1
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Advancing programmable gene expression in plants using CRISPRi-based Boolean gates. Nat Biotechnol 2024:10.1038/s41587-024-02273-5. [PMID: 38769425 DOI: 10.1038/s41587-024-02273-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
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2
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Khan MA, Herring G, Zhu JY, Oliva M, Fourie E, Johnston B, Zhang Z, Potter J, Pineda L, Pflueger J, Swain T, Pflueger C, Lloyd JPB, Secco D, Small I, Kidd BN, Lister R. CRISPRi-based circuits to control gene expression in plants. Nat Biotechnol 2024:10.1038/s41587-024-02236-w. [PMID: 38769424 DOI: 10.1038/s41587-024-02236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
The construction of synthetic gene circuits in plants has been limited by a lack of orthogonal and modular parts. Here, we implement a CRISPR (clustered regularly interspaced short palindromic repeats) interference (CRISPRi)-based reversible gene circuit platform in plants. We create a toolkit of engineered repressible promoters of different strengths and construct NOT and NOR gates in Arabidopsis thaliana protoplasts. We determine the optimal processing system to express single guide RNAs from RNA Pol II promoters to introduce NOR gate programmability for interfacing with host regulatory sequences. The performance of a NOR gate in stably transformed Arabidopsis plants demonstrates the system's programmability and reversibility in a complex multicellular organism. Furthermore, cross-species activity of CRISPRi-based logic gates is shown in Physcomitrium patens, Triticum aestivum and Brassica napus protoplasts. Layering multiple NOR gates together creates OR, NIMPLY and AND logic functions, highlighting the modularity of our system. Our CRISPRi circuits are orthogonal, compact, reversible, programmable and modular and provide a platform for sophisticated spatiotemporal control of gene expression in plants.
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Affiliation(s)
- Muhammad Adil Khan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Gabrielle Herring
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Yuan Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marina Oliva
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Elliott Fourie
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Benjamin Johnston
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Zhining Zhang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jarred Potter
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Luke Pineda
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Tessa Swain
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - David Secco
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Brendan N Kidd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland, Australia.
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
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3
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Beal J. Flow Cytometry Quantification of Transient Transfections in Mammalian Cells. Methods Mol Biol 2024; 2774:153-176. [PMID: 38441764 DOI: 10.1007/978-1-0716-3718-0_11] [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: 03/07/2024]
Abstract
Flow cytometry is a powerful quantitative assay supporting high-throughput collection of single-cell data with a high dynamic range. For flow cytometry to yield reproducible data with a quantitative relationship to the underlying biology, however, requires that (1) appropriate process controls are collected along with experimental samples, (2) these process controls are used for unit calibration and quality control, and (3) data are analyzed using appropriate statistics. To this end, this chapter describes methods for quantitative flow cytometry through the addition of process controls and analyses, thereby enabling better development, modeling, and debugging of engineered biological organisms. The methods described here have specifically been developed in the context of transient transfections in mammalian cells but may in many cases be adaptable to other categories of transfection and other types of cells.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, USA.
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4
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Zhang Y, Chen S, Yang L, Zhang Q. Application progress of CRISPR/Cas9 genome-editing technology in edible fungi. Front Microbiol 2023; 14:1169884. [PMID: 37303782 PMCID: PMC10248459 DOI: 10.3389/fmicb.2023.1169884] [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: 02/20/2023] [Accepted: 04/26/2023] [Indexed: 06/13/2023] Open
Abstract
Edible fungi are not only delicious but are also rich in nutritional and medicinal value, which is highly sought after by consumers. As the edible fungi industry continues to rapidly advance worldwide, particularly in China, the cultivation of superior and innovative edible fungi strains has become increasingly pivotal. Nevertheless, conventional breeding techniques for edible fungi can be arduous and time-consuming. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) is a powerful tool for molecular breeding due to its ability to mediate high-efficiency and high-precision genome modification, which has been successfully applied to many kinds of edible fungi. In this review, we briefly summarized the working mechanism of the CRISPR/Cas9 system and highlighted the application progress of CRISPR/Cas9-mediated genome-editing technology in edible fungi, including Agaricus bisporus, Ganoderma lucidum, Flammulina filiformis, Ustilago maydis, Pleurotus eryngii, Pleurotus ostreatus, Coprinopsis cinerea, Schizophyllum commune, Cordyceps militaris, and Shiraia bambusicola. Additionally, we discussed the limitations and challenges encountered using CRISPR/Cas9 technology in edible fungi and provided potential solutions. Finally, the applications of CRISPR/Cas9 system for molecular breeding of edible fungi in the future are explored.
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5
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Ewaisha R, Anderson KS. Immunogenicity of CRISPR therapeutics-Critical considerations for clinical translation. Front Bioeng Biotechnol 2023; 11:1138596. [PMID: 36873375 PMCID: PMC9978118 DOI: 10.3389/fbioe.2023.1138596] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
CRISPR offers new hope for many patients and promises to transform the way we think of future therapies. Ensuring safety of CRISPR therapeutics is a top priority for clinical translation and specific recommendations have been recently released by the FDA. Rapid progress in the preclinical and clinical development of CRISPR therapeutics leverages years of experience with gene therapy successes and failures. Adverse events due to immunogenicity have been a major setback that has impacted the field of gene therapy. As several in vivo CRISPR clinical trials make progress, the challenge of immunogenicity remains a significant roadblock to the clinical availability and utility of CRISPR therapeutics. In this review, we examine what is currently known about the immunogenicity of CRISPR therapeutics and discuss several considerations to mitigate immunogenicity for the design of safe and clinically translatable CRISPR therapeutics.
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Affiliation(s)
- Radwa Ewaisha
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Department of Microbiology and Immunology, School of Pharmacy, Newgiza University, Newgiza, Egypt
| | - Karen S. Anderson
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, United States
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6
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Aldulijan I, Beal J, Billerbeck S, Bouffard J, Chambonnier G, Ntelkis N, Guerreiro I, Holub M, Ross P, Selvarajah V, Sprent N, Vidal G, Vignoni A. Functional Synthetic Biology. Synth Biol (Oxf) 2023; 8:ysad006. [PMID: 37073284 PMCID: PMC10105873 DOI: 10.1093/synbio/ysad006] [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: 06/30/2022] [Revised: 02/17/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes abstraction difficult, reduces engineering flexibility and impairs predictability and design reuse. Functional Synthetic Biology aims to overcome these impediments by focusing the design of biological systems on function, rather than on sequence. This reorientation will decouple the engineering of biological devices from the specifics of how those devices are put to use, requiring both conceptual and organizational change, as well as supporting software tooling. Realizing this vision of Functional Synthetic Biology will allow more flexibility in how devices are used, more opportunity for reuse of devices and data, improvements in predictability and reductions in technical risk and cost.
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Affiliation(s)
- Ibrahim Aldulijan
- Systems Engineering, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, 07030, NJ, USA
| | | | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jeff Bouffard
- Centre for Applied Synthetic Biology, and Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, H4B 1R6, Québec, Canada
| | - Gaël Chambonnier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
| | - Nikolaos Ntelkis
- Specialized Metabolism research group, Center for Plant Systems Biology, VIB-Ghent University, Technologiepark 71, Zwijnaarde, 9052, Belgium
| | - Isaac Guerreiro
- iGEM Foundation, 45 Prospect Street, Cambridge, 02139, MA, USA
| | - Martin Holub
- Delft University of Technology, Van der Maasweg 9, 2629 HZ, The Netherlands
| | - Paul Ross
- BioStrat Marketing, 9965 Harbour Lake Circle, Boynton Beach, FL, 33437, USA
| | | | - Noah Sprent
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, SW7 2AZ, UK
| | - Gonzalo Vidal
- Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing, Newcastle University, Devonshire Building, Devonshire Terrace, NE1 7RU, Newcastle Upon Tyne, UK
| | - Alejandro Vignoni
- Synthetic Biology and Biosystems Control Lab, Instituto de Automatica e Informatica Industrial, Universitat Politecnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain
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7
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Virtual cells in a virtual microenvironment recapitulate early development-like patterns in human pluripotent stem cell colonies. Stem Cell Reports 2022; 18:377-393. [PMID: 36332630 PMCID: PMC9859929 DOI: 10.1016/j.stemcr.2022.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
The mechanism by which morphogenetic signals engage the regulatory networks responsible for early embryonic tissue patterning is incompletely understood. Here, we developed a minimal gene regulatory network (GRN) model of human pluripotent stem cell (hPSC) lineage commitment and embedded it into "cellular" agents that respond to a dynamic morphogenetic signaling microenvironment. Simulations demonstrated that GRN wiring had significant non-intuitive effects on tissue pattern order, composition, and dynamics. Experimental perturbation of GRN connectivities supported model predictions and demonstrated the role of OCT4 as a master regulator of peri-gastrulation fates. Our so-called GARMEN strategy provides a multiscale computational platform to understand how single-cell-based regulatory interactions scale to tissue domains. This foundation provides new opportunities to simulate the impact of network motifs on normal and aberrant tissue development.
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8
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Prochazka L, Michaels YS, Lau C, Jones RD, Siu M, Yin T, Wu D, Jang E, Vázquez‐Cantú M, Gilbert PM, Kaul H, Benenson Y, Zandstra PW. Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells. Mol Syst Biol 2022; 18:e10886. [PMID: 36366891 PMCID: PMC9650275 DOI: 10.15252/msb.202110886] [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: 12/21/2021] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
During development, cell state transitions are coordinated through changes in the identity of molecular regulators in a cell type‐ and dose‐specific manner. The ability to rationally engineer such transitions in human pluripotent stem cells (hPSC) will enable numerous applications in regenerative medicine. Herein, we report the generation of synthetic gene circuits that can detect a desired cell state using AND‐like logic integration of endogenous miRNAs (classifiers) and, upon detection, produce fine‐tuned levels of output proteins using an miRNA‐mediated output fine‐tuning technology (miSFITs). Specifically, we created an “hPSC ON” circuit using a model‐guided miRNA selection and circuit optimization approach. The circuit demonstrates robust PSC‐specific detection and graded output protein production. Next, we used an empirical approach to create an “hPSC‐Off” circuit. This circuit was applied to regulate the secretion of endogenous BMP4 in a state‐specific and fine‐tuned manner to control the composition of differentiating hPSCs. Our work provides a platform for customized cell state‐specific control of desired physiological factors in hPSC, laying the foundation for programming cell compositions in hPSC‐derived tissues and beyond.
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Affiliation(s)
- Laura Prochazka
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Yale S Michaels
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Charles Lau
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Ross D Jones
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Mona Siu
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Ting Yin
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Diana Wu
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Esther Jang
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Mercedes Vázquez‐Cantú
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biosystems Science and Engineering (D‐BSSE) Basel Switzerland
| | - Penney M Gilbert
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Department of Cell and Systems Biology University of Toronto Toronto ON Canada
| | - Himanshu Kaul
- School of Engineering University of Leicester Leicester UK
- Department of Respiratory Sciences University of Leicester Leicester UK
| | - Yaakov Benenson
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biosystems Science and Engineering (D‐BSSE) Basel Switzerland
| | - Peter W Zandstra
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
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9
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Presnell KV, Melhem O, Morse NJ, Alper HS. Modular, Synthetic Boolean Logic Gates Enabled in Saccharomyces cerevisiae through T7 Polymerases/CRISPR dCas9 Designs. ACS Synth Biol 2022; 11:3414-3425. [PMID: 36206523 DOI: 10.1021/acssynbio.2c00327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic control of gene expression, whether simply promoter selection or higher-order Boolean-style logic, is an important tool for metabolic engineering and synthetic biology. This work develops a suite of orthogonal T7 RNA polymerase systems capable of exerting AND/OR switchlike control over transcription in the yeastSaccharomyces cerevisiae. When linked with CRISPR dCas9-based regulation systems, more complex circuitry is possible including AND/OR/NAND/NOR style control in response to combinations of extracellular copper and galactose. Additionally, we demonstrate that these T7 system designs are modular and can accommodate alternative stimuli sensing as demonstrated through blue light induction. These designs should greatly reduce the time and labor necessary for developing Boolean gene circuits in yeast with novel applications including metabolic pathway control in the future.
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Affiliation(s)
- Kristin V Presnell
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Omar Melhem
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Nicholas J Morse
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
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10
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Wang J, Tao Y, Juan Y, Zhou H, Zhao X, Cheng X, Wang X, Quan X, Li J, Huang K, Wei W, Zhao J. Hierarchical Assembly of Flexible Biopolymer Polyphosphate-Manganese into Nanosheets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203200. [PMID: 36084167 DOI: 10.1002/smll.202203200] [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: 05/28/2022] [Revised: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Polyphosphate (polyP) is one of the most compact inorganic polyanionic biopolymers that participates in various physiological processes. However, the development of polyP-based nanomaterials is still in its infancy. Here, biocompatible polyphosphate-manganese nanosheets are designed and synthesized by a hierarchical assembly strategy. The thickness and the lateral size of the resulting polyP-Mn nanosheets (PMNSs) are 5 nm and 120-130 nm, respectively. Molecular dynamics simulations suggested that the polyP-hexadecyl trimethyl ammonium bromide flat structure possesses a strong aggregating capacity and serves as the template for the 2D assembly of polyP-Mn. The PMNSs can activate the inflammatory response of macrophages resulting in the recovery of innate immunological functions to inhibit tumor proliferation. This work has initiated a new direction in constructing layered polyP-based nanomaterials and provides guidance for biocompatible and biodegradable biopolymer-based materials in the regulation of innate responses.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Yucheng Tao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210008, China
| | - Yewen Juan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210008, China
| | - Hang Zhou
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xinyang Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xiaomei Cheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xiuxiu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
| | - Xuebo Quan
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Junyan Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Kai Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210008, China
- Shenzhen Research Institute, Nanjing University, Shenzhen, 518057, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210008, China
- Shenzhen Research Institute, Nanjing University, Shenzhen, 518057, China
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11
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Crone MA, MacDonald JT, Freemont PS, Siciliano V. gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells. NPJ Syst Biol Appl 2022; 8:34. [PMID: 36114193 PMCID: PMC9481559 DOI: 10.1038/s41540-022-00241-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Synthetic networks require complex intertwined genetic regulation often relying on transcriptional activation or repression of target genes. CRISPRi-based transcription factors facilitate the programmable modulation of endogenous or synthetic promoter activity and the process can be optimised by using software to select appropriate gRNAs and limit non-specific gene modulation. Here, we develop a computational software pipeline, gDesigner, that enables the automated selection of orthogonal gRNAs with minimized off-target effects and promoter crosstalk. We next engineered a Lachnospiraceae bacterium Cas12a (dLbCas12a)-based repression system that downregulates target gene expression by means of steric hindrance of the cognate promoter. Finally, we generated a library of orthogonal synthetic dCas12a-repressed promoters and experimentally demonstrated it in HEK293FT, U2OS and H1299 cells lines. Our system expands the toolkit of mammalian synthetic promoters with a new complementary and orthogonal CRISPRi-based system, ultimately enabling the design of synthetic promoter libraries for multiplex gene perturbation that facilitate the understanding of complex cellular phenotypes.
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Affiliation(s)
- Michael A Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom
- London Biofoundry, Imperial College Translation and Innovation Hub, White City Campus, 84 Wood Lane, London, United Kingdom
| | - James T MacDonald
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom.
| | - Paul S Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom.
- UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London, London, United Kingdom.
- London Biofoundry, Imperial College Translation and Innovation Hub, White City Campus, 84 Wood Lane, London, United Kingdom.
| | - Velia Siciliano
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom.
- Istituto Italiano di Tecnologia IIT, Department of Synthetic and Systems Biology for Biomedicine, Genoa, Italy.
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12
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CRISPR/Cas9 system: a reliable and facile genome editing tool in modern biology. Mol Biol Rep 2022; 49:12133-12150. [PMID: 36030476 PMCID: PMC9420241 DOI: 10.1007/s11033-022-07880-6] [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: 03/17/2022] [Accepted: 08/17/2022] [Indexed: 11/10/2022]
Abstract
Genome engineering has always been a versatile technique in biological research and medicine, with several applications. In the last several years, the discovery of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 technology has swept the scientific community and revolutionised the speed of modern biology, heralding a new era of disease detection and rapid biotechnology discoveries. It enables successful gene editing by producing targeted double-strand breaks in virtually any organism or cell type. So, this review presents a comprehensive knowledge about the mechanism and structure of Cas9-mediated RNA-guided DNA targeting and cleavage. In addition, genome editing via CRISPR-Cas9 technology in various animals which are being used as models in scientific research including Non-Human Primates Pigs, Dogs, Zebra, fish and Drosophila has been discussed in this review. This review also aims to understand the applications, serious concerns and future perspective of CRISPR/Cas9-mediated genome editing.
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13
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Hao Y, Li M, Zhang Q, Shi J, Li J, Li Q, Fan C, Wang F. DNA Origami‐Based Single‐Molecule CRISPR Machines for Spatially Resolved Searching. Angew Chem Int Ed Engl 2022; 61:e202205460. [DOI: 10.1002/anie.202205460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Yaya Hao
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Zhang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiye Shi
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Jiang Li
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- The Interdisciplinary Research Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
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14
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Braun CJ, Adames AC, Saur D, Rad R. Tutorial: design and execution of CRISPR in vivo screens. Nat Protoc 2022; 17:1903-1925. [PMID: 35840661 DOI: 10.1038/s41596-022-00700-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
Here we provide a detailed tutorial on CRISPR in vivo screening. Using the mouse as the model organism, we introduce a range of CRISPR tools and applications, delineate general considerations for 'transplantation-based' or 'direct in vivo' screening design, and provide details on technical execution, sequencing readouts, computational analyses and data interpretation. In vivo screens face unique pitfalls and limitations, such as delivery issues or library bottlenecking, which must be counteracted to avoid screening failure or flawed conclusions. A broad variety of in vivo phenotypes can be interrogated such as organ development, hematopoietic lineage decision and evolutionary licensing in oncogenesis. We describe experimental strategies to address various biological questions and provide an outlook on emerging CRISPR applications, such as genetic interaction screening. These technological advances create potent new opportunities to dissect the molecular underpinnings of complex organismal phenotypes.
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Affiliation(s)
- Christian J Braun
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany. .,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Andrés Carbonell Adames
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dieter Saur
- Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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15
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Hao Y, Li M, Zhang Q, Shi J, Li J, Li Q, Fan C, Wang F. DNA origami‐based single‐molecule CRISPR machines for spatially resolved searching. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yaya Hao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHRISTMAS ISLAND
| | - Mingqiang Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Qian Zhang
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Jiye Shi
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Division of Physical Biology CHINA
| | - Jiang Li
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Division of Physical Biology CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Chunhai Fan
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Rd 800 200240 Shanghai CHINA
| | - Fei Wang
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
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16
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Huang L, Liao Z, Liu Z, Chen Y, Huang T, Xiao H. Application and Prospect of CRISPR/Cas9 Technology in Reversing Drug Resistance of Non-Small Cell Lung Cancer. Front Pharmacol 2022; 13:900825. [PMID: 35620280 PMCID: PMC9127258 DOI: 10.3389/fphar.2022.900825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer drug resistance has always been a major factor affecting the treatment of non-small cell lung cancer, which reduces the quality of life of patients. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) technology, as an efficient and convenient new gene-editing technology, has provided a lot of help to the clinic and accelerated the research of cancer and drug resistance. In this review, we introduce the mechanisms of drug resistance in non-small cell lung cancer (NSCLC), discuss how the CRISPR/Cas9 system can reverse multidrug resistance in NSCLC, and focus on drug resistance gene mutations. To improve the prognosis of NSCLC patients and further improve patients' quality of life, it is necessary to utilize the CRISPR/Cas9 system in systematic research on cancer drug resistance.
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Affiliation(s)
- Lu Huang
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Zhi Liao
- Department of Gynecology and Obstetrics, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Zhixi Liu
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Yan Chen
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - Tingwenli Huang
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
| | - Hongtao Xiao
- Department of Clinical Pharmacy, Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China.,Personalized Drug Therapy Key Laboratory of Sichuan Province, Chengdu, China
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17
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Nash A, Capriotti P, Hoermann A, Papathanos PA, Windbichler N. Intronic gRNAs for the Construction of Minimal Gene Drive Systems. Front Bioeng Biotechnol 2022; 10:857460. [PMID: 35646834 PMCID: PMC9133698 DOI: 10.3389/fbioe.2022.857460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Gene drives are promising tools for the genetic control of insect vector or pest populations. CRISPR-based gene drives are generally highly complex synthetic constructs consisting of multiple transgenes and their respective regulatory elements. This complicates the generation of new gene drives and the testing of the behavior of their constituent functional modules. Here, we explored the minimal genetic components needed to constitute autonomous gene drives in Drosophila melanogaster. We first designed intronic gRNAs that can be located directly within coding transgene sequences and tested their functions in cell lines. We then integrated a Cas9 open reading frame hosting such an intronic gRNA within the Drosophila rcd-1r locus that drives the expression in the male and female germlines. We showed that upon removal of the fluorescent transformation marker, the rcd-1rd allele supports efficient gene drive. We assessed the propensity of this driver, designed to be neutral with regards to fitness and host gene function, to propagate in caged fly populations. Because of their simplicity, such integral gene drives could enable the modularization of drive and effector functions. We also discussed the possible biosafety implications of minimal and possibly recoded gene drives.
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Affiliation(s)
- Alexander Nash
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paolo Capriotti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Astrid Hoermann
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Phillipos Aris Papathanos
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Nikolai Windbichler,
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18
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Beal J, Teague B, Sexton JT, Castillo-Hair S, DeLateur NA, Samineni M, Tabor JJ, Weiss R. Meeting Measurement Precision Requirements for Effective Engineering of Genetic Regulatory Networks. ACS Synth Biol 2022; 11:1196-1207. [PMID: 35156365 DOI: 10.1021/acssynbio.1c00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reliable, predictable engineering of cellular behavior is one of the key goals of synthetic biology. As the field matures, biological engineers will become increasingly reliant on computer models that allow for the rapid exploration of design space prior to the more costly construction and characterization of candidate designs. The efficacy of such models, however, depends on the accuracy of their predictions, the precision of the measurements used to parametrize the models, and the tolerance of biological devices for imperfections in modeling and measurement. To better understand this relationship, we have derived an Engineering Error Inequality that provides a quantitative mathematical bound on the relationship between predictability of results, model accuracy, measurement precision, and device characteristics. We apply this relation to estimate measurement precision requirements for engineering genetic regulatory networks given current model and device characteristics, recommending a target standard deviation of 1.5-fold. We then compare these requirements with the results of an interlaboratory study to validate that these requirements can be met via flow cytometry with matched instrument channels and an independent calibrant. On the basis of these results, we recommend a set of best practices for quality control of flow cytometry data and discuss how these might be extended to other measurement modalities and applied to support further development of genetic regulatory network engineering.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Brian Teague
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - John T. Sexton
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | | | - Nicholas A. DeLateur
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Meher Samineni
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Jeffrey J. Tabor
- Department of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Ron Weiss
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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19
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Villegas Kcam MC, Chappell J. Design, Characterization, and Application of Targeted Gene Activation in Bacteria Using a Modular CRISPRa System. Methods Mol Biol 2022; 2518:203-215. [PMID: 35666447 DOI: 10.1007/978-1-0716-2421-0_12] [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: 06/15/2023]
Abstract
CRISPR-Cas regulators have provided an excellent toolbox to control gene expression due to the versatility of its components and the easy programming of the single guide RNA (sgRNA) to target DNA sequences. Included in this are CRISPR activation (CRISPRa) systems. These systems allow users to activate transcription of a target gene through the localization of transcription activation domains (ADs) near promoter elements, which in turn recruit RNA polymerase (RNAP) to turn on transcription. A variety of different CRISPRa systems have been described that vary in AD type, recruitment strategies, and CRISPR-Cas systems. Recently, a highly modular CRISPRa system was described that allows for facile exchange of ADs and CRISPR-Cas components. This allows for the creation of CRISPRa systems with unique properties, for example, ability to activate from specific positions upstream of a gene of interest. Here, we describe a protocol for designing, characterizing, and applying the modular CRISPRa system for gene activation in E. coli. We first focus on how to identify activating sites upstream of promoters and the cloning of the targeting sgRNA. We then describe how to perform a fluorescence experiment to evaluate activation of a single target site. Finally, we explain how to adapt the system to expand the target range and how to characterize the activation pattern obtained from different CRISPRa designs.
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Affiliation(s)
| | - James Chappell
- Department of BioSciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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20
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Simmons TR, Ellington AD, Contreras LM. RNP-Based Control Systems for Genetic Circuits in Synthetic Biology Beyond CRISPR. Methods Mol Biol 2022; 2518:1-31. [PMID: 35666436 DOI: 10.1007/978-1-0716-2421-0_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Ribonucleoproteins (RNPs) are RNA-protein complexes utilized natively in both prokaryotes and eukaryotes to regulate essential processes within the cell. Over the past few years, many of these native systems have been adapted to provide control over custom genetic targets. Engineered RNP-based control systems allow for fine-tune regulation of desired targets, by providing customizable nucleotide-nucleotide interactions. However, as there have been several engineered RNP systems developed recently, identifying an optimal system for various bioprocesses is challenging. Here, we review the most successful engineered RNP systems and their applications to survey the current state of the field. Additionally, we provide selection criteria to provide users a streamlined method for identifying an RNP control system most useful to their own work. Lastly, we discuss future applications of RNP control systems and how they can be utilized to address the current grand challenges of the synthetic biology community.
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Affiliation(s)
- Trevor R Simmons
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
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21
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CRISPR-Based Genetic Switches and Other Complex Circuits: Research and Application. Life (Basel) 2021; 11:life11111255. [PMID: 34833131 PMCID: PMC8621321 DOI: 10.3390/life11111255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-based enzymes have offered a unique capability to the design of genetic switches, with advantages in designability, modularity and orthogonality. CRISPR-based genetic switches operate on multiple levels of life, including transcription and translation. In both prokaryotic and eukaryotic cells, deactivated CRISPR endonuclease and endoribonuclease have served in genetic switches for activating or repressing gene expression, at both transcriptional and translational levels. With these genetic switches, more complex circuits have been assembled to achieve sophisticated functions including inducible switches, non-linear response and logical biocomputation. As more CRISPR enzymes continue to be excavated, CRISPR-based genetic switches will be used in a much wider range of applications.
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22
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Design of time-delayed safety switches for CRISPR gene therapy. Sci Rep 2021; 11:16908. [PMID: 34413448 PMCID: PMC8377138 DOI: 10.1038/s41598-021-96510-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
CRISPR system is a powerful gene editing tool which has already been reported to address a variety of gene relevant diseases in different cell lines. However, off-target effect and immune response caused by Cas9 remain two fundamental problems. Inspired by previously reported Cas9 self-elimination systems, time-delayed safety switches are designed in this work. Firstly, ultrasensitive relationship is constructed between Cas9-sgRNA (enzyme) and Cas9 plasmids (substrate), which generates the artificial time delay. Then intrinsic time delay in biomolecular activities is revealed by data fitting and utilized in constructing safety switches. The time-delayed safety switches function by separating the gene editing process and self-elimination process, and the tunable delay time may ensure a good balance between gene editing efficiency and side effect minimization. By addressing gene therapy efficiency, off-target effect, immune response and drug accumulation, we hope our safety switches may offer inspiration in realizing safe and efficient gene therapy in humans.
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23
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Gama-Brambila R, Chen J, Dabiri Y, Tascher G, Němec V, Münch C, Song G, Knapp S, Cheng X. A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins. JACS AU 2021; 1:777-785. [PMID: 34467332 PMCID: PMC8395650 DOI: 10.1021/jacsau.1c00007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Indexed: 06/01/2023]
Abstract
The discovery of clustered regularly interspaced short palindromic repeats and their associated proteins (Cas) has revolutionized the field of genome and epigenome editing. A number of new methods have been developed to precisely control the function and activity of Cas proteins, including fusion proteins and small-molecule modulators. Proteolysis-targeting chimeras (PROTACs) represent a new concept using the ubiquitin-proteasome system to degrade a protein of interest, highlighting the significance of chemically induced protein-E3 ligase interaction in drug discovery. Here, we engineered Cas proteins (Cas9, dCas9, Cas12, and Cas13) by inserting a Phe-Cys-Pro-Phe (FCPF) amino acid sequence (known as the π-clamp system) and demonstrate that the modified CasFCPF proteins can be (1) labeled in live cells by perfluoroaromatics carrying the fluorescein or (2) degraded by a perfluoroaromatics-functionalized PROTAC (PROTAC-FCPF). A proteome-wide analysis of PROTAC-FCPF-mediated Cas9FCPF protein degradation revealed a high target specificity, suggesting a wide range of applications of perfluoroaromatics-induced proximity in the regulation of stability, activity, and functionality of any FCPF-tagging protein.
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Affiliation(s)
- Rodrigo
A. Gama-Brambila
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Jie Chen
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Yasamin Dabiri
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Georg Tascher
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt am Main, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
| | - Václav Němec
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Christian Münch
- Institute
of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt am Main, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany
| | - Guangqi Song
- Department
of Gastroenterology, Zhongshan Hospital
of Fudan University, 180 Fenglin Road, Xuhui District, 200032 Shanghai, China
| | - Stefan Knapp
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
| | - Xinlai Cheng
- Buchmann
Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 15. R. 3.652, D-60438 Frankfurt am Main, Germany
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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24
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Shakiba N, Jones RD, Weiss R, Del Vecchio D. Context-aware synthetic biology by controller design: Engineering the mammalian cell. Cell Syst 2021; 12:561-592. [PMID: 34139166 PMCID: PMC8261833 DOI: 10.1016/j.cels.2021.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/19/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
The rise of systems biology has ushered a new paradigm: the view of the cell as a system that processes environmental inputs to drive phenotypic outputs. Synthetic biology provides a complementary approach, allowing us to program cell behavior through the addition of synthetic genetic devices into the cellular processor. These devices, and the complex genetic circuits they compose, are engineered using a design-prototype-test cycle, allowing for predictable device performance to be achieved in a context-dependent manner. Within mammalian cells, context effects impact device performance at multiple scales, including the genetic, cellular, and extracellular levels. In order for synthetic genetic devices to achieve predictable behaviors, approaches to overcome context dependence are necessary. Here, we describe control systems approaches for achieving context-aware devices that are robust to context effects. We then consider cell fate programing as a case study to explore the potential impact of context-aware devices for regenerative medicine applications.
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Affiliation(s)
- Nika Shakiba
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ross D Jones
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ron Weiss
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Domitilla Del Vecchio
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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25
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Pandelakis M, Delgado E, Ebrahimkhani MR. CRISPR-Based Synthetic Transcription Factors In Vivo: The Future of Therapeutic Cellular Programming. Cell Syst 2021; 10:1-14. [PMID: 31972154 DOI: 10.1016/j.cels.2019.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/14/2019] [Accepted: 10/09/2019] [Indexed: 01/04/2023]
Abstract
Pinpoint control over endogenous gene expression in vivo has long been a fevered dream for clinicians and researchers alike. With the recent repurposing of programmable, RNA-guided DNA endonucleases from the CRISPR bacterial immune system, this dream is becoming a powerful reality. Engineered CRISPR/Cas9-based transcriptional regulators and epigenome editors have enabled researchers to perturb endogenous gene expression in vivo, allowing for the therapeutic reprogramming of cell and tissue behavior. For this technology to be of maximal use, a variety of technological hurdles still need to be addressed. Better understanding of the design principle controlling gene expression together with technologies that enable spatiotemporal control of transcriptional engineering are fundamental for rational design, improved efficacy, and ultimately safe translation to humans. In this review, we will discuss recent advances and integrative strategies that can help pave the path toward a new class of transcriptional therapeutics.
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Affiliation(s)
- Matthew Pandelakis
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA
| | - Elizabeth Delgado
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA
| | - Mo R Ebrahimkhani
- School of Biological and Health Systems Engineering, Ira A. Fulton Schools of Engineering, Arizona State University, Tempe, AZ, USA; Department of Pathology, Division of Experimental Pathology, University of Pittsburgh, Pittsburgh, PA, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.
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26
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Villegas Kcam MC, Tsong AJ, Chappell J. Rational engineering of a modular bacterial CRISPR-Cas activation platform with expanded target range. Nucleic Acids Res 2021; 49:4793-4802. [PMID: 33823546 PMCID: PMC8096225 DOI: 10.1093/nar/gkab211] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 11/14/2022] Open
Abstract
CRISPR-Cas activator (CRISPRa) systems that selectively turn on transcription of a target gene are a potentially transformative technology for programming cellular function. While in eukaryotes versatile CRISPRa systems exist, in bacteria these systems suffer from a limited ability to activate different genes due to strict distance-dependent requirements of functional target binding sites, and require greater customization to optimize performance in different genetic and cellular contexts. To address this, we apply a rational protein engineering approach to create a new CRISPRa platform that is highly modular to allow for easy customization and has increased targeting flexibility through harnessing engineered Cas proteins. We first demonstrate that transcription activation domains can be recruited by CRISPR-Cas through noncovalent protein-protein interactions, which allows each component to be encoded on separate and easily interchangeable plasmid elements. We then exploit this modularity to rapidly screen a library of different activation domains, creating new systems with distinct regulatory properties. Furthermore, we demonstrate that by harnessing a library of circularly permuted Cas proteins, we can create CRISPRa systems that have different target binding site requirements, which together, allow for expanded target range.
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Affiliation(s)
| | - Annette J Tsong
- Department of BioSciences, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
| | - James Chappell
- Department of BioSciences, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, 6100 Main Street, MS 142, Houston, TX 77005, USA
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27
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Oligonucleotide-Based Therapies for Renal Diseases. Biomedicines 2021; 9:biomedicines9030303. [PMID: 33809425 PMCID: PMC8001091 DOI: 10.3390/biomedicines9030303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 02/07/2023] Open
Abstract
The global burden of chronic kidney disease (CKD) is increasing every year and represents a great cost for public healthcare systems, as the majority of these diseases are progressive. Therefore, there is an urgent need to develop new therapies. Oligonucleotide-based drugs are emerging as novel and promising alternatives to traditional drugs. Their expansion corresponds with new knowledge regarding the molecular basis underlying CKD, and they are already showing encouraging preclinical results, with two candidates being evaluated in clinical trials. However, despite recent technological advances, efficient kidney delivery remains challenging, and the presence of off-targets and side-effects precludes development and translation to the clinic. In this review, we provide an overview of the various oligotherapeutic strategies used preclinically, emphasizing the most recent findings in the field, together with the different strategies employed to achieve proper kidney delivery. The use of different nanotechnological platforms, including nanocarriers, nanoparticles, viral vectors or aptamers, and their potential for the development of more specific and effective treatments is also outlined.
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28
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Huang HH, Bellato M, Qian Y, Cárdenas P, Pasotti L, Magni P, Del Vecchio D. dCas9 regulator to neutralize competition in CRISPRi circuits. Nat Commun 2021; 12:1692. [PMID: 33727557 PMCID: PMC7966764 DOI: 10.1038/s41467-021-21772-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/29/2021] [Indexed: 12/17/2022] Open
Abstract
CRISPRi-mediated gene regulation allows simultaneous control of many genes. However, highly specific sgRNA-promoter binding is, alone, insufficient to achieve independent transcriptional regulation of multiple targets. Indeed, due to competition for dCas9, the repression ability of one sgRNA changes significantly when another sgRNA becomes expressed. To solve this problem and decouple sgRNA-mediated regulatory paths, we create a dCas9 concentration regulator that implements negative feedback on dCas9 level. This allows any sgRNA to maintain an approximately constant dose-response curve, independent of other sgRNAs. We demonstrate the regulator performance on both single-stage and layered CRISPRi-based genetic circuits, zeroing competition effects of up to 15-fold changes in circuit I/O response encountered without the dCas9 regulator. The dCas9 regulator decouples sgRNA-mediated regulatory paths, enabling concurrent and independent regulation of multiple genes. This allows predictable composition of CRISPRi-based genetic modules, which is essential in the design of larger scale synthetic genetic circuits.
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Affiliation(s)
- Hsin-Ho Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Massimo Bellato
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Yili Qian
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Paolo Magni
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Feng H, Guo J, Wang T, Zhang C, Xing XH. Guide-target mismatch effects on dCas9-sgRNA binding activity in living bacterial cells. Nucleic Acids Res 2021; 49:1263-1277. [PMID: 33503261 PMCID: PMC7897480 DOI: 10.1093/nar/gkaa1295] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
As an effective programmable DNA targeting tool, CRISPR-Cas9 system has been adopted in varieties of biotechnological applications. However, the off-target effects, derived from the tolerance towards guide-target mismatches, are regarded as the major problems in engineering CRISPR systems. To understand this, we constructed two sgRNA libraries carrying saturated single- and double-nucleotide mismatches in living bacteria cells, and profiled the comprehensive landscape of in vivo binding affinity of dCas9 toward DNA target guided by each individual sgRNA with particular mismatches. We observed a synergistic effect in seed, where combinatorial double mutations caused more severe activity loss compared with the two corresponding single mutations. Moreover, we found that a particular mismatch type, dDrG (D = A, T, G), only showed moderate impairment on binding. To quantitatively understand the causal relationship between mismatch and binding behaviour of dCas9, we further established a biophysical model, and found that the thermodynamic properties of base-pairing coupled with strand invasion process, to a large extent, can account for the observed mismatch-activity landscape. Finally, we repurposed this model, together with a convolutional neural network constructed based on the same mechanism, as a predictive tool to guide the rational design of sgRNA in bacterial CRISPR interference.
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Affiliation(s)
- Huibao Feng
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jiahui Guo
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Tianmin Wang
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chong Zhang
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Xin-hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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Muldoon JJ, Kandula V, Hong M, Donahue PS, Boucher JD, Bagheri N, Leonard JN. Model-guided design of mammalian genetic programs. SCIENCE ADVANCES 2021; 7:eabe9375. [PMID: 33608279 PMCID: PMC7895425 DOI: 10.1126/sciadv.abe9375] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/06/2021] [Indexed: 06/10/2023]
Abstract
Genetically engineering cells to perform customizable functions is an emerging frontier with numerous technological and translational applications. However, it remains challenging to systematically engineer mammalian cells to execute complex functions. To address this need, we developed a method enabling accurate genetic program design using high-performing genetic parts and predictive computational models. We built multifunctional proteins integrating both transcriptional and posttranslational control, validated models for describing these mechanisms, implemented digital and analog processing, and effectively linked genetic circuits with sensors for multi-input evaluations. The functional modularity and compositional versatility of these parts enable one to satisfy a given design objective via multiple synonymous programs. Our approach empowers bioengineers to predictively design mammalian cellular functions that perform as expected even at high levels of biological complexity.
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Affiliation(s)
- J J Muldoon
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - V Kandula
- Honors Program in Medical Education, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - M Hong
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - P S Donahue
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - J D Boucher
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - N Bagheri
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Chemistry of Life Processes Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
- Departments of Biology and Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - J N Leonard
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Chemistry of Life Processes Institute, and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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31
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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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32
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Velazquez JJ, LeGraw R, Moghadam F, Tan Y, Kilbourne J, Maggiore JC, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes SM, Plaisier C, Cahan P, Kiani S, Ebrahimkhani MR. Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids. Cell Syst 2020; 12:41-55.e11. [PMID: 33290741 PMCID: PMC8164844 DOI: 10.1016/j.cels.2020.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022]
Abstract
Pluripotent stem cell (PSC)-derived organoids have emerged as novel multicellular models of human tissue development but display immature phenotypes, aberrant tissue fates, and a limited subset of cells. Here, we demonstrate that integrated analysis and engineering of gene regulatory networks (GRNs) in PSC-derived multilineage human liver organoids direct maturation and vascular morphogenesis in vitro. Overexpression of PROX1 and ATF5, combined with targeted CRISPR-based transcriptional activation of endogenous CYP3A4, reprograms tissue GRNs and improves native liver functions, such as FXR signaling, CYP3A4 enzymatic activity, and stromal cell reactivity. The engineered tissues possess superior liver identity when compared with other PSC-derived liver organoids and show the presence of hepatocyte, biliary, endothelial, and stellate-like cell populations in single-cell RNA-seq analysis. Finally, they show hepatic functions when studied in vivo. Collectively, our approach provides an experimental framework to direct organogenesis in vitro by systematically probing molecular pathways and transcriptional networks that promote tissue development.
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Affiliation(s)
- Jeremy J Velazquez
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Ryan LeGraw
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Farzaneh Moghadam
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Yuqi Tan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Joseph C Maggiore
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Joshua Hislop
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Silvia Liu
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Davy Cats
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Einthovenweg, 2333 ZC Leiden, the Netherlands
| | - Susana M Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, Einthovenweg, 2333 ZC Leiden, the Netherlands
| | - Christopher Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Patrick Cahan
- Institute for Cell Engineering Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Samira Kiani
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, Division of Experimental Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA; Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Phoenix, AZ 85054, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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33
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Marsh S, Hanson B, Wood MJA, Varela MA, Roberts TC. Application of CRISPR-Cas9-Mediated Genome Editing for the Treatment of Myotonic Dystrophy Type 1. Mol Ther 2020; 28:2527-2539. [PMID: 33171139 PMCID: PMC7704741 DOI: 10.1016/j.ymthe.2020.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/03/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a debilitating multisystemic disorder, caused by expansion of a CTG microsatellite repeat in the 3' untranslated region of the DMPK (dystrophia myotonica protein kinase) gene. To date, novel therapeutic approaches have focused on transient suppression of the mutant, repeat-expanded RNA. However, recent developments in the field of genome editing have raised the exciting possibility of inducing permanent correction of the DM1 genetic defect. Specifically, repurposing of the prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) system has enabled programmable, site-specific, and multiplex genome editing. CRISPR-based strategies for the treatment of DM1 can be applied either directly to patients, or indirectly through the ex vivo modification of patient-derived cells, and they include excision of the repeat expansion, insertion of synthetic polyadenylation signals upstream of the repeat, steric interference with RNA polymerase II procession through the repeat leading to transcriptional downregulation of DMPK, and direct RNA targeting of the mutant RNA species. Potential obstacles to such therapies are discussed, including the major challenge of Cas9 and guide RNA transgene/ribonuclear protein delivery, off-target gene editing, vector genome insertion at cut sites, on-target unintended mutagenesis (e.g., repeat inversion), pre-existing immunity to Cas9 or AAV antigens, immunogenicity, and Cas9 persistence.
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Affiliation(s)
- Seren Marsh
- University of Oxford Medical School, Medical Sciences Division, University of Oxford, Oxford OX3 9DU, UK
| | - Britt Hanson
- Department of Physiology, Anatomy and Genetics, Oxford OX1 3QX, UK; Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK; MDUK Oxford Neuromuscular Centre, UK
| | - Miguel A Varela
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK
| | - Thomas C Roberts
- Department of Paediatrics, University of Oxford, Oxford OX1 3QX, UK; MDUK Oxford Neuromuscular Centre, UK.
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Santos-Moreno J, Schaerli Y. CRISPR-based gene expression control for synthetic gene circuits. Biochem Soc Trans 2020; 48:1979-1993. [PMID: 32964920 PMCID: PMC7609024 DOI: 10.1042/bst20200020] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/22/2022]
Abstract
Synthetic gene circuits allow us to govern cell behavior in a programmable manner, which is central to almost any application aiming to harness engineered living cells for user-defined tasks. Transcription factors (TFs) constitute the 'classic' tool for synthetic circuit construction but some of their inherent constraints, such as insufficient modularity, orthogonality and programmability, limit progress in such forward-engineering endeavors. Here we review how CRISPR (clustered regularly interspaced short palindromic repeats) technology offers new and powerful possibilities for synthetic circuit design. CRISPR systems offer superior characteristics over TFs in many aspects relevant to a modular, predictable and standardized circuit design. Thus, the choice of CRISPR technology as a framework for synthetic circuit design constitutes a valid alternative to complement or replace TFs in synthetic circuits and promises the realization of more ambitious designs.
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Affiliation(s)
- Javier Santos-Moreno
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
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35
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Kirkpatrick RL, Lewis K, Langan RA, Lajoie MJ, Boyken SE, Eakman M, Baker D, Zalatan JG. Conditional Recruitment to a DNA-Bound CRISPR-Cas Complex Using a Colocalization-Dependent Protein Switch. ACS Synth Biol 2020; 9:2316-2323. [PMID: 32816470 PMCID: PMC7976376 DOI: 10.1021/acssynbio.0c00012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To spatially control biochemical functions at specific sites within a genome, we have engineered a synthetic switch that activates when bound to its DNA target site. The system uses two CRISPR-Cas complexes to colocalize components of a de novo-designed protein switch (Co-LOCKR) to adjacent sites in the genome. Colocalization triggers a conformational change in the switch from an inactive closed state to an active open state with an exposed functional peptide. We prototype the system in yeast and demonstrate that DNA binding triggers activation of the switch, recruitment of a transcription factor, and expression of a downstream reporter gene. This DNA-triggered Co-LOCKR switch provides a platform to engineer sophisticated functions that should only be executed at a specific target site within the genome, with potential applications in a wide range of synthetic systems including epigenetic regulation, imaging, and genetic logic circuits.
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Affiliation(s)
- Robin L. Kirkpatrick
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA, 98195, United States
| | - Kieran Lewis
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - Robert A. Langan
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA, 98195, United States
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, United States
| | - Marc J. Lajoie
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, United States
| | - Scott E. Boyken
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, United States
| | - Madeleine Eakman
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, United States
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, United States
| | - Jesse G. Zalatan
- Department of Chemistry, University of Washington, Seattle, WA, 98195, United States
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36
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Cheng X. Valproic Acid Thermally Destabilizes and Inhibits SpyCas9 Activity. Mol Ther 2020; 28:2635-2641. [PMID: 32882179 DOI: 10.1016/j.ymthe.2020.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/24/2020] [Accepted: 08/19/2020] [Indexed: 01/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system plays an important role in prokaryotic adaptive immunity. Due to its capacity for sequence-specific gene editing, CRISPR-Cas9 has become one of the most important tools widely used for genome editing in molecular biotechnology. However, its clinical application is currently limited by unwanted mutations at off-target sites. Various strategies have been developed for precise control of Cas9 in order to reduce these off-target effects, including chemical-based approaches. From a chemical screening, I observed that valproic acid (VPA) binds to and destabilizes Streptococcus pyogenes Cas9 (SpyCas9) protein in vitro, as well as in cells, while within its therapeutical concentration range under conditions of hyperthermia as demonstrated. Conditions were generated either by an external heat bag or in combination with the photothermal therapeutic agent indocyanine green activated by a near-infrared laser. Use of other histone deacetylase inhibitors failed, suggesting a histone deacetylase inhibition-independent function of VPA. Thus, this finding provides an uncomplicated thermotherapeutical approach for timely regulation of the activity of the CRISPR-Cas9 system at desired locations.
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Affiliation(s)
- Xinlai Cheng
- Buchmann Institute for Molecular Life Sciences, Pharmaceutical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany; Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
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37
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The AssemblX Toolkit for Reliable and User-Friendly Multigene Assemblies. Methods Mol Biol 2020. [PMID: 32809192 DOI: 10.1007/978-1-0716-0908-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The implementation of complex cloning projects covering the assembly of entire biological pathways or large genetic circuits poses a major challenge in the field of biotechnology and synthetic biology, as such projects can be costly and time-consuming. To overcome these difficulties, we developed the software-assisted AssemblX toolkit, which allows even unexperienced users to design, build, and subsequently test large DNA constructs. Currently, AssemblX allows the assembly of up to 25 functional units (e.g., genes), from 75 or more subunits (e.g., promoters, coding sequences, terminators). At the first assembly level, AssemblX uses overlap-based, scar-free, and sequence-independent cloning methods. This allows the unrestricted design at the gene level without the need for laborious parts domestication. The standardized, polymerase chain reaction-free, and virtually sequence-independent assembly into multigene modules relies on rare cutting homing endonucleases and computationally optimized overlap sequences. Selection and marker switching strategies ensure an effective process, and the assembly product can be transferred to any desired expression host.
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38
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Abstract
Oligonucleotides can be used to modulate gene expression via a range of processes including RNAi, target degradation by RNase H-mediated cleavage, splicing modulation, non-coding RNA inhibition, gene activation and programmed gene editing. As such, these molecules have potential therapeutic applications for myriad indications, with several oligonucleotide drugs recently gaining approval. However, despite recent technological advances, achieving efficient oligonucleotide delivery, particularly to extrahepatic tissues, remains a major translational limitation. Here, we provide an overview of oligonucleotide-based drug platforms, focusing on key approaches - including chemical modification, bioconjugation and the use of nanocarriers - which aim to address the delivery challenge.
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Breunig CT, Köferle A, Neuner AM, Wiesbeck MF, Baumann V, Stricker SH. CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing. Physiol Rev 2020; 101:177-211. [PMID: 32525760 DOI: 10.1152/physrev.00034.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Given the large amount of genome-wide data that have been collected during the last decades, a good understanding of how and why cells change during development, homeostasis, and disease might be expected. Unfortunately, the opposite is true; triggers that cause cellular state changes remain elusive, and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret, and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools, namely, activation and/or repression of master transcription factors in their endogenous chromatin context; targeting transcription factors to endogenous, alternative, or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.
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Affiliation(s)
- Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Andrea M Neuner
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Maximilian F Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
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Abstract
Gene expression control based on CRISPRi (clustered regularly interspaced short palindromic repeats interference) has emerged as a powerful tool for creating synthetic gene circuits, both in prokaryotes and in eukaryotes; yet, its lack of cooperativity has been pointed out as a potential obstacle for dynamic or multistable synthetic circuit construction. Here we use CRISPRi to build a synthetic oscillator (“CRISPRlator”), bistable network (toggle switch) and stripe pattern-forming incoherent feed-forward loop (IFFL). Our circuit designs, conceived to feature high predictability and orthogonality, as well as low metabolic burden and context-dependency, allow us to achieve robust circuit behaviors in Escherichia coli populations. Mathematical modeling suggests that unspecific binding in CRISPRi is essential to establish multistability. Our work demonstrates the wide applicability of CRISPRi in synthetic circuits and paves the way for future efforts towards engineering more complex synthetic networks, boosted by the advantages of CRISPR technology. Synthetic circuits based on CRISPRi have not achieved multistable and dynamic behaviors. Here the authors build an oscillator, a toggle switch and an incoherent feed-forward loop using CRISPRi, and provide a mathematical model suggesting that unspecific binding in CRISPRi enables multistability.
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41
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Huang X, Chen Z, Liu Y. RNAi-mediated control of CRISPR functions. Theranostics 2020; 10:6661-6673. [PMID: 32550896 PMCID: PMC7295050 DOI: 10.7150/thno.44880] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas9 has become a versatile tool for genome editing and regulation, and strategies to effectively control its activity have attracted much attention. RNAi, also a gene-regulating tool, is used as another mechanism by which eukaryotes resist the invasion of foreign genetic material. Methods: In this study, we analyzed the quantitative inhibition of the CRISPR system by using artificial miRNAs (amiRNAs) combined with the RNAi enhancer enoxacin to improve the targeting specificity of the CRISPR system. Furthermore, we examined the feasibility of improving the efficiency of gene editing and regulation by blocking the effects of natural intracellular miRNAs on sgRNAs. Results: amiRNAs targeting the sgRNA were used to control its expression, and the small molecule drug denoxacin was utilized to enhance this effect, especially in the presence of Cas9. amiRNA/enoxacin inhibited CRISPR-mediated gene editing and regulation both in vitro and in vivo and could tune sgRNA-targeting specificity. Furthermore, CRISPR efficiency was increased by blocking the effects of endogenous miRNAs. Conclusion: Our study provides an efficient molecular switch for conditional regulation of CRISPR activities in mammalian cells and also presents potentially useful approaches for solving current key issues of off-target effects and low targeting efficiency.
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Affiliation(s)
- Xinbo Huang
- National and Local Joint Engineering Laboratory of Medical Synthetic Biology, Shenzhen, Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen518035, China
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health, Science Center, Shenzhen 518035, China
| | - Zhicong Chen
- National and Local Joint Engineering Laboratory of Medical Synthetic Biology, Shenzhen, Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen518035, China
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health, Science Center, Shenzhen 518035, China
| | - Yuchen Liu
- National and Local Joint Engineering Laboratory of Medical Synthetic Biology, Shenzhen, Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen518035, China
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen518035, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health, Science Center, Shenzhen 518035, China
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Fontana J, Dong C, Kiattisewee C, Chavali VP, Tickman BI, Carothers JM, Zalatan JG. Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements. Nat Commun 2020; 11:1618. [PMID: 32238808 PMCID: PMC7113249 DOI: 10.1038/s41467-020-15454-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 03/04/2020] [Indexed: 11/09/2022] Open
Abstract
In bacterial systems, CRISPR-Cas transcriptional activation (CRISPRa) has the potential to dramatically expand our ability to regulate gene expression, but we lack predictive rules for designing effective gRNA target sites. Here, we identify multiple features of bacterial promoters that impose stringent requirements on CRISPRa target sites. Notably, we observe narrow, 2-4 base windows of effective sites with a periodicity corresponding to one helical turn of DNA, spanning ~40 bases and centered ~80 bases upstream of the TSS. However, we also identify two features suggesting the potential for broad scope: CRISPRa is effective at a broad range of σ70-family promoters, and an expanded PAM dCas9 allows the activation of promoters that cannot be activated by S. pyogenes dCas9. These results provide a roadmap for future engineering efforts to further expand and generalize the scope of bacterial CRISPRa.
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Affiliation(s)
- Jason Fontana
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA
| | - Chen Dong
- Department of Chemistry, University of Washington, Seattle, 98195, WA, USA
| | - Cholpisit Kiattisewee
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA
| | - Venkata P Chavali
- Department of Chemical Engineering, University of Washington, Seattle, 98195, WA, USA
| | - Benjamin I Tickman
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA
| | - James M Carothers
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, 98195, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, 98195, WA, USA.
- Center for Synthetic Biology, University of Washington, Seattle, 98195, WA, USA.
| | - Jesse G Zalatan
- Department of Chemistry, University of Washington, Seattle, 98195, WA, USA.
- Department of Chemical Engineering, University of Washington, Seattle, 98195, WA, USA.
- Center for Synthetic Biology, University of Washington, Seattle, 98195, WA, USA.
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43
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Krawczyk K, Scheller L, Kim H, Fussenegger M. Rewiring of endogenous signaling pathways to genomic targets for therapeutic cell reprogramming. Nat Commun 2020; 11:608. [PMID: 32001704 PMCID: PMC6992713 DOI: 10.1038/s41467-020-14397-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022] Open
Abstract
Rewiring cellular sensors to trigger non-natural responses is fundamental for therapeutic cell engineering. Current designs rely on engineered receptors that are limited to single inputs, and often suffer from high leakiness and low fold induction. Here, we present Generalized Engineered Activation Regulators (GEARs) that overcome these limitations by being pathway-specific rather than input-specific. GEARs consist of the MS2 bacteriophage coat protein fused to regulatory or transactivation domains, and work by rerouting activation of the NFAT, NFκB, MAPK or SMAD pathways to dCas9-directed gene expression from genomic loci. This system enables membrane depolarization-induced activation of insulin expression in β-mimetic cells and IL-12 expression in activated Jurkat cells, as well as IL-12 production in response to the immunomodulatory cytokines TGFβ and TNFα in HEK293T cells. Engineered cells with the ability to reinterpret the extracellular milieu have potential for applications in immunotherapy and in the treatment of metabolic diseases.
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Affiliation(s)
- Krzysztof Krawczyk
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Leo Scheller
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Hyojin Kim
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland.
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland.
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44
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Li H, Yang Y, Hong W, Huang M, Wu M, Zhao X. Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduct Target Ther 2020; 5:1. [PMID: 32296011 PMCID: PMC6946647 DOI: 10.1038/s41392-019-0089-y] [Citation(s) in RCA: 908] [Impact Index Per Article: 227.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 09/21/2019] [Accepted: 09/21/2019] [Indexed: 02/06/2023] Open
Abstract
Based on engineered or bacterial nucleases, the development of genome editing technologies has opened up the possibility of directly targeting and modifying genomic sequences in almost all eukaryotic cells. Genome editing has extended our ability to elucidate the contribution of genetics to disease by promoting the creation of more accurate cellular and animal models of pathological processes and has begun to show extraordinary potential in a variety of fields, ranging from basic research to applied biotechnology and biomedical research. Recent progress in developing programmable nucleases, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas-associated nucleases, has greatly expedited the progress of gene editing from concept to clinical practice. Here, we review recent advances of the three major genome editing technologies (ZFNs, TALENs, and CRISPR/Cas9) and discuss the applications of their derivative reagents as gene editing tools in various human diseases and potential future therapies, focusing on eukaryotic cells and animal models. Finally, we provide an overview of the clinical trials applying genome editing platforms for disease treatment and some of the challenges in the implementation of this technology.
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Affiliation(s)
- Hongyi Li
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Yang Yang
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Weiqi Hong
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P. R. China
| | - Mengyuan Huang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, Chengdu, Sichuan, 610041, P. R. China
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA.
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, 610041, P. R. China.
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45
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Higashikuni Y, Lu TK. Advancing CRISPR-Based Programmable Platforms beyond Genome Editing in Mammalian Cells. ACS Synth Biol 2019; 8:2607-2619. [PMID: 31751114 DOI: 10.1021/acssynbio.9b00297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human diseases are caused by dysregulation of cellular biological programs that are encoded in DNA. Unveiling the endogenous programs and encoding new programs into the genome are key to creating novel diagnostic and therapeutic strategies. CRISPR/Cas9, originally identified in bacteria, has revolutionized genome editing in mammalian cells. Recent advances in CRISPR technologies have provided new programmable platforms for modifying cell function and behavior. CRISPR-based transcriptional regulators and modified gRNAs have enabled multiplexed regulation and visualization of genome dynamics with spatiotemporal precision. Using these toolkits, genome-scale screening platforms can identify key genetic elements or combinations thereof that modulate phenotypes in mammalian cells. In addition, imaging platforms for multiplexed genomic labeling have been created to study the conformation and dynamics of chromatin in living cells, which are essential for genome function. Furthermore, CRISPR-based computation and memory platforms have been built in living mammalian cells by using DNA as a data processing and storage medium to regulate and monitor cellular behaviors. The conditional regulation of CRISPR-based parts has enabled the design of complex multilayered biological programs. CRISPR-based memory platforms can continuously record biological events as mutations in defined DNA loci. By making use of base editors, CRISPR-based computation and memory platforms have been interconnected to perform logic operations based on past events. These technologies open up new avenues for understanding biological phenomena and designing mammalian cells as living machines for biomedical applications.
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46
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Synthetic biology for improving cell fate decisions and tissue engineering outcomes. Emerg Top Life Sci 2019; 3:631-643. [PMID: 33523179 DOI: 10.1042/etls20190091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Synthetic biology is a relatively new field of science that combines aspects of biology and engineering to create novel tools for the construction of biological systems. Using tools within synthetic biology, stem cells can then be reprogrammed and differentiated into a specified cell type. Stem cells have already proven to be largely beneficial in many different therapies and have paved the way for tissue engineering and regenerative medicine. Although scientists have made great strides in tissue engineering, there still remain many questions to be answered in regard to regeneration. Presented here is an overview of synthetic biology, common tools built within synthetic biology, and the way these tools are being used in stem cells. Specifically, this review focuses on how synthetic biologists engineer genetic circuits to dynamically control gene expression while also introducing emerging topics such as genome engineering and synthetic transcription factors. The findings mentioned in this review show the diverse use of stem cells within synthetic biology and provide a foundation for future research in tissue engineering with the use of synthetic biology tools. Overall, the work done using synthetic biology in stem cells is in its early stages, however, this early work is leading to new approaches for repairing diseased and damaged tissues and organs, and further expanding the field of tissue engineering.
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Geller SH, Antwi EB, Di Ventura B, McClean MN. Optogenetic Repressors of Gene Expression in Yeasts Using Light-Controlled Nuclear Localization. Cell Mol Bioeng 2019; 12:511-528. [PMID: 31719930 PMCID: PMC6816687 DOI: 10.1007/s12195-019-00598-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 09/03/2019] [Indexed: 01/30/2023] Open
Abstract
INTRODUCTION Controlling gene expression is a fundamental goal of basic and synthetic biology because it allows insight into cellular function and control of cellular activity. We explored the possibility of generating an optogenetic repressor of gene expression in the model organism Saccharomyces cerevisiae by using light to control the nuclear localization of nuclease-dead Cas9, dCas9. METHODS The dCas9 protein acts as a repressor for a gene of interest when localized to the nucleus in the presence of an appropriate guide RNA (sgRNA). We engineered dCas9, the mammalian transcriptional repressor Mxi1, and an optogenetic tool to control nuclear localization (LINuS) as parts in an existing yeast optogenetic toolkit. This allowed expression cassettes containing novel dCas9 repressor configurations and guide RNAs to be rapidly constructed and integrated into yeast. RESULTS Our library of repressors displays a range of basal repression without the need for inducers or promoter modification. Populations of cells containing these repressors can be combined to generate a heterogeneous population of yeast with a 100-fold expression range. We find that repression can be dialed modestly in a light dose- and intensity-dependent manner. We used this library to repress expression of the lanosterol 14-alpha-demethylase Erg11, generating yeast with a range of sensitivity to the important antifungal drug fluconazole. CONCLUSIONS This toolkit will be useful for spatiotemporal perturbation of gene expression in Saccharomyces cerevisiae. Additionally, we believe that the simplicity of our scheme will allow these repressors to be easily modified to control gene expression in medically relevant fungi, such as pathogenic yeasts.
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Affiliation(s)
- Stephanie H. Geller
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, WI 53706 USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, 1525 Linden Dr., Madison, WI 53706 USA
| | - Enoch B. Antwi
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), 69120 Heidelberg, Germany
| | - Barbara Di Ventura
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, WI 53706 USA
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48
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Bartley BA, Choi K, Samineni M, Zundel Z, Nguyen T, Myers CJ, Sauro HM. pySBOL: A Python Package for Genetic Design Automation and Standardization. ACS Synth Biol 2019; 8:1515-1518. [PMID: 30424601 DOI: 10.1021/acssynbio.8b00336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This paper presents pySBOL, a software library for computer-aided design of synthetic biological systems in the Python scripting language. This library provides an easy-to-use, object-oriented, application programming interface (API) with low barrier of entry for synthetic biology application developers. The pySBOL library enables reuse of genetic parts and designs through standardized data exchange with biological parts repositories and software tools that communicate using the Synthetic Biology Open Language (SBOL). In addition, pySBOL supports data management of design-build-test-learn workflows for individual laboratories as well as large, distributed teams of synthetic biologists. PySBOL also lets users add custom data to SBOL files to support the specific data requirements of their research. This extensibility helps users integrate software tool chains and develop workflows for new applications. These features and others make the pySBOL library a valuable tool for supporting engineering practices in synthetic biology. Documentation and installation instructions can be found at pysbol2.readthedocs.io .
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Affiliation(s)
- Bryan A. Bartley
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Kiri Choi
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
| | - Meher Samineni
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zach Zundel
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Tramy Nguyen
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Chris J. Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, Utah 84112, United States
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
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49
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Beal J, Overney C, Adler A, Yaman F, Tiberio L, Samineni M. TASBE Flow Analytics: A Package for Calibrated Flow Cytometry Analysis. ACS Synth Biol 2019; 8:1524-1529. [PMID: 31053031 DOI: 10.1021/acssynbio.8b00533] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Flow cytometry is a powerful method for high-throughput precision measurement of cell fluorescence and size. Effective use of this tool for quantification of synthetic biology devices and circuits, however, generally requires careful application of complex multistage workflows for calibration, filtering, and analysis with appropriate statistics. The TASBE Flow Analytics package provides a free, open, and accessible implementation of such workflows in a form designed for high-throughput analysis of large synthetic biology data sets. Given a set of experimental samples and controls, this package can process them to output calibrated data, quantitative analyses and comparisons, automatically generated figures, and detailed debugging and diagnostic reports in both human-readable and machine-readable forms. TASBE Flow Analytics can be used through a simple user-friendly interactive Excel interface, as a library supporting Matlab, Octave, or Python interactive sessions, or as a component integrated into automated workflows.
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Affiliation(s)
- Jacob Beal
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Cassandra Overney
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
- Olin College, Needham, Massachusetts 02492, United States
| | - Aaron Adler
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Fusun Yaman
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Lisa Tiberio
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
| | - Meher Samineni
- Raytheon BBN Technologies, Cambridge, Massachusetts 02138, United States
- University of Utah, Salt Lake City, Utah 84112, United States
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50
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Tewary M, Shakiba N, Zandstra PW. Stem cell bioengineering: building from stem cell biology. Nat Rev Genet 2019; 19:595-614. [PMID: 30089805 DOI: 10.1038/s41576-018-0040-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
New fundamental discoveries in stem cell biology have yielded potentially transformative regenerative therapeutics. However, widespread implementation of stem-cell-derived therapeutics remains sporadic. Barriers that impede the development of these therapeutics can be linked to our incomplete understanding of how the regulatory networks that encode stem cell fate govern the development of the complex tissues and organs that are ultimately required for restorative function. Bioengineering tools, strategies and design principles represent core components of the stem cell bioengineering toolbox. Applied to the different layers of complexity present in stem-cell-derived systems - from gene regulatory networks in single stem cells to the systemic interactions of stem-cell-derived organs and tissues - stem cell bioengineering can address existing challenges and advance regenerative medicine and cellular therapies.
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada.,Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada
| | - Peter W Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME) and The Donnelly Centre for Cellular and Biomolecular Research (CCBR), University of Toronto, Toronto, Ontario, Canada. .,Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada. .,Michael Smith Laboratories and School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
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