1
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Yan H, Tang W. Programmed RNA editing with an evolved bacterial adenosine deaminase. Nat Chem Biol 2024; 20:1361-1370. [PMID: 38969862 DOI: 10.1038/s41589-024-01661-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Teng X, Zhao X, Dai Y, Zhang X, Zhang Q, Wu Y, Hu D, Li J. ClickRNA-PROTAC for Tumor-Selective Protein Degradation and Targeted Cancer Therapy. J Am Chem Soc 2024. [PMID: 39320981 DOI: 10.1021/jacs.4c06402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Proteolysis-targeting chimeras (PROTACs) show promise in tumor treatment. However, the E3 ligases VHL and CRBN, commonly used in PROTAC, are highly expressed in only a few tumors, thus limiting the application scope and efficacy of PROTAC drugs. Furthermore, the lack of tumor specificity in PROTAC drugs can result in toxic side effects. Therefore, there is an urgent need to develop tumor-selective PROTAC drugs that do not rely on endogenous E3 ligases. In this study, we introduce the ClickRNA-PROTAC system, which involves the expression of a fusion protein of the E3 ubiquitin ligase SIAH1 and SNAPTag through mRNA transfection and recruits the protein of interest (POI) using bio-orthogonal click chemistry. ClickRNA-PROTAC can effectively degrade various proteins such as BRD4, KRAS, and NFκB simply by replacing the warhead molecules. By employing a tumor-specific mRNA-responsive translation strategy, ClickRNA-PROTAC can selectively degrade POIs in tumor cells. Furthermore, ClickRNA-PROTAC demonstrated strong efficacy in targeted cancer therapy in a xenograft mouse model of adrenocortical carcinoma. In conclusion, this approach offers several advantages, including independence from endogenous E3 ubiquitin ligases, tumor specificity, and programmability, thereby paving the way for the development of PROTAC drugs.
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Affiliation(s)
- Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Life Science Academy, Beijing 102209, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Xuan Zhao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yicong Dai
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xiangdong Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Qiushuang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yuncong Wu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Difei Hu
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Life Science Academy, Beijing 102209, China
- New Cornerstone Science Laboratory, Shenzhen 518054, China
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China
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3
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Aygün N, Vuong C, Krupa O, Mory J, Le BD, Valone JM, Liang D, Shafie B, Zhang P, Salinda A, Wen C, Gandal MJ, Love MI, de la Torre-Ubieta L, Stein JL. Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis. Am J Hum Genet 2024; 111:1877-1898. [PMID: 39168119 PMCID: PMC11393701 DOI: 10.1016/j.ajhg.2024.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk postmortem adult brain tissue. However, many brain-trait associated loci have unknown cellular or molecular function. These genetic variants may exert context-specific function on different molecular phenotypes including post-transcriptional changes. Here, we identified genetic regulation of RNA editing and alternative polyadenylation (APA) within a cell-type-specific population of human neural progenitors and neurons. More RNA editing and isoforms utilizing longer polyadenylation sequences were observed in neurons, likely due to higher expression of genes encoding the proteins mediating these post-transcriptional events. We also detected hundreds of cell-type-specific editing quantitative trait loci (edQTLs) and alternative polyadenylation QTLs (apaQTLs). We found colocalizations of a neuron edQTL in CCDC88A with educational attainment and a progenitor apaQTL in EP300 with schizophrenia, suggesting that genetically mediated post-transcriptional regulation during brain development leads to differences in brain function.
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Affiliation(s)
- Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Celine Vuong
- Intellectual and Developmental Disabilities Research Center, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica Mory
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brandon D Le
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan M Valone
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Beck Shafie
- Intellectual and Developmental Disabilities Research Center, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Intellectual and Developmental Disabilities Research Center, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Angelo Salinda
- Intellectual and Developmental Disabilities Research Center, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cindy Wen
- Intellectual and Developmental Disabilities Research Center, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael J Gandal
- Intellectual and Developmental Disabilities Research Center, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Luis de la Torre-Ubieta
- Intellectual and Developmental Disabilities Research Center, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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4
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Choi J, Chen W, Liao H, Li X, Shendure J. A molecular proximity sensor based on an engineered, dual-component guide RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.14.553235. [PMID: 37645782 PMCID: PMC10461971 DOI: 10.1101/2023.08.14.553235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
One of the goals of synthetic biology is to enable the design of arbitrary molecular circuits with programmable inputs and outputs. Such circuits bridge the properties of electronic and natural circuits, processing information in a predictable manner within living cells. Genome editing is a potentially powerful component of synthetic molecular circuits, whether for modulating the expression of a target gene or for stably recording information to genomic DNA. However, programming molecular events such as protein-protein interactions or induced proximity as triggers for genome editing remains challenging. Here we demonstrate a strategy termed "P3 editing", which links p rotein- p rotein p roximity to the formation of a functional CRISPR-Cas9 dual-component guide RNA. By engineering the crRNA:tracrRNA interaction, we demonstrate that various known protein-protein interactions, as well as the chemically-induced dimerization of protein domains, can be used to activate prime editing or base editing in human cells. Additionally, we explore how P3 editing can incorporate outputs from ADAR-based RNA sensors, potentially allowing specific RNAs to induce specific genome edits within a larger circuit. Our strategy enhances the controllability of CRISPR-based genome editing, facilitating its use in synthetic molecular circuits deployed in living cells.
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Affiliation(s)
- Junhong Choi
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Hanna Liao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Seattle Hub for Synthetic Biology, Seattle, WA 98195, USA
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5
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Zhou Y, Sheng P, Li J, Li Y, Xie M, Green AA. Conditional RNA interference in mammalian cells via RNA transactivation. Nat Commun 2024; 15:6855. [PMID: 39127751 PMCID: PMC11316766 DOI: 10.1038/s41467-024-50600-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 07/15/2024] [Indexed: 08/12/2024] Open
Abstract
RNA interference (RNAi) is a powerful tool for sequence-specific gene knockdown in therapeutic and research applications. However, spatiotemporal control of RNAi is required to decrease nonspecific targeting, potential toxicity, and allow targeting of essential genes. Herein we describe a class of de-novo-designed RNA switches that enable sequence-specific regulation of RNAi in mammalian cells. Using cis-repressing RNA elements, we engineer RNA devices that only initiate microRNA biogenesis when binding with cognate trigger RNAs. We demonstrate that this conditional RNAi system, termed Orthogonal RNA Interference induced by Trigger RNA (ORIENTR), provides up to 14-fold increases in artificial miRNA biogenesis upon activation in orthogonal libraries. We show that integration of ORIENTR triggers with dCas13d enhances dynamic range to up to 31-fold. We further demonstrate that ORIENTR can be applied to detect endogenous RNA signals and to conditionally knockdown endogenous genes, thus enabling regulatory possibilities including cell-type-specific RNAi and rewiring of transcriptional networks via RNA profile.
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Affiliation(s)
- Yu Zhou
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology (MGM), University of Florida, Gainesville, FL, USA
| | - Peike Sheng
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, Gainesville, FL, USA
| | - Jiayi Li
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Yudan Li
- Biological Design Center, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Mingyi Xie
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), University of Florida, Gainesville, FL, USA.
- UF Health Cancer Center, Gainesville, FL, USA.
| | - Alexander A Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA.
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6
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Seo JP, Trippett JS, Huang Z, Lee S, Nouraein S, Wang RZ, Szablowski JO. Acoustically targeted measurement of transgene expression in the brain. SCIENCE ADVANCES 2024; 10:eadj7686. [PMID: 39110811 PMCID: PMC11305388 DOI: 10.1126/sciadv.adj7686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Gene expression is a critical component of brain physiology, but monitoring this expression in the living brain represents a major challenge. Here, we introduce a new paradigm called recovery of markers through insonation (REMIS) for noninvasive measurement of gene expression in the brain with cell type, spatial, and temporal specificity. Our approach relies on engineered protein markers that are produced in neurons but exit into the brain's interstitium. When ultrasound is applied to targeted brain regions, it opens the blood-brain barrier and releases these markers into the bloodstream. Once in blood, the markers can be readily detected using biochemical techniques. REMIS can noninvasively confirm gene delivery and measure endogenous signaling in specific brain sites through a simple insonation and a subsequent blood test. REMIS is reliable and demonstrated consistent improvement in recovery of markers from the brain into the blood. Overall, this work establishes a noninvasive, spatially specific method of monitoring gene delivery and endogenous signaling in the brain.
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Affiliation(s)
- Joon Pyung Seo
- Applied Physics Program, Rice University, Houston, TX, USA
| | | | - Zhimin Huang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Sangsin Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Shirin Nouraein
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - Ryan Z. Wang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jerzy O. Szablowski
- Applied Physics Program, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
- Rice Neuroengineering Initiative, Rice University, Houston, TX, USA
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7
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Siebart JC, Chan CS, Yao X, Su FY, Kwong GA. In vivo gene delivery to immune cells. Curr Opin Biotechnol 2024; 88:103169. [PMID: 38972172 PMCID: PMC11316639 DOI: 10.1016/j.copbio.2024.103169] [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: 02/13/2023] [Revised: 11/16/2023] [Accepted: 06/14/2024] [Indexed: 07/09/2024]
Abstract
Immune cell therapies are an emerging class of living drugs that rely on the delivery of therapeutic transgenes to enhance, modulate, or restore cell function, such as those that encode for tumor-targeting receptors or replacement proteins. However, many cellular immunotherapies are autologous treatments that are limited by high manufacturing costs, typical vein-to-vein time of 3-4 weeks, and severe immune-related adverse effects. To address these issues, different classes of gene delivery vehicles are being developed to target specific immune cell subsets in vivo to address the limitations of ex vivo manufacturing, modulate therapeutic responses in situ, and reduce on- and off-target toxicity. The success of in vivo gene delivery to immune cells - which is being tested at the preclinical and clinical stages of development for the treatment of cancer, infectious diseases, and autoimmunity - is paramount for the democratization of cellular immunotherapies.
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Affiliation(s)
- Jamison C Siebart
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Ching S Chan
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Xinyi Yao
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Fang-Yi Su
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Gabriel A Kwong
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA; Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA 30332, USA; Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA; Integrated Cancer Research Center, Georgia Institute of Technology, Atlanta, GA 30332, USA; Georgia ImmunoEngineering Consortium, Emory University and Georgia Institute of Technology, Atlanta, GA 30332, USA.
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8
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Agmon A, Barth AL. A brief history of somatostatin interneuron taxonomy or: how many somatostatin subtypes are there, really? Front Neural Circuits 2024; 18:1436915. [PMID: 39091993 PMCID: PMC11292610 DOI: 10.3389/fncir.2024.1436915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024] Open
Abstract
We provide a brief (and unabashedly biased) overview of the pre-transcriptomic history of somatostatin interneuron taxonomy, followed by a chronological summary of the large-scale, NIH-supported effort over the last ten years to generate a comprehensive, single-cell RNA-seq-based taxonomy of cortical neurons. Focusing on somatostatin interneurons, we present the perspective of experimental neuroscientists trying to incorporate the new classification schemes into their own research while struggling to keep up with the ever-increasing number of proposed cell types, which seems to double every two years. We suggest that for experimental analysis, the most useful taxonomic level is the subdivision of somatostatin interneurons into ten or so "supertypes," which closely agrees with their more traditional classification by morphological, electrophysiological and neurochemical features. We argue that finer subdivisions ("t-types" or "clusters"), based on slight variations in gene expression profiles but lacking clear phenotypic differences, are less useful to researchers and may actually defeat the purpose of classifying neurons to begin with. We end by stressing the need for generating novel tools (mouse lines, viral vectors) for genetically targeting distinct supertypes for expression of fluorescent reporters, calcium sensors and excitatory or inhibitory opsins, allowing neuroscientists to chart the input and output synaptic connections of each proposed subtype, reveal the position they occupy in the cortical network and examine experimentally their roles in sensorimotor behaviors and cognitive brain functions.
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Affiliation(s)
- Ariel Agmon
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, United States
| | - Alison L. Barth
- Department of Biological Sciences, Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA, United States
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9
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Raudales R, Kim G, Kelly SM, Hatfield J, Guan W, Zhao S, Paul A, Qian Y, Li B, Huang ZJ. Specific and comprehensive genetic targeting reveals brain-wide distribution and synaptic input patterns of GABAergic axo-axonic interneurons. eLife 2024; 13:RP93481. [PMID: 39012795 PMCID: PMC11251723 DOI: 10.7554/elife.93481] [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: 07/18/2024] Open
Abstract
Axo-axonic cells (AACs), also called chandelier cells (ChCs) in the cerebral cortex, are the most distinctive type of GABAergic interneurons described in the neocortex, hippocampus, and basolateral amygdala (BLA). AACs selectively innervate glutamatergic projection neurons (PNs) at their axon initial segment (AIS), thus may exert decisive control over PN spiking and regulate PN functional ensembles. However, the brain-wide distribution, synaptic connectivity, and circuit function of AACs remain poorly understood, largely due to the lack of specific and reliable experimental tools. Here, we have established an intersectional genetic strategy that achieves specific and comprehensive targeting of AACs throughout the mouse brain based on their lineage (Nkx2.1) and molecular (Unc5b, Pthlh) markers. We discovered that AACs are deployed across essentially all the pallium-derived brain structures, including not only the dorsal pallium-derived neocortex and medial pallium-derived hippocampal formation, but also the lateral pallium-derived claustrum-insular complex, and the ventral pallium-derived extended amygdaloid complex and olfactory centers. AACs are also abundant in anterior olfactory nucleus, taenia tecta, and lateral septum. AACs show characteristic variations in density across neocortical areas and layers and across subregions of the hippocampal formation. Neocortical AACs comprise multiple laminar subtypes with distinct dendritic and axonal arborization patterns. Retrograde monosynaptic tracing from AACs across neocortical, hippocampal, and BLA regions reveal shared as well as distinct patterns of synaptic input. Specific and comprehensive targeting of AACs facilitates the study of their developmental genetic program and circuit function across brain structures, providing a ground truth platform for understanding the conservation and variation of a bona fide cell type across brain regions and species.
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Affiliation(s)
- Ricardo Raudales
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Program in Neurobiology, Stony Brook UniversityStony BrookUnited States
| | - Gukhan Kim
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Sean M Kelly
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Program in Neurobiology, Stony Brook UniversityStony BrookUnited States
| | - Joshua Hatfield
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Wuqiang Guan
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Shengli Zhao
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Anirban Paul
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Department of Neural and Behavioral Sciences, Penn State College of MedicineHersheyUnited States
| | - Yongjun Qian
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
| | - Bo Li
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
- Department of Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Z Josh Huang
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
- Department of Neurobiology, Duke UniversityDurhamUnited States
- Department of Biomedical Engineering, Duke UniversityDurhamUnited States
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10
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Wang L, Xu W, Zhang S, Gundberg GC, Zheng CR, Wan Z, Mustafina K, Caliendo F, Sandt H, Kamm R, Weiss R. Sensing and guiding cell-state transitions by using genetically encoded endoribonuclease-mediated microRNA sensors. Nat Biomed Eng 2024:10.1038/s41551-024-01229-z. [PMID: 38982158 DOI: 10.1038/s41551-024-01229-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/11/2024] [Indexed: 07/11/2024]
Abstract
Precisely sensing and guiding cell-state transitions via the conditional genetic activation of appropriate differentiation factors is challenging. Here we show that desired cell-state transitions can be guided via genetically encoded sensors, whereby endogenous cell-state-specific miRNAs regulate the translation of a constitutively transcribed endoribonuclease, which, in turn, controls the translation of a gene of interest. We used this approach to monitor several cell-state transitions, to enrich specific cell types and to automatically guide the multistep differentiation of human induced pluripotent stem cells towards a haematopoietic lineage via endothelial cells as an intermediate state. Such conditional activation of gene expression is durable and resistant to epigenetic silencing and could facilitate the monitoring of cell-state transitions in physiological and pathological conditions and eventually the 'rewiring' of cell-state transitions for applications in organoid-based disease modelling, cellular therapies and regenerative medicine.
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Affiliation(s)
- Lei Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Biology, Northeastern University, Boston, MA, USA.
| | - Wenlong Xu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shun Zhang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gregory C Gundberg
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christine R Zheng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengpeng Wan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kamila Mustafina
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fabio Caliendo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hayden Sandt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger Kamm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
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11
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Wu RY, Wu CQ, Xie F, Xing X, Xu L. Building RNA-Mediated Artificial Signaling Pathways between Endogenous Genes. Acc Chem Res 2024; 57:1777-1789. [PMID: 38872074 DOI: 10.1021/acs.accounts.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
ConspectusSophisticated genetic networks play a pivotal role in orchestrating cellular responses through intricate signaling pathways across diverse environmental conditions. Beyond the inherent complexity of natural cellular signaling networks, the construction of artificial signaling pathways (ASPs) introduces a vast array of possibilities for reshaping cellular responses, enabling programmable control of living organisms. ASPs can be integrated with existing cellular networks and redirect output responses as desired, allowing seamless communication and coordination with other cellular processes, thereby achieving designable transduction within cells. Among diversified ASPs, establishing connections between originally independent endogenous genes is of particular significance in modifying the genetic networks, so that cells can be endowed with new capabilities to sense and deal with abnormal factors related to differentiated gene expression (i.e., solve the issues of the aberrant gene expression induced by either external or internal stimuli). In a typical scenario, the two genes X and Y in the cell are originally expressed independently. After the introduction of an ASP, changes in the expression of gene X may exert a designed impact on gene Y, subsequently inducing the cellular response related to gene Y. If X represents a disease signal and Y serves as a therapeutic module, the introduction of the ASP empowers cells with a new spontaneous defense system to handle potential risks, which holds great potential for both fundamental and translational studies.In this Account, we primarily review our endeavors in the construction of RNA-mediated ASPs between endogenous genes that can respond to differentiated RNA expression. In contrast to other molecules that may be restricted to specific pathways, synthetic RNA circuits can be easily utilized and expanded as a general platform for constructing ASPs with a high degree of programmability and tunability for diversified functionalities through predictable Watson-Crick base pairing. We first provide an overview of recent advancements in RNA-based genetic circuits, encompassing but not limited to utilization of RNA toehold switches, siRNA and CRISPR systems. Despite notable progress, most reported RNA circuits have to contain at least one exogenous RNA X as input or one engineered RNA Y as a target, which is not suitable for establishing endogenous gene connections. While exogenous RNAs can be engineered and controlled as desired, constructing a general and efficient platform for manipulation of naturally occurring RNAs poses a formidable challenge, especially for the mammalian system. With a focus on this goal, we are devoted to developing efficient strategies to manipulate cell responses by establishing RNA-mediated ASPs between endogenous genes, particularly in mammalian cells. Our step-by-step progress in engineering customized cell signaling circuits, from bacterial cells to mammalian cells, from gene expression regulation to phenotype control, and from small RNA to long mRNA of low abundance and more complex secondary structures, is systematically described. Finally, future perspectives and potential applications of these RNA-mediated ASPs between endogenous genes are also discussed.
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Affiliation(s)
- Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiwen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
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12
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Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
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13
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Jiang G, Gao Y, Zhou N, Wang B. CRISPR-powered RNA sensing in vivo. Trends Biotechnol 2024:S0167-7799(24)00094-5. [PMID: 38734565 DOI: 10.1016/j.tibtech.2024.04.002] [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: 01/25/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/13/2024]
Abstract
RNA sensing in vivo evaluates past or ongoing endogenous RNA disturbances, which is crucial for identifying cell types and states and diagnosing diseases. Recently, the CRISPR-driven genetic circuits have offered promising solutions to burgeoning challenges in RNA sensing. This review delves into the cutting-edge developments of CRISPR-powered RNA sensors in vivo, reclassifying these RNA sensors into four categories based on their working mechanisms, including programmable reassembly of split single-guide RNA (sgRNA), RNA-triggered RNA processing and protein cleavage, miRNA-triggered RNA interference (RNAi), and strand displacement reactions. Then, we discuss the advantages and challenges of existing methodologies in diverse application scenarios and anticipate and analyze obstacles and opportunities in forthcoming practical implementations.
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Affiliation(s)
- Guo Jiang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China
| | - Yuanli Gao
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Nan Zhou
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China
| | - Baojun Wang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China.
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14
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Chamberland S, Grant G, Machold R, Nebet ER, Tian G, Stich J, Hanani M, Kullander K, Tsien RW. Functional specialization of hippocampal somatostatin-expressing interneurons. Proc Natl Acad Sci U S A 2024; 121:e2306382121. [PMID: 38640347 PMCID: PMC11047068 DOI: 10.1073/pnas.2306382121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 02/27/2024] [Indexed: 04/21/2024] Open
Abstract
Hippocampal somatostatin-expressing (Sst) GABAergic interneurons (INs) exhibit considerable anatomical and functional heterogeneity. Recent single-cell transcriptome analyses have provided a comprehensive Sst-IN subpopulations census, a plausible molecular ground truth of neuronal identity whose links to specific functionality remain incomplete. Here, we designed an approach to identify and access subpopulations of Sst-INs based on transcriptomic features. Four mouse models based on single or combinatorial Cre- and Flp- expression differentiated functionally distinct subpopulations of CA1 hippocampal Sst-INs that largely tiled the morpho-functional parameter space of the Sst-INs superfamily. Notably, the Sst;;Tac1 intersection revealed a population of bistratified INs that preferentially synapsed onto fast-spiking interneurons (FS-INs) and were sufficient to interrupt their firing. In contrast, the Ndnf;;Nkx2-1 intersection identified a population of oriens lacunosum-moleculare INs that predominantly targeted CA1 pyramidal neurons, avoiding FS-INs. Overall, our results provide a framework to translate neuronal transcriptomic identity into discrete functional subtypes that capture the diverse specializations of hippocampal Sst-INs.
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Affiliation(s)
- Simon Chamberland
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Gariel Grant
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Robert Machold
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Erica R. Nebet
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Guoling Tian
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Joshua Stich
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Monica Hanani
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Klas Kullander
- Developmental Genetics, Department of Neuroscience, Uppsala University, Uppsala, Uppsala län752 37, Sweden
| | - Richard W. Tsien
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Center for Neural Science, New York University, New York, NY10003
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15
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Wu CQ, Wu RY, Zhang QL, Wang LL, Wang Y, Dai C, Zhang CX, Xu L. Harnessing Catalytic RNA Circuits for Construction of Artificial Signaling Pathways in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202319309. [PMID: 38298112 DOI: 10.1002/anie.202319309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Engineering of genetic networks with artificial signaling pathways (ASPs) can reprogram cellular responses and phenotypes under different circumstances for a variety of diagnostic and therapeutic purposes. However, construction of ASPs between originally independent endogenous genes in mammalian cells is highly challenging. Here we report an amplifiable RNA circuit that can theoretically build regulatory connections between any endogenous genes in mammalian cells. We harness the system of catalytic hairpin assembly with combination of controllable CRISPR-Cas9 function to transduce the signals from distinct messenger RNA expression of trigger genes into manipulation of target genes. Through introduction of these RNA-based genetic circuits, mammalian cells are endowed with autonomous capabilities to sense the changes of RNA expression either induced by ligand stimuli or from various cell types and control the cellular responses and fates via apoptosis-related ASPs. Our design provides a generalized platform for construction of ASPs inside the genetic networks of mammalian cells based on differentiated RNA expression.
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Affiliation(s)
- Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
- School of Pharmacy and Medical Technology, Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine of Fujian Province, Putian University, Putian, 351100, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chu Dai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chen-Xi Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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16
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Witzenberger M, Schwartz S. Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges. Trends Genet 2024; 40:313-325. [PMID: 38350740 DOI: 10.1016/j.tig.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/15/2024]
Abstract
Over 170 chemical modifications can be naturally installed on RNA, all of which are catalyzed by dedicated machineries. These modifications can alter RNA sequence structure, stability, and translation as well as serving as quality control marks that record aspects of RNA processing. The diverse roles played by RNAs within cells has motivated endeavors to exogenously introduce RNA modifications at target sites for diverse purposes ranging from recording RNA:protein interactions to therapeutic applications. Here, we discuss these applications and the approaches that have been employed to engineer RNA-modifying machineries, and highlight persisting challenges and perspectives.
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Affiliation(s)
- Monika Witzenberger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7630031, Israel.
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17
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Raudales R, Kim G, Kelly SM, Hatfield J, Guan W, Zhao S, Paul A, Qian Y, Li B, Huang ZJ. Specific and comprehensive genetic targeting reveals brain-wide distribution and synaptic input patterns of GABAergic axo-axonic interneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.07.566059. [PMID: 37986757 PMCID: PMC10659298 DOI: 10.1101/2023.11.07.566059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Axo-axonic cells (AACs), also called chandelier cells (ChCs) in the cerebral cortex, are the most distinctive type of GABAergic interneurons described in the neocortex, hippocampus, and basolateral amygdala (BLA). AACs selectively innervate glutamatergic projection neurons (PNs) at their axon initial segment (AIS), thus may exert decisive control over PN spiking and regulate PN functional ensembles. However, the brain-wide distribution, synaptic connectivity, and circuit function of AACs remains poorly understood, largely due to the lack of specific and reliable experimental tools. Here, we have established an intersectional genetic strategy that achieves specific and comprehensive targeting of AACs throughout the mouse brain based on their lineage (Nkx2.1) and molecular (Unc5b, Pthlh) markers. We discovered that AACs are deployed across essentially all the pallium-derived brain structures, including not only the dorsal pallium-derived neocortex and medial pallium-derived hippocampal formation, but also the lateral pallium-derived claustrum-insular complex, and the ventral pallium-derived extended amygdaloid complex and olfactory centers. AACs are also abundant in anterior olfactory nucleus, taenia tecta and lateral septum. AACs show characteristic variations in density across neocortical areas and layers and across subregions of the hippocampal formation. Neocortical AACs comprise multiple laminar subtypes with distinct dendritic and axonal arborization patterns. Retrograde monosynaptic tracing from AACs across neocortical, hippocampal and BLA regions reveal shared as well as distinct patterns of synaptic input. Specific and comprehensive targeting of AACs facilitates the study of their developmental genetic program and circuit function across brain structures, providing a ground truth platform for understanding the conservation and variation of a bona fide cell type across brain regions and species.
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Affiliation(s)
- Ricardo Raudales
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Program in Neurobiology, Stony Brook University, NY, 11794, USA
| | - Gukhan Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sean M Kelly
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Program in Neurobiology, Stony Brook University, NY, 11794, USA
| | - Joshua Hatfield
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
| | - Wuqiang Guan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shengli Zhao
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
| | - Anirban Paul
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, PA, 17033
| | - Yongjun Qian
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
| | - Bo Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA
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18
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Ascanelli C, Dahir R, Wilson CH. Manipulating Myc for reparative regeneration. Front Cell Dev Biol 2024; 12:1357589. [PMID: 38577503 PMCID: PMC10991803 DOI: 10.3389/fcell.2024.1357589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024] Open
Abstract
The Myc family of proto-oncogenes is a key node for the signal transduction of external pro-proliferative signals to the cellular processes required for development, tissue homoeostasis maintenance, and regeneration across evolution. The tight regulation of Myc synthesis and activity is essential for restricting its oncogenic potential. In this review, we highlight the central role that Myc plays in regeneration across the animal kingdom (from Cnidaria to echinoderms to Chordata) and how Myc could be employed to unlock the regenerative potential of non-regenerative tissues in humans for therapeutic purposes. Mastering the fine balance of harnessing the ability of Myc to promote transcription without triggering oncogenesis may open the door to many exciting opportunities for therapeutic development across a wide array of diseases.
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Affiliation(s)
| | | | - Catherine H. Wilson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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19
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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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20
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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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21
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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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22
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Takahashi K, Galloway KE. RNA-based controllers for engineering gene and cell therapies. Curr Opin Biotechnol 2024; 85:103026. [PMID: 38052131 PMCID: PMC11214845 DOI: 10.1016/j.copbio.2023.103026] [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: 10/02/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023]
Abstract
Engineered RNA-based genetic controllers provide compact, tunable, post-transcriptional gene regulation. As RNA devices are generally small, these devices are portable to DNA and RNA viral vectors. RNA tools have recently expanded to allow reading and editing of endogenous RNAs for profiling and programming of transcriptional states. With their expanded capabilities and highly compact, modular, and programmable nature, RNA-based controllers will support greater safety, efficacy, and performance in gene and cell-based therapies. In this review, we highlight RNA-based controllers and their potential as user-guided and autonomous systems for control of gene and cell-based therapies.
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Affiliation(s)
- Kei Takahashi
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA
| | - Kate E Galloway
- Department of Chemical Engineering, MIT, 25 Ames St., Cambridge, MA 02139, USA.
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23
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Weng S, Yang X, Yu N, Wang PC, Xiong S, Ruan H. Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications. Int J Mol Sci 2023; 25:351. [PMID: 38203521 PMCID: PMC10779106 DOI: 10.3390/ijms25010351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
ADAR (Adenosine Deaminases Acting on RNA) proteins are a group of enzymes that play a vital role in RNA editing by converting adenosine to inosine in RNAs. This process is a frequent post-transcriptional event observed in metazoan transcripts. Recent studies indicate widespread dysregulation of ADAR-mediated RNA editing across many immune-related diseases, such as human cancer. We comprehensively review ADARs' function as pattern recognizers and their capability to contribute to mediating immune-related pathways. We also highlight the potential role of site-specific RNA editing in maintaining homeostasis and its relationship to various diseases, such as human cancers. More importantly, we summarize the latest cutting-edge computational approaches and data resources for predicting and analyzing RNA editing sites. Lastly, we cover the recent advancement in site-directed ADAR editing tool development. This review presents an up-to-date overview of ADAR-mediated RNA editing, how site-specific RNA editing could potentially impact disease pathology, and how they could be harnessed for therapeutic applications.
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Affiliation(s)
- Shenghui Weng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Xinyi Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Nannan Yu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Peng-Cheng Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Sidong Xiong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
| | - Hang Ruan
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.W.); (P.-C.W.)
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou 215123, China
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24
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Liu Y, Liu W, Wang B. Engineering CRISPR guide RNAs for programmable RNA sensors. Biochem Soc Trans 2023; 51:2061-2070. [PMID: 37955062 PMCID: PMC10754282 DOI: 10.1042/bst20221486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023]
Abstract
As the most valuable feature of the CRISPR system, the programmability based on Watson-Crick base pairing has been widely exploited in engineering RNA sensors. The base pairing in these systems offers a connection between the RNA of interest and the CRISPR effector, providing a highly specific mechanism for RNA detection both in vivo and in vitro. In the last decade, despite the many successful RNA sensing approaches developed during the era of CRISPR explosion, a deeper understanding of the characteristics of CRISPR systems and the continuous expansion of the CRISPR family members indicates that the CRISPR-based RNA sensor remains a promising area from which a variety of new functions and applications can be engineered. Here, we present a systematic overview of the various strategies of engineering CRISPR gRNA for programmable RNA detection with an aim to clarify the role of gRNA's programmability among the present limitations and future development of CRISPR-enabled RNA sensors.
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Affiliation(s)
- Yang Liu
- MRC Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Wei Liu
- MRC Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou 311100, China
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25
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Koonin EV, Gootenberg JS, Abudayyeh OO. Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox. Biochemistry 2023; 62:3465-3487. [PMID: 37192099 PMCID: PMC10734277 DOI: 10.1021/acs.biochem.3c00159] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Indexed: 05/18/2023]
Abstract
CRISPR systems mediate adaptive immunity in bacteria and archaea through diverse effector mechanisms and have been repurposed for versatile applications in therapeutics and diagnostics thanks to their facile reprogramming with RNA guides. RNA-guided CRISPR-Cas targeting and interference are mediated by effectors that are either components of multisubunit complexes in class 1 systems or multidomain single-effector proteins in class 2. The compact class 2 CRISPR systems have been broadly adopted for multiple applications, especially genome editing, leading to a transformation of the molecular biology and biotechnology toolkit. The diversity of class 2 effector enzymes, initially limited to the Cas9 nuclease, was substantially expanded via computational genome and metagenome mining to include numerous variants of Cas12 and Cas13, providing substrates for the development of versatile, orthogonal molecular tools. Characterization of these diverse CRISPR effectors uncovered many new features, including distinct protospacer adjacent motifs (PAMs) that expand the targeting space, improved editing specificity, RNA rather than DNA targeting, smaller crRNAs, staggered and blunt end cuts, miniature enzymes, promiscuous RNA and DNA cleavage, etc. These unique properties enabled multiple applications, such as harnessing the promiscuous RNase activity of the type VI effector, Cas13, for supersensitive nucleic acid detection. class 1 CRISPR systems have been adopted for genome editing, as well, despite the challenge of expressing and delivering the multiprotein class 1 effectors. The rich diversity of CRISPR enzymes led to rapid maturation of the genome editing toolbox, with capabilities such as gene knockout, base editing, prime editing, gene insertion, DNA imaging, epigenetic modulation, transcriptional modulation, and RNA editing. Combined with rational design and engineering of the effector proteins and associated RNAs, the natural diversity of CRISPR and related bacterial RNA-guided systems provides a vast resource for expanding the repertoire of tools for molecular biology and biotechnology.
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Affiliation(s)
- Eugene V. Koonin
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Jonathan S. Gootenberg
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Omar O. Abudayyeh
- McGovern
Institute for Brain Research at MIT, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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26
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Langlieb J, Sachdev NS, Balderrama KS, Nadaf NM, Raj M, Murray E, Webber JT, Vanderburg C, Gazestani V, Tward D, Mezias C, Li X, Flowers K, Cable DM, Norton T, Mitra P, Chen F, Macosko EZ. The molecular cytoarchitecture of the adult mouse brain. Nature 2023; 624:333-342. [PMID: 38092915 PMCID: PMC10719111 DOI: 10.1038/s41586-023-06818-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
The function of the mammalian brain relies upon the specification and spatial positioning of diversely specialized cell types. Yet, the molecular identities of the cell types and their positions within individual anatomical structures remain incompletely known. To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq1,2-a recently developed spatial transcriptomics method with near-cellular resolution-across the entire mouse brain. Integration of these datasets revealed the cell type composition of each neuroanatomical structure. Cell type diversity was found to be remarkably high in the midbrain, hindbrain and hypothalamus, with most clusters requiring a combination of at least three discrete gene expression markers to uniquely define them. Using these data, we developed a framework for genetically accessing each cell type, comprehensively characterized neuropeptide and neurotransmitter signalling, elucidated region-specific specializations in activity-regulated gene expression and ascertained the heritability enrichment of neurological and psychiatric phenotypes. These data, available as an online resource ( www.BrainCellData.org ), should find diverse applications across neuroscience, including the construction of new genetic tools and the prioritization of specific cell types and circuits in the study of brain diseases.
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Affiliation(s)
| | | | | | - Naeem M Nadaf
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mukund Raj
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | | | - Daniel Tward
- Departments of Computational Medicine and Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chris Mezias
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xu Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Dylan M Cable
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Partha Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Stem Cell and Regenerative Biology, Cambridge, MA, USA.
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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27
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Zhang Q, Liu X, Gong L, He M. Combinatorial genetic strategies for dissecting cell lineages, cell types, and gene function in the mouse brain. Dev Growth Differ 2023; 65:546-553. [PMID: 37963088 DOI: 10.1111/dgd.12902] [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: 09/05/2023] [Revised: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Research in neuroscience has greatly benefited from the development of genetic approaches that enable lineage tracing, cell type targeting, and conditional gene regulation. Recent advances in combinatorial strategies, which integrate multiple cellular features, have significantly enhanced the spatiotemporal precision and flexibility of these manipulations. In this minireview, we introduce the concept and design of these strategies and provide a few examples of their application in genetic fate mapping, cell type targeting, and reversible conditional gene regulation. These advancements have facilitated in-depth investigation into the developmental principles underlying the assembly of brain circuits, granting experimental access to highly specific cell lineages and subtypes, as well as offering valuable new tools for modeling and studying neurological diseases. Additionally, we discuss future directions aimed at expanding and improving the existing genetic toolkit for a better understanding of the development, structure, and function of healthy and diseased brains.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xue Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling Gong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miao He
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
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28
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Li B, Qu L, Yang J. RNA-Guided RNA Modifications: Biogenesis, Functions, and Applications. Acc Chem Res 2023; 56:3198-3210. [PMID: 37931323 DOI: 10.1021/acs.accounts.3c00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Post-transcriptional modifications are ubiquitous in both protein-coding and noncoding RNAs (ncRNAs), playing crucial functional roles in diverse biological processes across all kingdoms of life. These RNA modifications can be achieved through two distinct mechanisms: RNA-independent and RNA-guided (also known as RNA-dependent). In the RNA-independent mechanism, modifications are directly introduced onto RNA molecules by enzymes without the involvement of other RNA molecules, while the cellular RNA-guided RNA modification system exists in the form of RNA-protein complexes, wherein one guide RNA collaborates with a set of proteins, including the modifying enzyme. The primary function of guide RNAs lies in their ability to bind to complementary regions within the target RNAs, orchestrating the installation of specific modifications. Both mechanisms offer unique advantages and are critical to the diverse and dynamic landscape of RNA modifications. RNA-independent modifications provide rapid and direct modification of RNA molecules, while RNA-guided mechanisms offer precise and programmable means to introduce modifications at specific RNA sites. Recently, emerging evidence has shed light on RNA-guided RNA modifications as a captivating area of research, providing precise and programmable control over RNA sequences and functions.In this Account, we focus on RNA modifications synthesized in an RNA-guided manner, including 2'-O-methylated nucleotides (Nm), pseudouridine (Ψ), N4-acetylcytidine (ac4C), and inosine (I). This Account sheds light on the intricate processes of biogenesis and elucidates the regulatory roles of these modifications in RNA metabolism. These roles include pivotal functions such as RNA stability, translation, and splicing, where each modification contributes to the diverse and finely tuned regulatory landscape of RNA biology. In addition to elucidating the biogenesis and functions of these modifications, we also provide an overview of high-throughput methods and their underlying biochemical principles used for the transcriptome-wide investigation of these modifications and their fundamental interactions in RNA-guided systems. This includes exploring RNA-protein interactions and RNA-RNA interactions, which play crucial roles in the dynamic regulatory networks of RNA-guided modifications. The ever-advancing methodologies have greatly enhanced our understanding of the dynamic and widespread nature of RNA-guided RNA modifications and their regulatory functions. Furthermore, the applications of RNA-guided RNA modifications are discussed, illuminating their potential in diverse fields. From basic research to gene therapy, the programmable nature of RNA-guided modifications presents exciting opportunities for manipulating gene expression and developing innovative therapeutic strategies.
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Affiliation(s)
- Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
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29
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Chiou KL, Huang X, Bohlen MO, Tremblay S, DeCasien AR, O’Day DR, Spurrell CH, Gogate AA, Zintel TM, Andrews MG, Martínez MI, Starita LM, Montague MJ, Platt ML, Shendure J, Snyder-Mackler N. A single-cell multi-omic atlas spanning the adult rhesus macaque brain. SCIENCE ADVANCES 2023; 9:eadh1914. [PMID: 37824616 PMCID: PMC10569716 DOI: 10.1126/sciadv.adh1914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
Cataloging the diverse cellular architecture of the primate brain is crucial for understanding cognition, behavior, and disease in humans. Here, we generated a brain-wide single-cell multimodal molecular atlas of the rhesus macaque brain. Together, we profiled 2.58 M transcriptomes and 1.59 M epigenomes from single nuclei sampled from 30 regions across the adult brain. Cell composition differed extensively across the brain, revealing cellular signatures of region-specific functions. We also identified 1.19 M candidate regulatory elements, many previously unidentified, allowing us to explore the landscape of cis-regulatory grammar and neurological disease risk in a cell type-specific manner. Altogether, this multi-omic atlas provides an open resource for investigating the evolution of the human brain and identifying novel targets for disease interventions.
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Affiliation(s)
- Kenneth L. Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Martin O. Bohlen
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Sébastien Tremblay
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Alex R. DeCasien
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA
| | - Diana R. O’Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Cailyn H. Spurrell
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Aishwarya A. Gogate
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Trisha M. Zintel
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Cayo Biobank Research Unit
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
- Section on Developmental Neurogenomics, National Institute of Mental Health, Bethesda, MD, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, PR, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
- Marketing Department, University of Pennsylvania, Philadelphia, PA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Madeline G. Andrews
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Melween I. Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, PR, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Michael J. Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael L. Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, PA, USA
- Marketing Department, University of Pennsylvania, Philadelphia, PA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
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30
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Aygün N, Krupa O, Mory J, Le B, Valone J, Liang D, Love MI, Stein JL. Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555019. [PMID: 37693528 PMCID: PMC10491258 DOI: 10.1101/2023.08.30.555019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The function of some genetic variants associated with brain-relevant traits has been explained through colocalization with expression quantitative trait loci (eQTL) conducted in bulk post-mortem adult brain tissue. However, many brain-trait associated loci have unknown cellular or molecular function. These genetic variants may exert context-specific function on different molecular phenotypes including post-transcriptional changes. Here, we identified genetic regulation of RNA-editing and alternative polyadenylation (APA), within a cell-type-specific population of human neural progenitors and neurons. More RNA-editing and isoforms utilizing longer polyadenylation sequences were observed in neurons, likely due to higher expression of genes encoding the proteins mediating these post-transcriptional events. We also detected hundreds of cell-type-specific editing quantitative trait loci (edQTLs) and alternative polyadenylation QTLs (apaQTLs). We found colocalizations of a neuron edQTL in CCDC88A with educational attainment and a progenitor apaQTL in EP300 with schizophrenia, suggesting genetically mediated post-transcriptional regulation during brain development lead to differences in brain function.
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Affiliation(s)
- Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jessica Mory
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brandon Le
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan Valone
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I. Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lead contact
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31
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Wang WJ, Lin J, Wu CQ, Luo AL, Xing X, Xu L. Establishing artificial gene connections through RNA displacement-assembly-controlled CRISPR/Cas9 function. Nucleic Acids Res 2023; 51:7691-7703. [PMID: 37395400 PMCID: PMC10415155 DOI: 10.1093/nar/gkad558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023] Open
Abstract
Construction of synthetic circuits that can reprogram genetic networks and signal pathways is a long-term goal for manipulation of biosystems. However, it is still highly challenging to build artificial genetic communications among endogenous RNA species due to their sequence independence and structural diversities. Here we report an RNA-based synthetic circuit that can establish regulatory linkages between expression of endogenous genes in both Escherichiacoli and mammalian cells. This design employs a displacement-assembly approach to modulate the activity of guide RNA for function control of CRISPR/Cas9. Our experiments demonstrate the great effectiveness of this RNA circuit for building artificial connections between expression of originally unrelated genes. Both exogenous and naturally occurring RNAs, including small/microRNAs and long mRNAs, are capable of controlling expression of another endogenous gene through this approach. Moreover, an artificial signal pathway inside mammalian cells is also successfully established to control cell apoptosis through our designed synthetic circuit. This study provides a general strategy for constructing synthetic RNA circuits, which can introduce artificial connections into the genetic networks of mammalian cells and alter the cellular phenotypes.
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Affiliation(s)
- Wei-Jia Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiao Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ai-Ling Luo
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiwen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University Institution, Guangzhou 510632, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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32
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Ahuja N, Hwaun E, Pungor JR, Rafiq R, Nemes S, Sakmar T, Vogt MA, Grasse B, Diaz Quiroz J, Montague TG, Null RW, Dallis DN, Gavriouchkina D, Marletaz F, Abbo L, Rokhsar DS, Niell CM, Soltesz I, Albertin CB, Rosenthal JJC. Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity. Curr Biol 2023:S0960-9822(23)00739-X. [PMID: 37343558 DOI: 10.1016/j.cub.2023.05.066] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Cephalopods are remarkable among invertebrates for their cognitive abilities, adaptive camouflage, novel structures, and propensity for recoding proteins through RNA editing. Due to the lack of genetically tractable cephalopod models, however, the mechanisms underlying these innovations are poorly understood. Genome editing tools such as CRISPR-Cas9 allow targeted mutations in diverse species to better link genes and function. One emerging cephalopod model, Euprymna berryi, produces large numbers of embryos that can be easily cultured throughout their life cycle and has a sequenced genome. As proof of principle, we used CRISPR-Cas9 in E. berryi to target the gene for tryptophan 2,3 dioxygenase (TDO), an enzyme required for the formation of ommochromes, the pigments present in the eyes and chromatophores of cephalopods. CRISPR-Cas9 ribonucleoproteins targeting tdo were injected into early embryos and then cultured to adulthood. Unexpectedly, the injected specimens were pigmented, despite verification of indels at the targeted sites by sequencing in injected animals (G0s). A homozygote knockout line for TDO, bred through multiple generations, was also pigmented. Surprisingly, a gene encoding indoleamine 2,3, dioxygenase (IDO), an enzyme that catalyzes the same reaction as TDO in vertebrates, was also present in E. berryi. Double knockouts of both tdo and ido with CRISPR-Cas9 produced an albino phenotype. We demonstrate the utility of these albinos for in vivo imaging of Ca2+ signaling in the brain using two-photon microscopy. These data show the feasibility of making gene knockout cephalopod lines that can be used for live imaging of neural activity in these behaviorally sophisticated organisms.
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Affiliation(s)
- Namrata Ahuja
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Ernie Hwaun
- Department of Neurosurgery and Stanford Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Judit R Pungor
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Ruhina Rafiq
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Sal Nemes
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Taylor Sakmar
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Miranda A Vogt
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Bret Grasse
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Juan Diaz Quiroz
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Tessa G Montague
- Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Ryan W Null
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Danielle N Dallis
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0412, Japan
| | - Ferdinand Marletaz
- Centre for Life's Origin & Evolution, Department of Ecology, Evolution & Environment, University College London, WC1E 6BT London, UK
| | - Lisa Abbo
- Marine Resources Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0412, Japan; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Ivan Soltesz
- Department of Neurosurgery and Stanford Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Caroline B Albertin
- Eugene Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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Booth BJ, Nourreddine S, Katrekar D, Savva Y, Bose D, Long TJ, Huss DJ, Mali P. RNA editing: Expanding the potential of RNA therapeutics. Mol Ther 2023; 31:1533-1549. [PMID: 36620962 PMCID: PMC9824937 DOI: 10.1016/j.ymthe.2023.01.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/06/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
RNA therapeutics have had a tremendous impact on medicine, recently exemplified by the rapid development and deployment of mRNA vaccines to combat the COVID-19 pandemic. In addition, RNA-targeting drugs have been developed for diseases with significant unmet medical needs through selective mRNA knockdown or modulation of pre-mRNA splicing. Recently, RNA editing, particularly antisense RNA-guided adenosine deaminase acting on RNA (ADAR)-based programmable A-to-I editing, has emerged as a powerful tool to manipulate RNA to enable correction of disease-causing mutations and modulate gene expression and protein function. Beyond correcting pathogenic mutations, the technology is particularly well suited for therapeutic applications that require a transient pharmacodynamic effect, such as the treatment of acute pain, obesity, viral infection, and inflammation, where it would be undesirable to introduce permanent alterations to the genome. Furthermore, transient modulation of protein function, such as altering the active sites of enzymes or the interface of protein-protein interactions, opens the door to therapeutic avenues ranging from regenerative medicine to oncology. These emerging RNA-editing-based toolsets are poised to broadly impact biotechnology and therapeutic applications. Here, we review the emerging field of therapeutic RNA editing, highlight recent laboratory advancements, and discuss the key challenges on the path to clinical development.
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Affiliation(s)
| | - Sami Nourreddine
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | | | | | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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34
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Kim MH, Radaelli C, Thomsen ER, Monet D, Chartrand T, Jorstad NL, Mahoney JT, Taormina MJ, Long B, Baker K, Bakken TE, Campagnola L, Casper T, Clark M, Dee N, D'Orazi F, Gamlin C, Kalmbach BE, Kebede S, Lee BR, Ng L, Trinh J, Cobbs C, Gwinn RP, Keene CD, Ko AL, Ojemann JG, Silbergeld DL, Sorensen SA, Berg J, Smith KA, Nicovich PR, Jarsky T, Zeng H, Ting JT, Levi BP, Lein E. Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex. eLife 2023; 12:e81863. [PMID: 37249212 PMCID: PMC10332811 DOI: 10.7554/elife.81863] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably obtaining healthy tissue, conducting multiple patch-clamp recordings on inhibitory cell types, and identifying those cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings, post-hoc fluorescent in situ hybridization (FISH), machine learning-based cell type classification and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST-positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed by Patch-seq, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodent, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.
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Affiliation(s)
- Mean-Hwan Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Deja Monet
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | | | - Brian Long
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Tamara Casper
- Allen Institute for Brain ScienceSeattleUnited States
| | - Michael Clark
- Allen Institute for Brain ScienceSeattleUnited States
| | - Nick Dee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | - Clare Gamlin
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian E Kalmbach
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Sara Kebede
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian R Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lindsay Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jessica Trinh
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - C Dirk Keene
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - Andrew L Ko
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Daniel L Silbergeld
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | | | - Jim Berg
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jonathan T Ting
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Boaz P Levi
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
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35
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Seo JP, Trippett JS, Huang Z, Wang RZ, Lee S, Szablowski JO. Acoustically-Targeted Measurement of Transgene Expression in the Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541868. [PMID: 37292585 PMCID: PMC10245922 DOI: 10.1101/2023.05.23.541868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gene expression is a critical component of brain physiology and activity, but monitoring this expression in the living brain represents a significant challenge. Here, we introduce a new paradigm called Recovery of Markers through InSonation (REMIS) for noninvasive measurement of gene expression in the brain with cell-type, spatial, and temporal specificity. Our approach relies on engineered protein markers that are designed to be expressed in neurons and exit into the interstitium. By applying ultrasound to targeted brain regions, these markers are released into the bloodstream, where they can be readily detected using biochemical techniques. REMIS can noninvasively confirm gene delivery and measure endogenous signaling in specific brain sites through a simple insonation and a subsequent blood test. Using REMIS, we successfully measured chemogenetic induction of neuronal activity in ultrasound-tar-geted brain regions. REMIS recovery of markers is reliable and demonstrated improved recovery of markers from the brain into the blood in every tested animal. Overall, our work establishes a noninvasive, spatially-specific means of monitoring gene delivery outcomes and endogenous signaling in mammalian brains, opening up possibilities for brain research and noninvasive monitoring of gene therapies in the brain.
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36
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Chamberland S, Grant G, Machold R, Nebet ER, Tian G, Hanani M, Kullander K, Tsien RW. Functional specialization of hippocampal somatostatin-expressing interneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538511. [PMID: 37162922 PMCID: PMC10168348 DOI: 10.1101/2023.04.27.538511] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Hippocampal somatostatin-expressing (Sst) GABAergic interneurons (INs) exhibit considerable anatomical and functional heterogeneity. Recent single cell transcriptome analyses have provided a comprehensive Sst-IN subtype census, a plausible molecular ground truth of neuronal identity whose links to specific functionality remain incomplete. Here, we designed an approach to identify and access subpopulations of Sst-INs based on transcriptomic features. Four mouse models based on single or combinatorial Cre- and Flp- expression differentiated functionally distinct subpopulations of CA1 hippocampal Sst-INs that largely tiled the morpho-functional parameter space of the Sst-INs superfamily. Notably, the Sst;;Tac1 intersection revealed a population of bistratified INs that preferentially synapsed onto fast-spiking interneurons (FS-INs) and were both necessary and sufficient to interrupt their firing. In contrast, the Ndnf;;Nkx2-1 intersection identified a population of oriens lacunosum-moleculare (OLM) INs that predominantly targeted CA1 pyramidal neurons, avoiding FS-INs. Overall, our results provide a framework to translate neuronal transcriptomic identity into discrete functional subtypes that capture the diverse specializations of hippocampal Sst-INs.
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Affiliation(s)
- Simon Chamberland
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Gariel Grant
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Robert Machold
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Erica R. Nebet
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Guoling Tian
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Monica Hanani
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Klas Kullander
- Developmental Genetics, Department of Neuroscience, Uppsala University, Uppsala 752 37, Uppsala län, Sweden
| | - Richard W. Tsien
- NYU Neuroscience Institute and Department of Neuroscience and Physiology, NYU Langone Medical Center, New York, NY 10016, USA
- Center for Neural Science, New York University, New York, NY, 10003, USA
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37
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Dai C, Wang J, Tu L, Pan Z, Yang J, Zhou S, Luo Q, Zhu L, Ye Y. Genetically-encoded degraders as versatile modulators of intracellular therapeutic targets. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023. [DOI: 10.1016/j.cobme.2023.100458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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38
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Langlieb J, Sachdev NS, Balderrama KS, Nadaf NM, Raj M, Murray E, Webber JT, Vanderburg C, Gazestani V, Tward D, Mezias C, Li X, Cable DM, Norton T, Mitra P, Chen F, Macosko EZ. The cell type composition of the adult mouse brain revealed by single cell and spatial genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531307. [PMID: 36945580 PMCID: PMC10028805 DOI: 10.1101/2023.03.06.531307] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
The function of the mammalian brain relies upon the specification and spatial positioning of diversely specialized cell types. Yet, the molecular identities of the cell types, and their positions within individual anatomical structures, remain incompletely known. To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA-seq with Slide-seq-a recently developed spatial transcriptomics method with near-cellular resolution-across the entire mouse brain. Integration of these datasets revealed the cell type composition of each neuroanatomical structure. Cell type diversity was found to be remarkably high in the midbrain, hindbrain, and hypothalamus, with most clusters requiring a combination of at least three discrete gene expression markers to uniquely define them. Using these data, we developed a framework for genetically accessing each cell type, comprehensively characterized neuropeptide and neurotransmitter signaling, elucidated region-specific specializations in activity-regulated gene expression, and ascertained the heritability enrichment of neurological and psychiatric phenotypes. These data, available as an online resource (BrainCellData.org) should find diverse applications across neuroscience, including the construction of new genetic tools, and the prioritization of specific cell types and circuits in the study of brain diseases.
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Affiliation(s)
| | | | | | | | - Mukund Raj
- Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA USA
| | | | | | | | - Daniel Tward
- Departments of Computational Medicine and Neurology, University of California Los Angeles, Los Angeles, CA USA
| | - Chris Mezias
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Xu Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Dylan M. Cable
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | | | - Partha Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Harvard Stem Cell and Regenerative Biology, Cambridge, MA USA
| | - Evan Z. Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA USA
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39
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Autocatalytic base editing for RNA-responsive translational control. Nat Commun 2023; 14:1339. [PMID: 36906659 PMCID: PMC10008589 DOI: 10.1038/s41467-023-36851-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/20/2023] [Indexed: 03/13/2023] Open
Abstract
Genetic circuits that control transgene expression in response to pre-defined transcriptional cues would enable the development of smart therapeutics. To this end, here we engineer programmable single-transcript RNA sensors in which adenosine deaminases acting on RNA (ADARs) autocatalytically convert target hybridization into a translational output. Dubbed DART VADAR (Detection and Amplification of RNA Triggers via ADAR), our system amplifies the signal from editing by endogenous ADAR through a positive feedback loop. Amplification is mediated by the expression of a hyperactive, minimal ADAR variant and its recruitment to the edit site via an orthogonal RNA targeting mechanism. This topology confers high dynamic range, low background, minimal off-target effects, and a small genetic footprint. We leverage DART VADAR to detect single nucleotide polymorphisms and modulate translation in response to endogenous transcript levels in mammalian cells.
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40
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Crews LA, Ma W, Ladel L, Pham J, Balaian L, Steel SK, Mondala PK, Diep RH, Wu CN, Mason CN, van der Werf I, Oliver I, Reynoso E, Pineda G, Whisenant TC, Wentworth P, La Clair JJ, Jiang Q, Burkart MD, Jamieson CHM. Reversal of malignant ADAR1 splice isoform switching with Rebecsinib. Cell Stem Cell 2023; 30:250-263.e6. [PMID: 36803553 PMCID: PMC10134781 DOI: 10.1016/j.stem.2023.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 02/18/2023]
Abstract
Adenosine deaminase acting on RNA1 (ADAR1) preserves genomic integrity by preventing retroviral integration and retrotransposition during stress responses. However, inflammatory-microenvironment-induced ADAR1p110 to p150 splice isoform switching drives cancer stem cell (CSC) generation and therapeutic resistance in 20 malignancies. Previously, predicting and preventing ADAR1p150-mediated malignant RNA editing represented a significant challenge. Thus, we developed lentiviral ADAR1 and splicing reporters for non-invasive detection of splicing-mediated ADAR1 adenosine-to-inosine (A-to-I) RNA editing activation; a quantitative ADAR1p150 intracellular flow cytometric assay; a selective small-molecule inhibitor of splicing-mediated ADAR1 activation, Rebecsinib, which inhibits leukemia stem cell (LSC) self-renewal and prolongs humanized LSC mouse model survival at doses that spare normal hematopoietic stem and progenitor cells (HSPCs); and pre-IND studies showing favorable Rebecsinib toxicokinetic and pharmacodynamic (TK/PD) properties. Together, these results lay the foundation for developing Rebecsinib as a clinical ADAR1p150 antagonist aimed at obviating malignant microenvironment-driven LSC generation.
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Affiliation(s)
- Leslie A Crews
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wenxue Ma
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Luisa Ladel
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jessica Pham
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Larisa Balaian
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - S Kathleen Steel
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Phoebe K Mondala
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Raymond H Diep
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Christina N Wu
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Cayla N Mason
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Inge van der Werf
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Isabelle Oliver
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eduardo Reynoso
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Gabriel Pineda
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Thomas C Whisenant
- Center for Computational Biology & Bioinformatics (CCBB), Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peggy Wentworth
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - James J La Clair
- Departments of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qingfei Jiang
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Departments of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Catriona H M Jamieson
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, University of California, San Diego, La Jolla, CA 92037, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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41
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Ono H, Saito H. Sensing intracellular signatures with synthetic mRNAs. RNA Biol 2023; 20:588-602. [PMID: 37582192 PMCID: PMC10431736 DOI: 10.1080/15476286.2023.2244791] [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] [Revised: 06/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
The bottom-up assembly of biological components in synthetic biology has contributed to a better understanding of natural phenomena and the development of new technologies for practical applications. Over the past few decades, basic RNA research has unveiled the regulatory roles of RNAs underlying gene regulatory networks; while advances in RNA biology, in turn, have highlighted the potential of a wide variety of RNA elements as building blocks to construct artificial systems. In particular, synthetic mRNA-based translational regulators, which respond to signals in cells and regulate the production of encoded output proteins, are gaining attention with the recent rise of mRNA therapeutics. In this Review, we discuss recent progress in RNA synthetic biology, mainly focusing on emerging technologies for sensing intracellular protein and RNA molecules and controlling translation.
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Affiliation(s)
- Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
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42
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Burgess DJ. RADARs and READRs for programmable RNA sensing. Nat Rev Genet 2022; 23:711. [DOI: 10.1038/s41576-022-00548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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