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Rostovsky I, Wieler U, Kuzmina A, Taube R, Sal-Man N. Secretion of functional interferon by the type 3 secretion system of enteropathogenic Escherichia coli. Microb Cell Fact 2024; 23:163. [PMID: 38824527 PMCID: PMC11144349 DOI: 10.1186/s12934-024-02397-y] [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: 02/12/2024] [Accepted: 04/18/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Type I interferons (IFN-I)-a group of cytokines with immunomodulatory, antiproliferative, and antiviral properties-are widely used as therapeutics for various cancers and viral diseases. Since IFNs are proteins, they are highly susceptible to degradation by proteases and by hydrolysis in the strong acid environment of the stomach, and they are therefore administered parenterally. In this study, we examined whether the intestinal bacterium, enteropathogenic Escherichia coli (EPEC), can be exploited for oral delivery of IFN-Is. EPEC survives the harsh conditions of the stomach and, upon reaching the small intestine, expresses a type III secretion system (T3SS) that is used to translocate effector proteins across the bacterial envelope into the eukaryotic host cells. RESULTS In this study, we developed an attenuated EPEC strain that cannot colonize the host but can secrete functional human IFNα2 variant through the T3SS. We found that this bacteria-secreted IFN exhibited antiproliferative and antiviral activities similar to commercially available IFN. CONCLUSION These findings present a potential novel approach for the oral delivery of IFN via secreting bacteria.
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Affiliation(s)
- Irina Rostovsky
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel
| | - Uri Wieler
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel
| | - Alona Kuzmina
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel
| | - Ran Taube
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel
| | - Neta Sal-Man
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel.
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2
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Babamohamadi M, Mohammadi N, Faryadi E, Haddadi M, Merati A, Ghobadinezhad F, Amirian R, Izadi Z, Hadjati J. Anti-CTLA-4 nanobody as a promising approach in cancer immunotherapy. Cell Death Dis 2024; 15:17. [PMID: 38191571 PMCID: PMC10774412 DOI: 10.1038/s41419-023-06391-x] [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: 06/21/2023] [Revised: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
Cancer is one of the most common diseases and causes of death worldwide. Since common treatment approaches do not yield acceptable results in many patients, developing innovative strategies for effective treatment is necessary. Immunotherapy is one of the promising approaches that has been highly regarded for preventing tumor recurrence and new metastases. Meanwhile, inhibiting immune checkpoints is one of the most attractive methods of cancer immunotherapy. Cytotoxic T lymphocyte-associated protein-4 (CTLA-4) is an essential immune molecule that plays a vital role in cell cycle modulation, regulation of T cell proliferation, and cytokine production. This molecule is classically expressed by stimulated T cells. Inhibition of overexpression of immune checkpoints such as CTLA-4 receptors has been confirmed as an effective strategy. In cancer immunotherapy, immune checkpoint-blocking drugs can be enhanced with nanobodies that target immune checkpoint molecules. Nanobodies are derived from the variable domain of heavy antibody chains. These small protein fragments have evolved entirely without a light chain and can be used as a powerful tool in imaging and treating diseases with their unique structure. They have a low molecular weight, which makes them smaller than conventional antibodies while still being able to bind to specific antigens. In addition to low molecular weight, specific binding to targets, resistance to temperature, pH, and enzymes, high ability to penetrate tumor tissues, and low toxicity make nanobodies an ideal approach to overcome the disadvantages of monoclonal antibody-based immunotherapy. In this article, while reviewing the cellular and molecular functions of CTLA-4, the structure and mechanisms of nanobodies' activity, and their delivery methods, we will explain the advantages and challenges of using nanobodies, emphasizing immunotherapy treatments based on anti-CTLA-4 nanobodies.
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Affiliation(s)
- Mehregan Babamohamadi
- Department of Biology, School of Natural Sciences, University of Tabriz, Tabriz, Iran
- Stem Cell and Regenerative Medicine Innovation Center, Tehran University of Medical Sciences, Tehran, Iran
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nastaran Mohammadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Faryadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Maryam Haddadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhossein Merati
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Medical Laboratory Sciences, School of Paramedical, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farbod Ghobadinezhad
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Roshanak Amirian
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Zhila Izadi
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Jamshid Hadjati
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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3
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Asensio‐Calavia A, Ceballos‐Munuera Á, Méndez‐Pérez A, Álvarez B, Fernández LÁ. A tuneable genetic switch for tight control of tac promoters in Escherichia coli boosts expression of synthetic injectisomes. Microb Biotechnol 2024; 17:e14328. [PMID: 37608576 PMCID: PMC10832536 DOI: 10.1111/1751-7915.14328] [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: 04/25/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023] Open
Abstract
Biosafety of engineered bacteria as living therapeutics requires a tight regulation to control the specific delivery of protein effectors, maintaining minimum leakiness in the uninduced (OFF) state and efficient expression in the induced (ON) state. Here, we report a three repressors (3R) genetic circuit that tightly regulates the expression of multiple tac promoters (Ptac) integrated in the chromosome of E. coli and drives the expression of a complex type III secretion system injectisome for therapeutic protein delivery. The 3R genetic switch is based on the tetracycline repressor (TetR), the non-inducible lambda repressor cI (ind-) and a mutant lac repressor (LacIW220F ) with higher activity. The 3R switch was optimized with different protein translation and degradation signals that control the levels of LacIW220F . We demonstrate the ability of an optimized switch to fully repress the strong leakiness of the Ptac promoters in the OFF state while triggering their efficient activation in the ON state with anhydrotetracycline (aTc), an inducer suitable for in vivo use. The implementation of the optimized 3R switch in the engineered synthetic injector E. coli (SIEC) strain boosts expression of injectisomes upon aTc induction, while maintaining a silent OFF state that preserves normal growth in the absence of the inducer. Since Ptac is a commonly used promoter, the 3R switch may have multiple applications for tight control of protein expression in E. coli. In addition, the modularity of the 3R switch may enable its tuning for the control of Ptac promoters with different inducers.
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Affiliation(s)
- Alejandro Asensio‐Calavia
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Álvaro Ceballos‐Munuera
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Almudena Méndez‐Pérez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
- Programa de Doctorado en Biociencias MolecularesUniversidad Autónoma de Madrid (UAM)MadridSpain
| | - Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
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4
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Lynch JP, González-Prieto C, Reeves AZ, Bae S, Powale U, Godbole NP, Tremblay JM, Schmidt FI, Ploegh HL, Kansra V, Glickman JN, Leong JM, Shoemaker CB, Garrett WS, Lesser CF. Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut. Cell Host Microbe 2023; 31:634-649.e8. [PMID: 37003258 PMCID: PMC10101937 DOI: 10.1016/j.chom.2023.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/20/2022] [Accepted: 03/08/2023] [Indexed: 04/03/2023]
Abstract
Drug platforms that enable the directed delivery of therapeutics to sites of diseases to maximize efficacy and limit off-target effects are needed. Here, we report the development of PROT3EcT, a suite of commensal Escherichia coli engineered to secrete proteins directly into their surroundings. These bacteria consist of three modular components: a modified bacterial protein secretion system, the associated regulatable transcriptional activator, and a secreted therapeutic payload. PROT3EcT secrete functional single-domain antibodies, nanobodies (Nbs), and stably colonize and maintain an active secretion system within the intestines of mice. Furthermore, a single prophylactic dose of a variant of PROT3EcT that secretes a tumor necrosis factor-alpha (TNF-α)-neutralizing Nb is sufficient to ablate pro-inflammatory TNF levels and prevent the development of injury and inflammation in a chemically induced model of colitis. This work lays the foundation for developing PROT3EcT as a platform for the treatment of gastrointestinal-based diseases.
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Affiliation(s)
- Jason P Lynch
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Coral González-Prieto
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Analise Z Reeves
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sena Bae
- Departments of Immunology and Infectious Diseases and Harvard T.H. Chan Center for the Microbiome in Public Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Urmila Powale
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Neha P Godbole
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jacqueline M Tremblay
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA
| | - Florian I Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Hidde L Ploegh
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - Jonathan N Glickman
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - John M Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA; Tufts Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA 02111, USA
| | - Charles B Shoemaker
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA; Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Wendy S Garrett
- Departments of Immunology and Infectious Diseases and Harvard T.H. Chan Center for the Microbiome in Public Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of Harvard and MIT, Cambridge, MA 02139, USA.
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5
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Guzmán-Herrador DL, Fernández-Gómez A, Llosa M. Recruitment of heterologous substrates by bacterial secretion systems for transkingdom translocation. Front Cell Infect Microbiol 2023; 13:1146000. [PMID: 36949816 PMCID: PMC10025392 DOI: 10.3389/fcimb.2023.1146000] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
Bacterial secretion systems mediate the selective exchange of macromolecules between bacteria and their environment, playing a pivotal role in processes such as horizontal gene transfer or virulence. Among the different families of secretion systems, Type III, IV and VI (T3SS, T4SS and T6SS) share the ability to inject their substrates into human cells, opening up the possibility of using them as customized injectors. For this to happen, it is necessary to understand how substrates are recruited and to be able to engineer secretion signals, so that the transmembrane machineries can recognize and translocate the desired substrates in place of their own. Other factors, such as recruiting proteins, chaperones, and the degree of unfolding required to cross through the secretion channel, may also affect transport. Advances in the knowledge of the secretion mechanism have allowed heterologous substrate engineering to accomplish translocation by T3SS, and to a lesser extent, T4SS and T6SS into human cells. In the case of T4SS, transport of nucleoprotein complexes adds a bonus to its biotechnological potential. Here, we review the current knowledge on substrate recognition by these secretion systems, the many examples of heterologous substrate translocation by engineering of secretion signals, and the current and future biotechnological and biomedical applications derived from this approach.
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The Oncobiome in Gastroenteric and Genitourinary Cancers. Int J Mol Sci 2022; 23:ijms23179664. [PMID: 36077063 PMCID: PMC9456244 DOI: 10.3390/ijms23179664] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 12/24/2022] Open
Abstract
Early evidence suggests a strong association of microorganisms with several human cancers, and great efforts have been made to understand the pathophysiology underlying microbial carcinogenesis. Bacterial dysbiosis causes epithelial barrier failure, immune dysregulation and/or genotoxicity and, consequently, creates a tumor-permissive microenvironment. The majority of the bacteria in our body reside in the gastrointestinal tract, known as gut microbiota, which represents a complex and delicate ecosystem. Gut microbes can reach the pancreas, stomach and colon via the bloodstream. Oral bacterial translocations can also occur. In the stomach, pancreas and colon, low microbial diversity is associated with cancer, in particular with a bad prognosis. The urogenital tract also harbors unique microbiota, distinct from the gut microbiota, which might have a role in the urinary and female/male reproductive cancers’ pathogenesis. In healthy women, the majority of bacteria reside in the vagina and cervix and unlike other mucosal sites, the vaginal microbiota exhibits low microbial diversity. Genital dysbiosis might have an active role in the development and/or progression of gynecological malignancies through mechanisms including modulation of oestrogen metabolism. Urinary dysbiosis may influence the pathogenesis of bladder cancer and prostate cancer in males. Modulation of the microbiome via pre, pro and postbiotics, fecal or vaginal microbiota transplantation and engineering bacteria might prove useful in improving cancer treatment response and quality of life. Elucidating the complex host-microbiome interactions will result in prevention and therapeutic efficacy interventions.
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7
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Álvarez B, Muñoz-Abad V, Asensio-Calavia A, Fernández LÁ. Enhanced protein translocation to mammalian cells by expression of EtgA transglycosylase in a synthetic injector E. coli strain. Microb Cell Fact 2022; 21:133. [PMID: 35780105 PMCID: PMC9250224 DOI: 10.1186/s12934-022-01860-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/23/2022] [Indexed: 12/29/2022] Open
Abstract
Background Bacterial type III secretion systems (T3SSs) assemble a multiprotein complex termed the injectisome, which acts as a molecular syringe for translocation of specific effector proteins into the cytoplasm of host cells. The use of injectisomes for delivery of therapeutic proteins into mammalian cells is attractive for biomedical applications. With that aim, we previously generated a non-pathogenic Escherichia coli strain, called Synthetic Injector E. coli (SIEC), which assembles functional injectisomes from enteropathogenic E. coli (EPEC). The assembly of injectisomes in EPEC is assisted by the lytic transglycosylase EtgA, which degrades the peptidoglycan layer. As SIEC lacks EtgA, we investigated whether expression of this transglycosylase enhances the protein translocation capacity of the engineered bacterium. Results The etgA gene from EPEC was integrated into the SIEC chromosome under the control of the inducible tac promoter, generating the strain SIEC-eEtgA. The controlled expression of EtgA had no effect on the growth or viability of bacteria. Upon induction, injectisome assembly was ~ 30% greater in SIEC-eEtgA than in the parental strain, as determined by the level of T3SS translocon proteins, the hemolytic activity of the bacterial strain, and the impairment in flagellar motility. The functionality of SIEC-eEtgA injectisomes was evaluated in a derivative strain carrying a synthetic operon (eLEE5), which was capable of delivering Tir effector protein into the cytoplasm of HeLa cells triggering F-actin polymerization beneath the attached bacterium. Lastly, using β-lactamase as a reporter of T3SS-protein injection, we determined that the protein translocation capacity was ~ 65% higher in the SIEC-EtgA strain than in the parental SIEC strain. Conclusions We demonstrate that EtgA enhances the assembly of functional injectisomes in a synthetic injector E. coli strain, enabling the translocation of greater amounts of proteins into the cytoplasm of mammalian cells. Accordingly, EtgA expression may boost the protein translocation of SIEC strains programmed as living biotherapeutics.
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Affiliation(s)
- Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain
| | - Víctor Muñoz-Abad
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain.,Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid (UAM), Campus Cantoblanco, 28049, Madrid, Spain.,Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Nicolas Cabrera 1, Campus Cantoblanco, 28049, Madrid, Spain
| | - Alejandro Asensio-Calavia
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain.,Programa de Doctorado en Biociencias Moleculares, Universidad Autónoma de Madrid (UAM), Campus Cantoblanco, 28049, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus Cantoblanco, 28049, Madrid, Spain.
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Cable J, Leonard JN, Lu TK, Xie Z, Chang MW, Fernández LÁ, Lora JM, Kaufman HL, Quintana FJ, Geiger R, F Lesser C, Lynch JP, Hava DL, Cornish VW, Lee GK, DiAndreth B, Fero M, Srivastava R, De Coster T, Roybal KT, Rackham OJL, Kiani S, Zhu I, Hernandez-Lopez RA, Guo T, Chen WCW. Synthetic biology: at the crossroads of genetic engineering and human therapeutics-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:98-117. [PMID: 34786712 DOI: 10.1111/nyas.14710] [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: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/12/2022]
Abstract
Synthetic biology has the potential to transform cell- and gene-based therapies for a variety of diseases. Sophisticated tools are now available for both eukaryotic and prokaryotic cells to engineer cells to selectively achieve therapeutic effects in response to one or more disease-related signals, thus sparing healthy tissue from potentially cytotoxic effects. This report summarizes the Keystone eSymposium "Synthetic Biology: At the Crossroads of Genetic Engineering and Human Therapeutics," which took place on May 3 and 4, 2021. Given that several therapies engineered using synthetic biology have entered clinical trials, there was a clear need for a synthetic biology symposium that emphasizes the therapeutic applications of synthetic biology as opposed to the technical aspects. Presenters discussed the use of synthetic biology to improve T cell, gene, and viral therapies, to engineer probiotics, and to expand upon existing modalities and functions of cell-based therapies.
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Affiliation(s)
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Interdisciplinary Biological Sciences Program, Chemistry of Life Processes Institute; and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois
| | - Timothy K Lu
- Research Lab of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Senti Biosciences, South San Francisco, California
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Matthew Wook Chang
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - José M Lora
- Intergalactic Therapeutics, Cambridge, Massachusetts
| | - Howard L Kaufman
- Division of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston and The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Roger Geiger
- Institute for Research in Biomedicine, and Institute of Oncology Research, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Cammie F Lesser
- Department of Microbiology, Blavatnik Institute, Harvard Medical School and Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jason P Lynch
- Department of Microbiology, Blavatnik Institute, Harvard Medical School and Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - David L Hava
- Research Lab of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Gary K Lee
- Senti Biosciences, South San Francisco, California
| | | | - Michael Fero
- TeselaGen Biotechnology, San Francisco, California
| | - Rajkamal Srivastava
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute (HBNI), Kolkata, India
| | - Tim De Coster
- Laboratory of Experimental Cardiology, Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Kole T Roybal
- Department of Microbiology and Immunology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.,Chan Zuckerberg Biohub; Parker Institute for Cancer Immunotherapy, Gladstone-UCSF Institute for Genomic Immunology; and UCSF Cell Design Institute, San Francisco, California
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore
| | - Samira Kiani
- Division of Experimental Pathology, Department of Pathology, School of Medicine; and Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Iowis Zhu
- University of California, San Francisco, San Francisco, California
| | - Rogelio A Hernandez-Lopez
- Cell Design Institute, Department of Cellular and Molecular Pharmacology; and Center for Cellular Construction, University of California San Francisco, San Francisco, California
| | - Tingxi Guo
- Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - William C W Chen
- Research Laboratory of Electronics and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge; and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
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9
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Traenkle B, Segan S, Fagbadebo FO, Kaiser PD, Rothbauer U. A novel epitope tagging system to visualize and monitor antigens in live cells with chromobodies. Sci Rep 2020; 10:14267. [PMID: 32868807 PMCID: PMC7459311 DOI: 10.1038/s41598-020-71091-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Epitope tagging is a versatile approach to study different proteins using a well-defined and established methodology. To date, most epitope tags such as myc, HA, V5 and FLAG tags are recognized by antibodies, which limits their use to fixed cells, tissues or protein samples. Here we introduce a broadly applicable tagging strategy utilizing a short peptide tag (PepTag) which is specifically recognized by a nanobody (PepNB). We demonstrated that the PepNB can be easily functionalized for immunoprecipitation or direct immunofluorescence staining of Pep-tagged proteins in vitro. For in cellulo studies we converted the PepNB into a fluorescently labeled Pep-chromobody (PepCB) which is functionally expressed in living cells. The addition of the small PepTag does not interfere with the examined structures in different cellular compartments and its detection with the PepCB enables optical antigen tracing in real time. By employing the phenomenon of antigen-mediated chromobody stabilization (AMCBS) using a turnover-accelerated PepCB we demonstrated that the system is suitable to visualize and quantify changes in Pep-tagged antigen concentration by quantitative live-cell imaging. We expect that this novel tagging strategy offers new opportunities to study the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
- Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany.,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Sören Segan
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | | | - Philipp D Kaiser
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany. .,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany.
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10
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Zhang C, Ötjengerdes RM, Roewe J, Mejias R, Marschall ALJ. Applying Antibodies Inside Cells: Principles and Recent Advances in Neurobiology, Virology and Oncology. BioDrugs 2020; 34:435-462. [PMID: 32301049 PMCID: PMC7391400 DOI: 10.1007/s40259-020-00419-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To interfere with cell function, many scientists rely on methods that target DNA or RNA due to the ease with which they can be applied. Proteins are usually the final executors of function but are targeted only indirectly by these methods. Recent advances in targeted degradation of proteins based on proteolysis-targeting chimaeras (PROTACs), ubiquibodies, deGradFP (degrade Green Fluorescent Protein) and other approaches have demonstrated the potential of interfering directly at the protein level for research and therapy. Proteins can be targeted directly and very specifically by antibodies, but using antibodies inside cells has so far been considered to be challenging. However, it is possible to deliver antibodies or other proteins into the cytosol using standard laboratory equipment. Physical methods such as electroporation have been demonstrated to be efficient and validated thoroughly over time. The expression of intracellular antibodies (intrabodies) inside cells is another way to interfere with intracellular targets at the protein level. Methodological strategies to target the inside of cells with antibodies, including delivered antibodies and expressed antibodies, as well as applications in the research areas of neurobiology, viral infections and oncology, are reviewed here. Antibodies have already been used to interfere with a wide range of intracellular targets. Disease-related targets included proteins associated with neurodegenerative diseases such as Parkinson's disease (α-synuclein), Alzheimer's disease (amyloid-β) or Huntington's disease (mutant huntingtin [mHtt]). The applications of intrabodies in the context of viral infections include targeting proteins associated with HIV (e.g. HIV1-TAT, Rev, Vif, gp41, gp120, gp160) and different oncoviruses such as human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV) and Epstein-Barr virus, and they have been used to interfere with various targets related to different processes in cancer, including oncogenic pathways, proliferation, cell cycle, apoptosis, metastasis, angiogenesis or neo-antigens (e.g. p53, human epidermal growth factor receptor-2 [HER2], signal transducer and activator of transcription 3 [STAT3], RAS-related RHO-GTPase B (RHOB), cortactin, vascular endothelial growth factor receptor 2 [VEGFR2], Ras, Bcr-Abl). Interfering at the protein level allows questions to be addressed that may remain unanswered using alternative methods. This review addresses why direct targeting of proteins allows unique insights, what is currently feasible in vitro, and how this relates to potential therapeutic applications.
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Affiliation(s)
- Congcong Zhang
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rina M Ötjengerdes
- Hannover Medical School (MHH), Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Julian Roewe
- German Cancer Consortium (DKTK) Clinical Cooperation Unit (CCU) Neuroimmunology and Brain TumorImmunology (D170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rebeca Mejias
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea L J Marschall
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Brunswick, Germany.
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11
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Yang EY, Shah K. Nanobodies: Next Generation of Cancer Diagnostics and Therapeutics. Front Oncol 2020; 10:1182. [PMID: 32793488 PMCID: PMC7390931 DOI: 10.3389/fonc.2020.01182] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
The development of targeted medicine has greatly expanded treatment options and spurred new research avenues in cancer therapeutics, with monoclonal antibodies (mAbs) emerging as a prevalent treatment in recent years. With mixed clinical success, mAbs still hold significant shortcomings, as they possess limited tumor penetration, high manufacturing costs, and the potential to develop therapeutic resistance. However, the recent discovery of “nanobodies,” the smallest-known functional antibody fragment, has demonstrated significant translational potential in preclinical and clinical studies. This review highlights their various applications in cancer and analyzes their trajectory toward their translation into the clinic.
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Affiliation(s)
- Emily Y Yang
- Center for Stem Cell Therapeutics and Imaging, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Departments of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
| | - Khalid Shah
- Center for Stem Cell Therapeutics and Imaging, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Departments of Neurosurgery, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, United States
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12
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Hebbrecht T, Liu J, Zwaenepoel O, Boddin G, Van Leene C, Decoene K, Madder A, Braeckmans K, Gettemans J. Nanobody click chemistry for convenient site-specific fluorescent labelling, single step immunocytochemistry and delivery into living cells by photoporation and live cell imaging. N Biotechnol 2020; 59:33-43. [PMID: 32659511 DOI: 10.1016/j.nbt.2020.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/20/2020] [Accepted: 05/23/2020] [Indexed: 12/18/2022]
Abstract
While conventional antibodies have been an instrument of choice in immunocytochemistry for some time, their small counterparts known as nanobodies have been much less frequently used for this purpose. In this study we took advantage of the availability of nanobody cDNAs to site-specifically introduce a non-standard amino acid carrying an azide/alkyne moiety, allowing subsequent Cu(I)-catalyzed Azide-Alkyne Click Chemistry (CuAAC). This generated a fluorescently labelled nanobody that can be used in single step immunocytochemistry as compared to conventional two step immunocytochemistry. Two strategies were explored to label nanobodies with Alexa Fluor 488. The first involved enzymatic addition of an alkyne-containing peptide to nanobodies using sortase A, while the second consisted of incorporating para-azido phenylalanine at the nanobody C-terminus. Through these approaches, the fluorophore was covalently and site-specifically attached. It was demonstrated that cortactin and β-catenin, cytoskeletal and adherens junction proteins respectively, can be imaged in cells in this manner through single step immunocytochemistry. However, fixation and permeabilization of cells can alter native protein structure and form a dense cross-linked protein network, encumbering antibody binding. It was shown that photoporation prior to fixation not only allowed delivery of nanobodies into living cells, but also facilitated β-catenin nanobody Nb86 imaging of its target, which was not possible in fixed cells. Pharmacological inhibitors are lacking for many non-enzymatic proteins, and it is therefore expected that new biological information will be obtained through photoporation of fluorescent nanobodies, which allows the study of short term effects, independent of gene-dependent (intrabody) expression.
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Affiliation(s)
- Tim Hebbrecht
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Jing Liu
- Laboratory of General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent B-9000, Belgium
| | - Olivier Zwaenepoel
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Gaëlle Boddin
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Chloé Van Leene
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Klaas Decoene
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Ghent B-9000, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Ghent B-9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Ghent University, Ghent B-9000, Belgium; Center for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
| | - Jan Gettemans
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium.
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13
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Salmonella-based platform for efficient delivery of functional binding proteins to the cytosol. Commun Biol 2020; 3:342. [PMID: 32620833 PMCID: PMC7335062 DOI: 10.1038/s42003-020-1072-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/11/2020] [Indexed: 12/23/2022] Open
Abstract
Protein-based affinity reagents (like antibodies or alternative binding scaffolds) offer wide-ranging applications for basic research and therapeutic approaches. However, whereas small chemical molecules efficiently reach intracellular targets, the delivery of macromolecules into the cytosol of cells remains a major challenge; thus cytosolic applications of protein-based reagents are rather limited. Some pathogenic bacteria have evolved a conserved type III secretion system (T3SS) which allows the delivery of effector proteins into eukaryotic cells. Here, we enhance the T3SS of an avirulent strain of Salmonella typhimurium to reproducibly deliver multiple classes of recombinant proteins into eukaryotic cells. The efficacy of the system is probed with both DARPins and monobodies to functionally inhibit the paradigmatic and largely undruggable RAS signaling pathway. Thus, we develop a bacterial secretion system for potent cytosolic delivery of therapeutic macromolecules. To develop a bacterial secretion system for cytosolic delivery of therapeutic macromolecules, Chabloz et al. improve an “effectorless” Salmonella strain and combine it with a plasmid modified to boost the secretion of proteins of interest. With this system, they demonstrate efficient translocation of functional DARPins and monobodies into the cytosol of different eukaryotic cells lines and successfully block the paradigmatic RAS pathway.
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14
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LITESEC-T3SS - Light-controlled protein delivery into eukaryotic cells with high spatial and temporal resolution. Nat Commun 2020; 11:2381. [PMID: 32404906 PMCID: PMC7221075 DOI: 10.1038/s41467-020-16169-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/18/2020] [Indexed: 12/16/2022] Open
Abstract
Many bacteria employ a type III secretion system (T3SS) injectisome to translocate proteins into eukaryotic host cells. Although the T3SS can efficiently export heterologous cargo proteins, a lack of target cell specificity currently limits its application in biotechnology and healthcare. In this study, we exploit the dynamic nature of the T3SS to govern its activity. Using optogenetic interaction switches to control the availability of the dynamic cytosolic T3SS component SctQ, T3SS-dependent effector secretion can be regulated by light. The resulting system, LITESEC-T3SS (Light-induced translocation of effectors through sequestration of endogenous components of the T3SS), allows rapid, specific, and reversible activation or deactivation of the T3SS upon illumination. We demonstrate the light-regulated translocation of heterologous reporter proteins, and induction of apoptosis in cultured eukaryotic cells. LITESEC-T3SS constitutes a new method to control protein secretion and translocation into eukaryotic host cells with unparalleled spatial and temporal resolution.
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15
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Abstract
Humans are a colonized with trillions of commensal microorganisms which exert a profound effect on normal host physiology and immune function through an abundance of genetic and metabolic by-products. Although the commensal microbiome has beneficial functions to host physiology, perturbations of the composition of the commensal microbiome or the homeostatic mucosal environment can lead to the induction of immune pathology and systemic inflammation. In the context of cancer progression or response to immune therapy, this inflammation can be detrimental, resulting in tumor growth and the promotion of immune suppression. On the other hand, significant associations have been identified whereby certain commensal microorganisms are able to enhance T cell function or are required for tumor control in cancer patients treated with certain immune therapies and chemotherapies. The focus of this chapter is to highlight the role of the commensal microbiome during tumor progression and in response to immune therapies.
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16
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Keller BM, Maier J, Secker KA, Egetemaier SM, Parfyonova Y, Rothbauer U, Traenkle B. Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells. Mol Cell Proteomics 2018; 17:2518-2533. [PMID: 30228193 DOI: 10.1074/mcp.tir118.000914] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/04/2018] [Indexed: 11/06/2022] Open
Abstract
Understanding cellular processes requires the determination of dynamic changes in the concentration of genetically nonmodified, endogenous proteins, which, to date, is commonly accomplished by end-point assays in vitro Molecular probes such as fluorescently labeled nanobodies (chromobodies, CBs) are powerful tools to visualize the dynamic subcellular localization of endogenous proteins in living cells. Here, we employed the dependence of intracellular levels of chromobodies on the amount of their endogenous antigens, a phenomenon, which we termed antigen-mediated CB stabilization (AMCBS), for simultaneous monitoring of time-resolved changes in the concentration and localization of native proteins. To improve the dynamic range of AMCBS we generated turnover-accelerated CBs and demonstrated their application in visualization and quantification of fast reversible changes in antigen concentration upon compound treatment by quantitative live-cell imaging. We expect that this broadly applicable strategy will enable unprecedented insights into the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
| | - Julia Maier
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Kathy-Ann Secker
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | | | - Yana Parfyonova
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany; Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
| | - Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany.
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17
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Allegra A, Innao V, Gerace D, Vaddinelli D, Allegra AG, Musolino C. Nanobodies and Cancer: Current Status and New Perspectives. Cancer Invest 2018; 36:221-237. [DOI: 10.1080/07357907.2018.1458858] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Vanessa Innao
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Demetrio Gerace
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Doriana Vaddinelli
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Andrea Gaetano Allegra
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
| | - Caterina Musolino
- Division of Hematology, Dipartimento di Patologia Umana dell'Adulto e dell'Età evolutiva, University of Messina, Messina, Italy
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18
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Bai F, Li Z, Umezawa A, Terada N, Jin S. Bacterial type III secretion system as a protein delivery tool for a broad range of biomedical applications. Biotechnol Adv 2018; 36:482-493. [PMID: 29409784 DOI: 10.1016/j.biotechadv.2018.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/08/2018] [Accepted: 01/30/2018] [Indexed: 12/16/2022]
Abstract
A protein delivery tool based on bacterial type III secretion system (T3SS) has been broadly applied in biomedical researches. In this review, we summarize various applications of the T3SS-mediate protein delivery which enables translocation of proteins directly into mammalian cells without protein purification. Some of the remarkable advancements include delivery of antigens for therapeutic vaccines, nucleases for genome editing, transcription factors for cellular reprogramming and stem cells differentiation, and signaling molecules for post-translational proteomics studies. With continued improvement of the T3SS-mediated protein delivery tools, even wider application of the technology is anticipated.
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Affiliation(s)
- Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhenpeng Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Akihiro Umezawa
- Department of Reproductive Biology, National Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Naohiro Terada
- Department of Pathology College of Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States.
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19
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Rationale redesign of type III secretion systems: toward the development of non-pathogenic E. coli for in vivo delivery of therapeutic payloads. Curr Opin Microbiol 2017; 41:1-7. [PMID: 29141238 DOI: 10.1016/j.mib.2017.10.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 12/12/2022]
Abstract
Transkingdom secretion systems that bacteria use to inject proteins directly into the cytosol of mammalian host cells play an essential role in the virulence of many Gram-negative bacterial pathogens. Current efforts are underway to repurpose these machines as novel therapeutics; type III secretion systems as vectors for the delivery of proteins of therapeutic value including heterologous antigens for vaccine development and type IV secretion systems as vectors for DNA. While initial studies focused on the use of attenuated or replication incompetent pathogens, the recent development of non-pathogenic Escherichia coli that encode programmable type III secretion systems expands possibilities for the in vivo directed delivery of therapeutic payloads.
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20
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Hu Y, Liu C, Muyldermans S. Nanobody-Based Delivery Systems for Diagnosis and Targeted Tumor Therapy. Front Immunol 2017; 8:1442. [PMID: 29163515 PMCID: PMC5673844 DOI: 10.3389/fimmu.2017.01442] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 10/17/2017] [Indexed: 01/01/2023] Open
Abstract
The development of innovative targeted therapeutic approaches are expected to surpass the efficacy of current forms of treatments and cause less damage to healthy cells surrounding the tumor site. Since the first development of targeting agents from hybridoma’s, monoclonal antibodies (mAbs) have been employed to inhibit tumor growth and proliferation directly or to deliver effector molecules to tumor cells. However, the full potential of such a delivery strategy is hampered by the size of mAbs, which will obstruct the targeted delivery system to access the tumor tissue. By serendipity, a new kind of functional homodimeric antibody format was discovered in camelidae, known as heavy-chain antibodies (HCAbs). The cloning of the variable domain of HCAbs produces an attractive minimal-sized alternative for mAbs, referred to as VHH or nanobodies (Nbs). Apart from their dimensions in the single digit nanometer range, the unique characteristics of Nbs combine a high stability and solubility, low immunogenicity and excellent affinity and specificity against all possible targets including tumor markers. This stimulated the development of tumor-targeted therapeutic strategies. Some autonomous Nbs have been shown to act as antagonistic drugs, but more importantly, the targeting capacity of Nbs has been exploited to create drug delivery systems. Obviously, Nb-based targeted cancer therapy is mainly focused toward extracellular tumor markers, since the membrane barrier prevents antibodies to reach the most promising intracellular tumor markers. Potential strategies, such as lentiviral vectors and bacterial type 3 secretion system, are proposed to deliver target-specific Nbs into tumor cells and to block tumor markers intracellularly. Simultaneously, Nbs have also been employed for in vivo molecular imaging to diagnose diseased tissues and to monitor the treatment effects. Here, we review the state of the art and focus on recent developments with Nbs as targeting moieties for drug delivery systems in cancer therapy and cancer imaging.
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Affiliation(s)
- Yaozhong Hu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.,State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Changxiao Liu
- Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
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21
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Salema V, Fernández LÁ. Escherichia coli surface display for the selection of nanobodies. Microb Biotechnol 2017; 10:1468-1484. [PMID: 28772027 PMCID: PMC5658595 DOI: 10.1111/1751-7915.12819] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022] Open
Abstract
Nanobodies (Nbs) are the smallest functional antibody fragments known in nature and have multiple applications in biomedicine or environmental monitoring. Nbs are derived from the variable segment of camelid heavy chain-only antibodies, known as VHH. For selection, libraries of VHH gene segments from naïve, immunized animals or of synthetic origin have been traditionally cloned in E. coli phage display or yeast display systems, and clones binding the target antigen recovered, usually from plastic surfaces with the immobilized antigen (phage display) or using fluorescence-activated cell sorting (FACS; yeast display). This review briefly describes these conventional approaches and focuses on the distinct properties of an E. coli display system developed in our laboratory, which combines the benefits of both phage display and yeast display systems. We demonstrate that E. coli display using an N-terminal domain of intimin is an effective platform for the surface display of VHH libraries enabling selection of high-affinity Nbs by magnetic cell sorting and direct selection on live mammalian cells displaying the target antigen on their surface. Flow cytometry analysis of E. coli bacteria displaying the Nbs on their surface allows monitoring of the selection process, facilitates screening, characterization of antigen-binding clones, specificity, ligand competition and estimation of the equilibrium dissociation constant (KD ).
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Affiliation(s)
- Valencio Salema
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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22
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Attaching and effacing (A/E) lesion formation by enteropathogenic E. coli on human intestinal mucosa is dependent on non-LEE effectors. PLoS Pathog 2017; 13:e1006706. [PMID: 29084270 PMCID: PMC5685641 DOI: 10.1371/journal.ppat.1006706] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 11/14/2017] [Accepted: 10/20/2017] [Indexed: 01/31/2023] Open
Abstract
Enteropathogenic E. coli (EPEC) is a human pathogen that causes acute and chronic pediatric diarrhea. The hallmark of EPEC infection is the formation of attaching and effacing (A/E) lesions in the intestinal epithelium. Formation of A/E lesions is mediated by genes located on the pathogenicity island locus of enterocyte effacement (LEE), which encode the adhesin intimin, a type III secretion system (T3SS) and six effectors, including the essential translocated intimin receptor (Tir). Seventeen additional effectors are encoded by genes located outside the LEE, in insertion elements and prophages. Here, using a stepwise approach, we generated an EPEC mutant lacking the entire effector genes (EPEC0) and intermediate mutants. We show that EPEC0 contains a functional T3SS. An EPEC mutant expressing intimin but lacking all the LEE effectors but Tir (EPEC1) was able to trigger robust actin polymerization in HeLa cells and mucin-producing intestinal LS174T cells. However, EPEC1 was unable to form A/E lesions on human intestinal in vitro organ cultures (IVOC). Screening the intermediate mutants for genes involved in A/E lesion formation on IVOC revealed that strains lacking non-LEE effector/s have a marginal ability to form A/E lesions. Furthermore, we found that Efa1/LifA proteins are important for A/E lesion formation efficiency in EPEC strains lacking multiple effectors. Taken together, these results demonstrate the intricate relationships between T3SS effectors and the essential role non-LEE effectors play in A/E lesion formation on mucosal surfaces. Enteropathogenic E. coli (EPEC) causes diarrhea and generates the attaching and effacing (A/E) lesion in human gut epithelium. A/E lesion formation requires the locus of enterocyte effacement (LEE) in the bacterial genome, which encodes a protein injection system delivering the translocated intimin receptor (Tir), which binds to intimin on the bacterial surface. Intimin-Tir interaction is sufficient for bacterial attachment to epithelial cells in vitro but additional effectors may be needed for A/E lesion formation in the human gut. By generating deletion mutants lacking combinations or the whole repertoire of protein effectors encoded by EPEC, we show that intimin-Tir interaction is not sufficient and reveal an additive role of non-LEE effectors for A/E lesion formation in human intestinal tissue.
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23
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Beghein E, Gettemans J. Nanobody Technology: A Versatile Toolkit for Microscopic Imaging, Protein-Protein Interaction Analysis, and Protein Function Exploration. Front Immunol 2017; 8:771. [PMID: 28725224 PMCID: PMC5495861 DOI: 10.3389/fimmu.2017.00771] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/16/2017] [Indexed: 01/05/2023] Open
Abstract
Over the last two decades, nanobodies or single-domain antibodies have found their way in research, diagnostics, and therapy. These antigen-binding fragments, derived from Camelid heavy chain only antibodies, possess remarkable characteristics that favor their use over conventional antibodies or fragments thereof, in selected areas of research. In this review, we assess the current status of nanobodies as research tools in diverse aspects of fundamental research. We discuss the use of nanobodies as detection reagents in fluorescence microscopy and focus on recent advances in super-resolution microscopy. Second, application of nanobody technology in investigating protein–protein interactions is reviewed, with emphasis on possible uses in mass spectrometry. Finally, we discuss the potential value of nanobodies in studying protein function, and we focus on their recently reported application in targeted protein degradation. Throughout the review, we highlight state-of-the-art engineering strategies that could expand nanobody versatility and we suggest future applications of the technology in the selected areas of fundamental research.
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Affiliation(s)
- Els Beghein
- Nanobody Laboratory, Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jan Gettemans
- Nanobody Laboratory, Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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Böldicke T. Single domain antibodies for the knockdown of cytosolic and nuclear proteins. Protein Sci 2017; 26:925-945. [PMID: 28271570 PMCID: PMC5405437 DOI: 10.1002/pro.3154] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/03/2017] [Indexed: 12/12/2022]
Abstract
Single domain antibodies (sdAbs) from camels or sharks comprise only the variable heavy chain domain. Human sdAbs comprise the variable domain of the heavy chain (VH) or light chain (VL) and can be selected from human antibodies. SdAbs are stable, nonaggregating molecules in vitro and in vivo compared to complete antibodies and scFv fragments. They are excellent novel inhibitors of cytosolic/nuclear proteins because they are correctly folded inside the cytosol in contrast to scFv fragments. SdAbs are unique because of their excellent specificity and possibility to target posttranslational modifications such as phosphorylation sites, conformers or interaction regions of proteins that cannot be targeted with genetic knockout techniques and are impossible to knockdown with RNAi. The number of inhibiting cytosolic/nuclear sdAbs is increasing and usage of synthetic single pot single domain antibody libraries will boost the generation of these fascinating molecules without the need of immunization. The most frequently selected antigenic epitopes belong to viral and oncogenic proteins, followed by toxins, proteins of the nervous system as well as plant- and drosophila proteins. It is now possible to select functional sdAbs against virtually every cytosolic/nuclear protein and desired epitope. The development of new endosomal escape protein domains and cell-penetrating peptides for efficient transfection broaden the application of inhibiting sdAbs. Last but not least, the generation of relatively new cell-specific nanoparticles such as polymersomes and polyplexes carrying cytosolic/nuclear sdAb-DNA or -protein will pave the way to apply cytosolic/nuclear sdAbs for inhibition of viral infection and cancer in the clinic.
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Affiliation(s)
- Thomas Böldicke
- Helmholtz Centre for Infection Research, Structure and Function of ProteinsInhoffenstraße 7, D‐38124BraunschweigGermany
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25
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Abstract
Biologics are a promising new class of drugs based on complex macromolecules such as proteins and nucleic acids. However, delivery of these macromolecules into the cytoplasm of target cells remains a significant challenge. Here we present one potential solution: bacterial nanomachines that have evolved over millions of years to efficiently deliver proteins and nucleic acids across cell membranes and between cells. In this review, we provide a brief overview of the different bacterial systems capable of direct delivery into the eukaryotic cytoplasm and the medical applications for which they are being investigated, along with a perspective on the future directions of this exciting field.
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Steeland S, Vandenbroucke RE, Libert C. Nanobodies as therapeutics: big opportunities for small antibodies. Drug Discov Today 2016; 21:1076-113. [DOI: 10.1016/j.drudis.2016.04.003] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/26/2016] [Accepted: 04/04/2016] [Indexed: 12/28/2022]
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27
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Ittig SJ, Schmutz C, Kasper CA, Amstutz M, Schmidt A, Sauteur L, Vigano MA, Low SH, Affolter M, Cornelis GR, Nigg EA, Arrieumerlou C. A bacterial type III secretion-based protein delivery tool for broad applications in cell biology. J Cell Biol 2016; 211:913-31. [PMID: 26598622 PMCID: PMC4657163 DOI: 10.1083/jcb.201502074] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Methods enabling the delivery of proteins into eukaryotic cells are essential to address protein functions. Here we propose broad applications to cell biology for a protein delivery tool based on bacterial type III secretion (T3S). We show that bacterial, viral, and human proteins, fused to the N-terminal fragment of the Yersinia enterocolitica T3S substrate YopE, are effectively delivered into target cells in a fast and controllable manner via the injectisome of extracellular bacteria. This method enables functional interaction studies by the simultaneous injection of multiple proteins and allows the targeting of proteins to different subcellular locations by use of nanobody-fusion proteins. After delivery, proteins can be freed from the YopE fragment by a T3S-translocated viral protease or fusion to ubiquitin and cleavage by endogenous ubiquitin proteases. Finally, we show that this delivery tool is suitable to inject proteins in living animals and combine it with phosphoproteomics to characterize the systems-level impact of proapoptotic human truncated BID on the cellular network.
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Affiliation(s)
- Simon J Ittig
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | | | | | | | - Loïc Sauteur
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Shyan Huey Low
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Guy R Cornelis
- Research Unit in Biology of Microorganisms, Department of Biology, University of Namur, 5000 Namur, Belgium
| | - Erich A Nigg
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Cécile Arrieumerlou
- Biozentrum, University of Basel, 4056 Basel, Switzerland Institut National de la Santé et de la Recherche Médicale, U1016, Institut Cochin, 75014 Paris, France Centre National de la Recherche Scientifique, UMR8104, 75014 Paris, France Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
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Bieli D, Alborelli I, Harmansa S, Matsuda S, Caussinus E, Affolter M. Development and Application of Functionalized Protein Binders in Multicellular Organisms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:181-213. [DOI: 10.1016/bs.ircmb.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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29
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Moreno-Del Álamo M, de la Espina SMD, Fernández-Tresguerres ME, Giraldo R. Pre-amyloid oligomers of the proteotoxic RepA-WH1 prionoid assemble at the bacterial nucleoid. Sci Rep 2015; 5:14669. [PMID: 26423724 PMCID: PMC4589793 DOI: 10.1038/srep14669] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
Upon binding to short specific dsDNA sequences in vitro, the N-terminal WH1 domain of the plasmid DNA replication initiator RepA assembles as amyloid fibres. These are bundles of single or double twisted tubular filaments in which distorted RepA-WH1 monomers are the building blocks. When expressed in Escherichia coli, RepA-WH1 triggers the first synthetic amyloid proteinopathy in bacteria, recapitulating some of the features of mammalian prion diseases: it is vertically transmissible, albeit non-infectious, showing up in at least two phenotypically distinct and interconvertible strains. Here we report B3h7, a monoclonal antibody specific for oligomers of RepA-WH1, but which does not recognize the mature amyloid fibres. Unlike a control polyclonal antibody generated against the soluble protein, B3h7 interferes in vitro with DNA-promoted or amyloid-seeded assembly of RepA-WH1 fibres, thus the targeted oligomers are on-pathway amyloidogenic intermediates. Immuno-electron microscopy with B3h7 on thin sections of E. coli cells expressing RepA-WH1 consistently labels the bacterial nucleoid, but not the large cytoplasmic aggregates of the protein. This observation points to the nucleoid as the place where oligomeric amyloid precursors of RepA-WH1 are generated, and suggests that, once nucleated by DNA, further growth must continue in the cytoplasm due to entropic exclusion.
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Affiliation(s)
- María Moreno-Del Álamo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas - CSIC, Madrid E28040, Spain
| | | | | | - Rafael Giraldo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas - CSIC, Madrid E28040, Spain
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30
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Ruano-Gallego D, Álvarez B, Fernández LÁ. Engineering the Controlled Assembly of Filamentous Injectisomes in E. coli K-12 for Protein Translocation into Mammalian Cells. ACS Synth Biol 2015; 4:1030-41. [PMID: 26017572 PMCID: PMC4603727 DOI: 10.1021/acssynbio.5b00080] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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Bacterial pathogens containing type
III protein secretion systems
(T3SS) assemble large needle-like protein complexes in the bacterial
envelope, called injectisomes, for translocation of protein effectors
into host cells. The application of these “molecular syringes”
for the injection of proteins into mammalian cells is hindered by
their structural and genomic complexity, requiring multiple polypeptides
encoded along with effectors in various transcriptional units (TUs)
with intricate regulation. In this work, we have rationally designed
the controlled expression of the filamentous injectisomes found in
enteropathogenic Escherichia coli (EPEC) in the nonpathogenic strain E. coli K-12. All structural components of EPEC injectisomes, encoded in
a genomic island called the locus of enterocyte effacement
(LEE), were engineered in five TUs (eLEEs) excluding effectors, promoters
and transcriptional regulators. These eLEEs were placed under the
control of the IPTG-inducible promoter Ptac and integrated into specific
chromosomal sites of E. coli K-12 using a marker-less
strategy. The resulting strain, named synthetic injector E.
coli (SIEC), assembles filamentous injectisomes similar to
those in EPEC. SIEC injectisomes form pores in the host plasma membrane
and are able to translocate T3-substrate proteins (e.g., translocated intimin receptor, Tir) into the cytoplasm of HeLa
cells reproducing the phenotypes of intimate attachment and polymerization
of actin-pedestals elicited by EPEC bacteria. Hence, SIEC strain allows
the controlled expression of functional filamentous injectisomes for
efficient translocation of proteins with T3S-signals into mammalian
cells.
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Affiliation(s)
- David Ruano-Gallego
- Department of Microbial Biotechnology,
Centro Nacional de Biotecnología, Consejo Superior de Investigaciones
Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Beatriz Álvarez
- Department of Microbial Biotechnology,
Centro Nacional de Biotecnología, Consejo Superior de Investigaciones
Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology,
Centro Nacional de Biotecnología, Consejo Superior de Investigaciones
Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
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31
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Wong S, Slavcev R. Treating cancer with infection: a review on bacterial cancer therapy. Lett Appl Microbiol 2015; 61:107-12. [DOI: 10.1111/lam.12436] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 04/08/2015] [Accepted: 04/27/2015] [Indexed: 12/13/2022]
Affiliation(s)
- S. Wong
- School of Pharmacy; University of Waterloo; Waterloo ON Canada
| | - R.A. Slavcev
- School of Pharmacy; University of Waterloo; Waterloo ON Canada
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Piñero-Lambea C, Ruano-Gallego D, Fernández LÁ. Engineered bacteria as therapeutic agents. Curr Opin Biotechnol 2015; 35:94-102. [PMID: 26070111 DOI: 10.1016/j.copbio.2015.05.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 02/08/2023]
Abstract
Although bacteria are generally regarded as the causative agents of infectious diseases, most bacteria inhabiting the human body are non-pathogenic and some of them can be turned, after proper engineering, into 'smart' living therapeutics of defined properties for the treatment of different illnesses. This review focuses on recent developments to engineer bacteria for the treatment of diverse human pathologies, including inflammatory bowel diseases, autoimmune disorders, cancer, metabolic diseases and obesity, as well as to combat bacterial and viral infections. We discuss significant advances provided by synthetic biology to fully reprogram bacteria as human therapeutics, including novel measures for strict biocontainment.
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Affiliation(s)
- Carlos Piñero-Lambea
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - David Ruano-Gallego
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, 28049 Madrid, Spain.
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33
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Hassanzadeh-Ghassabeh G, Devoogdt N, De Pauw P, Vincke C, Muyldermans S. Nanobodies and their potential applications. Nanomedicine (Lond) 2013; 8:1013-26. [PMID: 23730699 DOI: 10.2217/nnm.13.86] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nanobodies are recombinant, antigen-specific, single-domain, variable fragments of camelid heavy chain-only antibodies. The innate supremacy of nanobodies as a renewable source of affinity reagents, together with their high production yield in a broad variety of expression systems, minimal size, great stability, reversible refolding and outstanding solubility in aqueous solutions, and ability to specifically recognize unique epitopes with subnanomolar affinity, have combined to make them a useful class of biomolecules for research and various medical diagnostic and therapeutic applications. This article speculates on a number of technological innovations that might be introduced in the nanobody identification platform to streamline the generation of more potent nanobodies and to expand their application range.
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34
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Van Impe K, Bethuyne J, Cool S, Impens F, Ruano-Gallego D, De Wever O, Vanloo B, Van Troys M, Lambein K, Boucherie C, Martens E, Zwaenepoel O, Hassanzadeh-Ghassabeh G, Vandekerckhove J, Gevaert K, Fernández LÁ, Sanders NN, Gettemans J. A nanobody targeting the F-actin capping protein CapG restrains breast cancer metastasis. Breast Cancer Res 2013; 15:R116. [PMID: 24330716 PMCID: PMC3979033 DOI: 10.1186/bcr3585] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 12/06/2013] [Indexed: 12/16/2022] Open
Abstract
Introduction Aberrant turnover of the actin cytoskeleton is intimately associated with cancer cell migration and invasion. Frequently however, evidence is circumstantial, and a reliable assessment of the therapeutic significance of a gene product is offset by lack of inhibitors that target biologic properties of a protein, as most conventional drugs do, instead of the corresponding gene. Proteomic studies have demonstrated overexpression of CapG, a constituent of the actin cytoskeleton, in breast cancer. Indirect evidence suggests that CapG is involved in tumor cell dissemination and metastasis. In this study, we used llama-derived CapG single-domain antibodies or nanobodies in a breast cancer metastasis model to address whether inhibition of CapG activity holds therapeutic merit. Methods We raised single-domain antibodies (nanobodies) against human CapG and used these as intrabodies (immunomodulation) after lentiviral transduction of breast cancer cells. Functional characterization of nanobodies was performed to identify which biochemical properties of CapG are perturbed. Orthotopic and tail vein in vivo models of metastasis in nude mice were used to assess cancer cell spreading. Results With G-actin and F-actin binding assays, we identified a CapG nanobody that binds with nanomolar affinity to the first CapG domain. Consequently, CapG interaction with actin monomers or actin filaments is blocked. Intracellular delocalization experiments demonstrated that the nanobody interacts with CapG in the cytoplasmic environment. Expression of the nanobody in breast cancer cells restrained cell migration and Matrigel invasion. Notably, the nanobody prevented formation of lung metastatic lesions in orthotopic xenograft and tail-vein models of metastasis in immunodeficient mice. We showed that CapG nanobodies can be delivered into cancer cells by using bacteria harboring a type III protein secretion system (T3SS). Conclusions CapG inhibition strongly reduces breast cancer metastasis. A nanobody-based approach offers a fast track for gauging the therapeutic merit of drug targets. Mapping of the nanobody-CapG interface may provide a platform for rational design of pharmacologic compounds.
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35
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Hochkoeppler A. Expanding the landscape of recombinant protein production in Escherichia coli. Biotechnol Lett 2013; 35:1971-81. [DOI: 10.1007/s10529-013-1396-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/26/2013] [Indexed: 12/11/2022]
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36
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Salema V, Marín E, Martínez-Arteaga R, Ruano-Gallego D, Fraile S, Margolles Y, Teira X, Gutierrez C, Bodelón G, Fernández LÁ. Selection of single domain antibodies from immune libraries displayed on the surface of E. coli cells with two β-domains of opposite topologies. PLoS One 2013; 8:e75126. [PMID: 24086454 PMCID: PMC3781032 DOI: 10.1371/journal.pone.0075126] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/08/2013] [Indexed: 01/21/2023] Open
Abstract
Screening of antibody (Ab) libraries by direct display on the surface of E. coli cells is hampered by the presence of the outer membrane (OM). In this work we demonstrate that the native β-domains of EhaA autotransporter and intimin, two proteins from enterohemorrhagic E. coli O157:H7 (EHEC) with opposite topologies in the OM, are effective systems for the display of immune libraries of single domain Abs (sdAbs) from camelids (nanobodies or VHH) on the surface of E. coli K-12 cells and for the selection of high affinity sdAbs using magnetic cell sorting (MACS). We analyzed the capacity of EhaA and intimin β-domains to display individual sdAbs and sdAb libraries obtained after immunization with the extracellular domain of the translocated intimin receptor from EHEC (TirMEHEC). We demonstrated that both systems displayed functional sdAbs on the surface of E. coli cells with little proteolysis and cellular toxicity, although E. coli cells displaying sdAbs with the β-domain of intimin showed higher antigen-binding capacity. Both E. coli display libraries were screened for TirMEHEC binding clones by MACS. High affinity binders were selected by both display systems, although more efficiently with the intimin β-domain. The specificity of the selected clones against TirMEHEC was demonstrated by flow cytometry of E. coli cells, along with ELISA and surface plasmon resonance with purified sdAbs. Finally, we employed the E. coli cell display systems to provide an estimation of the affinity of the selected sdAb by flow cytometry analysis under equilibrium conditions.
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Affiliation(s)
- Valencio Salema
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Elvira Marín
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Rocio Martínez-Arteaga
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - David Ruano-Gallego
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Sofía Fraile
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Yago Margolles
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Xema Teira
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Carlos Gutierrez
- Department of Animal Medicine and Surgery, Veterinary Faculty, Universidad de Las Palmas de Gran Canaria (UPGC), Las Palmas, Canary Islands, Spain
| | - Gustavo Bodelón
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM Cantoblanco, Madrid, Spain
- * E-mail:
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Van Audenhove I, Van Impe K, Ruano-Gallego D, De Clercq S, De Muynck K, Vanloo B, Verstraete H, Fernández LÁ, Gettemans J. Mapping cytoskeletal protein function in cells by means of nanobodies. Cytoskeleton (Hoboken) 2013; 70:604-22. [DOI: 10.1002/cm.21122] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 06/18/2013] [Accepted: 06/18/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Isabel Van Audenhove
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Belgium
| | - Katrien Van Impe
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Belgium
| | - David Ruano-Gallego
- Department of Microbial Biotechnology; Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas (CSIC), Campus Cantoblanco Universidad Autónoma de Madrid (UAM); Madrid Spain
| | - Sarah De Clercq
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Belgium
| | - Kevin De Muynck
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Belgium
| | - Berlinda Vanloo
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Belgium
| | - Hanne Verstraete
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Belgium
| | - Luis Á. Fernández
- Department of Microbial Biotechnology; Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas (CSIC), Campus Cantoblanco Universidad Autónoma de Madrid (UAM); Madrid Spain
| | - Jan Gettemans
- Department of Biochemistry; Faculty of Medicine and Health Sciences, Ghent University; Belgium
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Bodelón G, Palomino C, Fernández LÁ. Immunoglobulin domains inEscherichia coliand other enterobacteria: from pathogenesis to applications in antibody technologies. FEMS Microbiol Rev 2013; 37:204-50. [DOI: 10.1111/j.1574-6976.2012.00347.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 06/07/2012] [Accepted: 06/14/2012] [Indexed: 11/28/2022] Open
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Akeda Y, Kimura T, Yamasaki A, Kodama T, Iida T, Honda T, Oishi K. Functional cloning of Vibrio parahaemolyticus type III secretion system 1 in Escherichia coli K-12 strain as a molecular syringe. Biochem Biophys Res Commun 2012; 427:242-7. [PMID: 22995311 DOI: 10.1016/j.bbrc.2012.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/05/2012] [Indexed: 10/27/2022]
Abstract
The type III secretion system (T3SS) of gram-negative bacteria involves dedicated protein translocation machinery that directly injects proteins into target cells. Pathogenic bacteria already benefit from this unique system. The successful functional cloning of this useful tool into non-pathogenic bacteria would help establish novel clinical and basic biotechnology strategies in areas such as vaccine administration, the development of screening systems for anti-T3SS drugs and the target-specific delivery of bioactive compounds. In this study, we successfully cloned the Vibrio parahaemolyticus T3SS1 genetic locus into a non-pathogenic Escherichia coli K-12 strain. Assays performed here revealed that the T3SS1 cloned into the E. coli K-12 strain has the ability to translocate V. parahaemolyticus T3SS1 secreted proteins. Importantly, we also observed this system to allow the E. coli K-12 strain to inject foreign protein, as well as the V. parahaemolyticus T3SS effector, into cultured cells. These results demonstrate a prospective useful tool with experimental and therapeutic applications.
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Affiliation(s)
- Yukihiro Akeda
- Laboratory of Clinical Research on Infectious Diseases, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
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40
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Immunodetection of the recombinant GroEL by the Nanobody NbBruc02. World J Microbiol Biotechnol 2012; 28:2987-95. [DOI: 10.1007/s11274-012-1109-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/12/2012] [Indexed: 02/03/2023]
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41
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Abbady A, Al-Daoude A, Al-Mariri A, Zarkawi M, Muyldermans S. Chaperonin GroEL a Brucella immunodominant antigen identified using Nanobody and MALDI-TOF-MS technologies. Vet Immunol Immunopathol 2012; 146:254-63. [DOI: 10.1016/j.vetimm.2012.01.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 01/10/2012] [Accepted: 01/17/2012] [Indexed: 02/02/2023]
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Functional inhibition of transitory proteins by intrabody-mediated retention in the endoplasmatic reticulum. Methods 2011; 56:338-50. [PMID: 22037249 DOI: 10.1016/j.ymeth.2011.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 11/23/2022] Open
Abstract
Intrabodies are recombinantly expressed intracellular antibody fragments that can be used to specifically bind and inhibit the function of cellular proteins of interest. Intrabodies can be targeted to various cell compartments by attaching an appropriate localization peptide sequence to them. An efficient strategy with a high success rate is to anchor intrabodies in the endoplasmatic reticulum where they can inhibit transitory target proteins by binding and preventing them to reach their site of action. Intrabodies can be assembled from antibody gene fragments from various sources into dedicated expression vectors. Conventionally, antibody cDNA sequences are derived from selected hybridoma cell clones that express antibodies with the desired specificity. Alternatively, appropriate clones can be isolated by affinity selection from an antibody in vitro display library. Here an evaluation of endoplasmatic reticulum targeted intrabodies with respect to other knockdown approaches is given and the characteristics of various intrabody expression vectors are discussed. A step by step protocol is provided that was repeatedly used to construct intrabodies derived from diverse antibody isotypes producing hybridoma cell clones. The inactivation of the cell surface receptor neural cell adhesion molecule (NCAM) by a highly efficacious novel endoplasmatic reticulum-anchored intrabody is demonstrated.
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In Brief. Nat Rev Microbiol 2011. [DOI: 10.1038/nrmicro2517] [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]
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