative diseases. Post-transcriptional RNA modifications modulate mRNA coding properties, stability, translatability, expanding the coding capacity of the genome, and are involved in all cellular processes. Among mRNA post-transcriptional modifications, the A-to-I RNA editing, m6A RNA Methylation and Alternative Splicing play a critical role in all the phases of a neuronal cell life cycle and alterations in their mechanisms of action significantly contribute to aging and neurodegeneration. Here we review our current understanding of the contribution of A-to-I RNA editing, m6A RNA Methylation, and Alternative Splicing to physiological brain aging process and neurodegenerative diseases.
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Affiliation(s)
- Valentina Tassinari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Ambra Colopi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Sara Caratelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Francesca De Paolis
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Angela Gallo
- RNA Editing Lab., Oncohaematology Department, Cellular and Gene Therapy Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Cenciarelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Giuseppe Sconocchia
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Valeriana Cesarini
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
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53
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Diaz Quiroz JF, Siskel LD, Rosenthal JJC. Site-directed A → I RNA editing as a therapeutic tool: moving beyond genetic mutations. RNA (NEW YORK, N.Y.) 2023; 29:498-505. [PMID: 36669890 PMCID: PMC10019371 DOI: 10.1261/rna.079518.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Adenosine deamination by the ADAR family of enzymes is a natural process that edits genetic information as it passes through messenger RNA. Adenosine is converted to inosine in mRNAs, and this base is interpreted as guanosine during translation. Realizing the potential of this activity for therapeutics, a number of researchers have developed systems that redirect ADAR activity to new targets, ones that are not normally edited. These site-directed RNA editing (SDRE) systems can be broadly classified into two categories: ones that deliver an antisense RNA oligonucleotide to bind opposite a target adenosine, creating an editable structure that endogenously expressed ADARs recognize, and ones that tether the catalytic domain of recombinant ADAR to an antisense RNA oligonucleotide that serves as a targeting mechanism, much like with CRISPR-Cas or RNAi. To date, SDRE has been used mostly to try and correct genetic mutations. Here we argue that these applications are not ideal SDRE, mostly because RNA edits are transient and genetic mutations are not. Instead, we suggest that SDRE could be used to tune cell physiology to achieve temporary outcomes that are therapeutically advantageous, particularly in the nervous system. These include manipulating excitability in nociceptive neural circuits, abolishing specific phosphorylation events to reduce protein aggregation related to neurodegeneration or reduce the glial scarring that inhibits nerve regeneration, or enhancing G protein-coupled receptor signaling to increase nerve proliferation for the treatment of sensory disorders like blindness and deafness.
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Affiliation(s)
- Juan F Diaz Quiroz
- Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Louise D Siskel
- Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
| | - Joshua J C Rosenthal
- Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
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54
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Lipid nanoparticle-based ribonucleoprotein delivery for in vivo genome editing. J Control Release 2023; 355:406-416. [PMID: 36773957 DOI: 10.1016/j.jconrel.2023.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/12/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system is a technology that is used to perform site-specific gene disruption, repair, and the modification of genomic DNA via DNA repair mechanisms, and is expected to be a fundamental therapeutic strategy for the treatment of infectious diseases and genetic disorders. For clinical applications, the non-viral vector-based delivery of the CRISPR/Cas ribonucleoprotein (RNP) is important, but the poor efficiency of delivery and the lack of a practical method for its manufacture remains as an issue. We report herein on the development of a lipid nanoparticle (LNP)-based Cas RNP delivery system based on optimally designed single stranded oligonucleotides (ssODNs) that allow efficient in vivo genome editing. The formation of sequence-specific RNP-ssODN complexes was found to be important for the functional delivery of RNP. Furthermore, the melting temperature (Tm) between sgRNA and ssODN had a significant effect on in vivo gene knockout efficiency. An ssODN with a high Tm resulted in limited knockout (KO) activity while that at near room temperature showed the highest KO activity, indicating the importance of the cytosolic release of RNPs. Two consecutive intravenous injections of the Tm optimized formulation achieved approximately 70% and 80% transthyretin KO at the DNA and protein level, respectively, without any obvious toxicity. These findings represent a significant contribution to the development of safe in vivo CRISPR/Cas RNP delivery technology and its practical application in genome editing therapies.
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55
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Zhang P, Zhu Y, Guo Q, Li J, Zhan X, Yu H, Xie N, Tan H, Lundholm N, Garcia-Cuetos L, Martin MD, Subirats MA, Su YH, Ruiz-Trillo I, Martindale MQ, Yu JK, Gilbert MTP, Zhang G, Li Q. On the origin and evolution of RNA editing in metazoans. Cell Rep 2023; 42:112112. [PMID: 36795564 PMCID: PMC9989829 DOI: 10.1016/j.celrep.2023.112112] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.
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Affiliation(s)
- Pei Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Qunfei Guo
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Li
- BGI Research-Wuhan, BGI, Wuhan 430074, China
| | | | - Hao Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Nianxia Xie
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Lydia Garcia-Cuetos
- Natural History Museum of Denmark, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Theoretical Evolutionary Genomics, Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology, UPF-CSIC Barcelona, 08003 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Bilogia, Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan 26242, Taiwan
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guojie Zhang
- Center of Evolutionary and Organismal Biology, & Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Qiye Li
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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56
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CircRNA_0017076 acts as a sponge for miR-185-5p in the control of epithelial-to-mesenchymal transition of tubular epithelial cells during renal interstitial fibrosis. Hum Cell 2023; 36:1024-1040. [PMID: 36828974 DOI: 10.1007/s13577-023-00877-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/04/2023] [Indexed: 02/26/2023]
Abstract
Renal interstitial fibrosis (RIF) is a common pathological hallmark of progressive chronic kidney disease (CKD). Circular RNAs (circRNAs) are involved in certain renal diseases, but their role in RIF is largely unknown. The present study investigated the effects and potential mechanisms of circRNA_0017076 in RIF. CircRNA_0017076 expression was markedly upregulated in transforming growth factor-β1 (TGF-β1)-treated renal tubular epithelial cells (RTECs) and kidney biopsy samples from patients with RIF. Functional assays showed that circRNA_0017076 colocalized with microRNA-185-5p (miR-185-5p) and inhibited miR-185-5p function via direct binding to miR-185-5p. In vitro, the knockdown of circRNA_0017076 inhibited the calcium ion (Ca2+) influx-mediated epithelial-to-mesenchymal transition (EMT) of RTECs and downregulated the expression of stromal interaction molecule 1 (STIM1), which is a target protein of miR-185-5p. Silencing mmu_circ_0004488 reduced fibrotic lesions in the kidneys of unilateral ureteral obstruction (UUO) mice by targeting the miR-185-5p/Stim1 axis. For the first time, we identified circRNA_0017076 as a sponge for miR-185-5p, which regulates STIM1 gene expression and is involved in RIF. Our results support circRNA_0017076 as a potential therapeutic target for RIF disease.
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57
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Lei Z, Meng H, Zhuang Y, Zhu Q, Yi C. Chemical and Biological Approaches to Interrogate off-Target Effects of Genome Editing Tools. ACS Chem Biol 2023; 18:205-217. [PMID: 36731114 DOI: 10.1021/acschembio.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Various genome editing tools have been developed for programmable genome manipulation at specified genomic loci. However, it is crucial to comprehensively interrogate the off-target effect induced by these genome editing tools, especially when apply them onto the therapeutic applications. Here, we outlined the off-target effect that has been observed for various genome editing tools. We also reviewed detection methods to determine or evaluate the off-target editing, and we have discussed their advantages and limitations. Additionally, we have summarized current RNA editing tools for RNA therapy and medicine that may serve as alternative approaches for genome editing tools in both research and clinical applications.
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Affiliation(s)
- Zhixin Lei
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Haowei Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
| | - Yuan Zhuang
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing100871, China
| | - Qingguo Zhu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Chengqi Yi
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China.,Peking University Genome Editing Research Center, Peking University, Beijing100871, China
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58
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Tao J, Bauer DE, Chiarle R. Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing. Nat Commun 2023; 14:212. [PMID: 36639728 PMCID: PMC9838544 DOI: 10.1038/s41467-023-35886-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/06/2023] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas gene editing has revolutionized experimental molecular biology over the past decade and holds great promise for the treatment of human genetic diseases. Here we review the development of CRISPR-Cas9/Cas12/Cas13 nucleases, DNA base editors, prime editors, and RNA base editors, focusing on the assessment and improvement of their editing precision and safety, pushing the limit of editing specificity and efficiency. We summarize the capabilities and limitations of each CRISPR tool from DNA editing to RNA editing, and highlight the opportunities for future improvements and applications in basic research, as well as the therapeutic and clinical considerations for their use in patients.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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59
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Song J, Dong L, Sun H, Luo N, Huang Q, Li K, Shen X, Jiang Z, Lv Z, Peng L, Zhang M, Wang K, Liu K, Hong J, Yi C. CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons. Mol Cell 2023; 83:139-155.e9. [PMID: 36521489 DOI: 10.1016/j.molcel.2022.11.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/03/2022] [Accepted: 11/14/2022] [Indexed: 12/15/2022]
Abstract
Nonsense mutations, accounting for >20% of disease-associated mutations, lead to premature translation termination. Replacing uridine with pseudouridine in stop codons suppresses translation termination, which could be harnessed to mediate readthrough of premature termination codons (PTCs). Here, we present RESTART, a programmable RNA base editor, to revert PTC-induced translation termination in mammalian cells. RESTART utilizes an engineered guide snoRNA (gsnoRNA) and the endogenous H/ACA box snoRNP machinery to achieve precise pseudouridylation. We also identified and optimized gsnoRNA scaffolds to increase the editing efficiency. Unexpectedly, we found that a minor isoform of pseudouridine synthase DKC1, lacking a C-terminal nuclear localization signal, greatly improved the PTC-readthrough efficiency. Although RESTART induced restricted off-target pseudouridylation, they did not change the coding information nor the expression level of off-targets. Finally, RESTART enables robust pseudouridylation in primary cells and achieves functional PTC readthrough in disease-relevant contexts. Collectively, RESTART is a promising RNA-editing tool for research and therapeutics.
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Affiliation(s)
- Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Liting Dong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Nan Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Qiang Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Kai Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, PRC
| | - Xiaowen Shen
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC
| | - Zhe Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Zhicong Lv
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Luxin Peng
- College of Chemistry and Molecular Engineering, Peking University, Beijing, PRC
| | | | - Kun Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC
| | - Ke Liu
- Department of Otolaryngology Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, PRC
| | - Jiaxu Hong
- Department of Ophthalmology, Eye and Ear, Nose, Throat Hospital of Fudan University, Shanghai, PRC
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, PRC; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, PRC.
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60
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Hou Q, Jaffrey SR. Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells. RNA Biol 2023; 20:198-206. [PMID: 37129556 PMCID: PMC10155629 DOI: 10.1080/15476286.2023.2206248] [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] [Revised: 03/15/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023] Open
Abstract
RNA aptamers are structured RNAs that can bind to diverse ligands, including proteins, metabolites, and other small molecules. RNA aptamers are widely used as in vitro affinity reagents. However, RNA aptamers have not been highly successful as bioactive intracellular molecules that can bind target molecules and influence cellular processes. We describe how poor RNA aptamer expression and especially poor RNA aptamer folding have limited the use of RNA aptamers in RNA synthetic biology applications. We discuss innovative new approaches that promote RNA aptamer folding in living cells and how these approaches have improved the function of aptamers in mammalian cells. These new approaches are making RNA aptamer-based synthetic biology and RNA aptamer therapeutic applications much more achievable.
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Affiliation(s)
- Qian Hou
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R. Jaffrey
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
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61
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Li M, Yan C, Jiao Y, Xu Y, Bai C, Miao R, Jiang J, Liu J. Site-directed RNA editing by harnessing ADARs: advances and challenges. Funct Integr Genomics 2022; 22:1089-1103. [DOI: 10.1007/s10142-022-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
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62
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Qian Y, Li J, Zhao S, Matthews EA, Adoff M, Zhong W, An X, Yeo M, Park C, Yang X, Wang BS, Southwell DG, Huang ZJ. Programmable RNA sensing for cell monitoring and manipulation. Nature 2022; 610:713-721. [PMID: 36198803 PMCID: PMC10348343 DOI: 10.1038/s41586-022-05280-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 08/26/2022] [Indexed: 12/22/2022]
Abstract
RNA is a central and universal mediator of genetic information underlying the diversity of cell types and cell states, which together shape tissue organization and organismal function across species and lifespans. Despite numerous advances in RNA sequencing technologies and the massive accumulation of transcriptome datasets across the life sciences1,2, the dearth of technologies that use RNAs to observe and manipulate cell types remains a bottleneck in biology and medicine. Here we describe CellREADR (Cell access through RNA sensing by Endogenous ADAR), a programmable RNA-sensing technology that leverages RNA editing mediated by ADAR to couple the detection of cell-defining RNAs with the translation of effector proteins. Viral delivery of CellREADR conferred specific cell-type access in mouse and rat brains and in ex vivo human brain tissues. Furthermore, CellREADR enabled the recording and control of specific types of neurons in behaving mice. CellREADR thus highlights the potential for RNA-based monitoring and editing of animal cells in ways that are specific, versatile, simple and generalizable across organ systems and species, with wide applications in biology, biotechnology and programmable RNA medicine.
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Affiliation(s)
- Yongjun Qian
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Jiayun Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Shengli Zhao
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Elizabeth A Matthews
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michael Adoff
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Weixin Zhong
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Xu An
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Michele Yeo
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Christine Park
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Xiaolu Yang
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Bor-Shuen Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Derek G Southwell
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Z Josh Huang
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Durham, NC, USA.
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63
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Hajji K, Sedmík J, Cherian A, Amoruso D, Keegan LP, O'Connell MA. ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations. RNA (NEW YORK, N.Y.) 2022; 28:1281-1297. [PMID: 35863867 PMCID: PMC9479739 DOI: 10.1261/rna.079266.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes are essential for neuronal function and innate immune control. ADAR1 RNA editing prevents aberrant activation of antiviral dsRNA sensors through editing of long, double-stranded RNAs (dsRNAs). In this review, we focus on the ADAR2 proteins involved in the efficient, highly site-specific RNA editing to recode open reading frames first discovered in the GRIA2 transcript encoding the key GLUA2 subunit of AMPA receptors; ADAR1 proteins also edit many of these sites. We summarize the history of ADAR2 protein research and give an up-to-date review of ADAR2 structural studies, human ADARBI (ADAR2) mutants causing severe infant seizures, and mouse disease models. Structural studies on ADARs and their RNA substrates facilitate current efforts to develop ADAR RNA editing gene therapy to edit disease-causing single nucleotide polymorphisms (SNPs). Artificial ADAR guide RNAs are being developed to retarget ADAR RNA editing to new target transcripts in order to correct SNP mutations in them at the RNA level. Site-specific RNA editing has been expanded to recode hundreds of sites in CNS transcripts in Drosophila and cephalopods. In Drosophila and C. elegans, ADAR RNA editing also suppresses responses to self dsRNA.
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Affiliation(s)
- Khadija Hajji
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Jiří Sedmík
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Anna Cherian
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | | | - Liam P Keegan
- CEITEC Masaryk University, Brno 62500, Czech Republic
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64
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Grimm NB, Lee JT. Selective Xi reactivation and alternative methods to restore MECP2 function in Rett syndrome. Trends Genet 2022; 38:920-943. [PMID: 35248405 PMCID: PMC9915138 DOI: 10.1016/j.tig.2022.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
The human X-chromosome harbors only 4% of our genome but carries over 20% of genes associated with intellectual disability. Given that they inherit only one X-chromosome, males are more frequently affected by X-linked neurodevelopmental genetic disorders than females. However, despite inheriting two X-chromosomes, females can also be affected because X-chromosome inactivation enables only one of two X-chromosomes to be expressed per cell. For Rett syndrome and similar X-linked disorders affecting females, disease-specific treatments have remained elusive. However, a cure may be found within their own cells because every sick cell carries a healthy copy of the affected gene on the inactive X (Xi). Therefore, selective Xi reactivation may be a viable approach that would address the root cause of various X-linked disorders. Here, we discuss Rett syndrome and compare current approaches in the pharmaceutical pipeline to restore MECP2 function. We then focus on Xi reactivation and review available methods, lessons learned, and future directions.
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Affiliation(s)
- Niklas-Benedikt Grimm
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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Xiang Y, Katrekar D, Mali P. Methods for recruiting endogenous and exogenous ADAR enzymes for site-specific RNA editing. Methods 2022; 205:158-166. [PMID: 35779766 DOI: 10.1016/j.ymeth.2022.06.011] [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: 02/04/2022] [Revised: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 12/01/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) can be repurposed to achieve site-specific A-to-I RNA editing by recruiting them to a target of interest via an ADAR-recruiting guide RNA (adRNA). In this chapter, we present details towards experimental methods to enable this via two orthogonal strategies: one, via recruitment of endogenous ADARs (i.e. ADARs already natively expressed in cells); and two, via recruitment of exogenous ADARs (i.e. ADARs delivered into cells). Towards the former, we describe the use of circular adRNAs to recruit endogenous ADARs to a desired mRNA target. This results in robust, persistent and highly transcript specific editing both in vitro and in vivo. Towards the latter, we describe the use of a split-ADAR2 system, which allows for overexpression of ADAR2 variants that can be utilized to edit adenosines with high specificity, including at challenging to edit adenosines in non-preferred motifs such as those flanked by a 5' guanosine. We anticipate the described methods should facilitate RNA editing applications across research and biotechnology settings.
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Affiliation(s)
- Yichen Xiang
- Department of Bioengineering, University of California San Diego, USA
| | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, USA.
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66
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Brokowska J, Gaffke L, Pierzynowska K, Cyske Z, Węgrzyn G. Cell cycle disturbances in mucopolysaccharidoses: Transcriptomic and experimental studies on cellular models. Exp Biol Med (Maywood) 2022; 247:1639-1649. [PMID: 36000158 PMCID: PMC9597211 DOI: 10.1177/15353702221114872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mucopolysaccharidoses (MPS) are a group of lysosomal storage diseases caused by defects in genes coding for proteins involved in degradation of glycosaminoglycans (GAGs). These complex carbohydrates accumulate in cells causing their serious dysfunctions. Apart from the physical GAG storage, secondary and tertiary changes may contribute significantly to the pathomechanism of the disease. Among processes which were not systematically investigated in MPS cells to date there is the cell cycle. Here, we studied perturbances in this crucial cellular process in majority of MPS types. Transcriptomic analyses indicated that expression of many genes coding for proteins involved in the cell cycle is dysregulated in all tested MPS cells. Importantly, levels of transcripts of particular genes were changed in the same manner (i.e. either up- or down-regulated) in most or all types of the disease, indicating a common mechanism of the dysregulation. Flow cytometric studies demonstrated that the cell cycle is disturbed in all MPS types, with increased fractions of cells in the G0/G1 phase in most types and decreased fractions of cells in the G2/M phase in all types. We found that increased levels of cyclin D1 and disturbed timing of its appearance during the cell cycle may contribute to the mechanism of dysregulation of this process in MPS. Reduction of GAG levels by either a specific enzyme or genistein-mediated inhibition of synthesis of these compounds improved, but not fully corrected, the cell cycle in MPS fibroblasts. Therefore, it is suggested that combination of the therapeutic approaches devoted to reduction of GAG levels with cyclin D1 inhibitors might be considered in further works on developing effective treatment procedures for MPS.
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Sinnamon JR, Jacobson ME, Yung JF, Fisk JR, Jeng S, McWeeney SK, Parmelee LK, Chan CN, Yee SP, Mandel G. Targeted RNA editing in brainstem alleviates respiratory dysfunction in a mouse model of Rett syndrome. Proc Natl Acad Sci U S A 2022; 119:e2206053119. [PMID: 35939700 PMCID: PMC9388114 DOI: 10.1073/pnas.2206053119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/27/2022] [Indexed: 12/26/2022] Open
Abstract
Rett syndrome is a neurological disease due to loss-of-function mutations in the transcription factor, Methyl CpG binding protein 2 (MECP2). Because overexpression of endogenous MECP2 also causes disease, we have exploited a targeted RNA-editing approach to repair patient mutations where levels of MECP2 protein will never exceed endogenous levels. Here, we have constructed adeno-associated viruses coexpressing a bioengineered wild-type ADAR2 catalytic domain (Editasewt) and either Mecp2-targeting or nontargeting gfp RNA guides. The viruses are introduced systemically into male mice containing a guanosine to adenosine mutation that eliminates MeCP2 protein and causes classic Rett syndrome in humans. We find that in the mutant mice injected with the Mecp2-targeting virus, the brainstem exhibits the highest RNA-editing frequency compared to other brain regions. The efficiency is sufficient to rescue MeCP2 expression and function in the brainstem of mice expressing the Mecp2-targeting virus. Correspondingly, we find that abnormal Rett-like respiratory patterns are alleviated, and survival is prolonged, compared to mice injected with the control gfp guide virus. The levels of RNA editing among most brain regions corresponds to the distribution of guide RNA rather than Editasewt. Our results provide evidence that a targeted RNA-editing approach can alleviate a hallmark symptom in a mouse model of human disease.
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Affiliation(s)
- John R. Sinnamon
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239
| | | | - John F. Yung
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239
| | - Jenna R. Fisk
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239
| | - Shannon K. McWeeney
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239
- Division of Bioinformatics and Computational Biology, Oregon Health and Science University, Portland, OR 97239
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239
- Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239
| | - Lindsay K. Parmelee
- Integrated Pathology Core, Oregon National Primate Research Center, Beaverton, OR 97006
| | - Chi Ngai Chan
- Integrated Pathology Core, Oregon National Primate Research Center, Beaverton, OR 97006
| | - Siu-Pok Yee
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT 06030
| | - Gail Mandel
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239
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68
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CircRNA: An emerging star in the progression of glioma. Biomed Pharmacother 2022; 151:113150. [PMID: 35623170 DOI: 10.1016/j.biopha.2022.113150] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 11/21/2022] Open
Abstract
Circular RNAs (circRNAs), a class of single-stranded noncoding RNAs with a covalently closed loop structure, are recognized as promising biomarkers and targets for diagnosing and treating dozens of diseases, especially cancers. CircRNAs are extremely stable, abundant and conserved and have tissue- or developmental stage-specific expression. Currently, the biogenesis and biological functions of circRNAs have been increasingly revealed with deep sequencing and bioinformatics. Studies have indicated that circRNAs are frequently expressed in brain tissues and that their expression levels change in different stages of neural development, suggesting that circRNAs may play an important role in diseases of the nervous system, such as glioma. However, because the biogenesis and functions of circRNAs do not depend on a single mechanism but are coregulated by multiple factors, it is necessary to further explore the underlying mechanisms. In this review, we summarized the classification, mechanisms of biogenesis and biological functions of circRNAs. Meanwhile, we emphatically expounded on the process of abnormal expression of circRNAs, methods used in circRNA research, and their effects on the malignant biological capabilities of glioma.
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69
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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: 320] [Impact Index Per Article: 160.0] [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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70
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Zhang Y, Zhang X, Xu Y, Fang S, Ji Y, Lu L, Xu W, Qian H, Liang ZF. Circular RNA and Its Roles in the Occurrence, Development, Diagnosis of Cancer. Front Oncol 2022; 12:845703. [PMID: 35463362 PMCID: PMC9021756 DOI: 10.3389/fonc.2022.845703] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) are non-coding single-stranded covalently closed circular RNA, mainly produced by reverse splicing of exons of precursor mRNAs (pre-mRNAs). The characteristics of high abundance, strong specificity, and good stability of circRNAs have been discovered. A large number of studies have reported its various functions and mechanisms in biological events, such as the occurrence and development of cancer. In this review, we focus on the classification, characterization, biogenesis, functions of circRNAs, and the latest advances in cancer research. The development of circRNAs as biomarkers in cancer diagnosis and treatment also provides new ideas for studying circRNAs research.
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Affiliation(s)
- Yue Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xinyi Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yumeng Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shikun Fang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ying Ji
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ling Lu
- Child Healthcare Department, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Hui Qian
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Zhao Feng Liang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
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71
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Attwaters M. In vivo RNA base editing with circular RNAs. Nat Rev Genet 2022; 23:196-197. [PMID: 35194183 DOI: 10.1038/s41576-022-00463-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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