1
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Kang H, Park D, Kim J. Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs. Nucleic Acids Res 2024; 52:8595-8608. [PMID: 38943344 DOI: 10.1093/nar/gkae549] [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: 10/04/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
The CRISPR-Cas system provides a versatile RNA-guided approach for a broad range of applications. Thanks to advances in RNA synthetic biology, the engineering of guide RNAs (gRNAs) has enabled the conditional control of the CRISPR-Cas system. However, achieving precise regulation of the CRISPR-Cas system for efficient modulation of internal metabolic processes remains challenging. In this work, we developed a robust dCas9 regulator with engineered conditional gRNAs to enable tight control of endogenous genes. Our conditional gRNAs in Escherichia coli can control gene expression upon specific interaction with trigger RNAs with a dynamic range as high as 130-fold, evaluating up to a three-input logic A OR (B AND C). The conditional gRNA-mediated targeting of endogenous metabolic genes, lacZ, malT and poxB, caused differential regulation of growth in Escherichia coli via metabolic flux control. Further, conditional gRNAs could regulate essential cytoskeleton genes, ftsZ and mreB, to control cell filamentation and division. Finally, three types of two-input logic gates could be applied for the conditional control of ftsZ regulation, resulting in morphological changes. The successful operation and application of conditional gRNAs based on programmable RNA interactions suggests that our system could be compatible with other Cas-effectors and implemented in other host organisms.
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Affiliation(s)
- Hansol Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Dongwon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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2
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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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3
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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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4
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Bagheri N, Chamorro A, Idili A, Porchetta A. PAM-Engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications. Angew Chem Int Ed Engl 2024; 63:e202319677. [PMID: 38284432 DOI: 10.1002/anie.202319677] [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: 12/19/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
The RNA-programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio-engineering strategies are required to achieve control over Cas12a activity. Here, we show that Toehold Switch DNA hairpins, presenting a rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used to control Cas12a in response to molecular inputs. Reconfiguring the Toehold Switch DNA from a hairpin to a duplex conformation through a strand displacement reaction provides an effective means to modulate the accessibility of the PAM, thereby controlling the binding and cleavage activities of Cas12a. Through this approach, we showcase the potential to trigger downstream Cas12a activity by leveraging proximity-based strand displacement reactions in response to target binding. By utilizing the trans-cleavage activity of Cas12a as a signal transduction method, we demonstrate the versatility of our approach for sensing applications. Our system enables rapid, one-pot detection of IgG antibodies and small molecules with high sensitivity and specificity even within complex matrices. Besides the bioanalytical applications, the switchable PAM-engineered Toehold Switches serve as programmable tools capable of regulating Cas12a-based targeting and DNA processing in response to molecular inputs and hold promise for a wide array of biotechnological applications.
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Affiliation(s)
- Neda Bagheri
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alejandro Chamorro
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Andrea Idili
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
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5
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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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6
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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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7
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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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8
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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: 7] [Impact Index Per Article: 7.0] [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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9
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Jiang K, Koob J, Chen XD, Krajeski RN, Zhang Y, Volf V, Zhou W, Sgrizzi SR, Villiger L, Gootenberg JS, Chen F, Abudayyeh OO. Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Nat Biotechnol 2023; 41:698-707. [PMID: 36302988 DOI: 10.1038/s41587-022-01534-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Programmable approaches to sense and respond to the presence of specific RNAs in biological systems have broad applications in research, diagnostics, and therapeutics. Here we engineer a programmable RNA-sensing technology, reprogrammable ADAR sensors (RADARS), which harnesses RNA editing by adenosine deaminases acting on RNA (ADAR) to gate translation of a cargo protein by the presence of endogenous RNA transcripts. Introduction of a stop codon in a guide upstream of the cargo makes translation contingent on binding of an endogenous transcript to the guide, leading to ADAR editing of the stop codon and allowing translational readthrough. Through systematic sensor engineering, we achieve 277 fold improvement in sensor activation and engineer RADARS with diverse cargo proteins, including luciferases, fluorescent proteins, recombinases, and caspases, enabling detection sensitivity on endogenous transcripts expressed at levels as low as 13 transcripts per million. We show that RADARS are functional as either expressed DNA or synthetic mRNA and with either exogenous or endogenous ADAR. We apply RADARS in multiple contexts, including tracking transcriptional states, RNA-sensing-induced cell death, cell-type identification, and control of synthetic mRNA translation.
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Affiliation(s)
- Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeremy Koob
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xi Dawn Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Systems, Synthetic, and Quantitative Biology Program, Harvard Medical School, Boston, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yifan Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Verena Volf
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samantha R Sgrizzi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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10
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Genome editing in cancer: Challenges and potential opportunities. Bioact Mater 2023; 21:394-402. [PMID: 36185740 PMCID: PMC9483578 DOI: 10.1016/j.bioactmat.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Ever since its mechanism was discovered back in 2012, the CRISPR/Cas9 system have revolutionized the field of genome editing. While at first it was seen as a therapeutic tool mostly relevant for curing genetic diseases, it has been recently shown to also hold the potential to become a clinically relevant therapy for cancer. However, there are multiple challenges that must be addressed prior to clinical testing. Predominantly, the safety of the system when used for in-vivo therapies, including off-target activity and the effects of the double strand break induction on genomic stability. Here, we will focus on the inherent challenges in the CRISPR/Cas9 system and discuss various opportunities to overcoming these challenges. In recent years, several works have shown that knocking down key genes by CRISPR/Cas9 based could potentially be a new type of cancer therapy. This has been made possible due to advances in the fields of In-vivo delivery, such as lentiviral vectors and lipid nanoparticles. Limiting CRISPR/Cas9 activity to the tumor and minimizing off-target activity are challenges that must be overcome before proceeding to the clinic. We review approaches arising from multiple disciplines that could overcome these challenges. The combination of these multi-disciplinary approaches should be able to overcome the different challenges and open the way to the clinic.
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11
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Shaytan AK, Novikov RV, Vinnikov RS, Gribkova AK, Glukhov GS. From DNA-protein interactions to the genetic circuit design using CRISPR-dCas systems. Front Mol Biosci 2022; 9:1070526. [PMID: 36589238 PMCID: PMC9795063 DOI: 10.3389/fmolb.2022.1070526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023] Open
Abstract
In the last decade, the CRISPR-Cas technology has gained widespread popularity in different fields from genome editing and detecting specific DNA/RNA sequences to gene expression control. At the heart of this technology is the ability of CRISPR-Cas complexes to be programmed for targeting particular DNA loci, even when using catalytically inactive dCas-proteins. The repertoire of naturally derived and engineered dCas-proteins including fusion proteins presents a promising toolbox that can be used to construct functional synthetic genetic circuits. Rational genetic circuit design, apart from having practical relevance, is an important step towards a deeper quantitative understanding of the basic principles governing gene expression regulation and functioning of living organisms. In this minireview, we provide a succinct overview of the application of CRISPR-dCas-based systems in the emerging field of synthetic genetic circuit design. We discuss the diversity of dCas-based tools, their properties, and their application in different types of genetic circuits and outline challenges and further research directions in the field.
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Affiliation(s)
- A. K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Computer Science, HSE University, Moscow, Russia,*Correspondence: A. K. Shaytan,
| | - R. V. Novikov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - R. S. Vinnikov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - A. K. Gribkova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - G. S. Glukhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen, China
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12
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Bokhari RS, Beheshti A, Blutt SE, Bowles DE, Brenner D, Britton R, Bronk L, Cao X, Chatterjee A, Clay DE, Courtney C, Fox DT, Gaber MW, Gerecht S, Grabham P, Grosshans D, Guan F, Jezuit EA, Kirsch DG, Liu Z, Maletic-Savatic M, Miller KM, Montague RA, Nagpal P, Osenberg S, Parkitny L, Pierce NA, Porada C, Rosenberg SM, Sargunas P, Sharma S, Spangler J, Tavakol DN, Thomas D, Vunjak-Novakovic G, Wang C, Whitcomb L, Young DW, Donoviel D. Looking on the horizon; potential and unique approaches to developing radiation countermeasures for deep space travel. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:105-112. [PMID: 36336356 DOI: 10.1016/j.lssr.2022.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
Future lunar missions and beyond will require new and innovative approaches to radiation countermeasures. The Translational Research Institute for Space Health (TRISH) is focused on identifying and supporting unique approaches to reduce risks to human health and performance on future missions beyond low Earth orbit. This paper will describe three funded and complementary avenues for reducing the risk to humans from radiation exposure experienced in deep space. The first focus is on identifying new therapeutic targets to reduce the damaging effects of radiation by focusing on high throughput genetic screens in accessible, sometimes called lower, organism models. The second focus is to design innovative approaches for countermeasure development with special attention to nucleotide-based methodologies that may constitute a more agile way to design therapeutics. The final focus is to develop new and innovative ways to test radiation countermeasures in a human model system. While animal studies continue to be beneficial in the study of space radiation, they can have imperfect translation to humans. The use of three-dimensional (3D) complex in vitro models is a promising approach to aid the development of new countermeasures and personalized assessments of radiation risks. These three distinct and unique approaches complement traditional space radiation efforts and should provide future space explorers with more options to safeguard their short and long-term health.
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Affiliation(s)
- Rihana S Bokhari
- Agile Decision Sciences, NRESS, Arlington, VA 22202, United States of America.
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, United States of America; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, United States of America
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States of America; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States of America
| | - Dawn E Bowles
- Division of Surgical Sciences, Department of Surgery, Duke University, Durham NC, United States of America
| | - David Brenner
- Columbia University, New York, NY, 10027, United States of America
| | - Robert Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States of America
| | - Lawrence Bronk
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States of America
| | - Xu Cao
- Stanford University School of Medicine, Stanford, CA 94305, United States of America
| | - Anushree Chatterjee
- Sachi Bioworks, Louisville, CO 80027, United States of America; University of Colorado Boulder, Boulder, CO 80303, United States of America
| | - Delisa E Clay
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | | | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - M Waleed Gaber
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America
| | - Sharon Gerecht
- Chemical and Biomolecular Engineering and Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218 United States of America; Biomedical Engineering, Duke University, Durham, NC 27708, United States of America
| | - Peter Grabham
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, NY 10027 United States of America
| | - David Grosshans
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States of America
| | - Fada Guan
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States of America
| | - Erin A Jezuit
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - David G Kirsch
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Mirjana Maletic-Savatic
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, United States of America
| | - Ruth A Montague
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, United States of America
| | - Prashant Nagpal
- Sachi Bioworks, Louisville, CO 80027, United States of America
| | - Sivan Osenberg
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Luke Parkitny
- Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States of America; Jan and Dan Duncan Neurological Research Institute, 1250 Moursund St. Houston, TX 77030, United States of America
| | - Niles A Pierce
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States of America; Division of Engineering & Applied Science, California Institute of Technology, Pasadena, CA 91125, United States of America; Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Christopher Porada
- Wake Forest Institute for Regenerative Medicine, Fetal Research and Therapy Program Wake Forest School of Medicine, Winston-Salem, NC 27157, United States of America
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America; Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77303, United States of America
| | - Paul Sargunas
- Chemical and Biomolecular Engineering and Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218 United States of America
| | - Sadhana Sharma
- Sachi Bioworks, Louisville, CO 80027, United States of America
| | - Jamie Spangler
- Chemical and Biomolecular Engineering and Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218 United States of America
| | | | - Dilip Thomas
- Stanford University School of Medicine, Stanford, CA 94305, United States of America
| | | | - Chunbo Wang
- Division of Surgical Sciences, Department of Surgery, Duke University, Durham NC, United States of America
| | - Luke Whitcomb
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States of America
| | - Damian W Young
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, United States of America
| | - Dorit Donoviel
- Translational Research Institute for Space Health, Houston, TX 77030, United States of America; Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, United States of America.
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13
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Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022; 5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.
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Affiliation(s)
- Oana Pelea
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Address correspondence to: Oana Pelea, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
| | - Tudor A. Fulga
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA.,Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Address correspondence to: Tatjana Sauka-Spengler, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom,
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14
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Pothoulakis G, Nguyen MTA, Andersen E. Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control. Nucleic Acids Res 2022; 50:7176-7187. [PMID: 35648481 PMCID: PMC9262615 DOI: 10.1093/nar/gkac470] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/28/2022] [Accepted: 05/23/2022] [Indexed: 12/29/2022] Open
Abstract
Designer RNA scaffolds constitute a promising tool for synthetic biology, as they can be genetically expressed to perform specific functions in vivo such as scaffolding enzymatic cascades and regulating gene expression through CRISPR-dCas9 applications. RNA origami is a recently developed RNA design approach that allows construction of large RNA nanostructures that can position aptamer motifs to spatially organize other molecules, including proteins. However, it is still not fully understood how positioning multiple aptamers on a scaffold and the orientation of a scaffold affects functional properties. Here, we investigate fusions of single-guide RNAs and RNA origami scaffolds (termed sgRNAO) capable of recruiting activating domains for control of gene expression in yeast. Using MS2 and PP7 as orthogonal protein-binding aptamers, we observe a gradual increase in transcriptional activation for up to four aptamers. We demonstrate that different aptamer positions on a scaffold and scaffold orientation affect transcriptional activation. Finally, sgRNAOs are used to regulate expression of enzymes of the violacein biosynthesis pathway to control metabolic flux. The integration of RNA origami nanostructures at promoter sites achieved here, can in the future be expanded by the addition of functional motifs such as riboswitches, ribozymes and sensor elements to allow for complex gene regulation.
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Affiliation(s)
| | - Michael T A Nguyen
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| | - Ebbe S Andersen
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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15
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Enhancement of prime editing via xrRNA motif-joined pegRNA. Nat Commun 2022; 13:1856. [PMID: 35387980 PMCID: PMC8986804 DOI: 10.1038/s41467-022-29507-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
The prime editors (PEs) have shown great promise for precise genome modification. However, their suboptimal efficiencies present a significant technical challenge. Here, by appending a viral exoribonuclease-resistant RNA motif (xrRNA) to the 3'-extended portion of pegRNAs for their increased resistance against degradation, we develop an upgraded PE platform (xrPE) with substantially enhanced editing efficiencies in multiple cell lines. A pan-target average enhancement of up to 3.1-, 4.5- and 2.5-fold in given cell types is observed for base conversions, small deletions, and small insertions, respectively. Additionally, xrPE exhibits comparable edit:indel ratios and similarly minimal off-target editing as the canonical PE3. Of note, parallel comparison of xrPE to the most recently developed epegRNA-based PE system shows their largely equivalent editing performances. Our study establishes a highly adaptable platform of improved PE that shall have broad implications.
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16
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Lin J, Wang WJ, Wang Y, Liu Y, Xu L. Building Endogenous Gene Connections through RNA Self-Assembly Controlled CRISPR/Cas9 Function. J Am Chem Soc 2021; 143:19834-19843. [PMID: 34788038 DOI: 10.1021/jacs.1c09041] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Construction of synthetic circuits that can artificially establish endogenous gene connections is essential to introduce new phenotypes for cellular behaviors. Given the diversity of endogenous genes, it lacks a general and easy-to-design toolbox to manipulate the genetic network. Here we present a type of self-assembly-induced RNA circuit that can directly build regulatory connections between endogenous genes. Inspired from the natural assembling process of guide RNA in the CRISPR/Cas9 complex, this design employs an independent trigger RNA strand to induce the formation of a ternary guide RNA assembly for functional control of CRISPR/Cas9. With this general principle, expressional regulations of endogenous genes can be controlled by totally independent endogenous small RNAs and mRNAs in E. coli via activatable CRISPR/Cas9 function. Moreover, the cellular phenotype of E. coli is successfully programmed with introduction of new gene connections. In addition, the functionality of this design is also verified in the mammalian system. This self-assembly-based RNA circuit exhibits a great flexibility and simplicity of design and provides a unique approach to build endogenous gene connections, which paves a broad way toward manipulation of cellular genetic networks.
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Affiliation(s)
- Jiao Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wei-Jia 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
| | - Yan Liu
- 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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17
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Anderson DA, Voigt CA. Competitive dCas9 binding as a mechanism for transcriptional control. Mol Syst Biol 2021; 17:e10512. [PMID: 34747560 PMCID: PMC8574044 DOI: 10.15252/msb.202110512] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Catalytically dead Cas9 (dCas9) is a programmable transcription factor that can be targeted to promoters through the design of small guide RNAs (sgRNAs), where it can function as an activator or repressor. Natural promoters use overlapping binding sites as a mechanism for signal integration, where the binding of one can block, displace, or augment the activity of the other. Here, we implemented this strategy in Escherichia coli using pairs of sgRNAs designed to repress and then derepress transcription through competitive binding. When designed to target a promoter, this led to 27-fold repression and complete derepression. This system was also capable of ratiometric input comparison over two orders of magnitude. Additionally, we used this mechanism for promoter sequence-independent control by adopting it for elongation control, achieving 8-fold repression and 4-fold derepression. This work demonstrates a new genetic control mechanism that could be used to build analog circuit or implement cis-regulatory logic on CRISPRi-targeted native genes.
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Affiliation(s)
- Daniel A Anderson
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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