1
|
Hu SW, Lv J, Wang Z, Tang H, Wang H, Wang F, Wang D, Zhang J, Zhang L, Cao Q, Chen Y, Gao Z, Han Y, Wang W, Li GL, Shu Y, Li H. Engineering of the AAV-Compatible Hair Cell-Specific Small-Size Myo15 Promoter for Gene Therapy in the Inner Ear. RESEARCH (WASHINGTON, D.C.) 2024; 7:0341. [PMID: 38665848 PMCID: PMC11045262 DOI: 10.34133/research.0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/21/2024] [Indexed: 04/28/2024]
Abstract
Adeno-associated virus (AAV)-mediated gene therapy is widely applied to treat numerous hereditary diseases in animal models and humans. The specific expression of AAV-delivered transgenes driven by cell type-specific promoters should further increase the safety of gene therapy. However, current methods for screening cell type-specific promoters are labor-intensive and time-consuming. Herein, we designed a "multiple vectors in one AAV" strategy for promoter construction in vivo. Through this strategy, we truncated a native promoter for Myo15 expression in hair cells (HCs) in the inner ear, from 1,611 bp down to 1,157 bp, and further down to 956 bp. Under the control of these 2 promoters, green fluorescent protein packaged in AAV-PHP.eB was exclusively expressed in the HCs. The transcription initiation ability of the 2 promoters was further verified by intein-mediated otoferlin recombination in a dual-AAV therapeutic system. Driven by these 2 promoters, human otoferlin was selectively expressed in HCs, resulting in the restoration of hearing in treated Otof -/- mice for at least 52 weeks. In summary, we developed an efficient screening strategy for cell type-specific promoter engineering and created 2 truncated Myo15 promoters that not only restored hereditary deafness in animal models but also show great potential for treating human patients in future.
Collapse
Affiliation(s)
- Shao Wei Hu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Jun Lv
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Zijing Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Honghai Tang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Hui Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Fang Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Daqi Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Juan Zhang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Longlong Zhang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Qi Cao
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yuxin Chen
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Ziwen Gao
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yu Han
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Wuqing Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Geng-lin Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yilai Shu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Huawei Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| |
Collapse
|
2
|
Park S, Kim M, Lee JW. Optimizing Nucleic Acid Delivery Systems through Barcode Technology. ACS Synth Biol 2024; 13:1006-1018. [PMID: 38526308 DOI: 10.1021/acssynbio.3c00602] [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: 03/26/2024]
Abstract
Conventional biological experiments often focus on in vitro assays because of the inherent limitations when handling multiple variables in vivo, including labor-intensive and time-consuming procedures. Often only a subset of samples demonstrating significant efficacy in the in vitro assays can be evaluated in vivo. Nonetheless, because of the low correlation between the in vitro and in vivo tests, evaluation of the variables under examination in vivo and not solely in vitro is critical. An emerging approach to achieve high-throughput in vivo tests involves using a barcode system consisting of various nucleotide combinations. Unique barcodes for each variant enable the simultaneous testing of multiple entities, eliminating the need for separate individual tests. Subsequently, to identify crucial parameters, samples were collected and analyzed using barcode sequencing. This review explores the development of barcode design and its applications, including the evaluation of nucleic acid delivery systems and the optimization of gene expression in vivo.
Collapse
Affiliation(s)
- Soan Park
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
| | - Mibang Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 CheongamRo, Gyeongbuk, 37673 NamGu, Pohang, Republic of Korea
| |
Collapse
|
3
|
Sands C, Hedin KA, Vazquez-Uribe R, Sommer MOA. Saccharomyces boulardii promoters for control of gene expression in vivo. Microb Cell Fact 2024; 23:16. [PMID: 38185666 PMCID: PMC10771652 DOI: 10.1186/s12934-023-02288-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Interest in the use of engineered microbes to deliver therapeutic activities has increased in recent years. The probiotic yeast Saccharomyces boulardii has been investigated for production of therapeutics in the gastrointestinal tract. Well-characterised promoters are a prerequisite for robust therapeutic expression in the gut; however, S. boulardii promoters have not yet been thoroughly characterised in vitro and in vivo. RESULTS We present a thorough characterisation of the expression activities of 12 S. boulardii promoters in vitro in glucose, fructose, sucrose, inulin and acetate, under both aerobic and anaerobic conditions, as well as in the murine gastrointestinal tract. Green fluorescent protein was used to report on promoter activity. Promoter expression was found to be carbon-source dependent, with inulin emerging as a favourable carbon source. Furthermore, relative promoter expression in vivo was highly correlated with expression in sucrose (R = 0.99). CONCLUSIONS These findings provide insights into S. boulardii promoter activity and aid in promoter selection in future studies utilising S. boulardii to produce therapeutics in the gut.
Collapse
Affiliation(s)
- Carmen Sands
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| | - Morten Otto Alexander Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| |
Collapse
|
4
|
Rilievo G, Cecconello A, Fouladi Ghareshiran N, Magro M, Simmel FC, Vianello F. Integration of DNA-RNA-triplex-based regulation of transcription into molecular logic gates. FEBS Lett 2023; 597:2461-2472. [PMID: 37591635 DOI: 10.1002/1873-3468.14721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
In recent years, increasing numbers of noncoding RNA molecules were identified as possible components of endogenous DNA-RNA hybrid triplexes involved in gene regulation. Triplexes are potentially involved in complex molecular signaling networks that, if understood, would allow the engineering of biological computing components. Here, by making use of the enhancing and inhibiting effects of such triplexes, we demonstrate in vitro the construction of triplex-based molecular gates: 'exclusive OR' (XOR), 'exclusive NOT-OR' (XNOR), and a threshold gate, via transcription of a fluorogenic RNA aptamer. Precise modulation was displayed by the biomolecular-integrated systems over a wide interval of transcriptional outputs, ranging from drastic inhibition to significant enhancement. The present contribution represents a first example of molecular gates developed using DNA-RNA triplex nanostructures.
Collapse
Affiliation(s)
- Graziano Rilievo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Alessandro Cecconello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | | | - Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Friedrich C Simmel
- Physik Department, Technische Universitat München, Garching bei München, Germany
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| |
Collapse
|
5
|
Litteral V, Migliozzi R, Metzger D, McPherson C, Saldanha R. Engineering a Cortisol Sensing Enteric Probiotic. ACS Biomater Sci Eng 2023; 9:5163-5175. [PMID: 37647169 DOI: 10.1021/acsbiomaterials.2c01300] [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: 09/01/2023]
Abstract
Chronic stress can lead to prolonged adrenal gland secretion of cortisol, resulting in human ailments such as anxiety, post-traumatic stress disorder, metabolic syndrome, diabetes, immunosuppression, and cardiomyopathy. Real time monitoring of chronic increases in cortisol and intervening therapies to minimize the physiological effects of stress would be beneficial to prevent these endocrine related illnesses. Gut microbiota have shown the ability to secrete, respond, and even regulate endocrine hormones. One such microbe, Clostridium scindens, responds transcriptionally to cortisol. We engineered these cortisol responsive genetic elements from C. scindens into an enteric probiotic, E. coli Nissle 1917, to drive the expression of a fluorescent reporter allowing for the designing, testing, and building of a robust and physiologically relevant novel cortisol probiotic sensor. This smart probiotic was further engineered to be more sensitive and to respond to elevated cortisol by expressing tryptophan decarboxylase, thereby bestowing the ability to generate tryptamine and serotonin. Here we show that upon cortisol treatment the smart probiotic produces measurable amounts of tryptamine. Accumulated levels of these neuromodulators should improve mood, anxiety, and depression and drive down cortisol levels. Importantly, this work can serve as a model for the engineering of a sense-and-respond probiotic to modulate the gut-brain axis.
Collapse
Affiliation(s)
- Vaughn Litteral
- UES Corporation, 4401 Dayton-Xenia Avenue, Beavercreek, Ohio 45432-1805, United States
- Air Force Research Laboratory, 711 Human Performance Wing, Airman Bioengineering Division, Applied Biotechnology Branch, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Rebecca Migliozzi
- UES Corporation, 4401 Dayton-Xenia Avenue, Beavercreek, Ohio 45432-1805, United States
- Air Force Research Laboratory, 711 Human Performance Wing, Airman Bioengineering Division, Applied Biotechnology Branch, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - David Metzger
- UES Corporation, 4401 Dayton-Xenia Avenue, Beavercreek, Ohio 45432-1805, United States
- Air Force Research Laboratory, 711 Human Performance Wing, Airman Bioengineering Division, Applied Biotechnology Branch, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Craig McPherson
- UES Corporation, 4401 Dayton-Xenia Avenue, Beavercreek, Ohio 45432-1805, United States
- Air Force Research Laboratory, 711 Human Performance Wing, Airman Bioengineering Division, Applied Biotechnology Branch, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Roland Saldanha
- Air Force Research Laboratory, 711 Human Performance Wing, Airman Bioengineering Division, Applied Biotechnology Branch, Wright-Patterson Air Force Base, Ohio 45433, United States
| |
Collapse
|
6
|
Etter EL, Heavey MK, Errington M, Nguyen J. Microbe-loaded bioink designed to support therapeutic yeast growth. Biomater Sci 2023; 11:5262-5273. [PMID: 37341642 PMCID: PMC10529830 DOI: 10.1039/d3bm00514c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Live biotherapeutic products (LBPs) are an emerging class of therapeutics comprised of engineered living organisms such as bacteria or yeast. Bioprinting with living materials has now become possible using modern three-dimensional (3D) printing strategies. While there has been significant progress in bioprinting cells, bioprinting LBPs, specifically yeast, remains in its infancy and has not been optimized. Yeasts are a promising platform to develop into protein biofactories because they (1) grow rapidly, (2) are easy to engineer and manufacture, and (3) are inexpensive to produce. Here we developed an optimized method for loading yeast into hydrogel patches using digital light processing (DLP) 3D printing. We assessed the effects of patch geometry, bioink composition, and yeast concentration on yeast viability, patch stability, and protein release, and in doing so developed a patch formulation capable of supporting yeast growth and sustained protein release for at least ten days.
Collapse
Affiliation(s)
- Emma L Etter
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27599, USA, Raleigh, NC, 27695, USA.
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mairead K Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Errington
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juliane Nguyen
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27599, USA, Raleigh, NC, 27695, USA.
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
7
|
van ‘t Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA. High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinformatics 2022; 23:566. [PMID: 36585633 PMCID: PMC9801561 DOI: 10.1186/s12859-022-05108-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To aid in future engineering efforts, our aim was to construct an updated metabolic model of EcN with extended secondary metabolite representation. RESULTS An updated high-quality genome-scale metabolic model of EcN, iHM1533, was developed based on comparison with 55 E. coli/Shigella reference GEMs and manual curation, including expanded secondary metabolite pathways (enterobactin, salmochelins, aerobactin, yersiniabactin, and colibactin). The model was validated and improved using phenotype microarray data, resulting in an 82.3% accuracy in predicting growth phenotypes on various nutrition sources. Flux variability analysis with previously published 13C fluxomics data validated prediction of the internal central carbon fluxes. A standardised test suite called Memote assessed the quality of iHM1533 to have an overall score of 89%. The model was applied by using constraint-based flux analysis to predict targets for optimisation of secondary metabolite production. Modelling predicted design targets from across amino acid metabolism, carbon metabolism, and other subsystems that are common or unique for influencing the production of various secondary metabolites. CONCLUSION iHM1533 represents a well-annotated metabolic model of EcN with extended secondary metabolite representation. Phenotype characterisation and the iHM1533 model provide a better understanding of the metabolic capabilities of EcN and will help future metabolic engineering efforts.
Collapse
Affiliation(s)
- Max van ‘t Hof
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Omkar S. Mohite
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Tilmann Weber
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Bernhard O. Palsson
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Morten O. A. Sommer
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| |
Collapse
|
8
|
Robinson CM, Short NE, Riglar DT. Achieving spatially precise diagnosis and therapy in the mammalian gut using synthetic microbial gene circuits. Front Bioeng Biotechnol 2022; 10:959441. [PMID: 36118573 PMCID: PMC9478464 DOI: 10.3389/fbioe.2022.959441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian gut and its microbiome form a temporally dynamic and spatially heterogeneous environment. The inaccessibility of the gut and the spatially restricted nature of many gut diseases translate into difficulties in diagnosis and therapy for which novel tools are needed. Engineered bacterial whole-cell biosensors and therapeutics have shown early promise at addressing these challenges. Natural and engineered sensing systems can be repurposed in synthetic genetic circuits to detect spatially specific biomarkers during health and disease. Heat, light, and magnetic signals can also activate gene circuit function with externally directed spatial precision. The resulting engineered bacteria can report on conditions in situ within the complex gut environment or produce biotherapeutics that specifically target host or microbiome activity. Here, we review the current approaches to engineering spatial precision for in vivo bacterial diagnostics and therapeutics using synthetic circuits, and the challenges and opportunities this technology presents.
Collapse
|
9
|
Heavey MK, Durmusoglu D, Crook N, Anselmo AC. Discovery and delivery strategies for engineered live biotherapeutic products. Trends Biotechnol 2022; 40:354-369. [PMID: 34481657 PMCID: PMC8831446 DOI: 10.1016/j.tibtech.2021.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
Genetically engineered microbes that secrete therapeutics, sense and respond to external environments, and/or target specific sites in the gut fall under an emergent class of therapeutics, called live biotherapeutic products (LBPs). As live organisms that require symbiotic host interactions, LBPs offer unique therapeutic opportunities, but also face distinct challenges in the gut microenvironment. In this review, we describe recent approaches (often demonstrated using traditional probiotic microorganisms) to discover LBP chassis and genetic parts utilizing omics-based methods and highlight LBP delivery strategies, with a focus on addressing physiological challenges that LBPs encounter after oral administration. Finally, we share our perspective on the opportunity to apply an integrated approach, wherein discovery and delivery strategies are utilized synergistically, towards tailoring and optimizing LBP efficacy.
Collapse
Affiliation(s)
- Mairead K. Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Aaron C. Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Correspondence: (A.C. Anselmo), (N. Crook)
| |
Collapse
|
10
|
Al'Abri IS, Haller DJ, Li Z, Crook N. Inducible directed evolution of complex phenotypes in bacteria. Nucleic Acids Res 2022; 50:e58. [PMID: 35150576 PMCID: PMC9177967 DOI: 10.1093/nar/gkac094] [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: 03/09/2021] [Revised: 12/22/2021] [Accepted: 02/01/2022] [Indexed: 11/15/2022] Open
Abstract
Directed evolution is a powerful method for engineering biology in the absence of detailed sequence-function relationships. To enable directed evolution of complex phenotypes encoded by multigene pathways, we require large library sizes for DNA sequences >5–10 kb in length, elimination of genomic hitchhiker mutations, and decoupling of diversification and screening steps. To meet these challenges, we developed Inducible Directed Evolution (IDE), which uses a temperate bacteriophage to package large plasmids and transfer them to naive cells after intracellular mutagenesis. To demonstrate IDE, we evolved a 5-gene pathway from Bacillus licheniformis that accelerates tagatose catabolism in Escherichia coli, resulting in clones with 65% shorter lag times during growth on tagatose after only two rounds of evolution. Next, we evolved a 15.4 kb, 10-gene pathway from Bifidobacterium breve UC2003 that aids E. coli’s utilization of melezitose. After three rounds of IDE, we isolated evolved pathways that both reduced lag time by more than 2-fold and enabled 150% higher final optical density. Taken together, this work enhances the capacity and utility of a whole pathway directed evolution approach in E. coli.
Collapse
Affiliation(s)
- Ibrahim S Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Daniel J Haller
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
11
|
Kwak S, Mahmud B, Dantas G. A Tunable and Expandable Transactivation System in Probiotic Yeast Saccharomyces boulardii. ACS Synth Biol 2022; 11:508-514. [PMID: 34939781 PMCID: PMC9013468 DOI: 10.1021/acssynbio.1c00384] [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: 01/23/2023]
Abstract
Precise transcriptional modulation is a key requirement for developing synthetic probiotics with predictably tunable functionalities. In this study, an expandable and tunable transactivation system was constructed and validated in probiotic yeast Saccharomyces boulardii. The use of nuclease-null Cas9 and scaffold RNA (scRNA) directed regulation enabled transactivation under the control of a synthetic promoter in S. boulardii. A synthetic promoter consisting of the scRNA target sequence and the core GAL7 promoter region restricted interference from the native galactose regulon. The system was readily expanded by introducing new target sequences to the promoter and scRNA. Complementarity between the promoter and scRNA, and binding specificity between scRNA and transcriptional activator, served as two layers of orthogonality of the transactivation. In addition, activator expression under the control of an inducible promoter enabled control of the transactivation via chemical inducer. The described system has the potential to enable engineering of probiotic yeast to more precisely perform therapeutic functions.
Collapse
Affiliation(s)
- Suryang Kwak
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA, 63110
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA, 63110
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA, 63130,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Corresponding author (after review): G.D. ()
| |
Collapse
|
12
|
Armetta J, Schantz-Klausen M, Shepelin D, Vazquez-Uribe R, Bahl MI, Laursen MF, Licht TR, Sommer MO. Escherichia coli Promoters with Consistent Expression throughout the Murine Gut. ACS Synth Biol 2021; 10:3359-3368. [PMID: 34842418 DOI: 10.1021/acssynbio.1c00325] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Advanced microbial therapeutics have great potential as a novel modality to diagnose and treat a wide range of diseases. Yet, to realize this potential, robust parts for regulating gene expression and consequent therapeutic activity in situ are needed. In this study, we characterized the expression level of more than 8000 variants of the Escherichia coli sigma factor 70 (σ70) promoter in a range of different environmental conditions and growth states using fluorescence-activated cell sorting and deep sequencing. Sampled conditions include aerobic and anaerobic culture in the laboratory as well as growth in several locations of the murine gastrointestinal tract. We found that σ70 promoters in E. coli generally maintain consistent expression levels across the murine gut (R2: 0.55-0.85, p value < 1 × 10-5), suggesting a limited environmental influence but a higher variability between in vitro and in vivo expression levels, highlighting the challenges of translating in vitro promoter activity to in vivo applications. Based on these data, we design the Schantzetta library, composed of eight promoters spanning a wide expression range and displaying a high degree of robustness in both laboratory and in vivo conditions (R2 = 0.98, p = 0.000827). This study provides a systematic assessment of the σ70 promoter activity in E. coli as it transits the murine gut leading to the definition of robust expression cassettes that could be a valuable tool for reliable engineering and development of advanced microbial therapeutics.
Collapse
Affiliation(s)
- Jeremy Armetta
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Michael Schantz-Klausen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Denis Shepelin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | | | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Morten O.A. Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
| |
Collapse
|
13
|
Design and in situ biosynthesis of precision therapies against gastrointestinal pathogens. CURRENT OPINION IN PHYSIOLOGY 2021. [DOI: 10.1016/j.cophys.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
14
|
Durmusoglu D, Al’Abri IS, Collins SP, Cheng J, Eroglu A, Beisel CL, Crook N. In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii. ACS Synth Biol 2021; 10:1039-1052. [PMID: 33843197 DOI: 10.1021/acssynbio.0c00562] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Saccharomyces boulardii is a probiotic yeast that exhibits rapid growth at 37 °C, is easy to transform, and can produce therapeutic proteins in the gut. To establish its ability to produce small molecules encoded by multigene pathways, we measured the amount and variance in protein expression enabled by promoters, terminators, selective markers, and copy number control elements. We next demonstrated efficient (>95%) CRISPR-mediated genome editing in this strain, allowing us to probe engineered gene expression across different genomic sites. We leveraged these strategies to assemble pathways enabling a wide range of vitamin precursor (β-carotene) and drug (violacein) titers. We found that S. boulardii colonizes germ-free mice stably for over 30 days and competes for niche space with commensal microbes, exhibiting short (1-2 day) gut residence times in conventional and antibiotic-treated mice. Using these tools, we enabled β-carotene synthesis (194 μg total) in the germ-free mouse gut over 14 days, estimating that the total mass of additional β-carotene recovered in feces was 56-fold higher than the β-carotene present in the initial probiotic dose. This work quantifies heterologous small molecule production titers by S. boulardii living in the mammalian gut and provides a set of tools for modulating these titers.
Collapse
Affiliation(s)
- Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ibrahim S. Al’Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Scott P. Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Junrui Cheng
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Room 3204, Kannapolis, North Carolina 28081, United States
| | - Abdulkerim Eroglu
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Room 3204, Kannapolis, North Carolina 28081, United States
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, 120 Broughton Drive, Room 351, Raleigh, North Carolina 27695-7622, United States
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg 97080, Germany
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
15
|
Grandel NE, Reyes Gamas K, Bennett MR. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol 2021; 29:1095-1105. [PMID: 33966922 DOI: 10.1016/j.tim.2021.04.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/02/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity.
Collapse
Affiliation(s)
- Nicolas E Grandel
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Kiara Reyes Gamas
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA.
| |
Collapse
|