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Li B, Li Q, Qi Z, Li Z, Yan X, Chen Y, Xu X, Pan Q, Chen Y, Huang F, Ping Y. Supramolecular Genome Editing: Targeted Delivery and Endogenous Activation of CRISPR/Cas9 by Dynamic Host-Guest Recognition. Angew Chem Int Ed Engl 2024; 63:e202316323. [PMID: 38317057 DOI: 10.1002/anie.202316323] [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: 11/01/2023] [Revised: 02/04/2024] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
We synthesize supramolecular poly(disulfide) (CPS) containing covalently attached cucurbit[7]uril (CB[7]), which is exploited not only as a carrier to deliver plasmid DNA encoding destabilized Cas9 (dsCas9), but also as a host to include trimethoprim (TMP) by CB[7] moieties through the supramolecular complexation to form TMP@CPS/dsCas9. Once the plasmid is transfected into tumor cells by CPS, the presence of polyamines can competitively trigger the decomplexation of TMP@CPS, thereby displacing and releasing TMP from CB[7] to stabilize dsCas9 that can target and edit the genomic locus of PLK1 to inhibit the growth of tumor cells. Following the systemic administration of TMP@CPS/dsCas9 decorated with hyaluronic acid (HA), tumor-specific editing of PLK1 is detected due to the elevated polyamines in tumor microenvironment, greatly minimizing off-target editing in healthy tissues and non-targeted organs. As the metabolism of polyamines is dysregulated in a wide range of disorders, this study offers a supramolecular approach to precisely control CRISPR/Cas9 functions under particular pathological contexts.
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Affiliation(s)
- Bowen Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, P. R. China
| | - Qing Li
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, P. R. China
| | - Zidan Qi
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Zhiyao Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xiaojie Yan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Xiaojie Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, P. R. China
| | - Qi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yuxuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Feihe Huang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou, 310058, P. R. China
- Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, P. R. China
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, P. R. China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, 311121, P. R. China
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2
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Devarajan A. Optically Controlled CRISPR-Cas9 and Cre Recombinase for Spatiotemporal Gene Editing: A Review. ACS Synth Biol 2024; 13:25-44. [PMID: 38134336 DOI: 10.1021/acssynbio.3c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
CRISPR-Cas9 and Cre recombinase, two tools extensively used for genome interrogation, have catalyzed key breakthroughs in our understanding of complex biological processes and diseases. However, the immense complexity of biological systems and off-target effects hinder clinical applications, necessitating the development of platforms to control gene editing over spatial and temporal dimensions. Among the strategies developed for inducible control, light is particularly attractive as it is noninvasive and affords high spatiotemporal resolution. The principles for optical control of Cas9 and Cre recombinase are broadly similar and involve photocaged enzymes and small molecules, engineered split- and single-chain constructs, light-induced expression, and delivery by light-responsive nanocarriers. Few systems enable spatiotemporal control with a high dynamic range without loss of wild-type editing efficiencies. Such systems posit the promise of light-activatable systems in the clinic. While the prospect of clinical applications is palpably exciting, optimization and extensive preclinical validation are warranted. Judicious integration of optically activated CRISPR and Cre, tailored for the desired application, may help to bridge the "bench-to-bedside" gap in therapeutic gene editing.
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Affiliation(s)
- Archit Devarajan
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, Madhya Pradesh, India - 462066
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3
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Hasselbeck S, Cheng X. Molecular Marvels: Small Molecules Paving the Way for Enhanced Gene Therapy. Pharmaceuticals (Basel) 2023; 17:41. [PMID: 38256875 PMCID: PMC10818943 DOI: 10.3390/ph17010041] [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: 12/09/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
In the rapidly evolving landscape of genetic engineering, the advent of CRISPR-Cas technologies has catalyzed a paradigm shift, empowering scientists to manipulate the genetic code with unprecedented accuracy and efficiency. Despite the remarkable capabilities inherent to CRISPR-Cas systems, recent advancements have witnessed the integration of small molecules to augment their functionality, introducing new dimensions to the precision and versatility of gene editing applications. This review delves into the synergy between CRISPR-Cas technologies based specifically on Cas9 and small-molecule drugs, elucidating the pivotal role of chemicals in optimizing target specificity and editing efficiency. By examining a diverse array of applications, ranging from therapeutic interventions to agricultural advancements, we explore how the judicious use of chemicals enhances the precision of CRISPR-Cas9-mediated genetic modifications. In this review, we emphasize the significance of small-molecule drugs in fine-tuning the CRISPR-Cas9 machinery, which allows researchers to exert meticulous control over the editing process. We delve into the mechanisms through which these chemicals bolster target specificity, mitigate off-target effects, and contribute to the overall refinement of gene editing outcomes. Additionally, we discuss the potential of chemical integration in expanding the scope of CRISPR-Cas9 technologies, enabling tailored solutions for diverse genetic manipulation challenges. As CRISPR-Cas9 technologies continue to evolve, the integration of small-molecule drugs emerges as a crucial avenue for advancing the precision and applicability of gene editing techniques. This review not only synthesizes current knowledge but also highlights future prospects, paving the way for a deeper understanding of the synergistic interplay between CRISPR-Cas9 systems and chemical modulators in the pursuit of more controlled and efficient genetic modifications.
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Affiliation(s)
- Sebastian Hasselbeck
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Xinlai Cheng
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany;
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
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4
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Xu Y, Wang Y, Liang FS. Site-Specific m 6 A Erasing via Conditionally Stabilized CRISPR-Cas13b Editor. Angew Chem Int Ed Engl 2023; 62:e202309291. [PMID: 37713087 PMCID: PMC10592254 DOI: 10.1002/anie.202309291] [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: 06/30/2023] [Indexed: 09/16/2023]
Abstract
N6-methyladenosine (m6 A) on RNAs plays an important role in regulating various biological processes and CRIPSR technology has been employed for programmable m6 A editing. However, the bulky size of CRISPR protein and constitutively expressed CRISPR/RNA editing enzymes can interfere with the native function of target RNAs and cells. Herein, we reported a conditional m6 A editing platform (FKBP*-dCas13b-ALK) based on a ligand stabilized dCas13 editor. The inducible expression of this m6 A editing system was achieved by adding or removing the Shield-1 molecule. We further demonstrated that the targeted recruitment of dCas13b-m6 A eraser fusion protein and site-specific m6 A erasing were achieved under the control of Shield-1. Moreover, the release and degradation of dCas13b fusion protein occurred faster than the restoration of m6 A on the target RNAs after Shield-1 removal, which provides an ideal opportunity to study the m6 A function with minimal steric interference from bulky dCas13b fusion protein.
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Affiliation(s)
- Ying Xu
- Department of Chemistry, Case Western Reserve Universit, 2080 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Yufan Wang
- Department of Chemistry, Case Western Reserve Universit, 2080 Adelbert Rd, Cleveland, OH, 44106, USA
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve Universit, 2080 Adelbert Rd, Cleveland, OH, 44106, USA
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5
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Kulkarni A, Tanga S, Karmakar A, Hota A, Maji B. CRISPR-Based Precision Molecular Diagnostics for Disease Detection and Surveillance. ACS APPLIED BIO MATERIALS 2023; 6:3927-3945. [PMID: 37788375 DOI: 10.1021/acsabm.3c00439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Sensitive, rapid, and portable molecular diagnostics is the future of disease surveillance, containment, and therapy. The recent SARS-CoV-2 pandemic has reminded us of the vulnerability of lives from ever-evolving pathogens. At the same time, it has provided opportunities to bridge the gap by translating basic molecular biology into therapeutic tools. One such molecular biology technique is CRISPR (clustered regularly interspaced short palindromic repeat) which has revolutionized the field of molecular diagnostics at the need of the hour. The use of CRISPR-Cas systems has been widespread in biology research due to the ease of performing genetic manipulations. In 2012, CRISPR-Cas systems were, for the first time, shown to be reprogrammable, i.e., capable of performing sequence-specific gene editing. This discovery catapulted the field of CRISPR-Cas research and opened many unexplored avenues in the field of gene editing, from basic research to therapeutics. One such field that benefitted greatly from this discovery was molecular diagnostics, as using CRISPR-Cas technologies enabled existing diagnostic methods to become more sensitive, accurate, and portable, a necessity in disease control. This Review aims to capture some of the trajectories and advances made in this arena and provides a comprehensive understanding of the methods and their potential use as point-of-care diagnostics.
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Affiliation(s)
- Akshara Kulkarni
- Ashoka University, Department of Biology, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - Sadiya Tanga
- Ashoka University, Department of Chemistry, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - Arkadeep Karmakar
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
| | - Arpita Hota
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
| | - Basudeb Maji
- Ashoka University, Department of Biology, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
- Ashoka University, Department of Chemistry, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
- Bose Institute, Department of Biological Sciences, EN Block, Sector V, Kolkata 700091, West Bengal, India
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6
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Ji H, Xiong W, Guo S, Wang S, Xing X, Tian T, Zhou X. Isonitrile-Tetrazine Click-and-Release Chemistry for Controlling RNA-Guided Nucleic Acid Cleavage. ACS Chem Biol 2023; 18:1829-1837. [PMID: 37505910 DOI: 10.1021/acschembio.3c00255] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
With the increasing demand for the regulation of CRISPR systems, a considerable number of studies have been conducted to control their excessive activity levels. In this context, we propose a method that involves a bioorthogonal cleavage reaction between isonitrile and tetrazine to modulate the cleavage activity of the CRISPR system. Importantly, isonitrile demonstrates significant potential for modifying sgRNAs, making it a promising candidate for bioorthogonal reactions, a phenomenon that has not been previously reported. Our approach utilizes the 3-isocyanopropyl-carbonate group as a caging group to deactivate the CRISPR systems, while tetrazine acts as an activator to restore their activities. Through the implementation of post-synthetic modifications and click-and-release chemistry, we have successfully achieved the regulation of RNA-guided nucleic acid cleavage, which holds great promise for controlling gene editing in human cells.
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Affiliation(s)
- Huimin Ji
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Xiong
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Shaoyuan Guo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Shaoru Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiwen Xing
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China
| | - Tian Tian
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
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7
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Sreekanth V, Jan M, Zhao KT, Lim D, Davis JR, McConkey M, Kovalcik V, Barkal S, Law BK, Fife J, Tian R, Vinyard ME, Becerra B, Kampmann M, Sherwood RI, Pinello L, Liu DR, Ebert BL, Choudhary A. A molecular glue approach to control the half-life of CRISPR-based technologies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.531757. [PMID: 36945568 PMCID: PMC10028966 DOI: 10.1101/2023.03.12.531757] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Cas9 is a programmable nuclease that has furnished transformative technologies, including base editors and transcription modulators (e.g., CRISPRi/a), but several applications of these technologies, including therapeutics, mandatorily require precision control of their half-life. For example, such control can help avert any potential immunological and adverse events in clinical trials. Current genome editing technologies to control the half-life of Cas9 are slow, have lower activity, involve fusion of large response elements (> 230 amino acids), utilize expensive controllers with poor pharmacological attributes, and cannot be implemented in vivo on several CRISPR-based technologies. We report a general platform for half-life control using the molecular glue, pomalidomide, that binds to a ubiquitin ligase complex and a response-element bearing CRISPR-based technology, thereby causing the latter's rapid ubiquitination and degradation. Using pomalidomide, we were able to control the half-life of large CRISPR-based technologies (e.g., base editors, CRISPRi) and small anti-CRISPRs that inhibit such technologies, allowing us to build the first examples of on-switch for base editors. The ability to switch on, fine-tune and switch-off CRISPR-based technologies with pomalidomide allowed complete control over their activity, specificity, and genome editing outcome. Importantly, the miniature size of the response element and favorable pharmacological attributes of the drug pomalidomide allowed control of activity of base editor in vivo using AAV as the delivery vehicle. These studies provide methods and reagents to precisely control the dosage and half-life of CRISPR-based technologies, propelling their therapeutic development.
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Affiliation(s)
- Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Max Jan
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin T. Zhao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jessie R. Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Marie McConkey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Veronica Kovalcik
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sam Barkal
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Benjamin K. Law
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - James Fife
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ruilin Tian
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michael E. Vinyard
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Basheer Becerra
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Richard I. Sherwood
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Benjamin L. Ebert
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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8
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Xiong H, Xu Y, Kim B, Rha H, Zhang B, Li M, Yang GF, Kim JS. Photo-controllable biochemistry: Exploiting the photocages in phototherapeutic window. Chem 2022. [DOI: 10.1016/j.chempr.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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9
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Responsive MXene nanovehicles deliver CRISPR/Cas12a for boolean logic-controlled gene editing. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1376-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Shin S, Jang S, Lim D. Small Molecules for Enhancing the Precision and Safety of Genome Editing. Molecules 2022; 27:6266. [PMID: 36234804 PMCID: PMC9573751 DOI: 10.3390/molecules27196266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing technologies have revolutionized biology, biotechnology, and medicine, and have spurred the development of new therapeutic modalities. However, there remain several barriers to the safe use of CRISPR technologies, such as unintended off-target DNA cleavages. Small molecules are important resources to solve these problems, given their facile delivery and fast action to enable temporal control of the CRISPR systems. Here, we provide a comprehensive overview of small molecules that can precisely modulate CRISPR-associated (Cas) nucleases and guide RNAs (gRNAs). We also discuss the small-molecule control of emerging genome editors (e.g., base editors) and anti-CRISPR proteins. These molecules could be used for the precise investigation of biological systems and the development of safer therapeutic modalities.
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Affiliation(s)
- Siyoon Shin
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Seeun Jang
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Donghyun Lim
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
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11
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Mothersill C, Seymour C. Low dose radiation mechanisms: The certainty of uncertainty. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2022; 876-877:503451. [PMID: 35483782 DOI: 10.1016/j.mrgentox.2022.503451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 02/06/2023]
Abstract
This paper reviews the current understanding of low dose radiobiology, and how it has evolved from classical target theory. It highlights the uncertainty around low dose effects, which is due in part to the complexity of "context" surrounding the ultimate expression of biological effects following low dose exposure. The paper makes special reference to low dose non-targeted effects which, are currently ignored in radiation protection and population level risk assessment, because it is unclear what they mean for risk. The view of the authors is that this "lack of clarity" about what the effects mean is precisely the point. It indicates the uncertainty of outcomes after a given exposure. The uncertainty stems from multiple outcome options resulting from the intrinsic uncertainty of the stochastic interaction of low dose radiation with matter. This uncertainty should be embraced rather than eschewed. The impacts of the uncertainties identified in this paper is explored and an approach to quantifying mutation probability in relation to dose is presented.
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Affiliation(s)
- Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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12
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Zhao J, Hu H, Zhang J, Li Y, Wang L, Zhou H, Wang R. Endogenous hydrogen peroxide can efficiently regulate CRISPR-Cas9 based gene editing. NEW J CHEM 2022. [DOI: 10.1039/d1nj04203c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report controllable gene editing tools for the CRISPR-Cas9 system via genetic code expansion triggered by oxidative small molecule H2O2.
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Affiliation(s)
- Jizhong Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hongmei Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jingwen Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Wang
- Wuhan No. 1 Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Hongling Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
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13
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Yan X, Pan Q, Xin H, Chen Y, Ping Y. Genome-editing prodrug: Targeted delivery and conditional stabilization of CRISPR-Cas9 for precision therapy of inflammatory disease. SCIENCE ADVANCES 2021; 7:eabj0624. [PMID: 34878850 PMCID: PMC8654308 DOI: 10.1126/sciadv.abj0624] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Regulation of CRISPR-Cas9 functions in vivo is conducive to developing precise therapeutic genome editing. Here, we report a CRISPR-Cas9 prodrug nanosystem (termed NanoProCas9), which combines the targeted delivery and the conditional activation of CRISPR-Cas9 for the precision therapy of inflammatory bowel disease. NanoProCas9 is composed of (i) cationic poly(β-amino ester) (PBAE) capable of complexing plasmid DNA encoding destabilized Cas9 (dsCas9) nuclease, (ii) a layer of biomimetic cell membrane coated on PBAE/plasmid nanocomplexes for the targeted delivery of PBAE/dsCas9 complexes, and (iii) the stimuli-responsive precursory molecules anchored on the exofacial membrane. The systemic administration of NanoProCas9 enables the targeted delivery of dsCas9 plasmid into inflammatory lesions, where the precursory small molecule can be activated by ROS signals to stabilize expressed dsCas9, thereby activating Cas9 function for inflammatory genome editing. The proposed “genome-editing prodrug” presents a proof-of-concept example to precisely regulate CRISPR-Cas9 functions by virtue of particular pathological stimuli in vivo.
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Affiliation(s)
- Xiaojie Yan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huhu Xin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Corresponding author.
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14
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Zhu C, Kou T, Kadi AA, Li J, Zhang Y. Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets. Org Biomol Chem 2021; 19:9358-9368. [PMID: 34632469 DOI: 10.1039/d1ob01613j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoirradiation provides a convenient and biocompatible approach for spatiotemporal modulation of biological systems with photoresponsive components. The construction of molecular platforms with a photoresponse to be integrated into biomolecules for photomodulation has been of great research interest in optochemical biology. In this review, we summarize typical molecular platforms that are integratable with biomolecules for photomodulation purposes. We categorize these molecular platforms according to their excitation light source, namely ultraviolet (UV), visible (Vis) or near-infrared (NIR) light. The protype chemistry of these molecular platforms is introduced along with an overview of their most recent applications for spatiotemporal regulation of biomolecular function in living cells or mice models. Challenges and the outlook are also presented. We hope this review paper will contribute to further progress in the development of molecular platforms and their biomedical use.
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Affiliation(s)
- Chenghong Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Tianzhang Kou
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Adnan A Kadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Kingdom of Saudi Arabia.
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
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15
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Zhuo C, Zhang J, Lee JH, Jiao J, Cheng D, Liu L, Kim HW, Tao Y, Li M. Spatiotemporal control of CRISPR/Cas9 gene editing. Signal Transduct Target Ther 2021; 6:238. [PMID: 34148061 PMCID: PMC8214627 DOI: 10.1038/s41392-021-00645-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/09/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) gene editing technology, as a revolutionary breakthrough in genetic engineering, offers a promising platform to improve the treatment of various genetic and infectious diseases because of its simple design and powerful ability to edit different loci simultaneously. However, failure to conduct precise gene editing in specific tissues or cells within a certain time may result in undesirable consequences, such as serious off-target effects, representing a critical challenge for the clinical translation of the technology. Recently, some emerging strategies using genetic regulation, chemical and physical strategies to regulate the activity of CRISPR/Cas9 have shown promising results in the improvement of spatiotemporal controllability. Herein, in this review, we first summarize the latest progress of these advanced strategies involving cell-specific promoters, small-molecule activation and inhibition, bioresponsive delivery carriers, and optical/thermal/ultrasonic/magnetic activation. Next, we highlight the advantages and disadvantages of various strategies and discuss their obstacles and limitations in clinical translation. Finally, we propose viewpoints on directions that can be explored to further improve the spatiotemporal operability of CRISPR/Cas9.
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Grants
- the Guangdong Province Science and Technology Innovation Special Fund (International Scientific Cooperation, 2018A050506035), the National Natural Science Foundation of China (51903256).
- the National Key Research and Development Program of China (2016YFE0117100), the National Natural Science Foundation of China (21875289 and U1501243), the Guangdong-Hong Kong Joint Innovation Project (2016A050503026), the Major Project on the Integration of Industry, Education and Research of Guangzhou City (201704030123), the Science and Technology Program of Guangzhou (201704020016), the Guangdong Innovative and Entrepreneurial Research Team Program (2013S086)
- National Research Foundation, Republic of Korea (2015K1A1A2032163, 2018K1A4A3A01064257, 2018R1A2B3003446)
- the National Key Research and Development Program of China (2019YFA0111300, 2016YFE0117100), the National Natural Science Foundation of China (21907113), the Guangdong Provincial Pearl River Talents Program (2019QN01Y131), the Thousand Talents Plan.
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Affiliation(s)
- Chenya Zhuo
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiabin Zhang
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jung-Hwan Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, South Korea
| | - Ju Jiao
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Du Cheng
- PCFM Lab of Ministry of Education, School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, South Korea.
| | - Yu Tao
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, China.
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16
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Wu J, Peng H, Lu X, Lai M, Zhang H, Le XC. Binding-Mediated Formation of Ribonucleoprotein Corona for Efficient Delivery and Control of CRISPR/Cas9. Angew Chem Int Ed Engl 2021; 60:11104-11109. [PMID: 33354860 PMCID: PMC8252003 DOI: 10.1002/anie.202014162] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/27/2020] [Indexed: 01/26/2023]
Abstract
Protein coronae formed with nanoparticles confer several useful properties. However, the non-specific nature of protein corona formation makes it difficult to deliver specific proteins for therapeutic applications. Herein, we report on the construction of a new type of protein corona, termed binding-mediated protein corona. This new corona enables the efficient and controllable delivery of functional proteins, which is otherwise challenging for conventional protein coronae. We show the design and delivery of the ribonucleoprotein corona for the CRISPR/Cas9 system. Successful gene editing in human cell lines (Hela and HEK293) demonstrates the efficient delivery, high stability, low cytotoxicity, and well-controlled activity of the Cas9-guide RNA ribonucleoprotein. The binding-mediated protein corona strategy opens up new opportunities for therapeutic protein delivery.
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Affiliation(s)
- Jinjun Wu
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - Hanyong Peng
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - Xiufen Lu
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - Maode Lai
- Department of PathologyZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Hongquan Zhang
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - X. Chris Le
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
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17
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Wu J, Peng H, Lu X, Lai M, Zhang H, Le XC. Binding‐Mediated Formation of Ribonucleoprotein Corona for Efficient Delivery and Control of CRISPR/Cas9. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jinjun Wu
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - Xiufen Lu
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - Maode Lai
- Department of Pathology Zhejiang University School of Medicine Hangzhou Zhejiang 310058 China
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - X. Chris Le
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
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18
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Shivram H, Cress BF, Knott GJ, Doudna JA. Controlling and enhancing CRISPR systems. Nat Chem Biol 2021; 17:10-19. [PMID: 33328654 PMCID: PMC8101458 DOI: 10.1038/s41589-020-00700-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022]
Abstract
Many bacterial and archaeal organisms use clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) systems to defend themselves from mobile genetic elements. These CRISPR-Cas systems are classified into six types based on their composition and mechanism. CRISPR-Cas enzymes are widely used for genome editing and offer immense therapeutic opportunity to treat genetic diseases. To realize their full potential, it is important to control the timing, duration, efficiency and specificity of CRISPR-Cas enzyme activities. In this Review we discuss the mechanisms of natural CRISPR-Cas regulatory biomolecules and engineering strategies that enhance or inhibit CRISPR-Cas immunity by altering enzyme function. We also discuss the potential applications of these CRISPR regulators and highlight unanswered questions about their evolution and purpose in nature.
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Affiliation(s)
- Haridha Shivram
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Brady F Cress
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria, Australia
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
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19
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Weinstain R, Slanina T, Kand D, Klán P. Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials. Chem Rev 2020; 120:13135-13272. [PMID: 33125209 PMCID: PMC7833475 DOI: 10.1021/acs.chemrev.0c00663] [Citation(s) in RCA: 253] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.
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Affiliation(s)
- Roy Weinstain
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Tomáš Slanina
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Dnyaneshwar Kand
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Petr Klán
- Department
of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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20
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Sreekanth V, Zhou Q, Kokkonda P, Bermudez-Cabrera HC, Lim D, Law BK, Holmes BR, Chaudhary SK, Pergu R, Leger BS, Walker JA, Gifford DK, Sherwood RI, Choudhary A. Chemogenetic System Demonstrates That Cas9 Longevity Impacts Genome Editing Outcomes. ACS CENTRAL SCIENCE 2020; 6:2228-2237. [PMID: 33376784 PMCID: PMC7760466 DOI: 10.1021/acscentsci.0c00129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Indexed: 06/02/2023]
Abstract
Prolonged Cas9 activity can hinder genome engineering as it causes off-target effects, genotoxicity, heterogeneous genome-editing outcomes, immunogenicity, and mosaicism in embryonic editing-issues which could be addressed by controlling the longevity of Cas9. Though some temporal controls of Cas9 activity have been developed, only cumbersome systems exist for modifying the lifetime. Here, we have developed a chemogenetic system that brings Cas9 in proximity to a ubiquitin ligase, enabling rapid ubiquitination and degradation of Cas9 by the proteasome. Despite the large size of Cas9, we were able to demonstrate efficient degradation in cells from multiple species. Furthermore, by controlling the Cas9 lifetime, we were able to bias the DNA repair pathways and the genotypic outcome for both templated and nontemplated genome editing. Finally, we were able to dosably control the Cas9 activity and specificity to ameliorate the off-target effects. The ability of this system to change the Cas9 lifetime and, therefore, bias repair pathways and specificity in the desired direction allows precision control of the genome editing outcome.
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Affiliation(s)
- Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Qingxuan Zhou
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Heysol C. Bermudez-Cabrera
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Donghyun Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Benjamin K. Law
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Benjamin R. Holmes
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts 02142, United States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Santosh K. Chaudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Rajaiah Pergu
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Brittany S. Leger
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - James A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - David K. Gifford
- McGovern Institute for Brain Research at MIT, Cambridge, Massachusetts 02142, United States
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Richard I. Sherwood
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht 3584 CT, The Netherlands
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Divisions of Renal Medicine and Engineering, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
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21
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Modell AE, Siriwardena SU, Shoba VM, Li X, Choudhary A. Chemical and optical control of CRISPR-associated nucleases. Curr Opin Chem Biol 2020; 60:113-121. [PMID: 33253976 DOI: 10.1016/j.cbpa.2020.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system of bacteria has furnished programmable nucleases (e.g., Cas9) that are transforming the field of genome editing with applications in basic and biomedical research, biotechnology, and agriculture. However, broader real-world applications of Cas9 require precision control of its activity over dose, time, and space as off-target effects, embryonic mosaicism, chromosomal translocations, and genotoxicity have been observed with elevated and/or prolonged nuclease activity. Here, we review chemical and optical methods for precision control of Cas9's activity.
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Affiliation(s)
- Ashley E Modell
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Sachini U Siriwardena
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Veronika M Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xing Li
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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22
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Ma J, Ripp A, Wassy D, Dürr T, Qiu D, Häner M, Haas T, Popp C, Bezold D, Richert S, Esser B, Jessen HJ. Thiocoumarin Caged Nucleotides: Synthetic Access and Their Photophysical Properties. Molecules 2020; 25:E5325. [PMID: 33203096 PMCID: PMC7696096 DOI: 10.3390/molecules25225325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 11/21/2022] Open
Abstract
Photocages have been successfully applied in cellular signaling studies for the controlled release of metabolites with high spatio-temporal resolution. Commonly, coumarin photocages are activated by UV light and the quantum yields of uncaging are relatively low, which can limit their applications in vivo. Here, syntheses, the determination of the photophysical properties, and quantum chemical calculations of 7-diethylamino-4-hydroxymethyl-thiocoumarin (thio-DEACM) and caged adenine nucleotides are reported and compared to the widely used 7-diethylamino-4-hydroxymethyl-coumarin (DEACM) caging group. In this comparison, thio-DEACM stands out as a phosphate cage with improved photophysical properties, such as red-shifted absorption and significantly faster photolysis kinetics.
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Affiliation(s)
- Jiahui Ma
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Alexander Ripp
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
- Cluster of Excellence livMatS @ FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Daniel Wassy
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Tobias Dürr
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Thomas Haas
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Christoph Popp
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Dominik Bezold
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
| | - Sabine Richert
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany;
| | - Birgit Esser
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
- Cluster of Excellence livMatS @ FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Henning J. Jessen
- Institute of Organic Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany; (J.M.); (A.R.); (D.W.); (T.D.); (D.Q.); (M.H.); (T.H.); (C.P.); (D.B.); (B.E.)
- Cluster of Excellence livMatS @ FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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23
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Chen C, Wang Z, Jing N, Chen W, Tang X. Photomodulation of Caged RNA Oligonucleotide Functions in Living Systems. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Changmai Chen
- School of Pharmacy Fujian Medical University No.1 Xuefu N Rd, University Town Fuzhou 350122 China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Zhongyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Nannan Jing
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
| | - Wei Chen
- School of Pharmacy Fujian Medical University No.1 Xuefu N Rd, University Town Fuzhou 350122 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd, Haidian District Beijing 100191 China
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24
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Directed Evolution of CRISPR/Cas Systems for Precise Gene Editing. Trends Biotechnol 2020; 39:262-273. [PMID: 32828556 DOI: 10.1016/j.tibtech.2020.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
CRISPR technology is a universal tool for genome engineering that has revolutionized biotechnology. Recently identified unique CRISPR/Cas systems, as well as re-engineered Cas proteins, have rapidly expanded the functions and applications of CRISPR/Cas systems. The structures of Cas proteins are complex, containing multiple functional domains. These protein domains are evolutionarily conserved polypeptide units that generally show independent structural or functional properties. In this review, we propose using protein domains as a new way to classify protein engineering strategies for these proteins and discuss common ways to engineer key domains to modify the functions of CRISPR/Cas systems.
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25
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Lau CH, Tin C. The Synergy between CRISPR and Chemical Engineering. Curr Gene Ther 2020; 19:147-171. [PMID: 31267870 DOI: 10.2174/1566523219666190701100556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 02/06/2023]
Abstract
Gene therapy and transgenic research have advanced quickly in recent years due to the development of CRISPR technology. The rapid development of CRISPR technology has been largely benefited by chemical engineering. Firstly, chemical or synthetic substance enables spatiotemporal and conditional control of Cas9 or dCas9 activities. It prevents the leaky expression of CRISPR components, as well as minimizes toxicity and off-target effects. Multi-input logic operations and complex genetic circuits can also be implemented via multiplexed and orthogonal regulation of target genes. Secondly, rational chemical modifications to the sgRNA enhance gene editing efficiency and specificity by improving sgRNA stability and binding affinity to on-target genomic loci, and hence reducing off-target mismatches and systemic immunogenicity. Chemically-modified Cas9 mRNA is also more active and less immunogenic than the native mRNA. Thirdly, nonviral vehicles can circumvent the challenges associated with viral packaging and production through the delivery of Cas9-sgRNA ribonucleoprotein complex or large Cas9 expression plasmids. Multi-functional nanovectors enhance genome editing in vivo by overcoming multiple physiological barriers, enabling ligand-targeted cellular uptake, and blood-brain barrier crossing. Chemical engineering can also facilitate viral-based delivery by improving vector internalization, allowing tissue-specific transgene expression, and preventing inactivation of the viral vectors in vivo. This review aims to discuss how chemical engineering has helped improve existing CRISPR applications and enable new technologies for biomedical research. The usefulness, advantages, and molecular action for each chemical engineering approach are also highlighted.
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Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Chung Tin
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong
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26
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Li Y, Wang H, Zhang L, Ding Z, Xu S, Gu Z, Shi G. Efficient Genome Editing in Bacillus licheniformis Mediated by a Conditional CRISPR/Cas9 System. Microorganisms 2020; 8:microorganisms8050754. [PMID: 32429599 PMCID: PMC7285353 DOI: 10.3390/microorganisms8050754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022] Open
Abstract
Bacillus licheniformis is widely used to produce multiple enzymes and chemicals in industrial fermentation. It is also an organism that is hard to genetically manipulate, which is mainly attributed to its extremely low transformation efficiency. The lack of genetic modification technology severely limits its further application. In this study, an all-in-one conditional clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 plasmid was developed for B. licheniformis with the cas9 gene under the control of a xylose-inducible promoter. By means of this design, the expression of the cas9 gene could be repressed without xylose, which significantly improved the transformation ratio from less than 0.1 cfu/μg to 2.42 cfu/μg DNA. Compared with this conditional system, a constitutive overexpression system led to significant growth retardation in bacterial cells. Both the biomass and specific growth rate decreased greatly. After transformation, successful genome editing could be triggered by 0.5% xylose. When the α-amylase gene amyL was used as a genomic target, the efficiencies of its disruption using three different protospacer-adjacent motif (PAM) sequences were 64.3%, 70.9%, and 47.1%, respectively. Moreover, temperature plays a pivotal role in the function of the constructed CRISPR system. The maximum success rate reached 97% at 20 °C, while higher temperatures negatively impacted the function of the system. These results suggested that the design with a cas9 gene under the strict control of a xylose-inducible promoter significantly improved the success rate of genome editing in this host. This work contributes to the development of genetic manipulation and furthers the use of B. licheniformis as an efficient industrial workhorse.
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Affiliation(s)
- Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.L.); (H.W.); (L.Z.); (Z.D.); (S.X.); (Z.G.)
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Hanrong Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.L.); (H.W.); (L.Z.); (Z.D.); (S.X.); (Z.G.)
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.L.); (H.W.); (L.Z.); (Z.D.); (S.X.); (Z.G.)
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.L.); (H.W.); (L.Z.); (Z.D.); (S.X.); (Z.G.)
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.L.); (H.W.); (L.Z.); (Z.D.); (S.X.); (Z.G.)
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhenghua Gu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.L.); (H.W.); (L.Z.); (Z.D.); (S.X.); (Z.G.)
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Y.L.); (H.W.); (L.Z.); (Z.D.); (S.X.); (Z.G.)
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-0510-85918235
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27
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Simultaneous Control of Endogenous and User-Defined Genetic Pathways Using Unique ecDHFR Pharmacological Chaperones. Cell Chem Biol 2020; 27:622-634.e6. [PMID: 32330442 DOI: 10.1016/j.chembiol.2020.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/04/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
Destabilizing domains (DDs), such as a mutated form of Escherichia coli dihydrofolate reductase (ecDHFR), confer instability and promote protein degradation. However, when combined with small-molecule stabilizers (e.g., the antibiotic trimethoprim), DDs allow positive regulation of fusion protein abundance. Using a combinatorial screening approach, we identified and validated 17 unique 2,4-diaminopyrimidine/triazine-based ecDHFR DD stabilizers, at least 15 of which were ineffective antibiotics against E. coli and S. aureus. Identified stabilizers functioned in vivo to control an ecDHFR DD-firefly luciferase in the mouse eye and/or the liver. Next, stabilizers were leveraged to perform synergistic dual functions in vitro (HeLa cell death sensitization) and in vivo (repression of ocular inflammation) by stabilizing a user-defined ecDHFR DD while also controlling endogenous signaling pathways. Thus, these newly identified pharmacological chaperones allow for simultaneous control of compound-specific endogenous and user-defined genetic pathways, the combination of which may provide synergistic effects in complex biological scenarios.
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28
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Li J, Kong H, Zhu C, Zhang Y. Photo-controllable bioorthogonal chemistry for spatiotemporal control of bio-targets in living systems. Chem Sci 2020; 11:3390-3396. [PMID: 34109018 PMCID: PMC8152734 DOI: 10.1039/c9sc06540g] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/07/2020] [Indexed: 12/27/2022] Open
Abstract
The establishment of bioorthogonal chemistry is one of the most significant advances in chemical biology using exogenous chemistry to perturb and study biological processes. Photo-modulation of biological systems has realized temporal and spatial control on biomacromolecules in living systems. The combination of photo-modulation and bioorthogonal chemistry is therefore emerging as a new direction to develop new chemical biological tools with spatiotemporal resolution. This minireview will focus on recent development of bioorthogonal chemistry subject to spatiotemporal control through photo-irradiation. Different strategies to realize photo-control on bioorthogonal bond-forming reactions and biological applications of photo-controllable bioorthogonal reactions will be summarized to give a perspective on how the innovations on photo-chemistry can contribute to the development of optochemical biology. Future trends to develop more optochemical tools based on novel photochemistry will also be discussed to envision the development of chemistry-oriented optochemical biology.
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Affiliation(s)
- Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 China
| | - Hao Kong
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 China
| | - Chenghong Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 China
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29
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Abstract
Since the breakthrough discoveries that CRISPR-Cas9 nucleases can be easily programmed and employed to induce targeted double-strand breaks in mammalian cells, the gene editing field has grown exponentially. Today, CRISPR technologies based on engineered class II CRISPR effectors facilitate targeted modification of genes and RNA transcripts. Moreover, catalytically impaired CRISPR-Cas variants can be employed as programmable DNA binding domains and used to recruit effector proteins, such as transcriptional regulators, epigenetic modifiers or base-modifying enzymes, to selected genomic loci. The juxtaposition of CRISPR and optogenetics enables spatiotemporally confined and highly dynamic genome perturbations in living cells and animals and holds unprecedented potential for biology and biomedicine.Here, we provide an overview of the state-of-the-art methods for light-control of CRISPR effectors. We will detail the plethora of exciting applications enabled by these systems, including spatially confined genome editing, timed activation of endogenous genes, as well as remote control of chromatin-chromatin interactions. Finally, we will discuss limitations of current optogenetic CRISPR tools and point out routes for future innovation in this emerging field.
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Affiliation(s)
- Jan Mathony
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
| | - Mareike D Hoffmann
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Niopek
- Synthetic Biology Group, BioQuant Center, University of Heidelberg, Heidelberg, Germany.
- Health Data Science Unit, Heidelberg University Hospital and Medical Faculty of Heidelberg University, Heidelberg, Germany.
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30
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Engineering nucleic acid chemistry for precise and controllable CRISPR/Cas9 genome editing. Sci Bull (Beijing) 2019; 64:1841-1849. [PMID: 36659580 DOI: 10.1016/j.scib.2019.07.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 01/21/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) genome editing technology is revolutionizing our approach and capability to precisely manipulate the genetic flow of mammalians. The facile programmability of Cas9 protein and guide RNA (gRNA) sequence has recently expanded biomedical application of CRISPR/Cas9 technology from editing mammalian genome to various genetic manipulations. The therapeutic and clinical translation potential of CRISPR/Cas9 genome editing, however, are challenged by its off-target effect and low genome editing efficiency. In this regard, developing new Cas9 variants and conditional control of Cas9/gRNA activity are of great potential for improving genome editing accuracy and on-target efficiency. In this review, we summarize chemical strategies that have been developed recently to engineer the nucleic acid chemistry of gRNA to enhance CRISPR/Cas9 genome editing efficacy, specificity and controllability. This review aims to highlight the endeavor that has been made to solve bottleneck problems in the field of CRISPR/Cas9 and inspire innovative researches to fulfill the gap between bench and bed.
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31
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Peng H, Chau VQ, Phetsang W, Sebastian RM, Stone MRL, Datta S, Renwick M, Tamer YT, Toprak E, Koh AY, Blaskovich MA, Hulleman JD. Non-antibiotic Small-Molecule Regulation of DHFR-Based Destabilizing Domains In Vivo. Mol Ther Methods Clin Dev 2019; 15:27-39. [PMID: 31649953 PMCID: PMC6804886 DOI: 10.1016/j.omtm.2019.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
The E. coli dihydrofolate reductase (DHFR) destabilizing domain (DD), which shows promise as a biologic tool and potential gene therapy approach, can be utilized to achieve spatial and temporal control of protein abundance in vivo simply by administration of its stabilizing ligand, the routinely prescribed antibiotic trimethoprim (TMP). However, chronic TMP use drives development of antibiotic resistance (increasing likelihood of subsequent infections) and disrupts the gut microbiota (linked to autoimmune and neurodegenerative diseases), tempering translational excitement of this approach in model systems and for treating human diseases. Herein, we identified a TMP-based, non-antibiotic small molecule, termed 14a (MCC8529), and tested its ability to control multiple DHFR-based reporters and signaling proteins. We found that 14a is non-toxic and can effectively stabilize DHFR DDs expressed in mammalian cells. Furthermore, 14a crosses the blood-retinal barrier and stabilizes DHFR DDs expressed in the mouse eye with kinetics comparable to that of TMP (≤6 h). Surprisingly, 14a stabilized a DHFR DD in the liver significantly better than TMP did, while having no effect on the mouse gut microbiota. Our results suggest that alternative small-molecule DHFR DD stabilizers (such as 14a) may be ideal substitutes for TMP in instances when conditional, non-antibiotic control of protein abundance is desired in the eye and beyond.
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Affiliation(s)
- Hui Peng
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Viet Q. Chau
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Wanida Phetsang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Rebecca M. Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - M. Rhia L. Stone
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Shyamtanu Datta
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Marian Renwick
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Yusuf T. Tamer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Andrew Y. Koh
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Mark A.T. Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - John D. Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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