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Li J, Lu T, Chu Y, Zhang Y, Zhang J, Fu W, Sun J, Liu Y, Liao X, Zhou Y. Cinnamaldehyde targets SarA to enhance β-lactam antibiotic activity against methicillin-resistant Staphylococcus aureus. MLIFE 2024; 3:291-306. [PMID: 38948140 PMCID: PMC11211666 DOI: 10.1002/mlf2.12121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 07/02/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a current global public health problem due to its increasing resistance to the most recent antibiotic therapies. One critical approach is to develop ways to revitalize existing antibiotics. Here, we show that the phytogenic compound cinnamaldehyde (CIN) and β-lactam antibiotic combinations can functionally synergize and resensitize clinical MRSA isolates to β-lactam therapy and inhibit MRSA biofilm formation. Mechanistic studies indicated that the CIN potentiation effect on β-lactams was primarily the result of inhibition of the mecA expression by targeting the staphylococcal accessory regulator sarA. CIN alone or in combination with β-lactams decreased sarA gene expression and increased SarA protein phosphorylation that impaired SarA binding to the mecA promoter element and downregulated virulence genes such as those encoding biofilm, α-hemolysin, and adhesin. Perturbation of SarA-mecA binding thus interfered with PBP2a biosynthesis and this decreased MRSA resistance to β-lactams. Furthermore, CIN fully restored the anti-MRSA activities of β-lactam antibiotics in vivo in murine models of bacteremia and biofilm infections. Together, our results indicated that CIN acts as a β-lactam adjuvant and can be applied as an alternative therapy to combat multidrug-resistant MRSA infections.
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Affiliation(s)
- Jianguo Li
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Tingyin Lu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Yuefei Chu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Yuejun Zhang
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Jing Zhang
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
- Yantai Fushan Center for Animal Disease Control and PreventionYantaiChina
| | - Wenzhen Fu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Yahong Liu
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Xiao‐Ping Liao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
| | - Yu‐Feng Zhou
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety EvaluationSouth China Agricultural UniversityGuangzhouChina
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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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Su Y, Ding T. Targeting microbial quorum sensing: the next frontier to hinder bacterial driven gastrointestinal infections. Gut Microbes 2023; 15:2252780. [PMID: 37680117 PMCID: PMC10486307 DOI: 10.1080/19490976.2023.2252780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
Bacteria synchronize social behaviors via a cell-cell communication and interaction mechanism termed as quorum sensing (QS). QS has been extensively studied in monocultures and proved to be intensively involved in bacterial virulence and infection. Despite the role QS plays in pathogens during laboratory engineered infections has been proved, the potential functions of QS related to pathogenesis in context of microbial consortia remain poorly understood. In this review, we summarize the basic molecular mechanisms of QS, primarily focusing on pathogenic microbes driving gastrointestinal (GI) infections. We further discuss how GI pathogens disequilibrate the homeostasis of the indigenous microbial consortia, rebuild a realm dominated by pathogens, and interact with host under worsening infectious conditions via pathogen-biased QS signaling. Additionally, we present recent applications and main challenges of manipulating QS network in microbial consortia with the goal of better understanding GI bacterial sociality and facilitating novel therapies targeting bacterial infections.
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Affiliation(s)
- Ying Su
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Ministry of Education, Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Guangzhou, China
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Ministry of Education, Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Guangzhou, China
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4
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Jiang Y, Wu R, Zhang W, Xin F, Jiang M. Construction of stable microbial consortia for effective biochemical synthesis. Trends Biotechnol 2023; 41:1430-1441. [PMID: 37330325 DOI: 10.1016/j.tibtech.2023.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023]
Abstract
Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China.
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
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Khan F, Jeong GJ, Javaid A, Thuy Nguyen Pham D, Tabassum N, Kim YM. Surface adherence and vacuolar internalization of bacterial pathogens to the Candida spp. cells: Mechanism of persistence and propagation. J Adv Res 2023; 53:115-136. [PMID: 36572338 PMCID: PMC10658324 DOI: 10.1016/j.jare.2022.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The co-existence of Candida albicans with the bacteria in the host tissues and organs displays interactions at competitive, antagonistic, and synergistic levels. Several pathogenic bacteria take advantage of such types of interaction for their survival and proliferation. The chemical interaction involves the signaling molecules produced by the bacteria or Candida spp., whereas the physical attachment occurs by involving the surface proteins of the bacteria and Candida. In addition, bacterial pathogens have emerged to internalize inside the C. albicans vacuole, which is one of the inherent properties of the endosymbiotic relationship between the bacteria and the eukaryotic host. AIM OF REVIEW The interaction occurring by the involvement of surface protein from diverse bacterial species with Candida species has been discussed in detail in this paper. An in silico molecular docking study was performed between the surface proteins of different bacterial species and Als3P of C. albicans to explain the molecular mechanism involved in the Als3P-dependent interaction. Furthermore, in order to understand the specificity of C. albicans interaction with Als3P, the evolutionary relatedness of several bacterial surface proteins has been investigated. Furthermore, the environmental factors that influence bacterial pathogen internalization into the Candida vacuole have been addressed. Moreover, the review presented future perspectives for disrupting the cross-kingdom interaction and eradicating the endosymbiotic bacterial pathogens. KEY SCIENTIFIC CONCEPTS OF REVIEW With the involvement of cross-kingdom interactions and endosymbiotic relationships, the bacterial pathogens escape from the environmental stresses and the antimicrobial activity of the host immune system. Thus, the study of interactions between Candida and bacterial pathogens is of high clinical significance.
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Affiliation(s)
- Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
| | - Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Aqib Javaid
- Department of Biotechnology and Bioinformatics, University of Hyderabad, India
| | - Dung Thuy Nguyen Pham
- Institute of Applied Technology and Sustainable Development, Nguyen Tat Thanh University, Ho Chi Minh City 70000, Vietnam
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea.
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Huertas MG, Rodríguez M, Castro P, Cruz SD, Cifuentes EA, Yepes AF, Zambrano MM, Baldión AM. Description of the colonizing mycobiota of endotracheal tubes from patients admitted to two intensive care units in Bogotá, Colombia. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2023; 43:181-193. [PMID: 37721909 PMCID: PMC10586799 DOI: 10.7705/biomedica.6884] [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: 01/30/2023] [Accepted: 05/15/2023] [Indexed: 09/20/2023]
Abstract
Introduction. Medical device colonization by pathogenic microorganisms is a risk factor for increasing infections associated with health care and, consequently, the morbidity and mortality of intubated patients. In Colombia, fungal colonization of endotracheal tubes has not been described, and this information could lead to new therapeutic options for the benefit of patients. Objective. To describe the colonizing fungi of the endotracheal tubes from patients in the intensive care unit, along with its antifungal sensitivity profile. Materials and methods. We conducted a descriptive, observational study in two health centers for 12 months. Endotracheal tubes were collected from patients in intensive care units. Samples were processed for culture, fungi identification, and antifungal sensitivity profile assessment. Results. A total of 121 endotracheal tubes, obtained from 113 patients, were analyzed: 41.32 % of the tubes were colonized by Candida albicans (64.62%), C. non‑albicans (30.77%), Cryptococcus spp. (3.08%) or molds (1.54%). All fungi evaluated showed a high sensitivity to antifungals, with a mean of 91%. Conclusion. Fungal colonization was found in the endotracheal tubes of patients under invasive mechanical ventilation. The antifungal sensitivity profile in these patients was favorable. A clinical study is required to find possible correlations between the colonizing microorganisms and infectivity.
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Affiliation(s)
- Mónica Gabriela Huertas
- Genética Molecular, Corporación CorpoGen, Bogotá, D.C., Colombia; Escuela de Medicina, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia.
| | - Miguel Rodríguez
- Departamento de Patología y Laboratorios, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, D.C., Colombia.
| | - Patricia Castro
- Departamento de Patología y Laboratorios, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, D.C., Colombia.
| | - Sergio Danilo Cruz
- Departamento de Patología y Laboratorios, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, D.C., Colombia.
| | | | - Andrés Felipe Yepes
- Departamento de Patología y Laboratorios, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, D.C., Colombia.
| | | | - Ana Margarita Baldión
- Departamento de Patología y Laboratorios, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, D.C., Colombia.
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7
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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Zhang Y, Ma N, Tan P, Ma X. Quorum sensing mediates gut bacterial communication and host-microbiota interaction. Crit Rev Food Sci Nutr 2022; 64:3751-3763. [PMID: 36239296 DOI: 10.1080/10408398.2022.2134981] [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: 11/03/2022]
Abstract
Gut bacteria employ quorum sensing (QS) to coordinate their activities and communicate with one another, this process relies on the production, detection, and response to autoinducers, which are extracellular signaling molecules. In addition to synchronizing behavioral activities within the species, QS plays a crucial role in the gut host-microbiota interaction. In this review, an overview of classical QS systems is presented as well as the interspecies communication mediated by QS, and recent advances in the host-microbiota interaction mediated by QS. A greater knowledge of the communication network of gut microbiota is not only an opportunity and a challenge for developing nutritional and therapeutic strategies against bacterial illnesses, but also a means for improving gut health.
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Affiliation(s)
- Yucheng Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Peng Tan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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9
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Stefanov BA, Fussenegger M. Biomarker-driven feedback control of synthetic biology systems for next-generation personalized medicine. Front Bioeng Biotechnol 2022; 10:986210. [PMID: 36225597 PMCID: PMC9548536 DOI: 10.3389/fbioe.2022.986210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Many current clinical therapies for chronic diseases involve administration of drugs using dosage and bioavailability parameters estimated for a generalized population. This standard approach carries the risk of under dosing, which may result in ineffective treatment, or overdosing, which may cause undesirable side effects. Consequently, maintaining a drug concentration in the therapeutic window often requires frequent monitoring, adversely affecting the patient’s quality of life. In contrast, endogenous biosystems have evolved finely tuned feedback control loops that govern the physiological functions of the body based on multiple input parameters. To provide personalized treatment for chronic diseases, therefore, we require synthetic systems that can similarly generate a calibrated therapeutic response. Such engineered autonomous closed-loop devices should incorporate a sensor that actively tracks and evaluates the disease severity based on one or more biomarkers, as well as components that utilize these molecular inputs to bio compute and deliver the appropriate level of therapeutic output. Here, we review recent advances in applications of the closed-loop design principle in biomedical implants for treating severe and chronic diseases, highlighting translational studies of cellular therapies. We describe the engineering principles and components of closed-loop therapeutic devices, and discuss their potential to become a key pillar of personalized medicine.
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Affiliation(s)
| | - Martin Fussenegger
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, Switzerland
- Faculty of Life Science, University of Basel, Basel, Switzerland
- *Correspondence: Martin Fussenegger,
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10
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Mansouri M, Fussenegger M. Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells. Protein Cell 2022; 13:476-489. [PMID: 34586617 PMCID: PMC9226217 DOI: 10.1007/s13238-021-00876-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/02/2021] [Indexed: 12/01/2022] Open
Abstract
Cell therapy approaches that employ engineered mammalian cells for on-demand production of therapeutic agents in the patient's body are moving beyond proof-of-concept in translational medicine. The therapeutic cells can be customized to sense user-defined signals, process them, and respond in a programmable and predictable way. In this paper, we introduce the available tools and strategies employed to design therapeutic cells. Then, various approaches to control cell behaviors, including open-loop and closed-loop systems, are discussed. We also highlight therapeutic applications of engineered cells for early diagnosis and treatment of various diseases in the clinic and in experimental disease models. Finally, we consider emerging technologies such as digital devices and their potential for incorporation into future cell-based therapies.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland.
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11
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Machine learning aided construction of the quorum sensing communication network for human gut microbiota. Nat Commun 2022; 13:3079. [PMID: 35654892 PMCID: PMC9163137 DOI: 10.1038/s41467-022-30741-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 05/17/2022] [Indexed: 01/02/2023] Open
Abstract
Quorum sensing (QS) is a cell-cell communication mechanism that connects members in various microbial systems. Conventionally, a small number of QS entries are collected for specific microbes, which is far from being able to fully depict communication-based complex microbial interactions in human gut microbiota. In this study, we propose a systematic workflow including three modules and the use of machine learning-based classifiers to collect, expand, and mine the QS-related entries. Furthermore, we develop the Quorum Sensing of Human Gut Microbes (QSHGM) database (http://www.qshgm.lbci.net/) including 28,567 redundancy removal entries, to bridge the gap between QS repositories and human gut microbiota. With the help of QSHGM, various communication-based microbial interactions can be searched and a QS communication network (QSCN) is further constructed and analysed for 818 human gut microbes. This work contributes to the establishment of the QSCN which may form one of the key knowledge maps of the human gut microbiota, supporting future applications such as new manipulations to synthetic microbiota and potential therapies to gut diseases. Microbes communicate with each other by Quorum sensing (QS) languages. Here the authors construct a QS database and the QS communication network to decipher intricate QSbased communications and form one of the key knowledge maps for human gut microbiota.
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12
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Singh RP, Shadan A, Ma Y. Biotechnological Applications of Probiotics: A Multifarious Weapon to Disease and Metabolic Abnormality. Probiotics Antimicrob Proteins 2022; 14:1184-1210. [PMID: 36121610 PMCID: PMC9483357 DOI: 10.1007/s12602-022-09992-8] [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] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Consumption of live microorganisms "Probiotics" for health benefits and well-being is increasing worldwide. Their use as a therapeutic approach to confer health benefits has fascinated humans for centuries; however, its conceptuality gradually evolved with methodological advancement, thereby improving our understanding of probiotics-host interaction. However, the emerging concern regarding safety aspects of live microbial is enhancing the interest in non-viable or microbial cell extracts, as they could reduce the risks of microbial translocation and infection. Due to technical limitations in the production and formulation of traditionally used probiotics, the scientific community has been focusing on discovering new microbes to be used as probiotics. In many scientific studies, probiotics have been shown as potential tools to treat metabolic disorders such as obesity, type-2 diabetes, non-alcoholic fatty liver disease, digestive disorders (e.g., acute and antibiotic-associated diarrhea), and allergic disorders (e.g., eczema) in infants. However, the mechanistic insight of strain-specific probiotic action is still unknown. In the present review, we analyzed the scientific state-of-the-art regarding the mechanisms of probiotic action, its physiological and immuno-modulation on the host, and new direction regarding the development of next-generation probiotics. We discuss the use of recently discovered genetic tools and their applications for engineering the probiotic bacteria for various applications including food, biomedical applications, and other health benefits. Finally, the review addresses the future development of biological techniques in combination with clinical and preclinical studies to explain the molecular mechanism of action, and discover an ideal multifunctional probiotic bacterium.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand India
| | - Afreen Shadan
- Dr. Shyama Prasad Mukherjee University, Ranchi, Jharkhand India
| | - Ying Ma
- College of Resource and Environment, Southwest University, Chongqing, China
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13
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Ioannou P, Vouidaski A, Spernovasilis N, Alexopoulou C, Papazachariou A, Paraschou E, Achyropoulou A, Maraki S, Samonis G, Kofteridis DP. Candida spp. isolation from critically ill patients' respiratory tract. Does antifungal treatment affect survival? Germs 2021; 11:536-543. [PMID: 35096670 DOI: 10.18683/germs.2021.1288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Isolation of Candida spp. from bronchial samples of patients on mechanical ventilation is common. Even though it may not always reflect infection, it may induce immunological changes that can facilitate bacterial pneumonia. In this case, antifungal treatment is of uncertain value. This study examined the impact of antifungal treatment on the outcome of intensive care unit (ICU)-acquired respiratory tract infection (RTI) of critically ill, immunocompetent patients, with Candida isolation from their respiratory tract. METHODS This is a retrospective cohort study of adult patients hospitalized in the ICU of the University Hospital of Heraklion, Greece, from 2014 through 2016 with ICU-acquired RTI and Candida spp. isolated from their bronchial secretions. Data regarding medical history, demographics (gender, age), reason for ICU admission, previous antimicrobial use or hospitalization, SOFA and APACHE II score, clinical outcomes (primary clinical outcome: overall mortality during hospitalization; secondary clinical outcome: mortality during the ICU stay and duration of ICU and hospital stay) at the end of their ICU stay and at the end of their hospital stay were recorded and consequently evaluated. A logistic regression analysis model evaluated the effect of the recorded parameters in association with ICU mortality and overall mortality during hospitalization. RESULTS A total of 90 individuals were enrolled. Of them, 47 (52.2%) were treated with antifungals during their hospitalization around the time of Candida isolation. Patients treated with antifungals had higher SOFA and APACHE II scores, longer duration of stay in the ICU, more days on ventilator and higher total mortality during hospitalization. Multivariate logistic regression analysis identified antifungal use to be independently associated with total mortality during hospitalization. CONCLUSIONS Antifungal use in patients with ICU-acquired RTI was associated with higher overall mortality as compared to those not receiving such agents.
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Affiliation(s)
- Petros Ioannou
- MD, MSc, PhD Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Stavrakia and Voutes crossroad, Heraklion, PC 71110, Crete, Greece
| | - Alexandra Vouidaski
- MD, Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
| | - Nikolaos Spernovasilis
- MD, MSc Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
| | - Christina Alexopoulou
- MD, PhD, Intensive Care Unit, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
| | - Andria Papazachariou
- MD, Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
| | - Eleni Paraschou
- MD, Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
| | - Aikaterini Achyropoulou
- MD, Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
| | - Sofia Maraki
- MD, PhD, Department of Microbiology, University Hospital of Heraklion, Heraklion, PC 71110 Crete, Greece
| | - George Samonis
- MD, PhD, Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
| | - Diamantis P Kofteridis
- MD, PhD, Department of Internal Medicine & Infectious Diseases, University Hospital of Heraklion, Heraklion, PC 71110, Crete, Greece
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14
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Strittmatter T, Argast P, Buchman P, Krawczyk K, Fussenegger M. Control of gene expression in engineered mammalian cells with a programmable shear-stress inducer. Biotechnol Bioeng 2021; 118:4751-4759. [PMID: 34506645 PMCID: PMC9292429 DOI: 10.1002/bit.27939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/18/2021] [Accepted: 09/08/2021] [Indexed: 11/11/2022]
Abstract
In humans, cellular mechanoperception serves as the basis of touch sensation and proprioception, contributes to the proper programming of cell fate during embryonic development, and plays a pivotal role in the development of mechanosensitive tissues. Molecular mechanoreceptors can respond to their environment by mediating transient adjustments of ion homeostasis, which subsequently trigger calcium-dependent alteration of gene expression via specific signaling pathways such as the nuclear factor of the activated T-cells pathway. Although, mechanoreceptors are potential drug targets for various diseases, current techniques to study mechanically gated processes are often based on custom-tailored microfluidic systems, which require special setups or have limited throughput. Here, we present a platform to characterize shear-stress-triggered, calcium-mediated gene expression, which employs a programmable, 96-well-format, shear-stress induction device to examine the effects of imposing various mechanical loads on mammalian adherent cell lines. The presented method is suitable for high-throughput experiments and provides a large tunable parameter space to optimize conditions for different cell types. Our findings indicate that the device is an effective tool to explore conditions in terms of frequency, intensity, intervals as well as extracellular matrix composition alongside the evaluation of different combinations of mechanosensitive proteins for mechanically activated gene expression. We believe our results can serve as a platform for further investigations into shear stress-controlled gene expression in basic research and drug screening.
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Affiliation(s)
- Tobias Strittmatter
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Paul Argast
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Peter Buchman
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Krzysztof Krawczyk
- 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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Contreras-Ramos M, Mansell TJ. Leveraging quorum sensing to manipulate microbial dynamics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021. [DOI: 10.1016/j.cobme.2021.100306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Sedlmayer F, Woischnig AK, Unterreiner V, Fuchs F, Baeschlin D, Khanna N, Fussenegger M. 5-Fluorouracil blocks quorum-sensing of biofilm-embedded methicillin-resistant Staphylococcus aureus in mice. Nucleic Acids Res 2021; 49:e73. [PMID: 33856484 PMCID: PMC8287944 DOI: 10.1093/nar/gkab251] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 03/02/2021] [Accepted: 03/29/2021] [Indexed: 02/05/2023] Open
Abstract
Antibiotic-resistant pathogens often escape antimicrobial treatment by forming protective biofilms in response to quorum-sensing communication via diffusible autoinducers. Biofilm formation by the nosocomial pathogen methicillin-resistant Staphylococcus aureus (MRSA) is triggered by the quorum-sensor autoinducer-2 (AI-2), whose biosynthesis is mediated by methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) and S-ribosylhomocysteine lyase (LuxS). Here, we present a high-throughput screening platform for small-molecular inhibitors of either enzyme. This platform employs a cell-based assay to report non-toxic, bioavailable and cell-penetrating inhibitors of AI-2 production, utilizing engineered human cells programmed to constitutively secrete AI-2 by tapping into the endogenous methylation cycle via ectopic expression of codon-optimized MTAN and LuxS. Screening of a library of over 5000 commercial compounds yielded 66 hits, including the FDA-licensed cytostatic anti-cancer drug 5-fluorouracil (5-FU). Secondary screening and validation studies showed that 5-FU is a potent quorum-quencher, inhibiting AI-2 production and release by MRSA, Staphylococcus epidermidis, Escherichia coli and Vibrio harveyi. 5-FU efficiently reduced adherence and blocked biofilm formation of MRSA in vitro at an order-of-magnitude-lower concentration than that clinically relevant for anti-cancer therapy. Furthermore, 5-FU reestablished antibiotic susceptibility and enabled daptomycin-mediated prevention and clearance of MRSA infection in a mouse model of human implant-associated infection.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Anne-Kathrin Woischnig
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - Vincent Unterreiner
- Novartis Institutes for BioMedical Research (NIBR), Chemical Biology and Therapeutics (CBT), CH-4033, Basel, Switzerland
| | - Florian Fuchs
- Novartis Institutes for BioMedical Research (NIBR), Chemical Biology and Therapeutics (CBT), CH-4033, Basel, Switzerland
| | - Daniel Baeschlin
- Novartis Institutes for BioMedical Research (NIBR), Chemical Biology and Therapeutics (CBT), CH-4033, Basel, Switzerland
| | - Nina Khanna
- Laboratory of Infection Biology, Department of Biomedicine, University and University Hospital Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Basel, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
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17
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Mormile I, Rossi FW, Prevete N, Granata F, Pucino V, de Paulis A. The N-Formyl Peptide Receptors and Rheumatoid Arthritis: A Dangerous Liaison or Confusing Relationship? Front Immunol 2021; 12:685214. [PMID: 34220836 PMCID: PMC8253054 DOI: 10.3389/fimmu.2021.685214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/31/2021] [Indexed: 12/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by a progressive symmetric inflammation of the joints resulting in bone erosion and cartilage destruction with a progressive loss of function and joint deformity. An increased number of findings support the role of innate immunity in RA: many innate immune mechanisms are responsible for producing several cytokines and chemokines involved in RA pathogenesis, such as Tumor Necrosis Factor (TNF)-α, interleukin (IL)-6, and IL-1. Pattern recognition receptors (PRRs) play a crucial role in modulating the activity of the innate arm of the immune response. We focused our attention over the years on the expression and functions of a specific class of PRR, namely formyl peptide receptors (FPRs), which exert a key function in both sustaining and resolving the inflammatory response, depending on the context and/or the agonist. We performed a broad review of the data available in the literature on the role of FPRs and their ligands in RA. Furthermore, we queried a publicly available database collecting data from 90 RA patients with different clinic features to evaluate the possible association between FPRs and clinic-pathologic parameters of RA patients.
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Affiliation(s)
- Ilaria Mormile
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Francesca Wanda Rossi
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), World Allergy Organization (WAO) Center of Excellence, University of Naples Federico II, Naples, Italy
| | - Nella Prevete
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Naples, Italy
| | - Francescopaolo Granata
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Valentina Pucino
- College of Medical and Dental Sciences, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Amato de Paulis
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
- Center for Basic and Clinical Immunology Research (CISI), World Allergy Organization (WAO) Center of Excellence, University of Naples Federico II, Naples, Italy
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18
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Benítez-Chao DF, Balderas-Cisneros FDJ, León-Buitimea A, Morones-Ramírez JR. Design and in silico analysis of a whole-cell biosensor able to kill methicillin-resistant Staphylococcus aureus. Biotechnol Appl Biochem 2021; 69:1373-1382. [PMID: 34081352 DOI: 10.1002/bab.2210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/01/2021] [Indexed: 01/03/2023]
Abstract
The rise of methicillin-resistant Staphylococcus aureus (MRSA) infections has gained concern throughout the world over the past decades. Alternative therapeutic agents to antibiotics are rapidly growing to impede the proliferation of MRSA-caused infections. Lately, synthetic biology techniques have developed whole-cell biosensors by designing gene circuitry capable of sensing quorum-sensing (QS) molecules of pathogens and triggering expression of an antimicrobial moiety that kills MRSA and therefore prevents its further proliferation. Here, an E. coli was engineered in silico to act as a whole-cell biosensor that senses QS molecules from MRSA and triggers the expression of a bacteriocin that kills MRSA. To achieve this functionality, biosensor and bacteriocin modules were constructed and assembled into a vector. Both modules were codon-optimized to increase the yield production of the recombinant proteins. We then demonstrate in silico that the construction of a dual biosensor-killer plasmid, which holds two genetical modules known as biosensor and bacteriocin modules, enables the recombinant host to sense QS molecules from MRSA. Our designed whole-cell biosensor demonstrates in silico its ability to produce and secrete the bacteriocin as a function of the external concentration of autoinducer peptide from MRSA. These in silico results unravel the possibility of designing antimicrobial smarter therapeutics against resistant pathogens.
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Affiliation(s)
- Diego Francisco Benítez-Chao
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Av. Universidad, S/N, Ciudad Universitaria, San Nicolas de los Garza, N.L., 66455, México.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, México
| | - Francisco de Jesús Balderas-Cisneros
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Av. Universidad, S/N, Ciudad Universitaria, San Nicolas de los Garza, N.L., 66455, México.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, México
| | - Angel León-Buitimea
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Av. Universidad, S/N, Ciudad Universitaria, San Nicolas de los Garza, N.L., 66455, México.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, México
| | - José Rubén Morones-Ramírez
- Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Químicas, Av. Universidad, S/N, Ciudad Universitaria, San Nicolas de los Garza, N.L., 66455, México.,Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, Nuevo León, México
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19
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Wu S, Xu C, Liu J, Liu C, Qiao J. Vertical and horizontal quorum-sensing-based multicellular communications. Trends Microbiol 2021; 29:1130-1142. [PMID: 34020859 DOI: 10.1016/j.tim.2021.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022]
Abstract
Quorum sensing (QS) plays an important role in both natural and synthetic microbial systems. The complexity of QS entails multilayer controls, biomolecular crosstalk, and population-based interactions. In this review, we divide complex QS-based interactions into vertical and horizontal interactions. With respect to the former, we discuss QS-based interactions among phages, bacteria, and hosts in natural microbial systems, which are based on various QS signals and hormones. With regard to the latter, we highlight manipulations of QS-based interactions for multicomponent synthetic microbial consortia. We further present the recent and emerging applications of manipulating these interactions (collectively referred to as 'QS communication networks') in natural and synthetic microbiota. Finally, we identify key challenges in engineering diverse QS communication networks for various future applications.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Chengyang Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China.
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20
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Hayashi K, Yamamoto Y, Tamura M, Tokonami S, Iida T. Damage-free light-induced assembly of intestinal bacteria with a bubble-mimetic substrate. Commun Biol 2021; 4:385. [PMID: 33753856 PMCID: PMC7985151 DOI: 10.1038/s42003-021-01807-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
Rapid evaluation of functions in densely assembled bacteria is a crucial issue in the efficient study of symbiotic mechanisms. If the interaction between many living microbes can be controlled and accelerated via remote assembly, a cultivation process requiring a few days can be ommitted, thus leading to a reduction in the time needed to analyze the bacterial functions. Here, we show the rapid, damage-free, and extremely dense light-induced assembly of microbes over a submillimeter area with the "bubble-mimetic substrate (BMS)". In particular, we successfully assembled 104-105 cells of lactic acid bacteria (Lactobacillus casei), achieving a survival rate higher than 95% within a few minutes without cultivation process. This type of light-induced assembly on substrates like BMS, with the maintenance of the inherent functions of various biological samples, can pave the way for the development of innovative methods for rapid and highly efficient analysis of functions in a variety of microbes.
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Affiliation(s)
- Kota Hayashi
- Department of Physical Science, Graduate School of Science, Osaka Prefecture University, Osaka, Japan
- Research Institute for Light-induced Acceleration System (RILACS), Osaka Prefecture University, Osaka, Japan
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan
| | - Yasuyuki Yamamoto
- Department of Physical Science, Graduate School of Science, Osaka Prefecture University, Osaka, Japan
- Research Institute for Light-induced Acceleration System (RILACS), Osaka Prefecture University, Osaka, Japan
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan
| | - Mamoru Tamura
- Department of Physical Science, Graduate School of Science, Osaka Prefecture University, Osaka, Japan
- Research Institute for Light-induced Acceleration System (RILACS), Osaka Prefecture University, Osaka, Japan
| | - Shiho Tokonami
- Research Institute for Light-induced Acceleration System (RILACS), Osaka Prefecture University, Osaka, Japan.
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan.
| | - Takuya Iida
- Department of Physical Science, Graduate School of Science, Osaka Prefecture University, Osaka, Japan.
- Research Institute for Light-induced Acceleration System (RILACS), Osaka Prefecture University, Osaka, Japan.
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21
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Liu J, Yu YT, Xu CH, Chen DC. Candida Colonization in the Respiratory Tract: What Is the Significance? Front Med (Lausanne) 2021; 7:598037. [PMID: 33614672 PMCID: PMC7889970 DOI: 10.3389/fmed.2020.598037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/18/2020] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jiao Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue-Tian Yu
- Department of Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chun-Hui Xu
- Clinical Laboratory Center, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - De-Chang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Lv X, Cui T, Du H, Sun M, Bai F, Li J, Zhang D. Lactobacillus plantarum CY 1-1: A novel quorum quenching bacteria and anti-biofilm agent against Aeromonas sobria. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Wu S, Liu C, Feng J, Yang A, Guo F, Qiao J. QSIdb: quorum sensing interference molecules. Brief Bioinform 2020; 22:5916938. [PMID: 33003203 DOI: 10.1093/bib/bbaa218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/30/2022] Open
Abstract
Quorum sensing interference (QSI), the disruption and manipulation of quorum sensing (QS) in the dynamic control of bacteria populations could be widely applied in synthetic biology to realize dynamic metabolic control and develop potential clinical therapies. Conventionally, limited QSI molecules (QSIMs) were developed based on molecular structures or for specific QS receptors, which are in short supply for various interferences and manipulations of QS systems. In this study, we developed QSIdb (http://qsidb.lbci.net/), a specialized repository of 633 reported QSIMs and 73 073 expanded QSIMs including both QS agonists and antagonists. We have collected all reported QSIMs in literatures focused on the modifications of N-acyl homoserine lactones, natural QSIMs and synthetic QS analogues. Moreover, we developed a pipeline with SMILES-based similarity assessment algorithms and docking-based validations to mine potential QSIMs from existing 138 805 608 compounds in the PubChem database. In addition, we proposed a new measure, pocketedit, for assessing the similarities of active protein pockets or QSIMs crosstalk, and obtained 273 possible potential broad-spectrum QSIMs. We provided user-friendly browsing and searching facilities for easy data retrieval and comparison. QSIdb could assist the scientific community in understanding QS-related therapeutics, manipulating QS-based genetic circuits in metabolic engineering, developing potential broad-spectrum QSIMs and expanding new ligands for other receptors.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Chunjiang Liu
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, China
| | - Jie Feng
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Fei Guo
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University) and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
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24
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Kojima R, Aubel D, Fussenegger M. Building sophisticated sensors of extracellular cues that enable mammalian cells to work as "doctors" in the body. Cell Mol Life Sci 2020; 77:3567-3581. [PMID: 32185403 PMCID: PMC7452942 DOI: 10.1007/s00018-020-03486-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Abstract
Mammalian cells are inherently capable of sensing extracellular environmental signals and activating complex biological functions on demand. Advances in synthetic biology have made it possible to install additional capabilities, which can allow cells to sense the presence of custom biological molecules and provide defined outputs on demand. When implanted/infused in patients, such engineered cells can work as intrabody "doctors" that diagnose disease states and produce and deliver therapeutic molecules when and where necessary. The key to construction of such theranostic cells is the development of a range of sensor systems for detecting various extracellular environmental cues that can be rewired to custom outputs. In this review, we introduce the state-of-art engineering principles utilized in the design of sensor systems to detect soluble factors and also to detect specific cell contact, and we discuss their potential role in treating intractable diseases by delivering appropriate therapeutic functions on demand. We also discuss the challenges facing these emerging technologies.
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Affiliation(s)
- Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Dominque Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland.
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25
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Stephens K, Bentley WE. Synthetic Biology for Manipulating Quorum Sensing in Microbial Consortia. Trends Microbiol 2020; 28:633-643. [DOI: 10.1016/j.tim.2020.03.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022]
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26
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El-Mowafy M, Elgaml A, Shaaban M. New Approaches for Competing Microbial Resistance and Virulence. Microorganisms 2020. [DOI: 10.5772/intechopen.90388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Danchin A, Sekowska A, You C. One-carbon metabolism, folate, zinc and translation. Microb Biotechnol 2020; 13:899-925. [PMID: 32153134 PMCID: PMC7264889 DOI: 10.1111/1751-7915.13550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.
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Affiliation(s)
- Antoine Danchin
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongS.A.R. Hong KongChina
| | - Agnieszka Sekowska
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen University1066 Xueyuan Rd518055ShenzhenChina
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28
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VanArsdale E, Hörnström D, Sjöberg G, Järbur I, Pitzer J, Payne GF, van Maris AJA, Bentley WE. A Coculture Based Tyrosine-Tyrosinase Electrochemical Gene Circuit for Connecting Cellular Communication with Electronic Networks. ACS Synth Biol 2020; 9:1117-1128. [PMID: 32208720 DOI: 10.1021/acssynbio.9b00469] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is a growing interest in mediating information transfer between biology and electronics. By the addition of redox mediators to various samples and cells, one can both electronically obtain a redox "portrait" of a biological system and, conversely, program gene expression. Here, we have created a cell-based synthetic biology-electrochemical axis in which engineered cells process molecular cues, producing an output that can be directly recorded via electronics-but without the need for added redox mediators. The process is robust; two key components must act together to provide a valid signal. The system builds on the tyrosinase-mediated conversion of tyrosine to L-DOPA and L-DOPAquinone, which are both redox active. "Catalytic" transducer cells provide for signal-mediated surface expression of tyrosinase. Additionally, "reagent" transducer cells synthesize and export tyrosine, a substrate for tyrosinase. In cocultures, this system enables real-time electrochemical transduction of cell activating molecular cues. To demonstrate, we eavesdrop on quorum sensing signaling molecules that are secreted by Pseudomonas aeruginosa, N-(3-oxododecanoyl)-l-homoserine lactone and pyocyanin.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - David Hörnström
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Gustav Sjöberg
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Ida Järbur
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - Antonius J. A. van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
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29
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Zhou Z, Chen X, Sheng H, Shen X, Sun X, Yan Y, Wang J, Yuan Q. Engineering probiotics as living diagnostics and therapeutics for improving human health. Microb Cell Fact 2020; 19:56. [PMID: 32131831 PMCID: PMC7055047 DOI: 10.1186/s12934-020-01318-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/26/2020] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota that inhabit our gastrointestinal tract are well known to play an important role in maintaining human health in many aspects, including facilitating the digestion and absorption of nutrients, protecting against pathogens and regulating immune system. Gut microbiota dysbiosis is associated with a lot of diseases, such as inflammatory bowel disease, allergy, obesity, cardiovascular and neurodegenerative diseases and cancers. With the increasing knowledge of the microbiome, utilization of probiotic bacteria in modulating gut microbiota to prevent and treat a large number of disorders and diseases has gained much interest. In recent years, aided by the continuous development of tools and techniques, engineering probiotic microbes with desired characteristics and functionalities to benefit human health has made significant progress. In this paper, we summarize the recent advances in design and construction of probiotics as living diagnostics and therapeutics for probing and treating a series of diseases including metabolic disorders, inflammation and pathogenic bacteria infections. We also discuss the current challenges and future perspectives in expanding the application of probiotics for disease treatment and detection. We intend to provide insights and ideas for engineering of probiotics to better serve disease therapy and human health.
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Affiliation(s)
- Zhao Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15# Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xin Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15# Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Huakang Sheng
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15# Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15# Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15# Beisanhuan East Road, Chaoyang District, Beijing, 100029, China
| | - Yajun Yan
- College of Engineering, The University of Georgia, Athens, GA, 30602, USA
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15# Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15# Beisanhuan East Road, Chaoyang District, Beijing, 100029, China.
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30
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Liang W, Chen K, Gong W, Yoshimura T, Le Y, Wang Y, Wang JM. The Contribution of Chemoattractant GPCRs, Formylpeptide Receptors, to Inflammation and Cancer. Front Endocrinol (Lausanne) 2020; 11:17. [PMID: 32038501 PMCID: PMC6993212 DOI: 10.3389/fendo.2020.00017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/09/2020] [Indexed: 12/14/2022] Open
Abstract
A hallmark of inflammatory responses is leukocyte mobilization, which is mediated by pathogen and host released chemotactic factors that activate Gi-protein-coupled seven-transmembrane receptors (GPCRs) on host cell surface. Formylpeptide receptors (FPRs, Fprs in mice) are members of the chemoattractant GPCR family, shown to be critical in myeloid cell trafficking during infection, inflammation, immune responses, and cancer progression. Accumulating evidence demonstrates that both human FPRs and murine Fprs are involved in a number of patho-physiological processes because of their expression on a wide variety of cell types in addition to myeloid cells. The unique capacity of FPRs (Fprs) to interact with numerous structurally unrelated chemotactic ligands enables these receptors to participate in orchestrated disease initiation, progression, and resolution. One murine Fpr member, Fpr2, and its endogenous agonist peptide, Cathelicidin-related antimicrobial peptide (CRAMP), have been demonstrated as key mediators of colon mucosal homeostasis and protection from inflammation and associated tumorigenesis. Recent availability of genetically engineered mouse models greatly expanded the understanding of the role of FPRs (Fprs) in pathophysiology that places these molecules in the list of potential targets for therapeutic intervention of diseases.
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Affiliation(s)
- Weiwei Liang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
| | - Keqiang Chen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
| | - Wanghua Gong
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Teizo Yoshimura
- Department of Pathology and Experimental Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yingying Le
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Ji Ming Wang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
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31
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Genetic circuitry for personalized human cell therapy. Curr Opin Biotechnol 2019; 59:31-38. [DOI: 10.1016/j.copbio.2019.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/24/2019] [Accepted: 02/04/2019] [Indexed: 01/18/2023]
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32
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Chemotactic Ligands that Activate G-Protein-Coupled Formylpeptide Receptors. Int J Mol Sci 2019; 20:ijms20143426. [PMID: 31336833 PMCID: PMC6678346 DOI: 10.3390/ijms20143426] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 12/14/2022] Open
Abstract
Leukocyte infiltration is a hallmark of inflammatory responses. This process depends on the bacterial and host tissue-derived chemotactic factors interacting with G-protein-coupled seven-transmembrane receptors (GPCRs) expressed on the cell surface. Formylpeptide receptors (FPRs in human and Fprs in mice) belong to the family of chemoattractant GPCRs that are critical mediators of myeloid cell trafficking in microbial infection, inflammation, immune responses and cancer progression. Both murine Fprs and human FPRs participate in many patho-physiological processes due to their expression on a variety of cell types in addition to myeloid cells. FPR contribution to numerous pathologies is in part due to its capacity to interact with a plethora of structurally diverse chemotactic ligands. One of the murine Fpr members, Fpr2, and its endogenous agonist peptide, Cathelicidin-related antimicrobial peptide (CRAMP), control normal mouse colon epithelial growth, repair and protection against inflammation-associated tumorigenesis. Recent developments in FPR (Fpr) and ligand studies have greatly expanded the scope of these receptors and ligands in host homeostasis and disease conditions, therefore helping to establish these molecules as potential targets for therapeutic intervention.
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33
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Fleitas Martínez O, Cardoso MH, Ribeiro SM, Franco OL. Recent Advances in Anti-virulence Therapeutic Strategies With a Focus on Dismantling Bacterial Membrane Microdomains, Toxin Neutralization, Quorum-Sensing Interference and Biofilm Inhibition. Front Cell Infect Microbiol 2019; 9:74. [PMID: 31001485 PMCID: PMC6454102 DOI: 10.3389/fcimb.2019.00074] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/05/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance constitutes one of the major challenges facing humanity in the Twenty-First century. The spread of resistant pathogens has been such that the possibility of returning to a pre-antibiotic era is real. In this scenario, innovative therapeutic strategies must be employed to restrict resistance. Among the innovative proposed strategies, anti-virulence therapy has been envisioned as a promising alternative for effective control of the emergence and spread of resistant pathogens. This review presents some of the anti-virulence strategies that are currently being developed, it will cover strategies focused on quench pathogen quorum sensing (QS) systems, disassemble of bacterial functional membrane microdomains (FMMs), disruption of biofilm formation and bacterial toxin neutralization.
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Affiliation(s)
- Osmel Fleitas Martínez
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Marlon Henrique Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Suzana Meira Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Octavio Luiz Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
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34
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Wilken SE, Swift CL, Podolsky IA, Lankiewicz TS, Seppälä S, O'Malley MA. Linking ‘omics’ to function unlocks the biotech potential of non-model fungi. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Scheller L, Fussenegger M. From synthetic biology to human therapy: engineered mammalian cells. Curr Opin Biotechnol 2019; 58:108-116. [PMID: 30933864 DOI: 10.1016/j.copbio.2019.02.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/07/2019] [Accepted: 02/28/2019] [Indexed: 01/05/2023]
Abstract
Mammalian synthetic biology has evolved to become a key driver of biomedical innovation in the area of cell therapy. Advances in receptor engineering, immunotherapy and cell implants promise new treatment options for complex diseases. Synthetic receptors have already found applications in cellular immunotherapy for cancer treatment, and are being introduced into the field of cell implants. Here, we discuss prospects for the next generation of engineered mammalian cells for human therapy, highlighting selected recent studies.
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Affiliation(s)
- Leo Scheller
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland; University of Basel, Faculty of Science, Mattenstrasse 26, CH-4058, Basel, Switzerland.
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36
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Kojima R, Fussenegger M. Synthetic Biology: Engineering Mammalian Cells To Control Cell-to-Cell Communication at Will. Chembiochem 2019; 20:994-1002. [PMID: 30589185 DOI: 10.1002/cbic.201800682] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Indexed: 12/12/2022]
Abstract
Cell-to-cell communication plays a key role in the regulation of many natural biological processes. Recent advances in mammalian synthetic biology are making it possible to rationally engineer cell-to-cell communication for therapeutic and other purposes. Here, we review state-of-the-art engineering principles to control cell-to-cell communication, focusing on communication between mammalian cells with diffusible factors (e.g., small molecules or exosomes) or direct cell contact, and on interkingdom communication between mammalian cells and bacteria. Potential applications include construction of artificial tissues able to perform complex computations, sophisticated cell-based cancer therapies, use of mammalian cells as a new class of cargo delivery modality, development of design principles to control pattern formation of cell populations, and treatment of infectious diseases. We also discuss the challenges facing practical applications, and possible enabling technologies to overcome them.
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Affiliation(s)
- Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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37
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Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
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Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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38
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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