1
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Jin WY, Guo JX, Tang R, Wang J, Zhao H, Zhang M, Teng LZ, Sansonetti PJ, Gao YZ. In vivo detection of endogenous toxic phenolic compounds of intestine. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135526. [PMID: 39153300 DOI: 10.1016/j.jhazmat.2024.135526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/31/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Phenol and p-cresol are two common toxic small molecules related to various diseases. Existing reports confirmed that high L-tyrosine in the daily diet can increase the concentration of phenolic compounds in blood and urine. L-tyrosine is a common component of protein-rich foods. Some anaerobic bacteria in the gut can convert non-toxic l-tyrosine into these two toxic phenolic compounds, phenol and p-cresol. Existing methods have been constructed for measuring the concentration of phenolic compound in feces. However, there is still a lack of direct visual evidence to measure the phenolic compounds in the intestine. In this study, we aimed to construct a whole-cell biosensor for phenolic compounds detection based on the dmpR, the regulator from the phenol metabolism cluster. The commensal bacterium Citrobacter amalonaticus PS01 was selected and used as the chassis. Compared with the biosensor based on ECN1917, the biosensor PS01[dmpR] could better implant into the mouse gut through gavage and showed a higher sensitive to phenolic compound. And the concentration of phenolic compounds in the intestines could be observed with the help of in vivo imaging system using PS01[dmpR]. This paper demonstrated endogenous phenol synthesis in the gut and the strategy of using commensal bacteria to construct whole-cell biosensors for detecting small molecule compounds in the intestines.
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Affiliation(s)
- Wen-Yu Jin
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Guo
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rongkang Tang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jielin Wang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huan Zhao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng Zhang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; Pasteurian College, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215123, China
| | - Lin-Zuo Teng
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Philippe J Sansonetti
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Université de Paris, Paris, France.
| | - Yi-Zhou Gao
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Li Z, Lu X, Zhang Z, Yan S, Yang Y. Rapid Fingerprinting of Urinary Volatile Metabolites and Point-of-Care Diagnosis of Phenylketonuria on a Patterned Nanorod Sensor Array with Multiplexed Surface-Enhanced Raman Scattering Readouts. Anal Chem 2024; 96:14541-14549. [PMID: 39206680 DOI: 10.1021/acs.analchem.4c02822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Phenylketonuria (PKU) is one of the most common genetic metabolic diseases, especially among newborns. Traditional clinical examination of newborn blood samples for PKU is invasive, laborious, and limited to hospitals and healthcare facilities. We reported herein a SERS-based sensor array with three thiophenolic nanoreceptors built on a patterned nanorod vertical array for rapid and inexpensive detection of characteristic volatile biomarkers indicative of PKU in the urine and accurate classification of newborn baby patients all performed on a hand-held SERS spectrophotometer. The well-ordered array was generated from the volatility-driven assembly of gold nanorods (AuNRs) into an upright and closely packed hexagonal configuration. The uniformly distributed nanowells between AuNRs offered an intense and aspect-ratio-dependent plasmonic field for the molecular enhancement of SERS outputs. The SERS-based detector was integrated into a test chip for regular monitoring of volatile phenylketone bodies in the spiked solution or patients' urine within 5 min, allowing the quantification of a wide variety of normal or abnormal metabolites at their physiologically relevant concentration range. The detection limits for common biomarkers of PKU, including phenylpyruvic acid, 4-hydroxyphenylacetic acid, and phenylacetic acid, were at a few μM and well below the diagnostic thresholds. Moreover, the volatile headspace mixtures from a given urine sample could be fingerprinted by the sensor array and discriminated using machine-learning algorithms. Ultimately, the discrimination of baby patients among 26 cases of mild and classic PKU phenotypes and 17 cases of healthy volunteers could be realized with an overall accuracy of 97%. This hand-held SERS platform plays a pivotal role in advancing healthcare applications in quick screening of neonatal PKU through a facile urinary vapor test.
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Affiliation(s)
- Zheng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, P.R. China
| | - Xiaohui Lu
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, P.R. China
| | - Zhiyang Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Shandong Key Laboratory of Coastal Environmental Processes, Shandong Research Center for Coastal Environmental Engineering and Technology, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, P.R. China
| | - Shuoyang Yan
- School of Materials Science and Engineering, University of Jinan, Jinan 250022, P.R. China
| | - Yunli Yang
- Clinical Study and Evidence Based Medicine Institute, Gansu Provincial People's Hospital, Lanzhou 730000, P.R. China
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3
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Weibel N, Curcio M, Schreiber A, Arriaga G, Mausy M, Mehdy J, Brüllmann L, Meyer A, Roth L, Flury T, Pecina V, Starlinger K, Dernič J, Jungfer K, Ackle F, Earp J, Hausmann M, Jinek M, Rogler G, Antunes Westmann C. Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases. ACS Synth Biol 2024; 13:2376-2390. [PMID: 39115381 PMCID: PMC11334186 DOI: 10.1021/acssynbio.4c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 06/13/2024] [Accepted: 07/25/2024] [Indexed: 08/17/2024]
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation with no cure and limited treatment options that often have systemic side effects. In this study, we developed a target-specific system to potentially treat IBD by engineering the probiotic bacterium Escherichia coli Nissle 1917 (EcN). Our modular system comprises three components: a transcription factor-based sensor (NorR) capable of detecting the inflammation biomarker nitric oxide (NO), a type 1 hemolysin secretion system, and a therapeutic cargo consisting of a library of humanized anti-TNFα nanobodies. Despite a reduction in sensitivity, our system demonstrated a concentration-dependent response to NO, successfully secreting functional nanobodies with binding affinities comparable to the commonly used drug Adalimumab, as confirmed by enzyme-linked immunosorbent assay and in vitro assays. This newly validated nanobody library expands EcN therapeutic capabilities. The adopted secretion system, also characterized for the first time in EcN, can be further adapted as a platform for screening and purifying proteins of interest. Additionally, we provided a mathematical framework to assess critical parameters in engineering probiotic systems, including the production and diffusion of relevant molecules, bacterial colonization rates, and particle interactions. This integrated approach expands the synthetic biology toolbox for EcN-based therapies, providing novel parts, circuits, and a model for tunable responses at inflammatory hotspots.
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Affiliation(s)
- Nathalie Weibel
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Martina Curcio
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Atilla Schreiber
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Gabriel Arriaga
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Marine Mausy
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jana Mehdy
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lea Brüllmann
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Meyer
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Len Roth
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Tamara Flury
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Valerie Pecina
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Kim Starlinger
- University
of Zürich, Campus Irchel Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jan Dernič
- Institute
of Pharmacology and Toxicology, University
of Zürich, Winterthurerstrasse
190, CH-8057 Zürich, Switzerland
| | - Kenny Jungfer
- Department
of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Ackle
- Institute
of Medical Microbiology, University of Zürich, Gloriastrasse 28/30, CH-8006 Zürich, Switzerland
| | - Jennifer Earp
- Institute
of Medical Microbiology, University of Zürich, Gloriastrasse 28/30, CH-8006 Zürich, Switzerland
| | - Martin Hausmann
- Department
of Gastroenterology and Hepatology, University
Hospital Zürich and Zürich University, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Martin Jinek
- Department
of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gerhard Rogler
- Department
of Gastroenterology and Hepatology, University
Hospital Zürich and Zürich University, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Cauã Antunes Westmann
- Department
of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
- Swiss
Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015 Lausanne, Switzerland
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4
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Yang J, Ge S, Tan S, Liu H, Yang M, Liu W, Zhang K, Zhang Z, Liu J, Shi J, Wang ZH, Li J. Modified montmorillonite armed probiotics with enhanced on-site mucus-depleted intestinal colonization and H 2S scavenging for colitis treatment. J Control Release 2024; 374:140-153. [PMID: 39117113 DOI: 10.1016/j.jconrel.2024.07.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/08/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]
Abstract
Inflammatory bowel diseases (IBD) are often associated with dysregulated gut microbiota and excessive inflammatory microenvironment. Probiotic therapy combined with inflammation management is a promising approach to alleviate IBD, but the efficacy is hindered by the inferior colonization of probiotics in mucus-depleted inflammatory bowel segments. Here, we present modified montmorillonite armed probiotic Escherichia coli Nissle 1917 (MMT-Fe@EcN) with enhanced intestinal colonization and hydrogen sulfide (H2S) scavenging for synergistic alleviation of IBD. The montmorillonite layer that can protect EcN against environmental assaults in oral delivery and improve on-site colonization of EcN in the mucus-depleted intestinal segment due to its strong adhesive capability and electronegativity, with a 22.6-fold increase in colonization efficiency compared to EcN. Meanwhile, MMT-Fe@EcN can manage inflammation by scavenging H2S, which allows for enhancing probiotic viability and colonization for restoring the gut microbiota. As a result, MMT-Fe@EcN exhibits extraordinary therapeutic effects in the dextran sulfate sodium-induced mouse colitis models, including alleviating intestinal inflammation and restoring disrupted intestinal barrier function, and gut microbiota. These findings provide a promising strategy for clinical IBD treatment and potentially other mucus-depletion-related diseases.
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Affiliation(s)
- Jiali Yang
- Institute of Brain Science and Disease, School of Basic Medicine, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders, Qingdao University, Qingdao 266021, PR China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Shengchan Ge
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Shaochong Tan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Hua Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Mingzhu Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Wei Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Junjie Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China.
| | - Zhi-Hao Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, PR China.
| | - Jitian Li
- Henan Luoyang Orthopedic Hospital (Henan Provincial Orthopedic Hospital), 100 Yongping Road, Zhengzhou 450000, China.
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5
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Zheng B, Li M, Zhang T, Li B, Li Q, Saiding Q, Chen W, Guo M, Koo S, Ji X, Tao W. Functional modification of gut bacteria for disease diagnosis and treatment. MED 2024; 5:863-885. [PMID: 38964334 DOI: 10.1016/j.medj.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/15/2023] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
Intestinal bacteria help keep humans healthy by regulating lipid and glucose metabolism as well as the immunological and neurological systems. Oral treatment using intestinal bacteria is limited by the high acidity of stomach fluids and the immune system's attack on foreign bacteria. Scientists have created coatings and workarounds to overcome these limitations and improve bacterial therapy. These preparations have demonstrated promising outcomes, with advances in synthetic biology and optogenetics improving their focused colonization and controlled release. Engineering bacteria preparations have become a revolutionary therapeutic approach that converts intestinal bacteria into cellular factories for medicinal chemical synthesis. The present paper discusses various aspects of engineering bacteria preparations, including wrapping materials, biomedical uses, and future developments.
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Affiliation(s)
- Bin Zheng
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Mengyi Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Tiange Zhang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Bowen Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Qiuya Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Qimanguli Saiding
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mingming Guo
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Chemical and Molecular Engineering, Hanyang University ERICA, Ansan, Gyeonggi-do 15588, Republic of Korea.
| | - Xiaoyuan Ji
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China.
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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6
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Ke Z, Ma Q, Ye X, Wang Y, Jin Y, Zhao X, Su Z. Peptide GLP-1 receptor agonists: From injection to oral delivery strategies. Biochem Pharmacol 2024; 229:116471. [PMID: 39127152 DOI: 10.1016/j.bcp.2024.116471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/20/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Peptide glucagon-like peptide-1 receptor agonists (GLP-1RAs) are effective drugs for treating type 2 diabetes (T2DM) and have been proven to benefit the heart and kidney. Apart from oral semaglutide, which does not require injection, other peptide GLP-1RAs need to be subcutaneously administered. However, oral semaglutide also faces significant challenges, such as low bioavailability and frequent gastrointestinal discomfort. Thus, it is imperative that advanced oral strategies for peptide GLP-1RAs need to be explored. This review mainly compares the current advantages and disadvantages of various oral delivery strategies for peptide GLP-1RAs in the developmental stage and discusses the latest research progress of peptide GLP-1RAs, providing a useful guide for the development of new oral peptide GLP-1RA drugs.
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Affiliation(s)
- Zhiqiang Ke
- Protein Engineering and Biopharmaceuticals Science, Hubei University of Technology, Wuhan 430068, China; Hubei Key Laboratory of Diabetes and Angiopathy, National Demonstration Center for Experimental General Medicine Education, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei 437100, China
| | - Qianqian Ma
- Protein Engineering and Biopharmaceuticals Science, Hubei University of Technology, Wuhan 430068, China; School of Pharmaceutical Sciences and Institute of Materia Medica, Xinjiang University, Urumqi 830017, China
| | - Xiaonan Ye
- Protein Engineering and Biopharmaceuticals Science, Hubei University of Technology, Wuhan 430068, China
| | - Yanlin Wang
- Protein Engineering and Biopharmaceuticals Science, Hubei University of Technology, Wuhan 430068, China
| | - Yan Jin
- Protein Engineering and Biopharmaceuticals Science, Hubei University of Technology, Wuhan 430068, China
| | - Xinyuan Zhao
- Hubei Key Laboratory of Diabetes and Angiopathy, National Demonstration Center for Experimental General Medicine Education, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei 437100, China.
| | - Zhengding Su
- Protein Engineering and Biopharmaceuticals Science, Hubei University of Technology, Wuhan 430068, China; School of Pharmaceutical Sciences and Institute of Materia Medica, Xinjiang University, Urumqi 830017, China.
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7
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Radde N, Mortensen GA, Bhat D, Shah S, Clements JJ, Leonard SP, McGuffie MJ, Mishler DM, Barrick JE. Measuring the burden of hundreds of BioBricks defines an evolutionary limit on constructability in synthetic biology. Nat Commun 2024; 15:6242. [PMID: 39048554 PMCID: PMC11269670 DOI: 10.1038/s41467-024-50639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
Engineered DNA will slow the growth of a host cell if it redirects limiting resources or otherwise interferes with homeostasis. Escape mutants that alleviate this burden can rapidly evolve and take over cell populations, making genetic engineering less reliable and predictable. Synthetic biologists often use genetic parts encoded on plasmids, but their burden is rarely characterized. We measured how 301 BioBrick plasmids affected Escherichia coli growth and found that 59 (19.6%) were burdensome, primarily because they depleted the limited gene expression resources of host cells. Overall, no BioBricks reduced the growth rate of E. coli by >45%, which agreed with a population genetic model that predicts such plasmids should be unclonable. We made this model available online for education ( https://barricklab.org/burden-model ) and added our burden measurements to the iGEM Registry. Our results establish a fundamental limit on what DNA constructs and genetic modifications can be successfully engineered into cells.
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Affiliation(s)
- Noor Radde
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Genevieve A Mortensen
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Diya Bhat
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Shireen Shah
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Joseph J Clements
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Sean P Leonard
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Matthew J McGuffie
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Dennis M Mishler
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
- The Freshman Research Initiative, College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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8
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Won C, Yim SS. Emerging methylation-based approaches in microbiome engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:96. [PMID: 38987811 PMCID: PMC11238421 DOI: 10.1186/s13068-024-02529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.
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Affiliation(s)
- Changhee Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Sun Yim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
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9
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Sancho-Alonso M, Sarriés-Serrano U, Miquel-Rio L, Yanes Castilla C, Paz V, Meana JJ, Perello M, Bortolozzi A. New insights into the effects of serotonin on Parkinson's disease and depression through its role in the gastrointestinal tract. SPANISH JOURNAL OF PSYCHIATRY AND MENTAL HEALTH 2024:S2950-2853(24)00039-5. [PMID: 38992345 DOI: 10.1016/j.sjpmh.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/12/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
Neuropsychiatric and neurodegenerative disorders are frequently associated with gastrointestinal (GI) co-pathologies. Although the central and enteric nervous systems (CNS and ENS, respectively) have been studied separately, there is increasing interest in factors that may contribute to conditions affecting both systems. There is compelling evidence that serotonin (5-HT) may play an important role in several gut-brain disorders. It is well known that 5-HT is essential for the development and functioning of the CNS. However, most of the body's 5-HT is produced in the GI tract. A deeper understanding of the specific effects of enteric 5-HT on gut-brain disorders may provide the basis for the development of new therapeutic targets. This review summarizes current data focusing on the important role of 5-HT in ENS development and motility, with particular emphasis on novel aspects of 5-HT signaling in conditions where CNS and ENS comorbidities are common, such as Parkinson's disease and depressive disorders.
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Affiliation(s)
- María Sancho-Alonso
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain; Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain; Anatomy and Human Embryology Department, Faculty of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Unai Sarriés-Serrano
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain; Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain; University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain
| | - Lluis Miquel-Rio
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain; Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - Claudia Yanes Castilla
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain
| | - Verónica Paz
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain; Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
| | - José Javier Meana
- Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain; University of the Basque Country UPV/EHU, E-48940 Leioa, Bizkaia, Spain; Biobizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - Mario Perello
- Grupo de Neurofisiología, Instituto Multidisciplinario de Biología Celular (IMBICE), Universidad Nacional La Plata (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA), La Plata, Argentina
| | - Analia Bortolozzi
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), 08036 Barcelona, Spain; Systems Neuropharmacology Research Group, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain; Biomedical Research Networking Center for Mental Health (CIBERSAM), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain.
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10
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Siguenza N, Brevi A, Zhang JT, Pabani A, Bhushan A, Das M, Ding Y, Hasty J, Ghosh P, Zarrinpar A. Engineered bacterial therapeutics for detecting and treating CRC. Trends Cancer 2024; 10:588-597. [PMID: 38693003 DOI: 10.1016/j.trecan.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024]
Abstract
Despite an overall decrease in occurrence, colorectal cancer (CRC) remains the third most common cause of cancer deaths in the USA. Detection of CRC is difficult in high-risk groups, including those with genetic predispositions, with disease traits, or from certain demographics. There is emerging interest in using engineered bacteria to identify early CRC development, monitor changes in the adenoma and CRC microenvironment, and prevent cancer progression. Novel genetic circuits for cancer therapeutics or functions to enhance existing treatment modalities have been tested and verified in vitro and in vivo. Inclusion of biocontainment measures would prepare strains to meet therapeutic standards. Thus, engineered bacteria present an opportunity for detection and treatment of CRC lesions in a highly sensitive and specific manner.
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Affiliation(s)
- Nicole Siguenza
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Arianna Brevi
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Joanna T Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Arman Pabani
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Abhinav Bhushan
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA; Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Amir Zarrinpar
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA; Jennifer Moreno Department of Veterans Affairs, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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11
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Parthasarathy G, Malhi H, Bajaj JS. Therapeutic manipulation of the microbiome in liver disease. Hepatology 2024:01515467-990000000-00932. [PMID: 38922826 DOI: 10.1097/hep.0000000000000987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Myriad associations between the microbiome and various facets of liver physiology and pathology have been described in the literature. Building on descriptive and correlative sequencing studies, metagenomic studies are expanding our collective understanding of the functional and mechanistic role of the microbiome as mediators of the gut-liver axis. Based on these mechanisms, the functional activity of the microbiome represents an attractive, tractable, and precision medicine therapeutic target in several liver diseases. Indeed, several therapeutics have been used in liver disease even before their description as a microbiome-dependent approach. To bring successful microbiome-targeted and microbiome-inspired therapies to the clinic, a comprehensive appreciation of the different approaches to influence, collaborate with, or engineer the gut microbiome to coopt a disease-relevant function of interest in the right patient is key. Herein, we describe the various levels at which the microbiome can be targeted-from prebiotics, probiotics, synbiotics, and antibiotics to microbiome reconstitution and precision microbiome engineering. Assimilating data from preclinical animal models, human studies as well as clinical trials, we describe the potential for and rationale behind studying such therapies across several liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cirrhosis, HE as well as liver cancer. Lastly, we discuss lessons learned from previous attempts at developing such therapies, the regulatory framework that needs to be navigated, and the challenges that remain.
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Affiliation(s)
| | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
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12
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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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13
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Durmusoglu D, Haller DJ, Al'Abri IS, Day K, Sands C, Clark A, San-Miguel A, Vazquez-Uribe R, Sommer MOA, Crook NC. Programming Probiotics: Diet-Responsive Gene Expression and Colonization Control in Engineered S. boulardii. ACS Synth Biol 2024; 13:1851-1865. [PMID: 38787439 DOI: 10.1021/acssynbio.4c00145] [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: 05/25/2024]
Abstract
Saccharomyces boulardii (Sb) is an emerging probiotic chassis for delivering biomolecules to the mammalian gut, offering unique advantages as the only eukaryotic probiotic. However, precise control over gene expression and gut residence time in Sb have remained challenging. To address this, we developed five ligand-responsive gene expression systems and repaired galactose metabolism in Sb, enabling inducible gene expression in this strain. Engineering these systems allowed us to construct AND logic gates, control the surface display of proteins, and turn on protein production in the mouse gut in response to dietary sugar. Additionally, repairing galactose metabolism expanded Sb's habitat within the intestines and resulted in galactose-responsive control over gut residence time. This work opens new avenues for precise dosing of therapeutics by Sb via control over its in vivo gene expression levels and localization within the gastrointestinal tract.
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Affiliation(s)
- Deniz Durmusoglu
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Daniel J Haller
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ibrahim S Al'Abri
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Katie Day
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Carmen Sands
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andrew Clark
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Adriana San-Miguel
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nathan C Crook
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
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14
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Galvan S, Teixeira AP, Fussenegger M. Enhancing cell-based therapies with synthetic gene circuits responsive to molecular stimuli. Biotechnol Bioeng 2024. [PMID: 38867466 DOI: 10.1002/bit.28770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/21/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024]
Abstract
Synthetic biology aims to contribute to the development of next-generation patient-specific cell-based therapies for chronic diseases especially through the construction of sophisticated synthetic gene switches to enhance the safety and spatiotemporal controllability of engineered cells. Indeed, switches that sense and process specific cues, which may be either externally administered triggers or endogenous disease-associated molecules, have emerged as powerful tools for programming and fine-tuning therapeutic outputs. Living engineered cells, often referred to as designer cells, incorporating such switches are delivered to patients either as encapsulated cell implants or by infusion, as in the case of the clinically approved CAR-T cell therapies. Here, we review recent developments in synthetic gene switches responsive to molecular stimuli, spanning regulatory mechanisms acting at the transcriptional, translational, and posttranslational levels. We also discuss current challenges facing clinical translation of cell-based therapies employing these devices.
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Affiliation(s)
- Silvia Galvan
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana P Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
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15
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Payne S, Wick S, Carr PA, Guido NJ. A Methodology for the Assessment and Prioritization of Genetic Biocontainment Technologies for Engineered Microbes. APPLIED BIOSAFETY 2024; 29:108-119. [PMID: 39144101 PMCID: PMC11319856 DOI: 10.1089/apb.2023.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Introduction Organisms engineered with synthetic genes and genomes have the potential to play critical roles to address important issues in the environment, human health, and manufacturing. Engineered genetic biocontainment technologies are needed to manage the risks of unintended consequences when deploying these biological systems in consultation with the biosafety and biosecurity communities. Metrics measuring genetic biocontainment and a methodology to apply them are required to determine which genetic biocontainment technologies warrant further development for real-world applications. In this study, we develop and apply a systems analysis of the current technical landscape using expert opinion and a metric-based scoring system resulting in a semiquantitative comparative assessment of genetic biocontainment technologies in microorganisms. Methods Genetic biocontainment technologies were evaluated according to multiple metrics, falling into two broad classes: feasibility and applicability. Specific genetic biocontainment example scenarios and generalized categories were scored with these metrics. Gap analysis was carried out, indicating particular areas where genetic biocontainment can be improved. Results Metric analysis scoring of feasibility and applicability enabled prioritization of genetic biocontainment technologies for real-world applications. Gap analysis showed that technology readiness and containment stability scored low for a number of scenarios and categories, indicating a general need for further development before they can be ready for deployment. Conclusion Developing an assessment framework with defined metrics produced a straightforward system for evaluating genetic biocontainment strategies intended for various real-world applications. Use of the methodology also provided insights into existing gaps in genetic biocontainment strategies, and by altering the metrics, can be applied to other biotechnologies.
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Affiliation(s)
- Stephen Payne
- MIT Lincoln Laboratory, Lexington, Massachusetts, USA
| | - Scott Wick
- MIT Lincoln Laboratory, Lexington, Massachusetts, USA
| | - Peter A. Carr
- MIT Lincoln Laboratory, Lexington, Massachusetts, USA
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16
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Geng F, Wu M, Yang P, Li X, Pan X, Wang Y, Lü J. Engineered probiotic cocktail with two cascade metabolic Escherichia coli for the treatment of hyperlysinemia. Front Microbiol 2024; 15:1366017. [PMID: 38873158 PMCID: PMC11169572 DOI: 10.3389/fmicb.2024.1366017] [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: 01/05/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Engineering probiotics have emerged as a potential strategy for the treatment of metabolic diseases. However, due to the exceptional complexity of these metabolic disorders and the intricate relationship between gut microbes, it is difficult to achieve an ideal therapeutic effect in a specific metabolic disorder using only a single engineered strain. In this work, we proposed a probiotic cocktail strategy by engineering two cascade metabolic bacteria to treat hyperlysinemia, an inherited lysine metabolic disorder with loss of α-aminoadipate semialdehyde synthase (AASS) activity. A probiotic E. coli Nissle 1917 strain EcNT (pTLS) with a heterologous enzyme pathway in Saccharomyces cerevisiae was engineered to metabolize the excess lysine. Another one EcNT (pK25) was engineered to consume the products of lysine metabolism. The bacterial cocktail enables the maintenance of a metabolic cascade with AASS-like functional activity to maintain the blood lysine concentrations and downstream metabolites. In vitro experimental results showed that the cocktail bacteria had a better metabolic capacity and metabolites balance at a ratio of EcNT (pTLS) and EcNT (pK25) of 1:2. Feeding of the cocktail bacteria to the mouse model effectively reduced the concentration of lysine and balanced saccharopine in the plasma of hyperlysinemia-like mice. These findings not only provide a promising strategy of probiotic stains for the treatment of hyperlysinemia but also highlight the potential of engineered cascade cocktails to intervene and even cure other inherited metabolic diseases.
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Affiliation(s)
- Feng Geng
- College of Pharmacy, Binzhou Medical University, Yantai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Mingyu Wu
- College of Pharmacy, Binzhou Medical University, Yantai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Pan Yang
- College of Pharmacy, Binzhou Medical University, Yantai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Xueling Li
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- College of Public Health, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xiaohong Pan
- College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yadi Wang
- College of Pharmacy, Binzhou Medical University, Yantai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Junhong Lü
- College of Pharmacy, Binzhou Medical University, Yantai, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
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17
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Delbreil P, Dhondt S, Kenaan El Rahbani RM, Banquy X, Mitchell JJ, Brambilla D. Current Advances and Material Innovations in the Search for Novel Treatments of Phenylketonuria. Adv Healthc Mater 2024:e2401353. [PMID: 38801163 DOI: 10.1002/adhm.202401353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/22/2024] [Indexed: 05/29/2024]
Abstract
Phenylketonuria (PKU) is a genetically inherited disease caused by a mutation of the gene encoding phenylalanine hydroxylase (PAH) and is the most common inborn error of amino acid metabolism. A deficiency of PAH leads to increased blood and brain levels of phenylalanine (Phe), which may cause permanent neurocognitive symptoms and developmental delays if untreated. Current management strategies for PKU consist of early detection through neonatal screening and implementation of a restrictive diet with minimal amounts of natural protein in combination with Phe-free supplements and low-protein foods to meet nutritional requirements. For milder forms of PKU, oral treatment with synthetic sapropterin (BH4), the cofactor of PAH, may improve metabolic control of Phe and allow for more natural protein to be included in the patient's diet. For more severe forms, daily injections of pegvaliase, a PEGylated variant of phenylalanine ammonia-lyase (PAL), may allow for normalization of blood Phe levels. However, the latter treatment has considerable drawbacks, notably a strong immunogenicity of the exogenous enzyme and the attached polymeric chains. Research for novel therapies of PKU makes use of innovative materials for drug delivery and state-of-the-art protein engineering techniques to develop treatments which are safer, more effective, and potentially permanent.
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Affiliation(s)
- Philippe Delbreil
- Faculty of Pharmacy, Université de Montréal, Québec, H3T 1J4, Canada
| | - Sofie Dhondt
- Faculty of Pharmacy, Université de Montréal, Québec, H3T 1J4, Canada
| | | | - Xavier Banquy
- Faculty of Pharmacy, Université de Montréal, Québec, H3T 1J4, Canada
| | - John J Mitchell
- Department of Pediatrics, Faculty of Medicine and Health Sciences, McGill University, Québec, H4A 3J1, Canada
| | - Davide Brambilla
- Faculty of Pharmacy, Université de Montréal, Québec, H3T 1J4, Canada
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18
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Vazquez-Uribe R, Hedin KA, Licht TR, Nieuwdorp M, Sommer MOA. Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases. Trends Endocrinol Metab 2024:S1043-2760(24)00115-2. [PMID: 38782649 DOI: 10.1016/j.tem.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The rising prevalence of metabolic diseases calls for innovative treatments. Peptide-based drugs have transformed the management of conditions such as obesity and type 2 diabetes. Yet, challenges persist in oral delivery of these peptides. This review explores the potential of 'advanced microbiome therapeutics' (AMTs), which involve engineered microbes for delivery of peptides in situ, thereby enhancing their bioavailability. Preclinical work on AMTs has shown promise in treating animal models of metabolic diseases, including obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease. Outstanding challenges toward realizing the potential of AMTs involve improving peptide expression, ensuring predictable colonization control, enhancing stability, and managing safety and biocontainment concerns. Still, AMTs have potential for revolutionizing the treatment of metabolic diseases, potentially offering dynamic and personalized novel therapeutic approaches.
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Affiliation(s)
- Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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19
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Gao T, Niu L, Wu X, Dai D, Zhou Y, Liu M, Wu K, Yu Y, Guan N, Ye H. Sonogenetics-controlled synthetic designer cells for cancer therapy in tumor mouse models. Cell Rep Med 2024; 5:101513. [PMID: 38608697 PMCID: PMC11148564 DOI: 10.1016/j.xcrm.2024.101513] [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: 08/10/2023] [Revised: 02/21/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
Bacteria-based therapies are powerful strategies for cancer therapy, yet their clinical application is limited by a lack of tunable genetic switches to safely regulate the local expression and release of therapeutic cargoes. Rapid advances in remote-control technologies have enabled precise control of biological processes in time and space. We developed therapeutically active engineered bacteria mediated by a sono-activatable integrated gene circuit based on the thermosensitive transcriptional repressor TlpA39. Through promoter engineering and ribosome binding site screening, we achieved ultrasound (US)-induced protein expression and secretion in engineered bacteria with minimal noise and high induction efficiency. Specifically, delivered either intratumorally or intravenously, engineered bacteria colonizing tumors suppressed tumor growth through US-irradiation-induced release of the apoptotic protein azurin and an immune checkpoint inhibitor, a nanobody targeting programmed death-ligand 1, in different tumor mouse models. Beyond developing safe and high-performance designer bacteria for tumor therapy, our study illustrates a sonogenetics-controlled therapeutic platform that can be harnessed for bacteria-based precision medicine.
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Affiliation(s)
- Tian Gao
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Lingxue Niu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; The Radiology Department of Shanxi Provincial People's Hospital, The Fifth Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Di Dai
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China
| | - Mengyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ke Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Yuanhuan Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Ningzi Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China.
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Dongchuan Road 500, Shanghai 200241, China; Wuhu Hospital, Health Science Center, East China Normal University, Middle Jiuhua Road 263, Wuhu City, China.
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20
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Zhai L, Fu L, Wei W, Zheng D. Advances of Bacterial Biomaterials for Disease Therapy. ACS Synth Biol 2024; 13:1400-1411. [PMID: 38605650 DOI: 10.1021/acssynbio.4c00022] [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: 04/13/2024]
Abstract
Bacteria have immense potential as biological therapeutic agents that can be used to treat diseases, owing to their inherent immunomodulatory activity, targeting capabilities, and biosynthetic functions. The integration of synthetic biomaterials with natural bacteria has led to the construction of bacterial biomaterials with enhanced functionality and exceptional safety features. In this review, recent progress in the field of bacterial biomaterials, including bacterial drug delivery systems, bacterial drug-producing factories, bacterial biomaterials for metabolic engineering, bacterial biomaterials that can be remotely controlled, and living bacteria hydrogel formulations, is described and summarized. Furthermore, future trends in advancing next-generation bacterial biomaterials for enhanced clinical applications are proposed in the conclusion.
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Affiliation(s)
- Lin Zhai
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, PR China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Laiying Fu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, PR China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, PR China
- School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Diwei Zheng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing 100190, PR China
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21
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Chen H, Zhu Y, Zhang C, Hu L, Yang K. Engineered bacteria in tumor immunotherapy. Cancer Lett 2024; 589:216817. [PMID: 38492769 DOI: 10.1016/j.canlet.2024.216817] [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: 12/14/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
As the limitations of cancer immunotherapy become increasingly apparent, there is considerable anticipation regarding the utilization of biological tools to enhance treatment efficacy, particularly bacteria and their derivatives. Leveraging advances in genetic and synthetic biology technologies, engineered bacteria now play important roles far beyond those of conventional immunoregulatory agents, and they could function as tumor-targeting vehicles and in situ pharmaceutical factories. In recent years, these engineered bacteria play a role in almost every aspect of immunotherapy. It is nothing short of impressive to keep seeing different strain of bacteria modified in diverse ways for unique immunological enhancement. In this review, we have scrutinized the intricate interplay between the immune system and these engineered bacteria. These interactions generate strategies that can directly or indirectly optimize immunotherapy and even modulate the effects of combination therapies. Collectively, these engineered bacteria present a promising novel therapeutic strategy that promises to change the current landscape of immunotherapy.
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Affiliation(s)
- Hua Chen
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou, 215123, China
| | - Yinrui Zhu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou, 215123, China
| | - Chonghai Zhang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou, 215123, China
| | - Lin Hu
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou, 215123, China.
| | - Kai Yang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, 199 Renai Road, Suzhou, 215123, China.
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22
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Meng J, Liu S, Wu X. Engineered probiotics as live biotherapeutics for diagnosis and treatment of human diseases. Crit Rev Microbiol 2024; 50:300-314. [PMID: 36946080 DOI: 10.1080/1040841x.2023.2190392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 03/23/2023]
Abstract
The use of probiotics to regulate the intestinal microbiota to prevent and treat a large number of disorders and diseases has been an international research hotspot. Although conventional probiotics have a certain regulatory role in nutrient metabolism, inhibiting pathogens, inducing immune regulation, and maintaining intestinal epithelial barrier function, they are unable to treat certain diseases. In recent years, aided by the continuous development of synthetic biology, engineering probiotics with desired characteristics and functionalities to benefit human health has made significant progress. In this article, we summarise the mechanism of action of conventional probiotics and their limitations and highlight the latest developments in the design and construction of probiotics as living diagnostics and therapeutics for the detection and treatment of a series of diseases, including pathogen infections, cancer, intestinal inflammation, metabolic disorders, vaccine delivery, cognitive health, and fatty liver. Besides we discuss the concerns regarding engineered probiotics and corresponding countermeasures and outline the desired features in the future development of engineered live biotherapeutics.
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Affiliation(s)
- Jiao Meng
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
| | - Shufan Liu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology; College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xin Wu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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23
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Thöny B, Ng J, Kurian MA, Mills P, Martinez A. Mouse models for inherited monoamine neurotransmitter disorders. J Inherit Metab Dis 2024; 47:533-550. [PMID: 38168036 DOI: 10.1002/jimd.12710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/07/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
Several mouse models have been developed to study human defects of primary and secondary inherited monoamine neurotransmitter disorders (iMND). As the field continues to expand, current defects in corresponding mouse models include enzymes and a molecular co-chaperone involved in monoamine synthesis and metabolism (PAH, TH, PITX3, AADC, DBH, MAOA, DNAJC6), tetrahydrobiopterin (BH4) cofactor synthesis and recycling (adGTPCH1/DRD, arGTPCH1, PTPS, SR, DHPR), and vitamin B6 cofactor deficiency (ALDH7A1), as well as defective monoamine neurotransmitter packaging (VMAT1, VMAT2) and reuptake (DAT). No mouse models are available for human DNAJC12 co-chaperone and PNPO-B6 deficiencies, disorders associated with recessive variants that result in decreased stability and function of the aromatic amino acid hydroxylases and decreased neurotransmitter synthesis, respectively. More than one mutant mouse is available for some of these defects, which is invaluable as different variant-specific (knock-in) models may provide more insights into underlying mechanisms of disorders, while complete gene inactivation (knock-out) models often have limitations in terms of recapitulating complex human diseases. While these mouse models have common phenotypic traits also observed in patients, reflecting the defective homeostasis of the monoamine neurotransmitter pathways, they also present with disease-specific manifestations with toxic accumulation or deficiency of specific metabolites related to the specific gene affected. This review provides an overview of the currently available models and may give directions toward selecting existing models or generating new ones to investigate novel pathogenic mechanisms and precision therapies.
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Affiliation(s)
- Beat Thöny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zürich, Switzerland
| | - Joanne Ng
- Genetic Therapy Accelerator Centre, University College London, Queen Square Institute of Neurology, London, UK
| | - Manju A Kurian
- Zayed Centre for Research into Rare Disease in Children, GOS Institute of Child Health, University College London, London, UK
- Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Philippa Mills
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Aurora Martinez
- Department of Biomedicine and Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, Bergen, Norway
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24
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Zoghi S, Sadeghpour Heravi F, Nikniaz Z, Shirmohamadi M, Moaddab SY, Ebrahimzadeh Leylabadlo H. Gut microbiota and childhood malnutrition: Understanding the link and exploring therapeutic interventions. Eng Life Sci 2024; 24:2300070. [PMID: 38708416 PMCID: PMC11065333 DOI: 10.1002/elsc.202300070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 05/07/2024] Open
Abstract
Childhood malnutrition is a metabolic condition that affects the physical and mental well-being of children and leads to resultant disorders in maturity. The development of childhood malnutrition is influenced by a number of physiological and environmental factors including metabolic stress, infections, diet, genetic variables, and gut microbiota. The imbalanced gut microbiota is one of the main environmental risk factors that significantly influence host physiology and childhood malnutrition progression. In this review, we have evaluated the gut microbiota association with undernutrition and overnutrition in children, and then the quantitative and qualitative significance of gut dysbiosis in order to reveal the impact of gut microbiota modification using probiotics, prebiotics, synbiotics, postbiotics, fecal microbiota transplantation, and engineering biology methods as new therapeutic challenges in the management of disturbed energy homeostasis. Understanding the host-microbiota interaction and the remote regulation of other organs and pathways by gut microbiota can improve the effectiveness of new therapeutic approaches and mitigate the negative consequences of childhood malnutrition.
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Affiliation(s)
- Sevda Zoghi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | | | - Zeinab Nikniaz
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Masoud Shirmohamadi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Seyed Yaghoub Moaddab
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
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25
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Murali SK, Mansell TJ. Next generation probiotics: Engineering live biotherapeutics. Biotechnol Adv 2024; 72:108336. [PMID: 38432422 DOI: 10.1016/j.biotechadv.2024.108336] [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: 09/16/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.
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Affiliation(s)
- Sanjeeva Kumar Murali
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA.
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26
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Lubkowicz D, Hava DL, Lewis K, Isabella VM. Rational Engineering of Escherichia coli Nissle 1917 as Live Biotherapeutic to Degrade Uremic Toxin Precursors. ACS Synth Biol 2024; 13:1077-1084. [PMID: 38588591 DOI: 10.1021/acssynbio.3c00686] [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: 04/10/2024]
Abstract
Uremic toxins (UTs) are microbiota-derived metabolites that accelerate the progression of kidney damage in patients with chronic kidney disease (CKD). One of the major UTs involved in CKD progression is p-cresol-sulfate (PCS), derived from dietary l-tyrosine (l-Tyr). Here, we engineered a probiotic strain of Escherichia coli Nissle 1917, to convert l-Tyr to the nontoxic compound p-coumaric acid via tyrosine ammonia lyase (TAL). First, a small metagenomic library was assessed to identify the TAL with the greatest whole-cell activity. Second, accessory genes implicated in the import of l-Tyr and export of PCA were overexpressed to enhance l-Tyr degradation by 106% and 56%, respectively. Last, random mutagenesis coupled to a novel selection and screening strategy was developed that identified a TAL variant with a 25% increase in whole-cell activity. Taken together, the final strain exhibits a 183% improvement over initial whole-cell activity and provides a promising candidate to degrade l-Tyr mediated PCS accumulation.
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Affiliation(s)
- David Lubkowicz
- Synlogic Inc., Cambridge, Massachusetts 02142, United States
| | - David L Hava
- Synlogic Inc., Cambridge, Massachusetts 02142, United States
| | - Kim Lewis
- Northeastern University, Boston, Massachusetts 02115, United States
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27
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Su H, Zhang H, Wu J, Huang L, Zhang M, Xu W, Cao J, Liu W, Liu N, Jiang H, Gu X, Qian K. Fast Label-Free Metabolic Profile Recognition Identifies Phenylketonuria and Subtypes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305701. [PMID: 38348590 PMCID: PMC11022714 DOI: 10.1002/advs.202305701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/25/2024] [Indexed: 04/18/2024]
Abstract
Phenylketonuria (PKU) is the most common inherited metabolic disease in humans. Clinical screening of newborn heel blood samples for PKU is costly and time-consuming because it requires multiple procedures, like isotope labeling and derivatization, and PKU subtype identification requires an additional urine sample. Delayed diagnosis of PKU, or subtype identification can result in mental disability. Here, plasmonic silver nanoshells are used for laser desorption/ionization mass spectrometry (MS) detection of PKU with label-free assay by recognizing metabolic profile in dried blood spot (DBS) samples. A total of 1100 subjects are recruited and each DBS sample can be processed in seconds. This platform achieves PKU screening with a sensitivity of 0.985 and specificity of 0.995, which is comparable to existing clinical liquid chromatography MS (LC-MS) methods. This method can process 360 samples per hour, compared with the LC-MS method which processes only 30 samples per hour. Moreover, this assay enables precise identification of PKU subtypes without the need for a urine sample. It is demonstrated that this platform enables high-performance and fast, low-cost PKU screening and subtype identification. This approach might be suitable for the detection of other clinically relevant biomarkers in blood or other clinical samples.
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Affiliation(s)
- Haiyang Su
- Henan Key Laboratory of Rare DiseasesEndocrinology and Metabolism CenterThe First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and TechnologyLuoyang471003P. R. China
- State Key Laboratory of Systems Medicine for CancerSchool of Biomedical EngineeringInstitute of Medical Robotics and Shanghai Academy of Experimental MedicineShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Huiwen Zhang
- Xinhua HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200092P. R. China
| | - Jiao Wu
- State Key Laboratory of Systems Medicine for CancerSchool of Biomedical EngineeringInstitute of Medical Robotics and Shanghai Academy of Experimental MedicineShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Lin Huang
- Country Department of Clinical Laboratory MedicineShanghai Chest HospitalShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Mengji Zhang
- State Key Laboratory of Systems Medicine for CancerSchool of Biomedical EngineeringInstitute of Medical Robotics and Shanghai Academy of Experimental MedicineShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Wei Xu
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai200127P. R. China
| | - Jing Cao
- State Key Laboratory of Systems Medicine for CancerSchool of Biomedical EngineeringInstitute of Medical Robotics and Shanghai Academy of Experimental MedicineShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Wanshan Liu
- Xinhua HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200092P. R. China
| | - Ning Liu
- School of Electronics Information and Electrical EngineeringShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Hongwei Jiang
- Henan Key Laboratory of Rare DiseasesEndocrinology and Metabolism CenterThe First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and TechnologyLuoyang471003P. R. China
| | - Xuefan Gu
- Xinhua HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200092P. R. China
| | - Kun Qian
- State Key Laboratory of Systems Medicine for CancerSchool of Biomedical EngineeringInstitute of Medical Robotics and Shanghai Academy of Experimental MedicineShanghai Jiao Tong UniversityShanghai200030P. R. China
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28
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Wang X, Kang L, Kong D, Wu X, Zhou Y, Yu G, Dai D, Ye H. A programmable protease-based protein secretion platform for therapeutic applications. Nat Chem Biol 2024; 20:432-442. [PMID: 37872400 DOI: 10.1038/s41589-023-01433-z] [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: 01/19/2023] [Accepted: 09/02/2023] [Indexed: 10/25/2023]
Abstract
Cell-based therapies represent potent enabling technologies in biomedical science. However, current genetic control systems for engineered-cell therapies are predominantly based on the transcription or translation of therapeutic outputs. Here we report a protease-based rapid protein secretion system (PASS) that regulates the secretion of pretranslated proteins retained in the endoplasmic reticulum (ER) owing to an ER-retrieval signal. Upon cleavage by inducible proteases, these proteins are secreted. Three PASS variants (chemPASS, antigenPASS and optoPASS) are developed. With chemPASS, we demonstrate the reversal of hyperglycemia in diabetic mice within minutes via drug-induced insulin secretion. AntigenPASS-equipped cells recognize the tumor antigen and secrete granzyme B and perforin, inducing targeted cell apoptosis. Finally, results from mouse models of diabetes, hypertension and inflammatory pain demonstrate light-induced, optoPASS-mediated therapeutic peptide secretion within minutes, conferring anticipated therapeutic benefits. PASS is a flexible platform for rapid delivery of therapeutic proteins that can facilitate the development and adoption of cell-based precision therapies.
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Affiliation(s)
- Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liping Kang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- Wuhu Hospital, Health Science Center, East China Normal University, Wuhu City, China
| | - Guiling Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Di Dai
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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29
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Barati M, Mosharkesh E, Tahmassian AH, Khodaei M, Jabbari M, Kalhori A, Alipour M, Ghavidel AA, Khalili-Moghadam S, Fathollahi A, Davoodi SH. Engineered Probiotics for the Management of Congenital Metabolic Diseases: A Systematic Review. Prev Nutr Food Sci 2024; 29:1-7. [PMID: 38576877 PMCID: PMC10987387 DOI: 10.3746/pnf.2024.29.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/29/2023] [Accepted: 12/29/2023] [Indexed: 04/06/2024] Open
Abstract
Engineered probiotics (EPs) can be used to treat/manage chronic and congenital diseases. However, to the best of our knowledge, no systematic review has evaluated the effects of EPs on congenital metabolic disorders in murine models and human subjects. Thus, the present study systematically reviewed interventional studies that assessed the effects of EPs on congenital metabolic disorders. PubMed, Web of Science, and Scopus databases were searched up to February 2023 to retrieve related publications. Seventy-six articles were obtained in the primary step. After screening the titles/abstracts based on the inclusion and exclusion criteria, 11 papers were included. Finally, only seven articles were included after performing full-text evaluation. The included articles evaluated the effects of EPs on managing phenylketonuria (PKU, n=4) and hyperammonemia (n=3). Moreover, these studies examined mice and/or rats (n=6), monkeys (n=1), and humans (n=2). Studies on EPs and hyperammonemia revealed that some wild strains such as Lactobacillus plantarum have an innate ammonia-hyper-consuming potential; thus, there was no need to manipulate them. However, manipulation is needed to obtain a phenylalanine-metabolizing strain. In conclusion, EPs can be used to manage or treat congenital metabolic diseases including PKU.
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Affiliation(s)
- Meisam Barati
- Student Research Committee, Department of Clinical Nutrition, National Nutrition and Food Technology Research Institute, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
| | - Erfan Mosharkesh
- Faculty of Veterinary Medicine, University of Tabriz, Tabriz 5166616471, Iran
| | - Amir Hossein Tahmassian
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9138813944, Iran
| | - Maryam Khodaei
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
| | - Masoumeh Jabbari
- Department of Community Nutrition, National Nutrition and Food Technology Research Institute, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran 151674581, Iran
| | - Ali Kalhori
- Department of Food Science and Technology, Nutritional Science, The Ohio State University, Columbus, OH 43210, USA
| | - Mohsen Alipour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
| | - Afshin Abdi Ghavidel
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
| | - Sajad Khalili-Moghadam
- Student Research Committee, Department of Clinical Nutrition, National Nutrition and Food Technology Research Institute, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
| | - Anwar Fathollahi
- Saqqez School of Nursing, Kurdistan University of Medical Sciences, Sanandaj 66177-13446, Iran
| | - Sayed Hossein Davoodi
- Student Research Committee, Department of Clinical Nutrition, National Nutrition and Food Technology Research Institute, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran 1516745811, Iran
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran 1461965381, Iran
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30
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Perreault M, Means J, Gerson E, James M, Cotton S, Bergeron CG, Simon M, Carlin DA, Schmidt N, Moore TC, Blasbalg J, Sondheimer N, Ndugga-Kabuye K, Denney WS, Isabella VM, Lubkowicz D, Brennan A, Hava DL. The live biotherapeutic SYNB1353 decreases plasma methionine via directed degradation in animal models and healthy volunteers. Cell Host Microbe 2024; 32:382-395.e10. [PMID: 38309259 DOI: 10.1016/j.chom.2024.01.005] [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: 08/24/2023] [Revised: 12/07/2023] [Accepted: 01/12/2024] [Indexed: 02/05/2024]
Abstract
Methionine is an essential proteinogenic amino acid, but its excess can lead to deleterious effects. Inborn errors of methionine metabolism resulting from loss of function in cystathionine β-synthase (CBS) cause classic homocystinuria (HCU), which is managed by a methionine-restricted diet. Synthetic biotics are gastrointestinal tract-targeted live biotherapeutics that can be engineered to replicate the benefits of dietary restriction. In this study, we assess whether SYNB1353, an E. coli Nissle 1917 derivative, impacts circulating methionine and homocysteine levels in animals and healthy volunteers. In both mice and nonhuman primates (NHPs), SYNB1353 blunts the appearance of plasma methionine and plasma homocysteine in response to an oral methionine load. A phase 1 clinical study conducted in healthy volunteers subjected to an oral methionine challenge demonstrates that SYNB1353 is well tolerated and blunts plasma methionine by 26%. Overall, SYNB1353 represents a promising approach for methionine reduction with potential utility for the treatment of HCU.
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31
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Mahdizade Ari M, Dadgar L, Elahi Z, Ghanavati R, Taheri B. Genetically Engineered Microorganisms and Their Impact on Human Health. Int J Clin Pract 2024; 2024:6638269. [PMID: 38495751 PMCID: PMC10944348 DOI: 10.1155/2024/6638269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/20/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
The emergence of antibiotic-resistant strains, the decreased effectiveness of conventional therapies, and the side effects have led researchers to seek a safer, more cost-effective, patient-friendly, and effective method that does not develop antibiotic resistance. With progress in synthetic biology and genetic engineering, genetically engineered microorganisms effective in treatment, prophylaxis, drug delivery, and diagnosis have been developed. The present study reviews the types of genetically engineered bacteria and phages, their impacts on diseases, cancer, and metabolic and inflammatory disorders, the biosynthesis of these modified strains, the route of administration, and their effects on the environment. We conclude that genetically engineered microorganisms can be considered promising candidates for adjunctive treatment of diseases and cancers.
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Affiliation(s)
- Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Leila Dadgar
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | | | - Behrouz Taheri
- Department of Biotechnology, School of Medicine, Ahvaz Jundishapour University of medical Sciences, Ahvaz, Iran
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32
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Hayashi N, Lai Y, Fuerte-Stone J, Mimee M, Lu TK. Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements. Nat Commun 2024; 15:2096. [PMID: 38453913 PMCID: PMC10920895 DOI: 10.1038/s41467-024-45893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/07/2024] [Indexed: 03/09/2024] Open
Abstract
Sophisticated gene circuits built by synthetic biology can enable bacteria to sense their environment and respond predictably. Engineered biosensing bacteria outfitted with such circuits can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. To provide robust biocontainment for engineered bacteria, we devised a Cas9-assisted auxotrophic biocontainment system combining thymidine auxotrophy, an Engineered Riboregulator (ER) for controlled gene expression, and a CRISPR Device (CD). The CD prevents the engineered bacteria from acquiring thyA via horizontal gene transfer, which would disrupt the biocontainment system, and inhibits the spread of genetic elements by killing bacteria harboring the gene cassette. This system tunably controlled gene expression in the human gut commensal bacterium Bacteroides thetaiotaomicron, prevented escape from thymidine auxotrophy, and blocked transgene dissemination. These capabilities were validated in vitro and in vivo. This biocontainment system exemplifies a powerful strategy for bringing genetically engineered microorganisms safely into biomedicine.
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Affiliation(s)
- Naoki Hayashi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Yong Lai
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA
- Research Laboratory of Electronics, MIT, Cambridge, MA, 02139, USA
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR
| | - Jay Fuerte-Stone
- Department of Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Mark Mimee
- Department of Microbiology, The University of Chicago, Chicago, IL, 60637, USA.
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, 60637, USA.
| | - Timothy K Lu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- Research Laboratory of Electronics, MIT, Cambridge, MA, 02139, USA.
- Broad Institute, Cambridge, MA, 02139, USA.
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA.
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Lücke J, Huber S. E. coli´s fight against TYROnny: Designing a bacterial strain to tackle tyrosinemia type 1. J Hepatol 2024; 80:394-396. [PMID: 38008262 DOI: 10.1016/j.jhep.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Affiliation(s)
- Jöran Lücke
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Samuel Huber
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany; Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany.
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Gu P, Xie L, Chen T, Yang Q, Zhang X, Liu R, Guo J, Wei R, Li D, Jiang Y, Chen Y, Gong W, Chen P. An engineered Escherichia coli Nissle strain prevents lethal liver injury in a mouse model of tyrosinemia type 1. J Hepatol 2024; 80:454-466. [PMID: 37952766 DOI: 10.1016/j.jhep.2023.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/13/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND & AIMS Hereditary tyrosinemia type 1 (HT1) results from the loss of fumarylacetoacetate hydrolase (FAH) activity and can lead to lethal liver injury. Therapeutic options for HT1 remain limited. In this study, we aimed to construct an engineered bacterium capable of reprogramming host metabolism and thereby provide a potential alternative approach for the treatment of HT1. METHODS Escherichia coli Nissle 1917 (EcN) was engineered to express genes involved in tyrosine metabolism in the anoxic conditions that are characteristic of the intestine (EcN-HT). Bodyweight, survival rate, plasma (tyrosine/liver function), H&E staining and RNA sequencing were used to assess its ability to degrade tyrosine and protect against lethal liver injury in Fah-knockout (KO) mice, a well-accepted model of HT1. RESULTS EcN-HT consumed tyrosine and produced L-DOPA (levodopa) in an in vitro system. Importantly, in Fah-KO mice, the oral administration of EcN-HT enhanced tyrosine degradation, reduced the accumulation of toxic metabolites, and protected against lethal liver injury. RNA sequencing analysis revealed that EcN-HT rescued the global gene expression pattern in the livers of Fah-KO mice, particularly of genes involved in metabolic signaling and liver homeostasis. Moreover, EcN-HT treatment was found to be safe and well-tolerated in the mouse intestine. CONCLUSIONS This is the first report of an engineered live bacterium that can degrade tyrosine and alleviate lethal liver injury in mice with HT1. EcN-HT represents a novel engineered probiotic with the potential to treat this condition. IMPACT AND IMPLICATIONS Patients with hereditary tyrosinemia type 1 (HT1) are characterized by an inability to metabolize tyrosine normally and suffer from liver failure, renal dysfunction, neurological impairments, and cancer. Given the overlap and complementarity between the host and microbial metabolic pathways, the gut microbiome provides a potential chance to regulate host metabolism through degradation of tyrosine and reduction of byproducts that might be toxic. Herein, we demonstrated that an engineered live bacterium, EcN-HT, could enhance tyrosine breakdown, reduce the accumulation of toxic tyrosine byproducts, and protect against lethal liver injury in Fah-knockout mice. These findings suggested that engineered live biotherapeutics that can degrade tyrosine in the gut may represent a viable and safe strategy for the prevention of lethal liver injury in HT1 as well as the mitigation of its associated pathologies.
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Affiliation(s)
- Peng Gu
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, China; Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Li Xie
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Tao Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China; Department of Physiology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Qin Yang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China; Department of Gastroenterology, The Seventh Affiliated Hospital of Southern Medical University, Foshan, 528000, China
| | - Xianglong Zhang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ruofan Liu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jiayin Guo
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Rongjuan Wei
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Dongping Li
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yong Jiang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ye Chen
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, China.
| | - Wei Gong
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, China.
| | - Peng Chen
- Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, China; Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China; Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510515, China.
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Foo GW, Leichthammer CD, Saita IM, Lukas ND, Batko IZ, Heinrichs DE, Edgell DR. Intein-based thermoregulated meganucleases for containment of genetic material. Nucleic Acids Res 2024; 52:2066-2077. [PMID: 38180814 PMCID: PMC10899782 DOI: 10.1093/nar/gkad1247] [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: 08/23/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/07/2024] Open
Abstract
Limiting the spread of synthetic genetic information outside of the intended use is essential for applications where biocontainment is critical. In particular, biocontainment of engineered probiotics and plasmids that are excreted from the mammalian gastrointestinal tract is needed to prevent escape and acquisition of genetic material that could confer a selective advantage to microbial communities. Here, we built a simple and lightweight biocontainment system that post-translationally activates a site-specific DNA endonuclease to degrade DNA at 18°C and not at higher temperatures. We constructed an orthogonal set of temperature-sensitive meganucleases (TSMs) by inserting the yeast VMA1 L212P temperature-sensitive intein into the coding regions of LAGLIDADG homing endonucleases. We showed that the TSMs eliminated plasmids carrying the cognate TSM target site from laboratory strains of Escherichia coli at the permissive 18°C but not at higher restrictive temperatures. Plasmid elimination is dependent on both TSM endonuclease activity and intein splicing. TSMs eliminated plasmids from E. coli Nissle 1917 after passage through the mouse gut when fecal resuspensions were incubated at 18°C but not at 37°C. Collectively, our data demonstrates the potential of thermoregulated meganucleases as a means of restricting engineered plasmids and probiotics to the mammalian gut.
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Affiliation(s)
- Gary W Foo
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | | | - Ibrahim M Saita
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - Nicholas D Lukas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - Izabela Z Batko
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - David E Heinrichs
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, London, Ontario N6A 5C1, Canada
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Lethe MCL, Paris V, Wang X, Chan CTY. Similarities in Structure and Function of UDP-Glycosyltransferase Homologs from Human and Plants. Int J Mol Sci 2024; 25:2782. [PMID: 38474028 PMCID: PMC10932239 DOI: 10.3390/ijms25052782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
The uridine diphosphate glycosyltransferase (UGT) superfamily plays a key role in the metabolism of xenobiotics and metabolic wastes, which is essential for detoxifying those species. Over the last several decades, a huge effort has been put into studying human and mammalian UGT homologs, but family members in other organisms have been explored much less. Potentially, other UGT homologs can have desirable substrate specificity and biological activities that can be harnessed for detoxification in various medical settings. In this review article, we take a plant UGT homology, UGT71G1, and compare its structural and biochemical properties with the human homologs. These comparisons suggest that even though mammalian and plant UGTs are functional in different environments, they may support similar biochemical activities based on their protein structure and function. The known biological functions of these homologs are discussed so as to provide insights into the use of UGT homologs from other organisms for addressing human diseases related to UGTs.
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Affiliation(s)
- Mary Caroline L. Lethe
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA (V.P.)
| | - Vincent Paris
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA (V.P.)
| | - Xiaoqiang Wang
- Department of Biological Sciences, College of Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA;
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Clement T. Y. Chan
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA (V.P.)
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
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37
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Parvin T, Sadras SR. Advanced probiotics: bioengineering and their therapeutic application. Mol Biol Rep 2024; 51:361. [PMID: 38403783 DOI: 10.1007/s11033-024-09309-8] [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: 12/27/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
The role of gut bacteria in human health has long been acknowledged and dysbiosis of the gut microbiota has been correlated with a variety of disorders. Synthetic biology has rapidly grown over the past few years offering a variety of biological applications such as harnessing the relationship between bacteria and human health. Lactic acid bacteria (LAB) are thought to be appropriate chassis organisms for genetic modification with potential biomedical applications. A thorough understanding of the molecular mechanisms behind their beneficial qualities is essential to assist the multifunctional medicinal sectors. Effective genome editing will aid in the creation of next-generation designer probiotics with enhanced resilience and specialized capabilities, furthering our knowledge of the molecular mechanisms behind the physiological impacts of probiotics and their interactions with the host and microbiota. The goal of this review is to provide a brief overview of the methods used to create modified probiotics with the scientific rationale behind gene editing technology, the mechanism of action of engineered probiotics along with their application to treat conditions like inflammatory bowel disease, cancer, bacterial infections, and various metabolic diseases. In addition, application concerns and future directions are also presented.
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Affiliation(s)
- Tamanna Parvin
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India.
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India
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Kim TH, Ju K, Kim SK, Woo SG, Lee JS, Lee CH, Rha E, Shin J, Kwon KK, Lee H, Kim H, Lee SG, Lee DH. Novel Signal Peptides and Episomal Plasmid System for Enhanced Protein Secretion in Engineered Bacteroides Species. ACS Synth Biol 2024; 13:648-657. [PMID: 38224571 DOI: 10.1021/acssynbio.3c00649] [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: 01/17/2024]
Abstract
The genus Bacteroides, a predominant group in the human gut microbiome, presents significant potential for microbiome engineering and the development of live biotherapeutics aimed at treating gut diseases. Despite its promising capabilities, tools for effectively engineering Bacteroides species have been limited. In our study, we have made a breakthrough by identifying novel signal peptides in Bacteroides thetaiotaomicron and Akkermansia muciniphila. These peptides facilitate efficient protein transport across cellular membranes in Bacteroides, a critical step for therapeutic applications. Additionally, we have developed an advanced episomal plasmid system. This system demonstrates superior protein secretion capabilities compared to traditional chromosomal integration plasmids, making it a vital tool for enhancing the delivery of therapeutic proteins in Bacteroides species. Initially, the stability of this episomal plasmid posed a challenge; however, we have overcome this by incorporating an essential gene-based selection system. This novel strategy not only ensures plasmid stability but also aligns with the growing need for antibiotic-free selection methods in clinical settings. Our work, therefore, not only provides a more robust secretion system for Bacteroides but also sets a new standard for the development of live biotherapeutics.
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Affiliation(s)
- Tae Hyun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Kowoon Ju
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Gyun Woo
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si 56212, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jonghyeok Shin
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Hahn J, Ding S, Im J, Harimoto T, Leong KW, Danino T. Bacterial therapies at the interface of synthetic biology and nanomedicine. NATURE REVIEWS BIOENGINEERING 2024; 2:120-135. [PMID: 38962719 PMCID: PMC11218715 DOI: 10.1038/s44222-023-00119-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 07/05/2024]
Abstract
Bacteria are emerging as living drugs to treat a broad range of disease indications. However, the inherent advantages of these replicating and immunostimulatory therapies also carry the potential for toxicity. Advances in synthetic biology and the integration of nanomedicine can address this challenge through the engineering of controllable systems that regulate spatial and temporal activation for improved safety and efficacy. Here, we review recent progress in nanobiotechnology-driven engineering of bacteria-based therapies, highlighting limitations and opportunities that will facilitate clinical translation.
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Affiliation(s)
- Jaeseung Hahn
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Suwan Ding
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jongwon Im
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Tetsuhiro Harimoto
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
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40
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Zhou T, Wu J, Tang H, Liu D, Jeon BH, Jin W, Wang Y, Zheng Y, Khan A, Han H, Li X. Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer. NPJ Biofilms Microbiomes 2024; 10:6. [PMID: 38245564 PMCID: PMC10799920 DOI: 10.1038/s41522-024-00479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
Probiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.
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Affiliation(s)
- Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jingyuan Wu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Haibo Tang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Korea
| | - Weilin Jin
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yiqing Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | | | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Huawen Han
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China.
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China.
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41
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Lebovich M, Lora MA, Gracia-David J, Andrews LB. Genetic Circuits for Feedback Control of Gamma-Aminobutyric Acid Biosynthesis in Probiotic Escherichia coli Nissle 1917. Metabolites 2024; 14:44. [PMID: 38248847 PMCID: PMC10819706 DOI: 10.3390/metabo14010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024] Open
Abstract
Engineered microorganisms such as the probiotic strain Escherichia coli Nissle 1917 (EcN) offer a strategy to sense and modulate the concentration of metabolites or therapeutics in the gastrointestinal tract. Here, we present an approach to regulate the production of the depression-associated metabolite gamma-aminobutyric acid (GABA) in EcN using genetic circuits that implement negative feedback. We engineered EcN to produce GABA by overexpressing glutamate decarboxylase and applied an intracellular GABA biosensor to identify growth conditions that improve GABA biosynthesis. We next employed characterized genetically encoded NOT gates to construct genetic circuits with layered feedback to control the rate of GABA biosynthesis and the concentration of GABA produced. Looking ahead, this approach may be utilized to design feedback control of microbial metabolite biosynthesis to achieve designable smart microbes that act as living therapeutics.
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Affiliation(s)
- Matthew Lebovich
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Marcos A. Lora
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Jared Gracia-David
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Biology, Amherst College, Amherst, MA 01002, USA
| | - Lauren B. Andrews
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Biotechnology Training Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
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Knödlseder N, Fábrega MJ, Santos-Moreno J, Manils J, Toloza L, Marín Vilar M, Fernández C, Broadbent K, Maruotti J, Lemenager H, Carolis C, Zouboulis CC, Soler C, Lood R, Brüggemann H, Güell M. Delivery of a sebum modulator by an engineered skin microbe in mice. Nat Biotechnol 2024:10.1038/s41587-023-02072-4. [PMID: 38195987 DOI: 10.1038/s41587-023-02072-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/17/2023] [Indexed: 01/11/2024]
Abstract
Microorganisms can be equipped with synthetic genetic programs for the production of targeted therapeutic molecules. Cutibacterium acnes is the most abundant commensal of the human skin, making it an attractive chassis to create skin-delivered therapeutics. Here, we report the engineering of this bacterium to produce and secrete the therapeutic molecule neutrophil gelatinase-associated lipocalin, in vivo, for the modulation of cutaneous sebum production.
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Affiliation(s)
- Nastassia Knödlseder
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - María-José Fábrega
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier Santos-Moreno
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joan Manils
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Toloza
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria Marín Vilar
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Cristina Fernández
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Katrina Broadbent
- Protein Technologies Facility, Center of Genomic Regulation, Barcelona, Spain
| | | | | | - Carlo Carolis
- Protein Technologies Facility, Center of Genomic Regulation, Barcelona, Spain
| | - Christos C Zouboulis
- Hochschulklinik für Dermatologie, Venerologie und Allergologie, Immunologisches Zentrum; Städtisches Klinikum Dessau; and Medizinische Hochschule Brandenburg Theodor Fontane und Fakultät für Gesundheitswissenschaften Brandenburg, Dessau-Roßlau, Germany
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Rolf Lood
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | | | - Marc Güell
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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Heinken A, El Kouche S, Guéant-Rodriguez RM, Guéant JL. Towards personalized genome-scale modeling of inborn errors of metabolism for systems medicine applications. Metabolism 2024; 150:155738. [PMID: 37981189 DOI: 10.1016/j.metabol.2023.155738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023]
Abstract
Inborn errors of metabolism (IEMs) are a group of more than 1000 inherited diseases that are individually rare but have a cumulative global prevalence of 50 per 100,000 births. Recently, it has been recognized that like common diseases, patients with rare diseases can greatly vary in the manifestation and severity of symptoms. Here, we review omics-driven approaches that enable an integrated, holistic view of metabolic phenotypes in IEM patients. We focus on applications of Constraint-based Reconstruction and Analysis (COBRA), a widely used mechanistic systems biology approach, to model the effects of inherited diseases. Moreover, we review evidence that the gut microbiome is also altered in rare diseases. Finally, we outline an approach using personalized metabolic models of IEM patients for the prediction of biomarkers and tailored therapeutic or dietary interventions. Such applications could pave the way towards personalized medicine not just for common, but also for rare diseases.
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Affiliation(s)
- Almut Heinken
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France.
| | - Sandra El Kouche
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Rosa-Maria Guéant-Rodriguez
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
| | - Jean-Louis Guéant
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
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Debnath N, Yadav P, Mehta PK, Gupta P, Kumar D, Kumar A, Gautam V, Yadav AK. Designer probiotics: Opening the new horizon in diagnosis and prevention of human diseases. Biotechnol Bioeng 2024; 121:100-117. [PMID: 37881101 DOI: 10.1002/bit.28574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/19/2023] [Accepted: 09/23/2023] [Indexed: 10/27/2023]
Abstract
Probiotic microorganisms have been used for therapeutic purposes for over a century, and recent advances in biotechnology and genetic engineering have opened up new possibilities for developing therapeutic approaches using indigenous probiotic microorganisms. Diseases are often related to metabolic and immunological factors, which play a critical role in their onset. With the help of advanced genetic tools, probiotics can be modified to produce or secrete important therapeutic peptides directly into mucosal sites, increasing their effectiveness. One potential approach to enhancing human health is through the use of designer probiotics, which possess immunogenic characteristics. These genetically engineered probiotics hold promise in providing novel therapeutic options. In addition to their immunogenic properties, designer probiotics can also be equipped with sensors and genetic circuits, enabling them to detect a range of diseases with remarkable precision. Such capabilities may significantly advance disease diagnosis and management. Furthermore, designer probiotics have the potential to be used in diagnostic applications, offering a less invasive and more cost-effective alternative to conventional diagnostic techniques. This review offers an overview of the different functional aspects of the designer probiotics and their effectiveness on different diseases and also, we have emphasized their limitations and future implications. A comprehensive understanding of these functional attributes may pave the way for new avenues of prevention and the development of effective therapies for a range of diseases.
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Affiliation(s)
- Nabendu Debnath
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Pooja Yadav
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Praveen K Mehta
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
| | - Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashwani Kumar
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, Haryana, India
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashok K Yadav
- Centre for Molecular Biology, Central University of Jammu, Samba, Jammu and Kashmir (UT), India
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Nezhad SRK, Aligoodarzi PN, Rostami G, Shariati G, Galehdari H, Saberi A, Sedaghat A, Hamid M. Genotypic variants of the tetrahydrobiopterin (BH4) biosynthesis genes in patients with hyperphenylalaninemia from different regions of Iran. Mol Genet Genomic Med 2024; 12:e2294. [PMID: 37818795 PMCID: PMC10767420 DOI: 10.1002/mgg3.2294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Hyperphenylalaninemia (HPA) is a metabolic disorder classified into phenylalanine-4-hydroxylase (PAH) and non-PAH deficiency. The latter is produced by mutations in genes involved in the tetrahydrobiopterin (BH4) biosynthesis pathway and DNAJC12 pathogenetic variants. The BH4 metabolism, including de novo biosynthesis involved genes (i.e., guanosine 5'-triphosphate cyclohydrolase I (GTPCH/GCH1), sepiapterin reductase (SR/SPR), 6-pyruvoyl-tetrahydropterin synthase (PTPS/PTS)), and two genes that play roles in cofactor regeneration pathway (i.e., dihydropteridine reductase (DHPR/QDPR) and pterin-4α-carbinolamine dehydratase (PCD/PCBD1)). The subsequent systemic hyperphenylalaninemia and monoamine neurotransmitter deficiency lead to neurological consequences. The high rate of consanguineous marriages in Iran substantially increases the incidence of BH4 deficiency. METHODS We utilized the Sanger sequencing technique in this study to investigate 14 Iranian patients with non-PAH deficiency. All affected subjects in this study had HPA and no mutation was detected in their PAH gene. RESULTS We successfully identified six mutant alleles in BH4-deficiency-associated genes, including three novel mutations: one in QDPR, one in PTS, and one in the PCBD1 gene, thus giving a definite diagnosis to these patients. CONCLUSION In this light, appropriate patient management may follow. The clinical effect of reported variants is essential for genetic counseling and prenatal diagnosis in the patients' families and significant for the improvement of precision medicine.
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Affiliation(s)
| | | | - Golale Rostami
- Department of Molecular Medicine, Biotechnology Research CenterPasteur Institute of IranTehranIran
| | - Gholamreza Shariati
- Department of Medical Genetics, Faculty of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Hamid Galehdari
- Department of Genetics, Faculty of SciencesShahid Chamran University of AhvazAhvazIran
| | - Alihossein Saberi
- Department of Medical Genetics, Faculty of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Alireza Sedaghat
- Department of EndocrinologyAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Mohammad Hamid
- Department of Molecular Medicine, Biotechnology Research CenterPasteur Institute of IranTehranIran
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Ba F, Zhang Y, Ji X, Liu WQ, Ling S, Li J. Expanding the toolbox of probiotic Escherichia coli Nissle 1917 for synthetic biology. Biotechnol J 2024; 19:e2300327. [PMID: 37800393 DOI: 10.1002/biot.202300327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023]
Abstract
Escherichia coli Nissle 1917 (EcN) is a probiotic microbe that has the potential to be developed as a promising chassis for synthetic biology applications. However, the molecular tools and techniques for utilizing EcN remain to be further explored. To address this opportunity, the EcN-based toolbox was systematically expanded, enabling EcN as a powerful platform for more applications. First, two EcN cryptic plasmids and other compatible plasmids were genetically engineered to enrich the manipulable plasmid toolbox for multiple gene coexpression. Next, two EcN-based technologies were developed, including the conjugation strategy for DNA transfer, and quantification of protein expression capability. Finally, the EcN-based applications were further expanded by developing EcN native integrase-mediated genetic engineering and establishing an in vitro cell-free protein synthesis (CFPS) system. Overall, this study expanded the toolbox for manipulating and making full use of EcN as a commonly used probiotic chassis, providing several simplified, dependable, and predictable strategies for researchers working in synthetic biology fields.
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Affiliation(s)
- Fang Ba
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yufei Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiangyang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wan-Qiu Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
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Yamchi A, Rahimi M, Javan B, Abdollahi D, Salmanian M, Shahbazi M. Evaluation of the impact of polypeptide-p on diabetic rats upon its cloning, expression, and secretion in Saccharomyces boulardii. Arch Microbiol 2023; 206:37. [PMID: 38142245 DOI: 10.1007/s00203-023-03773-9] [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: 09/25/2023] [Revised: 11/16/2023] [Accepted: 11/25/2023] [Indexed: 12/25/2023]
Abstract
This study was designed to evaluate the effectiveness of recombinant polypeptide-p derived from Momordica charantia on diabetic rats. In this research, the optimized sequence of polypeptide-p gene fused to a secretion signal tag was cloned into the expression vector and transformed into probiotic Saccharomyces boulardii. The production of recombinant secretion protein was verified by western blotting, HPLC, and mass spectrometry. To assay recombinant yeast bioactivity in the gut, diabetic rats were orally fed wild-type and recombinant S. boulardii, in short SB and rSB, respectively, at two low and high doses as well as glibenclamide as a reference drug. In untreated diabetic and treated diabetic + SB rats (low and high doses), the blood glucose increased from 461, 481, and 455 (mg/dl), respectively, to higher than 600 mg/dl on the 21st day. Whereas glibenclamide and rSB treatments showed a significant reduction in the blood glucose level. The result of this study promised a safe plant-source supplement for diabetes through probiotic orchestration.
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Affiliation(s)
- Ahad Yamchi
- Department of Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
- Genetic Engineering and Molecular Genetics, Gorgan University of Agricultural Science and Natural Resources, P.O. Box: 4934174515, Gorgan, Iran.
| | - Maryam Rahimi
- Department of Horticulture, University of Zabol, Zabol, Iran
| | - Bita Javan
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Dorsa Abdollahi
- Department of Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Mojgan Salmanian
- Department of Animal Science and Poultry Nutrition, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Majid Shahbazi
- Medical Cellular and Molecular Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Amrofell MB, Rengarajan S, Vo ST, Ramirez Tovar ES, LoBello L, Dantas G, Moon TS. Engineering E. coli strains using antibiotic-resistance-gene-free plasmids. CELL REPORTS METHODS 2023; 3:100669. [PMID: 38086386 PMCID: PMC10753387 DOI: 10.1016/j.crmeth.2023.100669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/29/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
We created a generalizable pipeline for antibiotic-resistance-gene-free plasmid (ARGFP)-based cloning using a dual auxotrophic- and essential-gene-based selection strategy. We use auxotrophic selection to construct plasmids in engineered E. coli DH10B cloning strains and both auxotrophic- and essential-gene-based selection to (1) select for recombinant strains and (2) maintain a plasmid in E. coli Nissle 1917, a common chassis for engineered probiotic applications, and E. coli MG1655, the laboratory "wild-type" E. coli strain. We show that our approach has comparable efficiency to that of antibiotic-resistance-gene-based cloning. We also show that the double-knockout Nissle and MG1655 strains are simple to transform with plasmids of interest. Notably, we show that the engineered Nissle strains are amenable to long-term plasmid maintenance in repeated culturing as well as in the mouse gut, demonstrating the potential for broad applications while minimizing the risk of antibiotic resistance spread via horizontal gene transfer.
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Affiliation(s)
- Matthew B Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sunaina Rengarajan
- Department of Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven T Vo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erick S Ramirez Tovar
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Larissa LoBello
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Yeh YH, Kelly VW, Pour RR, Sirk SJ. A molecular toolkit for heterologous protein secretion across Bacteroides species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571725. [PMID: 38168418 PMCID: PMC10760143 DOI: 10.1101/2023.12.14.571725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Bacteroides species are abundant and prevalent stably colonizing members of the human gut microbiota, making them a promising chassis for developing long-term interventions for chronic diseases. Engineering these bacteria as on-site production and delivery vehicles for biologic drugs or diagnostics, however, requires efficient heterologous protein secretion tools, which are currently lacking. To address this limitation, we systematically investigated methods to enable heterologous protein secretion in Bacteroides using both endogenous and exogenous secretion systems. Here, we report a collection of secretion carriers that can export functional proteins across multiple Bacteroides species at high titers. To understand the mechanistic drivers of Bacteroides secretion, we characterized signal peptide sequence features as well as post-secretion extracellular fate and cargo size limit of protein cargo. To increase titers and enable flexible control of protein secretion, we developed a strong, self-contained, inducible expression circuit. Finally, we validated the functionality of our secretion carriers in vivo in a mouse model. This toolkit should enable expanded development of long-term living therapeutic interventions for chronic gastrointestinal disease.
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Affiliation(s)
- Yu-Hsuan Yeh
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Vince W. Kelly
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Rahman Rahman Pour
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Perlumi, Berkeley, CA 94704, USA
| | - Shannon J. Sirk
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Lead Contact
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50
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Guo J, Zhou B, Niu Y, Liu L, Yang L. Engineered probiotics introduced to improve intestinal microecology for the treatment of chronic diseases: present state and perspectives. J Diabetes Metab Disord 2023; 22:1029-1038. [PMID: 37975092 PMCID: PMC10638336 DOI: 10.1007/s40200-023-01279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/05/2023] [Indexed: 11/19/2023]
Abstract
Purpose Correcting intestinal microecological imbalance has become one of the core strategies to treat chronic diseases. Some traditional microecology-based therapies targeting intestine, such as prebiotic therapy, probiotic therapy and fecal microbiota transplantation therapy, have been used in the prevention and treatment of clinical chronic diseases, which still facing low safety and poor controllability problems. The development of synthetic biology technology has promoted the development of intestinal microecology-based therapeutics for chronic diseases, which exhibiting higher robustness and controllability, and become an important part of the next generation of microecological therapy. The purpose of this review is to summarize the application of synthetic biology in intestinal microecology-based therapeutics for chronic diseases. Methods The available literatures were searched to find out experimental studies and relevant review articles on the application of synthetic biology in intestinal microecology-based therapeutics for chronic diseases from year 1990 to 2023. Results Evidence proposed that synthetic biology has been applied in the intestinal microecology-based therapeutics for chronic diseases, covering metabolic diseases (e.g. diabetes, obesity, nonalcoholic fatty liver disease and phenylketonuria), digestive diseases (e.g. inflammatory bowel disease and colorectal cancer), and neurodegenerative diseases (e.g. Alzheimer's disease and Parkinson's disease). Conclusion This review summarizes the application of synthetic biology in intestinal microecology-based therapeutics for major chronic diseases and discusses the opportunities and challenges in the above process, providing clinical possibilities of synthetic biology technology applied in microecological therapies.
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Affiliation(s)
- Jianquan Guo
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, (Shanxi Medical University), Ministry of Education, Taiyuan, PR China
- School of Public Health, Shanxi Medical University, Taiyuan, 030001 Shanxi PR China
| | - Bangyuan Zhou
- School of Public Health, Shanxi Medical University, Taiyuan, 030001 Shanxi PR China
| | - Yali Niu
- School of Public Health, Shanxi Medical University, Taiyuan, 030001 Shanxi PR China
| | - Liangpo Liu
- School of Public Health, Shanxi Medical University, Taiyuan, 030001 Shanxi PR China
| | - Liyang Yang
- School of Basic Medical Sciences, Shanxi University of Chinese Medicine, 030619 Jinzhong, PR China
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