1
|
Chen M, Xia L, Wu C, Wang Z, Ding L, Xie Y, Feng W, Chen Y. Microbe-material hybrids for therapeutic applications. Chem Soc Rev 2024. [PMID: 39005165 DOI: 10.1039/d3cs00655g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
As natural living substances, microorganisms have emerged as useful resources in medicine for creating microbe-material hybrids ranging from nano to macro dimensions. The engineering of microbe-involved nanomedicine capitalizes on the distinctive physiological attributes of microbes, particularly their intrinsic "living" properties such as hypoxia tendency and oxygen production capabilities. Exploiting these remarkable characteristics in combination with other functional materials or molecules enables synergistic enhancements that hold tremendous promise for improved drug delivery, site-specific therapy, and enhanced monitoring of treatment outcomes, presenting substantial opportunities for amplifying the efficacy of disease treatments. This comprehensive review outlines the microorganisms and microbial derivatives used in biomedicine and their specific advantages for therapeutic application. In addition, we delineate the fundamental strategies and mechanisms employed for constructing microbe-material hybrids. The diverse biomedical applications of the constructed microbe-material hybrids, encompassing bioimaging, anti-tumor, anti-bacteria, anti-inflammation and other diseases therapy are exhaustively illustrated. We also discuss the current challenges and prospects associated with the clinical translation of microbe-material hybrid platforms. Therefore, the unique versatility and potential exhibited by microbe-material hybrids position them as promising candidates for the development of next-generation nanomedicine and biomaterials with unique theranostic properties and functionalities.
Collapse
Affiliation(s)
- Meng Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China.
| | - Lili Xia
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Chenyao Wu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Zeyu Wang
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Li Ding
- Department of Medical Ultrasound, National Clinical Research Center of Interventional Medicine, Shanghai Tenth People's Hospital, Tongji University Cancer Center, Tongji University School of Medicine, Tongji University, Shanghai, 200072, P. R. China.
| | - Yujie Xie
- School of Medicine, Shanghai University, Shanghai 200444, P. R. China.
| | - Wei Feng
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China.
- Shanghai Institute of Materdicine, Shanghai 200051, P. R. China
| |
Collapse
|
2
|
Kang H, Park D, Kim J. Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs. Nucleic Acids Res 2024:gkae549. [PMID: 38943344 DOI: 10.1093/nar/gkae549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
The CRISPR-Cas system provides a versatile RNA-guided approach for a broad range of applications. Thanks to advances in RNA synthetic biology, the engineering of guide RNAs (gRNAs) has enabled the conditional control of the CRISPR-Cas system. However, achieving precise regulation of the CRISPR-Cas system for efficient modulation of internal metabolic processes remains challenging. In this work, we developed a robust dCas9 regulator with engineered conditional gRNAs to enable tight control of endogenous genes. Our conditional gRNAs in Escherichia coli can control gene expression upon specific interaction with trigger RNAs with a dynamic range as high as 130-fold, evaluating up to a three-input logic A OR (B AND C). The conditional gRNA-mediated targeting of endogenous metabolic genes, lacZ, malT and poxB, caused differential regulation of growth in Escherichia coli via metabolic flux control. Further, conditional gRNAs could regulate essential cytoskeleton genes, ftsZ and mreB, to control cell filamentation and division. Finally, three types of two-input logic gates could be applied for the conditional control of ftsZ regulation, resulting in morphological changes. The successful operation and application of conditional gRNAs based on programmable RNA interactions suggests that our system could be compatible with other Cas-effectors and implemented in other host organisms.
Collapse
Affiliation(s)
- Hansol Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Dongwon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Foppa C, Rizkala T, Repici A, Hassan C, Spinelli A. Microbiota and IBD: Current knowledge and future perspectives. Dig Liver Dis 2024; 56:911-922. [PMID: 38008696 DOI: 10.1016/j.dld.2023.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.
Collapse
Affiliation(s)
- Caterina Foppa
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Colon and Rectal Surgery, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Tommy Rizkala
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy
| | - Alessandro Repici
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Gastroenterology and Digestive Endoscopy Unit, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Cesare Hassan
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Gastroenterology and Digestive Endoscopy Unit, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Antonino Spinelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Colon and Rectal Surgery, via Manzoni 56, Rozzano, 20089, Milan, Italy.
| |
Collapse
|
5
|
Wu YQ, Zou ZP, Zhou Y, Ye BC. Dual engineered bacteria improve inflammatory bowel disease in mice. Appl Microbiol Biotechnol 2024; 108:333. [PMID: 38739270 DOI: 10.1007/s00253-024-13163-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024]
Abstract
Currently, there are many different therapies available for inflammatory bowel disease (IBD), including engineered live bacterial therapeutics. However, most of these studies focus on producing a single therapeutic drug using individual bacteria, which may cause inefficacy. The use of dual drugs can enhance therapeutic effects. However, expressing multiple therapeutic drugs in one bacterial chassis increases the burden on the bacterium and hinders good secretion and expression. Therefore, a dual-bacterial, dual-drug expression system allows for the introduction of two probiotic chassis and enhances both therapeutic and probiotic effects. In this study, we constructed a dual bacterial system to simultaneously neutralize pro-inflammatory factors and enhance the anti-inflammatory pathway. These bacteria for therapy consist of Escherichia coli Nissle 1917 that expressed and secreted anti-TNF-α nanobody and IL-10, respectively. The oral administration of genetically engineered bacteria led to a decrease in inflammatory cell infiltration in colon and a reduction in the levels of pro-inflammatory cytokines. Additionally, the administration of engineered bacteria did not markedly aggravate gut fibrosis and had a moderating effect on intestinal microbes. This system proposes a dual-engineered bacterial drug combination treatment therapy for inflammatory bowel disease, which provides a new approach to intervene and treat IBD. KEY POINTS: • The paper discusses the effects of using dual engineered bacteria on IBD • Prospects of engineered bacteria in the clinical treatment of IBD.
Collapse
Affiliation(s)
- Yong-Qi Wu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhen-Ping Zou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China.
| |
Collapse
|
6
|
Murali SK, Mansell TJ. Next generation probiotics: Engineering live biotherapeutics. Biotechnol Adv 2024; 72:108336. [PMID: 38432422 DOI: 10.1016/j.biotechadv.2024.108336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.
Collapse
Affiliation(s)
- Sanjeeva Kumar Murali
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA.
| |
Collapse
|
7
|
Manigat F, Connell LB, Stewart BN, LePabic AR, Tessier CJG, Emlaw JR, Calvert ND, Rössl A, Shuhendler AJ, daCosta CJB, Campbell-Valois FX. pUdOs: Concise Plasmids for Bacterial and Mammalian Cells. ACS Synth Biol 2024; 13:485-497. [PMID: 38235654 PMCID: PMC10878396 DOI: 10.1021/acssynbio.3c00408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024]
Abstract
The plasmids from the Université d'Ottawa (pUdOs) are 28 small plasmids each comprising one of four origins of replication and one of seven selection markers, which together afford flexible use in Escherichia coli and several related gram-negative bacteria. The promoterless multicloning site is insulated from upstream spurious promoters by strong transcription terminators and contains type IIP or IIS restriction sites for conventional or Golden Gate cloning. pUdOs can be converted into efficient expression vectors through the insertion of a promoter at the user's discretion. For example, we demonstrate the utility of pUdOs as the backbone for an improved version of a Type III Secretion System reporter in Shigella. In addition, we derive a series of pUdO-based mammalian expression vectors, affording distinct levels of expression and transfection efficiency comparable to commonly used mammalian expression plasmids. Thus, pUdOs could advantageously replace traditional plasmids in a wide variety of cell types and applications.
Collapse
Affiliation(s)
- France
O. Manigat
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Louise B. Connell
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Brittany N. Stewart
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Abdel-Rahman LePabic
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Christian J. G. Tessier
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Johnathon R. Emlaw
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Nicholas D. Calvert
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Anthony Rössl
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Adam J. Shuhendler
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- University
of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Corrie J. B. daCosta
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - François-Xavier Campbell-Valois
- Center
for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular
Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- bioGARAGE,
Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Centre
for Infection, Immunity and Inflammation, Department of Biochemistry,
Microbiology and Immunology, University
of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| |
Collapse
|
8
|
Abele TJ, Billman ZP, Harvest CK, Bryan AK, Larson HN, Coers J, Miao EA. Overexpression of T3SS translocation signals in Salmonella causes delayed attenuation. Infect Immun 2024; 92:e0032923. [PMID: 38084951 PMCID: PMC10790824 DOI: 10.1128/iai.00329-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/21/2023] [Indexed: 01/17/2024] Open
Abstract
Engineering pathogens is a useful method for discovering new details of microbial pathogenesis and host defense. However, engineering can result in off-target effects. We previously engineered Salmonella enterica serovar Typhimurium to overexpress the secretion signal of the type 3 secretion system effector SspH1 fused with domains of other proteins as cargo. Such engineering had no virulence cost to the bacteria for the first 48 hours post infection in mice. Here, we show that after 48 hours, the engineered bacteria manifest an attenuation that correlates with the quantity of the SspH1 translocation signal expressed. In IFN-γ-deficient mice, this attenuation was weakened. Conversely, the attenuation was accelerated in the context of a pre-existing infection. We speculate that inflammatory signals change aspects of the target cell's physiology, which makes host cells less permissive to S. Typhimurium infection. This increased degree of difficulty requires the bacteria to utilize its T3SS at peak efficiency, which can be disrupted by engineered effectors.
Collapse
Affiliation(s)
- Taylor J. Abele
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Zachary P. Billman
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carissa K. Harvest
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alexia K. Bryan
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Durham, North Carolina, USA
| | - Heather N. Larson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jörn Coers
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Edward A. Miao
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| |
Collapse
|
9
|
Kandalai S, Li H, Zhang N, Peng H, Zheng Q. The human microbiome and cancer: a diagnostic and therapeutic perspective. Cancer Biol Ther 2023; 24:2240084. [PMID: 37498047 PMCID: PMC10376920 DOI: 10.1080/15384047.2023.2240084] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Recent evidence has shown that the human microbiome is associated with various diseases, including cancer. The salivary microbiome, fecal microbiome, and circulating microbial DNA in blood plasma have all been used experimentally as diagnostic biomarkers for many types of cancer. The microbiomes present within local tissue, other regions, and tumors themselves have been shown to promote and restrict the development and progression of cancer, most often by affecting cancer cells or the host immune system. These microbes have also been shown to impact the efficacy of various cancer therapies, including radiation, chemotherapy, and immunotherapy. Here, we review the research advances focused on how microbes impact these different facets and why they are important to the clinical care of cancer. It is only by better understanding the roles these microbes play in the diagnosis, development, progression, and treatment of cancer, that we will be able to catch and treat cancer early.
Collapse
Affiliation(s)
- Shruthi Kandalai
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Huapeng Li
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Haidong Peng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
10
|
Yeh YH, Kelly VW, Pour RR, Sirk SJ. A molecular toolkit for heterologous protein secretion across Bacteroides species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571725. [PMID: 38168418 PMCID: PMC10760143 DOI: 10.1101/2023.12.14.571725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Bacteroides species are abundant and prevalent stably colonizing members of the human gut microbiota, making them a promising chassis for developing long-term interventions for chronic diseases. Engineering these bacteria as on-site production and delivery vehicles for biologic drugs or diagnostics, however, requires efficient heterologous protein secretion tools, which are currently lacking. To address this limitation, we systematically investigated methods to enable heterologous protein secretion in Bacteroides using both endogenous and exogenous secretion systems. Here, we report a collection of secretion carriers that can export functional proteins across multiple Bacteroides species at high titers. To understand the mechanistic drivers of Bacteroides secretion, we characterized signal peptide sequence features as well as post-secretion extracellular fate and cargo size limit of protein cargo. To increase titers and enable flexible control of protein secretion, we developed a strong, self-contained, inducible expression circuit. Finally, we validated the functionality of our secretion carriers in vivo in a mouse model. This toolkit should enable expanded development of long-term living therapeutic interventions for chronic gastrointestinal disease.
Collapse
Affiliation(s)
- Yu-Hsuan Yeh
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Vince W. Kelly
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Rahman Rahman Pour
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Perlumi, Berkeley, CA 94704, USA
| | - Shannon J. Sirk
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Lead Contact
| |
Collapse
|
11
|
González-Prieto C, Lynch JP, Lesser CF. PROT 3EcT, engineered Escherichia coli for the targeted delivery of therapeutics. Trends Mol Med 2023; 29:968-969. [PMID: 37574350 PMCID: PMC10592157 DOI: 10.1016/j.molmed.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Affiliation(s)
- 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
| | - 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
| | - 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.
| |
Collapse
|
12
|
López-Sanz C, Jiménez-Saiz R, Nuñez-Borque E. Mapping the way to strengthening epithelial barriers: Neuronal circuits in mucus regulation. Allergy 2023; 78:2799-2801. [PMID: 37151124 DOI: 10.1111/all.15760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/28/2023] [Indexed: 05/09/2023]
Affiliation(s)
- Celia López-Sanz
- Department of Immunology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Rodrigo Jiménez-Saiz
- Department of Immunology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Department of Medicine, McMaster Immunology Research Centre (MIRC), Schroeder Allergy and Immunology Research Institute (SAIRI), McMaster University, Hamilton, Ontario, Canada
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria (UFV), Madrid, Spain
| | - Emilio Nuñez-Borque
- Department of Allergy and Immunology, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| |
Collapse
|
13
|
Mulik S, Berber E, Sehrawat S, Rouse BT. Controlling viral inflammatory lesions by rebalancing immune response patterns. Front Immunol 2023; 14:1257192. [PMID: 37671156 PMCID: PMC10475736 DOI: 10.3389/fimmu.2023.1257192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/07/2023] [Indexed: 09/07/2023] Open
Abstract
In this review, we discuss a variety of immune modulating approaches that could be used to counteract tissue-damaging viral immunoinflammatory lesions which typify many chronic viral infections. We make the point that in several viral infections the lesions can be largely the result of one or more aspects of the host response mediating the cell and tissue damage rather than the virus itself being directly responsible. However, within the reactive inflammatory lesions along with the pro-inflammatory participants there are also other aspects of the host response that may be acting to constrain the activity of the damaging components and are contributing to resolution. This scenario should provide the prospect of rebalancing the contributions of different host responses and hence diminish or even fully control the virus-induced lesions. We identify several aspects of the host reactions that influence the pattern of immune responsiveness and describe approaches that have been used successfully, mainly in model systems, to modulate the activity of damaging participants and which has led to lesion control. We emphasize examples where such therapies are, or could be, translated for practical use in the clinic to control inflammatory lesions caused by viral infections.
Collapse
Affiliation(s)
- Sachin Mulik
- Center for Biomedical Research, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Engin Berber
- Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Sharvan Sehrawat
- Indian Institute of Science Education and Research, Department of Biological Sciences, Mohali, Punjab, India
| | - Barry Tyrrell Rouse
- College of Veterinary Medicine, University of Tennessee, Knoxville, TN, United States
| |
Collapse
|
14
|
Arnold J, Glazier J, Mimee M. Genetic Engineering of Resident Bacteria in the Gut Microbiome. J Bacteriol 2023; 205:e0012723. [PMID: 37382533 PMCID: PMC10367592 DOI: 10.1128/jb.00127-23] [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] [Indexed: 06/30/2023] Open
Abstract
Techniques by which to genetically manipulate members of the microbiota enable both the evaluation of host-microbe interactions and an avenue by which to monitor and modulate human physiology. Genetic engineering applications have traditionally focused on model gut residents, such as Escherichia coli and lactic acid bacteria. However, emerging efforts by which to develop synthetic biology toolsets for "nonmodel" resident gut microbes could provide an improved foundation for microbiome engineering. As genome engineering tools come online, so too have novel applications for engineered gut microbes. Engineered resident gut bacteria facilitate investigations of the roles of microbes and their metabolites on host health and allow for potential live microbial biotherapeutics. Due to the rapid pace of discovery in this burgeoning field, this minireview highlights advancements in the genetic engineering of all resident gut microbes.
Collapse
Affiliation(s)
- Jack Arnold
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Joshua Glazier
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Mark Mimee
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|