1
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Yan H, Tang W. Programmed RNA editing with an evolved bacterial adenosine deaminase. Nat Chem Biol 2024:10.1038/s41589-024-01661-x. [PMID: 38969862 DOI: 10.1038/s41589-024-01661-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
Programmed RNA editing presents an attractive therapeutic strategy for genetic disease. In this study, we developed bacterial deaminase-enabled recoding of RNA (DECOR), which employs an evolved Escherichia coli transfer RNA adenosine deaminase, TadA8e, to deposit adenosine-to-inosine editing to CRISPR-specified sites in the human transcriptome. DECOR functions in a variety of cell types, including human lung fibroblasts, and delivers on-target activity similar to ADAR-overexpressing RNA-editing platforms with 88% lower off-target effects. High-fidelity DECOR further reduces off-target effects to basal level. We demonstrate the clinical potential of DECOR by targeting Van der Woude syndrome-causing interferon regulatory factor 6 (IRF6) insufficiency. DECOR-mediated RNA editing removes a pathogenic upstream open reading frame (uORF) from the 5' untranslated region of IRF6 and rescues primary ORF expression from 12.3% to 36.5%, relative to healthy transcripts. DECOR expands the current portfolio of effector proteins and opens new territory in programmed RNA editing.
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Affiliation(s)
- Hao Yan
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Weixin Tang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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2
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Johnson GA, Gould SI, Sánchez-Rivera FJ. Deconstructing cancer with precision genome editing. Biochem Soc Trans 2024; 52:803-819. [PMID: 38629716 PMCID: PMC11088927 DOI: 10.1042/bst20230984] [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: 02/01/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Recent advances in genome editing technologies are allowing investigators to engineer and study cancer-associated mutations in their endogenous genetic contexts with high precision and efficiency. Of these, base editing and prime editing are quickly becoming gold-standards in the field due to their versatility and scalability. Here, we review the merits and limitations of these precision genome editing technologies, their application to modern cancer research, and speculate how these could be integrated to address future directions in the field.
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Affiliation(s)
- Grace A. Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Samuel I. Gould
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
| | - Francisco J. Sánchez-Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge 02142, MA, U.S.A
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3
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Zhang D, Zhu L, Gao Y, Wang Y, Li P. RNA editing enzymes: structure, biological functions and applications. Cell Biosci 2024; 14:34. [PMID: 38493171 PMCID: PMC10944622 DOI: 10.1186/s13578-024-01216-6] [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: 09/24/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
With the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.
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Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Yanyan Gao
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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4
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Song J, Luo N, Dong L, Peng J, Yi C. RNA base editors: The emerging approach of RNA therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1844. [PMID: 38576085 DOI: 10.1002/wrna.1844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
RNA-based therapeutics offer a flexible and reversible approach for treating genetic disorders, such as antisense oligonucleotides, RNA interference, aptamers, mRNA vaccines, and RNA editing. In recent years, significant advancements have been made in RNA base editing to correct disease-relevant point mutations. These achievements have significantly influenced the fields of biotechnology, biomedical research and therapeutics development. In this article, we provide a comprehensive overview of the design and performance of contemporary RNA base editors, including A-to-I, C-to-U, A-to-m6A, and U-to-Ψ. We compare recent innovative developments and highlight their applications in disease-relevant contexts. Lastly, we discuss the limitations and future prospects of utilizing RNA base editing for therapeutic purposes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Nan Luo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Liting Dong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing, China
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5
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Song J, Zhuang Y, Yi C. Programmable RNA base editing via targeted modifications. Nat Chem Biol 2024; 20:277-290. [PMID: 38418907 DOI: 10.1038/s41589-023-01531-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/18/2023] [Indexed: 03/02/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editors are powerful tools in biology and hold great promise for the treatment of human diseases. Advanced DNA base editing tools, such as cytosine base editor and adenine base editor, have been developed to correct permanent mistakes in genetic material. However, undesired off-target edits would also be permanent, which poses a considerable risk for therapeutics. Alternatively, base editing at the RNA level is capable of correcting disease-causing mutations but does not lead to lasting genotoxic effects. RNA base editors offer temporary and reversible therapies and have been catching on in recent years. Here, we summarize some emerging RNA editors based on A-to-inosine, C-to-U and U-to-pseudouridine changes. We review the programmable RNA-targeting systems as well as modification enzyme-based effector proteins and highlight recent technological breakthroughs. Finally, we compare editing tools, discuss limitations and opportunities, and provide insights for the future directions of RNA base editing.
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Affiliation(s)
- Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Yuan Zhuang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, People's Republic of China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, People's Republic of China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China.
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6
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Pfeiffer LS, Stafforst T. Precision RNA base editing with engineered and endogenous effectors. Nat Biotechnol 2023; 41:1526-1542. [PMID: 37735261 DOI: 10.1038/s41587-023-01927-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
RNA base editing refers to the rewriting of genetic information within an intact RNA molecule and serves various functions, such as evasion of the endogenous immune system and regulation of protein function. To achieve this, certain enzymes have been discovered in human cells that catalyze the conversion of one nucleobase into another. This natural process could be exploited to manipulate and recode any base in a target transcript. In contrast to DNA base editing, analogous changes introduced in RNA are not permanent or inheritable but rather allow reversible and doseable effects that appeal to various therapeutic applications. The current practice of RNA base editing involves the deamination of adenosines and cytidines, which are converted to inosines and uridines, respectively. In this Review, we summarize current site-directed RNA base-editing strategies and highlight recent achievements to improve editing efficiency, precision, codon-targeting scope and in vivo delivery into disease-relevant tissues. Besides engineered editing effectors, we focus on strategies to harness endogenous adenosine deaminases acting on RNA (ADAR) enzymes and discuss limitations and future perspectives to apply the tools in basic research and as a therapeutic modality. We expect the field to realize the first RNA base-editing drug soon, likely on a well-defined genetic disease. However, the long-term challenge will be to carve out the sweet spot of the technology where its unique ability is exploited to modulate signaling cues, metabolism or other clinically relevant processes in a safe and doseable manner.
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Affiliation(s)
- Laura S Pfeiffer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center, Faculty of Medicine, University of Tübingen, Tübingen, Germany.
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7
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Ai X, Zhou S, Chen M, Du F, Yuan Y, Cui X, Dong J, Huang X, Tang Z. Leveraging Small Molecule-Induced Aptazyme Cleavage for Directed A-to-I RNA Editing. ACS Synth Biol 2023. [PMID: 37384927 DOI: 10.1021/acssynbio.3c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
As a promising therapeutic approach for the correction of pathogenic mutations, the RNA editing process is reversible and tunable without permanently altering the genome. RNA editing mediated by human ADAR proteins offers distinct advantages, including high specificity and low propensity to cause immunogenicity. Herein, we describe a small molecule-inducible RNA editing strategy by incorporating aptazymes into the guide RNA of ADAR-based RNA editing technology. Once small molecules are added or removed, aptazymes trigger self-cleavage to release the guide RNA, achieving small molecule-controlled RNA editing. To satisfy different RNA editing applications, both turn-on and turn-off A-to-I RNA editing of target mRNA have been realized by using on/off-switch aptazymes. Theoretically speaking, this strategy can be applied to various ADAR-based editing systems, which could improve the safety and potential clinical applications of RNA editing technology.
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Affiliation(s)
- Xilei Ai
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Shan Zhou
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Meiyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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8
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Chen ZB, He M, Li JYS, Shyy JYJ, Chien S. Epitranscriptional Regulation: From the Perspectives of Cardiovascular Bioengineering. Annu Rev Biomed Eng 2023; 25:157-184. [PMID: 36913673 DOI: 10.1146/annurev-bioeng-081922-021233] [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] [Indexed: 03/11/2023]
Abstract
The central dogma of gene expression involves DNA transcription to RNA and RNA translation into protein. As key intermediaries and modifiers, RNAs undergo various forms of modifications such as methylation, pseudouridylation, deamination, and hydroxylation. These modifications, termed epitranscriptional regulations, lead to functional changes in RNAs. Recent studies have demonstrated crucial roles for RNA modifications in gene translation, DNA damage response, and cell fate regulation. Epitranscriptional modifications play an essential role in development, mechanosensing, atherogenesis, and regeneration in the cardiovascular (CV) system, and their elucidation is critically important to understanding the molecular mechanisms underlying CV physiology and pathophysiology. This review aims at providing biomedical engineers with an overview of the epitranscriptome landscape, related key concepts, recent findings in epitranscriptional regulations, and tools for epitranscriptome analysis. The potential applications of this important field in biomedical engineering research are discussed.
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Affiliation(s)
- Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Ming He
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Julie Yi-Shuan Li
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
| | - John Y-J Shyy
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Shu Chien
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
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9
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Zhang Y, Feng D, Mu G, Wang Q, Wang J, Luo Y, Tang X. Light-triggered site-directed RNA editing by endogenous ADAR1 with photolabile guide RNA. Cell Chem Biol 2023:S2451-9456(23)00149-6. [PMID: 37295425 DOI: 10.1016/j.chembiol.2023.05.006] [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: 09/20/2022] [Revised: 03/21/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
RNA A-to-I editing is a post-transcriptional modification pervasively occurring in cells. Artificial intervention of A-to-I editing at specific sites of RNA could also be achieved with guide RNA and exogenous ADAR enzymes. In contrast to previous fused SNAP-ADAR enzymes for light-driven RNA A-to-I editing, we developed photo-caged antisense guide RNA oligonucleotides with simple 3'-terminal cholesterol modification, and successfully achieved light-triggered site-specific RNA A-to-I editing for the first time utilizing endogenous ADAR enzymes. Our caged A-to-I editing system effectively implemented light-dependent point mutation of mRNA transcripts of both exogenous and endogenous genes in living cells and 3D tumorspheres, as well as spatial regulation of EGFP expression, which provides a new approach for precise manipulation of RNA editing.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Di Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Guanqun Mu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yun Luo
- Shanghai Primerna Biotechnology Co. Ltd, Shanghai 201600, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, Jiangsu, China.
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10
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Morelli KH, Smargon AA, Yeo GW. Programmable macromolecule-based RNA-targeting therapies to treat human neurological disorders. RNA (NEW YORK, N.Y.) 2023; 29:489-497. [PMID: 36693761 PMCID: PMC10019361 DOI: 10.1261/rna.079519.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Disruptions in RNA processing play critical roles in the pathogenesis of neurological diseases. In this Perspective, we discuss recent progress in the development of RNA-targeting therapeutic modalities. We focus on progress, limitations, and opportunities in a new generation of therapies engineered from RNA binding proteins and other endogenous RNA regulatory macromolecules to treat human neurological disorders.
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Affiliation(s)
- Kathryn H Morelli
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, California 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California 92039, USA
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11
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The genome editing revolution. Trends Biotechnol 2023; 41:396-409. [PMID: 36709094 DOI: 10.1016/j.tibtech.2022.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/28/2023]
Abstract
A series of spectacular scientific discoveries and technological advances in the second half of the 20th century have provided the basis for the ongoing genome editing revolution. The elucidation of structural and functional features of DNA and RNA was followed by pioneering studies on genome editing: Molecular biotechnology was born. Since then, four decades followed during which progress of scientific insights and technological methods continued at an overwhelming pace. Fundamental insights into microbial host-virus interactions led to the development of tools for genome editing using restriction enzymes or the revolutionary CRISPR-Cas technology. In this review, we provide a historical overview of milestones that led to the genome editing revolution and speculate about future trends in biotechnology.
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12
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Therapeutic strategies for autism: targeting three levels of the central dogma of molecular biology. Transl Psychiatry 2023; 13:58. [PMID: 36792602 PMCID: PMC9931756 DOI: 10.1038/s41398-023-02356-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
The past decade has yielded much success in the identification of risk genes for Autism Spectrum Disorder (ASD), with many studies implicating loss-of-function (LoF) mutations within these genes. Despite this, no significant clinical advances have been made so far in the development of therapeutics for ASD. Given the role of LoF mutations in ASD etiology, many of the therapeutics in development are designed to rescue the haploinsufficient effect of genes at the transcriptional, translational, and protein levels. This review will discuss the various therapeutic techniques being developed from each level of the central dogma with examples including: CRISPR activation (CRISPRa) and gene replacement at the DNA level, antisense oligonucleotides (ASOs) at the mRNA level, and small-molecule drugs at the protein level, followed by a review of current delivery methods for these therapeutics. Since central nervous system (CNS) penetrance is of utmost importance for ASD therapeutics, it is especially necessary to evaluate delivery methods that have higher efficiency in crossing the blood-brain barrier (BBB).
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13
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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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14
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Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
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15
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Raghava Kurup R, Oakes EK, Manning AC, Mukherjee P, Vadlamani P, Hundley HA. RNA binding by ADAR3 inhibits adenosine-to-inosine editing and promotes expression of immune response protein MAVS. J Biol Chem 2022; 298:102267. [PMID: 35850307 PMCID: PMC9418441 DOI: 10.1016/j.jbc.2022.102267] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 12/13/2022] Open
Abstract
Members of the ADAR family of double-stranded RNA–binding proteins regulate one of the most abundant RNA modifications in humans, the deamination of adenosine to inosine. Several transcriptome-wide studies have been carried out to identify RNA targets of the active deaminases ADAR1 and ADAR2. However, our understanding of ADAR3, the brain-specific deaminase-deficient ADAR family member, is limited to a few transcripts. In this study, we identified over 3300 transcripts bound by ADAR3 and observed that binding of ADAR3 correlated with reduced editing of over 400 sites in the glioblastoma transcriptome. We further investigated the impact of ADAR3 on gene regulation of the transcript that encodes MAVS, an essential protein in the innate immune response pathway. We observed reduced editing in the MAVS 3′ UTR in cells expressing increased ADAR3 or reduced ADAR1 suggesting ADAR3 acts as a negative regulator of ADAR1-mediated editing. While neither ADAR1 knockdown or ADAR3 overexpression affected MAVS mRNA expression, we demonstrate increased ADAR3 expression resulted in upregulation of MAVS protein expression. In addition, we created a novel genetic mutant of ADAR3 that exhibited enhanced RNA binding and MAVS upregulation compared with wildtype ADAR3. Interestingly, this ADAR3 mutant no longer repressed RNA editing, suggesting ADAR3 has a unique regulatory role beyond altering editing levels. Altogether, this study provides the first global view of ADAR3-bound RNAs in glioblastoma cells and identifies both a role for ADAR3 in repressing ADAR1-mediated editing and an RNA-binding dependent function of ADAR3 in regulating MAVS expression.
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Affiliation(s)
| | - Eimile K Oakes
- Department of Biology, Indiana University, Bloomington IN 47405, USA
| | - Aidan C Manning
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN 47405, USA
| | - Priyanka Mukherjee
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN 47405, USA
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN 47405, USA
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington IN 47405, USA.
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16
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Dykstra PB, Kaplan M, Smolke CD. Engineering synthetic RNA devices for cell control. Nat Rev Genet 2022; 23:215-228. [PMID: 34983970 PMCID: PMC9554294 DOI: 10.1038/s41576-021-00436-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
The versatility of RNA in sensing and interacting with small molecules, proteins and other nucleic acids while encoding genetic instructions for protein translation makes it a powerful substrate for engineering biological systems. RNA devices integrate cellular information sensing, processing and actuation of specific signals into defined functions and have yielded programmable biological systems and novel therapeutics of increasing sophistication. However, challenges centred on expanding the range of analytes that can be sensed and adding new mechanisms of action have hindered the full realization of the field's promise. Here, we describe recent advances that address these limitations and point to a significant maturation of synthetic RNA-based devices.
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Affiliation(s)
- Peter B. Dykstra
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matias Kaplan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,
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17
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Xu W, Biswas J, Singer RH, Rosbash M. Targeted RNA editing: novel tools to study post-transcriptional regulation. Mol Cell 2022; 82:389-403. [PMID: 34739873 PMCID: PMC8792254 DOI: 10.1016/j.molcel.2021.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/22/2023]
Abstract
RNA binding proteins (RBPs) regulate nearly all post-transcriptional processes within cells. To fully understand RBP function, it is essential to identify their in vivo targets. Standard techniques for profiling RBP targets, such as crosslinking immunoprecipitation (CLIP) and its variants, are limited or suboptimal in some situations, e.g. when compatible antibodies are not available and when dealing with small cell populations such as neuronal subtypes and primary stem cells. This review summarizes and compares several genetic approaches recently designed to identify RBP targets in such circumstances. TRIBE (targets of RNA binding proteins identified by editing), RNA tagging, and STAMP (surveying targets by APOBEC-mediated profiling) are new genetic tools useful for the study of post-transcriptional regulation and RBP identification. We describe the underlying RNA base editing technology, recent applications, and therapeutic implications.
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Affiliation(s)
- Weijin Xu
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | - Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, MA 02451, USA.
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18
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Genome Editing among Bioethics and Regulatory Practices. Biomolecules 2021; 12:biom12010013. [PMID: 35053161 PMCID: PMC8774098 DOI: 10.3390/biom12010013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 12/26/2022] Open
Abstract
In the last decade, genome editing technologies became very effective and several clinical trials have been started in order to use them for treating some genetic diseases. Interestingly, despite more than 50 years of discussion about the frontiers of genetics in human health and evolution, the debate about the bioethics and the regulatory practices of genome editing is still far from satisfactory answers. This delay results from an excessive emphasis on the effectiveness of the genome editing technologies that is relevant for the regulatory practices, but not at a bioethical level. Indeed, other factors (such as accessibility and acceptability) could make these techniques not accepted at the bioethical level, even in the presence of their 100% effectiveness.
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19
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Knutson SD, Heemstra JM. Protein-based molecular recognition tools for detecting and profiling RNA modifications. Curr Opin Struct Biol 2021; 69:1-10. [PMID: 33445115 PMCID: PMC8272725 DOI: 10.1016/j.sbi.2020.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/18/2022]
Abstract
RNA undergoes extensive biochemical modification following transcription. In addition to RNA splicing, transcripts are processed by a suite of enzymes that alter the chemical structure of different nucleobases. Broadly termed as 'RNA editing,' these modifications impart significant functional changes to translation, localization, and stability of individual transcripts within the cell. These changes are dynamic and required for a number of critical cellular processes, and dysregulation of these pathways is responsible for several disease states. Accurately detecting, measuring, and mapping different RNA modifications across the transcriptome is vital to understanding their broader functions as well as leveraging these events as diagnostic biomarkers. Here, we review recent advances in profiling several types of RNA modifications, with particular emphasis on adenosine-to-inosine (A-to-I) and N6-methyladenosine (m6A) RNA editing. We especially highlight approaches that utilize proteins to detect or enrich modified RNA transcripts before sequencing, and we summarize recent insights yielded from these techniques.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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20
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Ojha N, Diaz Quiroz JF, Rosenthal JJC. In vitro and in cellula site-directed RNA editing using the λNDD-BoxB system. Methods Enzymol 2021; 658:335-358. [PMID: 34517953 DOI: 10.1016/bs.mie.2021.06.009] [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] [Indexed: 01/04/2023]
Abstract
Site-directed RNA editing (SDRE) exploits the enzymatic activity of Adenosine Deaminases Acting on RNAs (ADAR) to program changes in genetic information as it passes through RNA. ADARs convert adenosine (A) to inosine (I) through a hydrolytic deamination and since I can be read as guanosine (G) during translation, this change can regulate gene function and correct G→A genetic mutations. In SDRE, ADARs are redirected to convert user-defined A's to I's. SDRE also has certain advantages over genome editing because the changes in RNA are reversible and thus safer. In addition, ADARs are endogenously expressed in humans and therefore unlikely to provoke immunological complications when administered. Recently, a variety of systems for SDRE have been developed. Some rely on harnessing endogenously expressed ADARs and other deliver engineered versions of ADAR's catalytic domain. All systems are currently under refinement, and there are still challenges associated with raising their efficiency and specificity to levels that are adequate for therapeutics. This chapter provides a detailed protocol for in vitro and in cellula editing assays using the λNDD-BoxB system, one of the first systems developed for SDRE. The λNDD-BoxB system relies on gRNAs that are linked to the catalytic domain of human ADAR2 through a small RNA binding protein-RNA stem/loop interaction. We provide step-by-step protocols for (a) the construction of guide RNAs and editing enzyme plasmids, and (b) their use in vitro and in cellula for editing assays using a fluorescent protein-based reporter system containing a premature termination codon that can be corrected by editing.
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Affiliation(s)
- Namrata Ojha
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, MA, United States
| | | | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, MA, United States.
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21
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Tang T, Han Y, Wang Y, Huang H, Qian P. Programmable System of Cas13-Mediated RNA Modification and Its Biological and Biomedical Applications. Front Cell Dev Biol 2021; 9:677587. [PMID: 34386490 PMCID: PMC8353156 DOI: 10.3389/fcell.2021.677587] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13 has drawn broad interest to control gene expression and cell fate at the RNA level in general. Apart from RNA interference mediated by its endonuclease activity, the nuclease-deactivated form of Cas13 further provides a versatile RNA-guided RNA-targeting platform for manipulating kinds of RNA modifications post-transcriptionally. Chemical modifications modulate various aspects of RNA fate, including translation efficiency, alternative splicing, RNA–protein affinity, RNA–RNA interaction, RNA stability and RNA translocation, which ultimately orchestrate cellular biologic activities. This review summarizes the history of the CRISPR-Cas13 system, fundamental components of RNA modifications and the related physiological and pathological functions. We focus on the development of epi-transcriptional editing toolkits based on catalytically inactive Cas13, including RNA Editing for Programmable A to I Replacement (REPAIR) and xABE (adenosine base editor) for adenosine deamination, RNA Editing for Specific C-to-U Exchange (RESCUE) and xCBE (cytidine base editor) for cytidine deamination and dm6ACRISPR, as well as the targeted RNA methylation (TRM) and photoactivatable RNA m6A editing system using CRISPR-dCas13 (PAMEC) for m6A editing. We further highlight the emerging applications of these useful toolkits in cell biology, disease and imaging. Finally, we discuss the potential limitations, such as off-target editing, low editing efficiency and limitation for AAV delivery, and provide possible optimization strategies.
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Affiliation(s)
- Tian Tang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
| | - Yingli Han
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
| | - Yuran Wang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Pengxu Qian
- Center of Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.,Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, China
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22
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Liu H, Rauch S, Dickinson BC. Programmable technologies to manipulate gene expression at the RNA level. Curr Opin Chem Biol 2021; 64:27-37. [PMID: 33930627 DOI: 10.1016/j.cbpa.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
RNA has long been an enticing therapeutic target, but is now garnering increased attention, largely driven by clinical successes of RNA interference-based drugs. While gene knockdown by well-established RNA interference- and other oligonucleotide-based strategies continues to advance in the clinic, the repertoire of targetable effectors capable of altering gene expression at the RNA level is also rapidly expanding. In this review, we focus on several recently developed bifunctional molecular technologies that both interact with and act upon a target RNA. These new approaches for programmable RNA knockdown, editing, splicing, translation, and chemical modifications stand to provide impactful new modalities for therapeutic development in the coming decades.
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Affiliation(s)
- Huachun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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23
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Han RC, Fry LE, Kantor A, McClements ME, Xue K, MacLaren RE. Is subretinal AAV gene replacement still the only viable treatment option for choroideremia? Expert Opin Orphan Drugs 2021; 9:13-24. [PMID: 34040899 PMCID: PMC7610829 DOI: 10.1080/21678707.2021.1882300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/25/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Choroideremia is an X-linked inherited retinal degeneration resulting from mutations in the CHM gene, encoding Rab escort protein-1 (REP1), a protein regulating intracellular vesicular transport. Loss-of-function mutations in CHM lead to progressive loss of retinal pigment epithelium (RPE) with photoreceptor and choriocapillaris degeneration, leading to progressive visual field constriction and loss of visual acuity. Three hundred and fifty-four unique mutations have been reported in CHM. While gene augmentation remains an ideal therapeutic option for choroideremia, other potential future clinical strategies may exist. AREAS COVERED The authors examine the pathophysiology and genetic basis of choroideremia. They summarize the status of ongoing gene therapy trials and discuss CHM mutations amenable to other therapeutic approaches including CRISPR/Cas-based DNA and RNA editing, nonsense suppression of premature termination codons, and antisense oligonucleotides for splice modification. The authors undertook a literature search in PubMed and NIH Clinical Trials in October 2020. EXPERT OPINION The authors conclude that AAV-mediated gene augmentation remains the most effective approach for choroideremia. Given the heterogeneity of CHM mutations and potential risks and benefits, genome-editing approaches currently do not offer significant advantages. Nonsense suppression strategies and antisense oligonucleotides are exciting novel therapeutic options; however, their clinical viability remains to be determined.
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Affiliation(s)
- Ruofan Connie Han
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Lewis E. Fry
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ariel Kantor
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Kanmin Xue
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Robert E. MacLaren
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
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24
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Schaefer MR. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics? Genes (Basel) 2021; 12:genes12030345. [PMID: 33652758 PMCID: PMC7996938 DOI: 10.3390/genes12030345] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
RNA modifications, long considered to be molecular curiosities embellishing just abundant and non-coding RNAs, have now moved into the focus of both academic and applied research. Dedicated research efforts (epitranscriptomics) aim at deciphering the underlying principles by determining RNA modification landscapes and investigating the molecular mechanisms that establish, interpret and modulate the information potential of RNA beyond the combination of four canonical nucleotides. This has resulted in mapping various epitranscriptomes at high resolution and in cataloguing the effects caused by aberrant RNA modification circuitry. While the scope of the obtained insights has been complex and exciting, most of current epitranscriptomics appears to be stuck in the process of producing data, with very few efforts to disentangle cause from consequence when studying a specific RNA modification system. This article discusses various knowledge gaps in this field with the aim to raise one specific question: how are the enzymes regulated that dynamically install and modify RNA modifications? Furthermore, various technologies will be highlighted whose development and use might allow identifying specific and context-dependent regulators of epitranscriptomic mechanisms. Given the complexity of individual epitranscriptomes, determining their regulatory principles will become crucially important, especially when aiming at modifying specific aspects of an epitranscriptome both for experimental and, potentially, therapeutic purposes.
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Affiliation(s)
- Matthias R Schaefer
- Centre for Anatomy & Cell Biology, Division of Cell-and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Haus C, 1st Floor, 1090 Vienna, Austria
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25
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Challenges and advances in clinical applications of mesenchymal stromal cells. J Hematol Oncol 2021; 14:24. [PMID: 33579329 PMCID: PMC7880217 DOI: 10.1186/s13045-021-01037-x] [Citation(s) in RCA: 254] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Mesenchymal stromal cells (MSCs), also known as mesenchymal stem cells, have been intensely investigated for clinical applications within the last decades. However, the majority of registered clinical trials applying MSC therapy for diverse human diseases have fallen short of expectations, despite the encouraging pre-clinical outcomes in varied animal disease models. This can be attributable to inconsistent criteria for MSCs identity across studies and their inherited heterogeneity. Nowadays, with the emergence of advanced biological techniques and substantial improvements in bio-engineered materials, strategies have been developed to overcome clinical challenges in MSC application. Here in this review, we will discuss the major challenges of MSC therapies in clinical application, the factors impacting the diversity of MSCs, the potential approaches that modify MSC products with the highest therapeutic potential, and finally the usage of MSCs for COVID-19 pandemic disease.
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