1
|
Blum JE, Kong R, Schulman E, Chen FM, Upadhyay R, Romero-Meza G, Littman DR, Fischbach MA, Nagashima K, Sattely ES. Discovery and characterization of dietary antigens in oral tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.593976. [PMID: 38853977 PMCID: PMC11160622 DOI: 10.1101/2024.05.26.593976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Food antigens elicit immune tolerance through the action of regulatory T cells (Tregs) in the intestine. Although antigens that trigger common food allergies are known, the epitopes that mediate tolerance to most foods have not been described. Here, we identified murine T cell receptors specific for maize, wheat, and soy, and used expression cloning to de-orphan their cognate epitopes. All of the epitopes derive from seed storage proteins that are resistant to degradation and abundant in the edible portion of the plant. Multiple unrelated T cell clones were specific for an epitope at the C-terminus of 19 kDa alpha-zein, a protein from maize kernel. An MHC tetramer loaded with this antigen revealed that zein-specific T cells are predominantly Tregs localized to the intestine. These cells, which develop concurrently with weaning, constitute up to 2% of the peripheral Treg pool. Bulk and single-cell RNA sequencing revealed that these cells express higher levels of immunosuppressive markers and chemokines compared to other Tregs. These data suggest that immune tolerance to plant-derived foods is focused on a specific class of antigens with common features, and they reveal the functional properties of naturally occurring food-specific Tregs.
Collapse
Affiliation(s)
- Jamie E. Blum
- Department of Chemical Engineering; Stanford University; Stanford, CA 94305 USA
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
| | - Ryan Kong
- Department of Chemical Engineering; Stanford University; Stanford, CA 94305 USA
| | - E.A. Schulman
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
| | - Francis M. Chen
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
| | - Rabi Upadhyay
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
- Perlmutter Cancer Center, New York University Langone Health; New York, NY 10016 USA
| | - Gabriela Romero-Meza
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
| | - Dan R. Littman
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
| | - Michael A. Fischbach
- Department of Bioengineering; Stanford University; Stanford, CA 94305 USA
- Department of Microbiology and Immunology; Stanford University School of Medicine, Stanford University, Stanford CA 94305 USA
- ChEM-H Institute, Stanford University; Stanford, CA 94305 USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Kazuki Nagashima
- Department of Bioengineering; Stanford University; Stanford, CA 94305 USA
- Department of Microbiology and Immunology; Stanford University School of Medicine, Stanford University, Stanford CA 94305 USA
- ChEM-H Institute, Stanford University; Stanford, CA 94305 USA
| | - Elizabeth S. Sattely
- Department of Chemical Engineering; Stanford University; Stanford, CA 94305 USA
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
| |
Collapse
|
2
|
Miao X, Niu H, Sun M, Dong X, Hua M, Su Y, Wang J, Li D. A comparative study on the nutritional composition, protein structure and effects on gut microbiota of 5 fermented soybean products (FSPs). Food Res Int 2024; 183:114199. [PMID: 38760132 DOI: 10.1016/j.foodres.2024.114199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 05/19/2024]
Abstract
In this study, we conducted an analysis of the differences in nutrient composition and protein structure among various fermented soybean products and their impacts on the gut microbiota of rats. Conventional physicochemical analysis was employed to analyze the fundamental physicochemical composition of the samples. Additionally, we utilized high-performance liquid chromatography and ELISA techniques to quantify the presence of antinutritional compounds. Fourier infrared spectroscopy was applied to delineate the protein structure, while 16 s rRNA gene sequencing was conducted to evaluate alterations in gut microbiota abundance. Subsequently, KEGG was utilized for metabolic pathway analysis. Our findings revealed that fermented soybean products improved the nutritional profile of soybeans. Notably, Douchi exhibited the highest protein content at 52.18 g/100 g, denoting a 26.58 % increase, whereas natto showed a 24.98 % increase. Douchi and natto demonstrated the most substantial relative amino acid content, comprising 50.86 % and 49.04 % of the total samples, respectively. Moreover, the levels of antinutritional factors markedly decreased post-fermentation. Specifically, the α-helix content in doujiang decreased by 13.87 %, while the random coil content in soybean yogurt surged by 132.39 %. Rats that were fed FSP showcased notable enhancements in gut microbiota and associated metabolic pathways. A strong correlation was observed between nutrient composition, protein structure, and gut microbiota abundance. This study furnishes empirical evidence supporting the heightened nutritional attributes of FSPs.
Collapse
Affiliation(s)
- Xinyu Miao
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Honghong Niu
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Mubai Sun
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Xin Dong
- Center for Disease Control and Prevention of Hinggan League, Hinggan League 137400, China
| | - Mei Hua
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Ying Su
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China
| | - Jinghui Wang
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China.
| | - Da Li
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun 130033, China.
| |
Collapse
|
3
|
Li C, Lanasa D, Park JH. Pathways and mechanisms of CD4 +CD8αα + intraepithelial T cell development. Trends Immunol 2024; 45:288-302. [PMID: 38514370 PMCID: PMC11015970 DOI: 10.1016/j.it.2024.02.006] [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: 02/02/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
The mammalian small intestine epithelium harbors a peculiar population of CD4+CD8αα+ T cells that are derived from mature CD4+ T cells through reprogramming of lineage-specific transcription factors. CD4+CD8αα+ T cells occupy a unique niche in T cell biology because they exhibit mixed phenotypes and functional characteristics of both CD4+ helper and CD8+ cytotoxic T cells. The molecular pathways driving their generation are not fully mapped. However, recent studies demonstrate the unique role of the commensal gut microbiota as well as distinct cytokine and chemokine requirements in the differentiation and survival of these cells. We review the established and newly identified factors involved in the generation of CD4+CD8αα+ intraepithelial lymphocytes (IELs) and place them in the context of the molecular machinery that drives their phenotypic and functional differentiation.
Collapse
Affiliation(s)
- Can Li
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Lanasa
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jung-Hyun Park
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
4
|
Li F, Gong X, Zhou Y, Geng Q, Jiang Y, Yao L, Qu M, Tan Z. Integrated evidence of transcriptional, metabolic, and intestinal microbiota changes in Ruditapes philippinarum due to perfluorooctanoic acid-induced immunotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170341. [PMID: 38272093 DOI: 10.1016/j.scitotenv.2024.170341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Perfluorooctanoic acid (PFOA) is a toxic pollutant that bioaccumulates and is a significant public health concern due to its ubiquitous and persistent occurrence in global environments. Few studies have evaluated the adverse effects of PFOA on immune system, and this is particularly true for mollusks. Here, the PFOA-associated effects on immune system were evaluated in Ruditapes philippinarum using integrated analysis of metabolomes, microbiomes, and transcriptomes, providing evidence for possible mechanisms related to immunotoxicity. PFOA exposure caused clear variation in several important metabolites related to immune regulatory function within the haemolyph from R. philippinarum, while also altering key metabolic pathways, including those of lipids, unsaturated fatty acids (UFAs), and bile acids (BAs). After exposure to PFOAs, intestinal bacterial communities also clearly changed, with the predominant microflora becoming Mycoplasma and Bacteroidetes that are related to intestinal inflammation. Molecular analyses provided consistent results, wherein the expression of immune-related genes was significantly altered. Integration of the multi-'omics' analyses suggested that the TLR/MyD88/NF-kB pathway, along with PI3K-Akt-mTOR pathway, PPAR-mediated lipid metabolism and the autophagy signaling pathway, likely play important roles in initiating immunotoxic effects in R. philippinarum after PFOA exposure. These results provide further evidence that PFOA exposure can lead to immunologic dysfunction and also provide new insights into the mechanisms of PFAS alteration of bivalve immune function.
Collapse
Affiliation(s)
- Fengling Li
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Xiuqiong Gong
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Yang Zhou
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, People's Republic of China
| | - Qianqian Geng
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Yanhua Jiang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Lin Yao
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Meng Qu
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Zhijun Tan
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China; Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, People's Republic of China.
| |
Collapse
|
5
|
Zhao H, Shang L, Zhang Y, Liang Z, Wang N, Zhang Q, Gao C, Luo J. IL-17A inhibitors alleviate Psoriasis with concomitant restoration of intestinal/skin microbiota homeostasis and altered microbiota function. Front Immunol 2024; 15:1344963. [PMID: 38482003 PMCID: PMC10933079 DOI: 10.3389/fimmu.2024.1344963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/12/2024] [Indexed: 04/12/2024] Open
Abstract
Background Disturbed gut microbiota and associated metabolic dysfunction exist in Psoriasis. Despite the growing use of interleukin-17 inhibitor (anti-IL17) therapy, the effect of anti-IL17 on gut/skin microbiota function is not fully understood in patients with Psoriasis. Objective Therefore, we explored whether Psoriasis is associated with alterations in selected gut/skin microbiota in a study cohort, and a longitudinal cohort study to reveal the effects of IL-17A inhibitor treatment on gut microbiota in Psoriasis. Methods In a case-control study, 14 patients with Psoriasis and 10 age, sex and body mass index-matched Healthy Controls were recruited. Longitudinal mapping of the gut microbiome was performed using 16S rRNA gene sequencing. Mouse models were used to further study and validate the interrelationship between the skin microbiome and the gut microbiome in Psoriasis. PICRUST2 was applied to predict the function of the bacterial community. Results In Psoriasis patients, gut microbiota dysbiosis was present with increased heterogeneity: decreased Bacteroidota and increased Firmicutes as well as Actinobacteriota predominating in Psoriasis. Escherichia-Shigella enrichment was associated with reduction in serum levels of total bile acid and markers in Apoptotic pathways. After IL-17A inhibitor treatment in Psoriasis patients, longitudinal studies observed a trend toward a normal distribution of the gut microbiome and modulation of apoptosis-related metabolic pathways. Results from a mouse model showed dysregulation of the skin microbiota in Psoriasis characterized by Staphylococcus colonization. Conclusion The psoriatic gut/skin microbiota exhibits loss of community stability and pathogen enrichment. IL-17A inhibitors restore microbiota homeostasis and metabolic pathways, reduce pro-inflammatory cytokine expression, and alleviate symptoms in patients with Psoriasis.
Collapse
Affiliation(s)
- Huixia Zhao
- Department of Dermatology, Heji Hospital of Changzhi Medical College, Changzhi, China
| | - Lili Shang
- Department of Rheumatology, The Second Clinical Medical College of Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory for immunomicroecology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuting Zhang
- Department of Dermatology, Heji Hospital of Changzhi Medical College, Changzhi, China
| | - Zhaojun Liang
- Shanxi Key Laboratory for immunomicroecology, The Second Hospital of Shanxi Medical University, Taiyuan, China
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Nan Wang
- Shanxi Key Laboratory for immunomicroecology, The Second Hospital of Shanxi Medical University, Taiyuan, China
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Qian Zhang
- Department of Dermatology, Heji Hospital of Changzhi Medical College, Changzhi, China
| | - Chong Gao
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Jing Luo
- Shanxi Key Laboratory for immunomicroecology, The Second Hospital of Shanxi Medical University, Taiyuan, China
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| |
Collapse
|
6
|
Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, Lewis KE, Hopkin JM, Chung KF, O'Carroll O, Faul J, Creaser-Thomas J, Andrews M, Ghosal R, Piatek S, Willis-Owen SAG, Bartolomaeus TUP, Birkner T, Dwyer S, Kumar N, Turek EM, William Musk A, Hui J, Hunter M, James A, Dumas ME, Filippi S, Cox MJ, Lawley TD, Forslund SK, Moffatt MF, Cookson WOC. Genomic attributes of airway commensal bacteria and mucosa. Commun Biol 2024; 7:171. [PMID: 38347162 PMCID: PMC10861553 DOI: 10.1038/s42003-024-05840-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.
Collapse
Affiliation(s)
- Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ulrike Löber
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Jonathan S Ish-Horowicz
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
| | - Claire N McBrien
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Colin Churchward
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jeremy C Parker
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Conor Burke
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Aisling McGowan
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Gwyneth A Davies
- Population Data Science and Health Data Research UK BREATHE Hub, Swansea University Medical School, Swansea University, Swansea, UK
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Keir E Lewis
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Julian M Hopkin
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Orla O'Carroll
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - John Faul
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Joy Creaser-Thomas
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Mark Andrews
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Robin Ghosal
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Stefan Piatek
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Theda U P Bartolomaeus
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Till Birkner
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Sarah Dwyer
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena M Turek
- National Heart and Lung Institute, Imperial College London, London, UK
| | - A William Musk
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Jennie Hui
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Michael Hunter
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Alan James
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Marc-Emmanuel Dumas
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- U1283 INSERM / UMR8199 CNRS, Institut Pasteur de Lille, Lille University Hospital, European Genomic Institute for Diabetes, University of Lille, Lille, France
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Sarah Filippi
- Department of Mathematics, Imperial College London, London, UK
| | - Michael J Cox
- University of Birmingham College of Medical and Dental Sciences, 150183, Institute of Microbiology and Infection, Birmingham, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sofia K Forslund
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany.
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, UK.
| | | |
Collapse
|
7
|
Akama Y, Murao A, Aziz M, Wang P. Extracellular CIRP induces CD4CD8αα intraepithelial lymphocyte cytotoxicity in sepsis. Mol Med 2024; 30:17. [PMID: 38302880 PMCID: PMC10835974 DOI: 10.1186/s10020-024-00790-2] [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: 10/26/2023] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND In sepsis, intestinal barrier dysfunction is often caused by the uncontrolled death of intestinal epithelial cells (IECs). CD4CD8αα intraepithelial lymphocytes (IELs), a subtype of CD4+ T cells residing within the intestinal epithelium, exert cytotoxicity by producing granzyme B (GrB) and perforin (Prf). Extracellular cold-inducible RNA-binding protein (eCIRP) is a recently identified alarmin which stimulates TLR4 on immune cells to induce proinflammatory responses. Here, we hypothesized that eCIRP enhances CD4CD8αα IEL cytotoxicity and induces IEC death in sepsis. METHODS We subjected wild-type (WT) and CIRP-/- mice to sepsis by cecal ligation and puncture (CLP) and collected the small intestines to isolate IELs. The expression of GrB and Prf in CD4CD8αα IELs was assessed by flow cytometry. IELs isolated from WT and TLR4-/- mice were challenged with recombinant mouse CIRP (eCIRP) and assessed the expression of GrB and Prf in CD4CD8αα by flow cytometry. Organoid-derived IECs were co-cultured with eCIRP-treated CD4CD8αα cells in the presence/absence of GrB and Prf inhibitors and assessed IEC death by flow cytometry. RESULTS We found a significant increase in the expression of GrB and Prf in CD4CD8αα IELs of septic mice compared to sham mice. We found that GrB and Prf levels in CD4CD8αα IELs were increased in the small intestines of WT septic mice, while CD4CD8αα IELs of CIRP-/- mice did not show an increase in those cytotoxic granules after sepsis. We found that eCIRP upregulated GrB and Prf in CD4CD8αα IELs isolated from WT mice but not from TLR4-/- mice. Furthermore, we also revealed that eCIRP-treated CD4CD8αα cells induced organoid-derived IEC death, which was mitigated by GrB and Prf inhibitors. Finally, histological analysis of septic mice revealed that CIRP-/- mice were protected from tissue injury and cell death in the small intestines compared to WT mice. CONCLUSION In sepsis, the cytotoxicity initiated by the eCIRP/TLR4 axis in CD4CD8αα IELs is associated with intestinal epithelial cell (IEC) death, which could lead to gut injury.
Collapse
Affiliation(s)
- Yuichi Akama
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr, 11030, Manhasset, NY, USA
| | - Atsushi Murao
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr, 11030, Manhasset, NY, USA
| | - Monowar Aziz
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr, 11030, Manhasset, NY, USA.
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA.
| | - Ping Wang
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, 350 Community Dr, 11030, Manhasset, NY, USA.
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA.
| |
Collapse
|
8
|
Shin JH, Tillotson G, MacKenzie TN, Warren CA, Wexler HM, Goldstein EJC. Bacteroides and related species: The keystone taxa of the human gut microbiota. Anaerobe 2024; 85:102819. [PMID: 38215933 DOI: 10.1016/j.anaerobe.2024.102819] [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: 09/06/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp. are known to be major players in the maintenance of eubiosis in the human gastrointestinal tract. Here we review the critical role that Bacteroides play in the human gut, their potential pathogenic role outside of the gut, and their various methods of adapting to the environment, with a focus on data for B. fragilis and B. thetaiotaomicron. Bacteroides are anaerobic non-sporing Gram negative organisms that are also resistant to bile acids, generally thriving in the gut and having a beneficial relationship with the host. While they are generally commensal organisms, some Bacteroides spp. can be opportunistic pathogens in scenarios of GI disease, trauma, cancer, or GI surgery, and cause infection, most commonly intra-abdominal infection. B. fragilis can develop antimicrobial resistance through multiple mechanisms in large part due to its plasticity and fluid genome. Bacteroidota (formerly, Bacteroidetes) have a very broad metabolic potential in the GI microbiota and can rapidly adapt their carbohydrate metabolism to the available nutrients. Gastrointestinal Bacteroidota species produce short-chain fatty acids such as succinate, acetate, butyrate, and occasionally propionate, as the major end-products, which have wide-ranging and many beneficial influences on the host. Bacteroidota, via bile acid metabolism, also play a role in in colonization-resistance of other organisms, including Clostridioides difficile, and maintenance of gut integrity.
Collapse
Affiliation(s)
- Jae Hyun Shin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | | | | | - Cirle A Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Hannah M Wexler
- GLAVAHCS, Los Angeles, CA, USA; David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| | | |
Collapse
|
9
|
Bousbaine D, Bauman KD, Chen YE, Yu VK, Lalgudi PV, Naziripour A, Veinbachs A, Phung JL, Nguyen TTD, Swenson JM, Lee YE, Dimas A, Jain S, Meng X, Pham TPT, Zhao A, Barkal L, Gribonika I, Van Rompay KKA, Belkaid Y, Barnes CO, Fischbach MA. Discovery and engineering of the antibody response against a prominent skin commensal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576900. [PMID: 38328052 PMCID: PMC10849572 DOI: 10.1101/2024.01.23.576900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The ubiquitous skin colonist Staphylococcus epidermidis elicits a CD8 + T cell response pre-emptively, in the absence of an infection 1 . However, the scope and purpose of this anti-commensal immune program are not well defined, limiting our ability to harness it therapeutically. Here, we show that this colonist also induces a potent, durable, and specific antibody response that is conserved in humans and non-human primates. A series of S. epidermidis cell-wall mutants revealed that the cell surface protein Aap is a predominant target. By colonizing mice with a strain of S. epidermidis in which the parallel β-helix domain of Aap is replaced by tetanus toxin fragment C, we elicit a potent neutralizing antibody response that protects mice against a lethal challenge. A similar strain of S. epidermidis expressing an Aap-SpyCatcher chimera can be conjugated with recombinant immunogens; the resulting labeled commensal elicits high titers of antibody under conditions of physiologic colonization, including a robust IgA response in the nasal mucosa. Thus, immunity to a common skin colonist involves a coordinated T and B cell response, the latter of which can be redirected against pathogens as a novel form of topical vaccination.
Collapse
|
10
|
Yonemoto Y, Nemoto Y, Morikawa R, Shibayama N, Oshima S, Nagaishi T, Mizutani T, Ito G, Fujii S, Okamoto R. Single cell analysis revealed that two distinct, unique CD4 + T cell subsets were increased in the small intestinal intraepithelial lymphocytes of aged mice. Front Immunol 2024; 15:1340048. [PMID: 38327516 PMCID: PMC10848332 DOI: 10.3389/fimmu.2024.1340048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Recent advances in research suggest that aging has a controllable chronic inflammatory disease aspect. Aging systemic T cells, which secrete pro-inflammatory factors, affect surrounding somatic cells, and accelerate the aging process through chronic inflammation, have attracted attention as potential therapeutic targets in aging. On the other hand, there are few reports on the aging of the intestinal immune system, which differs from the systemic immune system in many ways. In the current study, we investigated the age-related changes in the intestinal immune system, particularly in T cells. The most significant changes were observed in the CD4+ T cells in the small intestinal IEL, with a marked increase in this fraction in old mice and reduced expression of CD27 and CD28, which are characteristic of aging systemic T cells. The proliferative capacity of aging IEL CD4+ T cells was significantly more reduced than that of aging systemic T cells. Transcriptome analysis showed that the expression of inflammatory cytokines was not upregulated, whereas Cd8α, NK receptors, and Granzymes were upregulated in aging IEL CD4+ T cells. Functional analysis showed that aging IEL T cells had a higher cytotoxic function against intestinal tumor organoids in vitro than young IEL T cells. scRNAseq revealed that splenic T cells show a transition from naïve to memory T cells, whereas intestinal T cells show the emergence of a CD8αα+CD4+ T cell fraction in aged mice, which is rarely seen in young cells. Further analysis of the aging IEL CD4+ T cells showed that two unique subsets are increased that are distinct from the systemic CD4+ T cells. Subset 1 has a pro-inflammatory component, with expression of IFNγ and upregulation of NFkB signaling pathways. Subset 2 does not express IFNγ, but upregulates inhibitory molecules and nIEL markers. Expression of granzymes and Cd8a was common to both. These fractions were in opposite positions in the clustering by UMAP and had different TCR repertoires. They may be involved in the suppression of intestinal aging and longevity through anti-tumor immunity, elimination of senescent cells and stressed cells in the aging environment. This finding could be a breakthrough in aging research.
Collapse
Affiliation(s)
- Yuki Yonemoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yasuhiro Nemoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryo Morikawa
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Nana Shibayama
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shigeru Oshima
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takashi Nagaishi
- Department of Advanced Therapeutics for Gastrointestinal Diseases, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomohiro Mizutani
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Go Ito
- Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Satoru Fujii
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| |
Collapse
|
11
|
Li D, Luo ZB, Zhu J, Wang JX, Jin ZY, Qi S, Jin M, Quan LH. Ginsenoside F2-Mediated Intestinal Microbiota and Its Metabolite Propionic Acid Positively Impact the Gut-Skin Axis in Atopic Dermatitis Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:339-350. [PMID: 38150707 DOI: 10.1021/acs.jafc.3c06015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Atopic dermatitis (AD) is a complex inflammatory skin disease induced by multiple factors. AD can also cause intestinal inflammation and disorders of the gut microbiota. Ginseng is a kind of edible and medicinal plant; its main active components are ginsenosides. Ginsenosides have a variety of anti-inflammatory effects and regulate the gut microbiota; however, their role in AD and the underlying mechanisms are unclear. In this study, we found that intragastric administration of ginsenoside F2 improved AD-like skin symptoms and reduced inflammatory cell infiltration, serum immunoglobulin E levels, and mRNA expression of inflammatory cytokines in AD mice. 16s rRNA sequencing analysis showed that ginsenoside F2 altered the intestinal microbiota structure and enriched the short-chain fatty acid-producing microbiota in AD mice. Metabolomic analysis revealed that ginsenoside F2 significantly increased the propionic acid (Pa) content of feces and serum in AD mice, which was positively correlated with significant enrichment of Parabacteroides goldsteinii and Lactobacillus plantarum in the intestines. Pa inhibits inflammatory responses in the gut and skin of AD mice through the G-protein-coupled receptor43/NF-κB pathway, thereby improving skin AD symptoms. These results revealed, for the first time, the mechanism by which ginsenoside F2 improves AD through the Pa (a metabolite of intestinal microbiota)-gut-skin axis.
Collapse
Affiliation(s)
- Dongxu Li
- College of Integration Science, Yanbian University, Yanji 133002, China
| | - Zhao-Bo Luo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Jun Zhu
- College of Integration Science, Yanbian University, Yanji 133002, China
| | - Jun-Xia Wang
- Department of Animal Science, College of Agricultural, Yanbian University, Yanji 133002, China
| | - Zheng-Yun Jin
- Department of Animal Science, College of Agricultural, Yanbian University, Yanji 133002, China
| | - Shaobo Qi
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Meiling Jin
- Department of Pharmacology, College of Medicine, Yanbian University, Yanji 133002, China
| | - Lin-Hu Quan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| |
Collapse
|
12
|
Brabec T, Schwarzer M, Kováčová K, Dobešová M, Schierová D, Březina J, Pacáková I, Šrůtková D, Ben-Nun O, Goldfarb Y, Šplíchalová I, Kolář M, Abramson J, Filipp D, Dobeš J. Segmented filamentous bacteria-induced epithelial MHCII regulates cognate CD4+ IELs and epithelial turnover. J Exp Med 2024; 221:e20230194. [PMID: 37902602 PMCID: PMC10615894 DOI: 10.1084/jem.20230194] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/16/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023] Open
Abstract
Intestinal epithelial cells have the capacity to upregulate MHCII molecules in response to certain epithelial-adhesive microbes, such as segmented filamentous bacteria (SFB). However, the mechanism regulating MHCII expression as well as the impact of epithelial MHCII-mediated antigen presentation on T cell responses targeting those microbes remains elusive. Here, we identify the cellular network that regulates MHCII expression on the intestinal epithelium in response to SFB. Since MHCII on the intestinal epithelium is dispensable for SFB-induced Th17 response, we explored other CD4+ T cell-based responses induced by SFB. We found that SFB drive the conversion of cognate CD4+ T cells to granzyme+ CD8α+ intraepithelial lymphocytes. These cells accumulate in small intestinal intraepithelial space in response to SFB. Yet, their accumulation is abrogated by the ablation of MHCII on the intestinal epithelium. Finally, we show that this mechanism is indispensable for the SFB-driven increase in the turnover of epithelial cells in the ileum. This study identifies a previously uncharacterized immune response to SFB, which is dependent on the epithelial MHCII function.
Collapse
Affiliation(s)
- Tomáš Brabec
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czech Republic
| | - Katarína Kováčová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Dobešová
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dagmar Schierová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Březina
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Iva Pacáková
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Dagmar Šrůtková
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czech Republic
| | - Osher Ben-Nun
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iva Šplíchalová
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Kolář
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dominik Filipp
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Dobeš
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
13
|
Zhang H, Xie Y, Cao F, Song X. Gut microbiota-derived fatty acid and sterol metabolites: biotransformation and immunomodulatory functions. Gut Microbes 2024; 16:2382336. [PMID: 39046079 PMCID: PMC11271093 DOI: 10.1080/19490976.2024.2382336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/26/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
Commensal microorganisms in the human gut produce numerous metabolites by using small molecules derived from the host or diet as precursors. Host or dietary lipid molecules are involved in energy metabolism and maintaining the structural integrity of cell membranes. Notably, gut microbes can convert these lipids into bioactive signaling molecules through their biotransformation and synthesis pathways. These microbiota-derived lipid metabolites can affect host physiology by influencing the body's immune and metabolic processes. This review aims to summarize recent advances in the microbial transformation and host immunomodulatory functions of these lipid metabolites, with a special focus on fatty acids and steroids produced by our gut microbiota.
Collapse
Affiliation(s)
- Haohao Zhang
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yadong Xie
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Fei Cao
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xinyang Song
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
14
|
Yang Q, Cai Y, Guo S, Wang Z, Wang Y, Yu X, Sun W, Qiu S, Zhang A. Decoding immune interactions of gut microbiota for understanding the mechanisms of diseases and treatment. Front Microbiol 2023; 14:1238822. [PMID: 38130945 PMCID: PMC10733502 DOI: 10.3389/fmicb.2023.1238822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Affiliation(s)
- Qiang Yang
- Good Agricultural Practices Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ying Cai
- Good Agricultural Practices Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| | - Sifan Guo
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| | - Zhibo Wang
- Good Agricultural Practices Center and Graduate School, Heilongjiang University of Chinese Medicine, Harbin, China
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| | - Yan Wang
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| | - Xiaodan Yu
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| | - Wanying Sun
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| | - Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, International Joint Research Center on Traditional Chinese and Modern Medicine, Hainan Engineering Research Center for Biological Sample Resources of Major Diseases (First Affiliated Hospital of Hainan Medical University), Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Hainan Medical University, Haikou, China
| |
Collapse
|
15
|
Meng H, Xu D, Wang Q, Liu L, Liu W, Wang J. Maintaining immune homeostasis with Coptis Chinensis water extract to mitigate sepsis severity via modulating gut microbiome and metabolism. J Pharm Biomed Anal 2023; 236:115719. [PMID: 37742503 DOI: 10.1016/j.jpba.2023.115719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Sepsis arises from an uncontrolled inflammatory response to infection that can lead to organ failure. The gut microbiome is increasingly recognized as a key modulator of sepsis progression. This study investigated whether Coptis chinensis water extract (CCWE) could attenuate sepsis by modulating the gut microbiome and immune response. A rat model of sepsis induced by cecum ligation and perforation was used. 16 S ribosomal ribonucleic acid (rRNA) sequencing, proton nuclear magnetic resonance (1H NMR) metabolomics and flow cytometry assays were used to evaluate microbial, metabolic and immune profiles. CCWE treatment reversed sepsis-induced loss of beneficial bacteria like Firmicutes and Bacteroidetes and restored gut microbial balance. CCWE increased short-chain fatty acids, carnitine and phenylacetate, which provide energy and curb inflammation. By enhancing immune homeostasis and maintaining regulatory T cells (Tregs), CCWE treatment also exerted bidirectional regulation on T cells for initially suppressing hyperactivation then enabling recovery. Overall, CCWE may benefit sepsis by regulating the gut-microbiome-immune axis. By restoring microbiome balance, improving metabolism, and modulating immunity, CCWE treatment shows potential for alleviating sepsis severity and progression. The increases in beneficial bacteria, Tregs, and anti-inflammatory metabolites coupled with decreases in opportunistic pathogens likely contributed collectively to CCWE's protective effects. CCWE may emerge as an alternative or adjunctive option for managing disorders of dangerous inflammation like sepsis. Future research should explore CCWE's mechanisms of action clinically to determine its potential as a safe, effective means of modulating health through natural regulation of the gut microbiome and immune function.
Collapse
Affiliation(s)
- Huihui Meng
- Center of Molecular Metabolism, School of Environmental & Biological Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China
| | - Di Xu
- Center of Molecular Metabolism, School of Environmental & Biological Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China
| | - Qing Wang
- Department of Interventional Surgery, Zibo Central Hospital, No.54 Gongqingtuan Road (W), Zhangdian District, Zibo City, Shandong, China
| | - Lin Liu
- Department of Interventional Surgery, Zibo Central Hospital, No.54 Gongqingtuan Road (W), Zhangdian District, Zibo City, Shandong, China
| | - Wenya Liu
- Center of Molecular Metabolism, School of Environmental & Biological Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China
| | - Junsong Wang
- Center of Molecular Metabolism, School of Environmental & Biological Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
| |
Collapse
|
16
|
Maseda D, Manfredo-Vieira S, Payne AS. T cell and bacterial microbiota interaction at intestinal and skin epithelial interfaces. DISCOVERY IMMUNOLOGY 2023; 2:kyad024. [PMID: 38567051 PMCID: PMC10917213 DOI: 10.1093/discim/kyad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/28/2023] [Accepted: 11/24/2023] [Indexed: 04/04/2024]
Abstract
Graphical Abstract.
Collapse
Affiliation(s)
- Damian Maseda
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Silvio Manfredo-Vieira
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aimee S Payne
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
17
|
Xu J, Kong X, Li J, Mao H, Zhu Y, Zhu X, Xu Y. Pediatric intensive care unit treatment alters the diversity and composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children. Front Microbiol 2023; 14:1237993. [PMID: 38029168 PMCID: PMC10679412 DOI: 10.3389/fmicb.2023.1237993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Common critical illnesses are a growing economic burden on healthcare worldwide. However, therapies targeting the gut microbiota for critical illnesses have not been developed on a large scale. This study aimed to investigate the changes in the characteristics of the gut microbiota in critically ill children after short-term pediatric intensive care unit (PICU) treatments. Methods Anal swab samples were prospectively collected from March 2021 to March 2022 from children admitted to the PICU of Xinhua Hospital who received broad-spectrum antibiotics on days 1 (the D1 group) and 7 (the D7 group) of the PICU treatment. The structural and functional characteristics of the gut microbiota of critically ill children were explored using metagenomic next-generation sequencing (mNGS) technology, and a comparative analysis of samples from D1 and D7 was conducted. Results After 7 days of PICU admission, a significant decrease was noted in the richness of the gut microbiota in critically ill children, while the bacterial diversity and the community structure between groups remained stable to some extent. The relative abundance of Bacilli and Lactobacillales was significantly higher, and that of Campylobacter hominis was significantly lower in the D7 group than in the D1 group. The random forest model revealed that Prevotella coporis and Enterobacter cloacae were bacterial biomarkers between groups. LEfSe revealed that two Gene Ontology entries, GO:0071555 (cell wall organization) and GO:005508 (transmembrane transport), changed significantly after the short-term treatment in the PICU. In addition, 30 KEGG pathways were mainly related to the activity of enzymes and proteins during the processes of metabolism, DNA catabolism and repair, and substance transport. Finally, 31 antimicrobial resistance genes had significantly different levels between the D7 and D1 groups. The top 10 up-regulated genes were Erm(A), ErmX, LptD, eptB, SAT-4, tetO, adeJ, adeF, APH(3')-IIIa, and tetM. Conclusion The composition, gene function, and resistance genes of gut microbiota of critically ill children can change significantly after short PICU treatments. Our findings provide a substantial basis for a better understanding of the structure and function of gut microbiota and their role in critical illnesses.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Yaya Xu
- Department of Pediatric Intensive Care Medicine, Xinhua Hospital, Affiliated to the Medical School, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
18
|
Ramanan D, Pratama A, Zhu Y, Venezia O, Sassone-Corsi M, Chowdhary K, Galván-Peña S, Sefik E, Brown C, Gélineau A, Mathis D, Benoist C. Regulatory T cells in the face of the intestinal microbiota. Nat Rev Immunol 2023; 23:749-762. [PMID: 37316560 DOI: 10.1038/s41577-023-00890-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
Regulatory T cells (Treg cells) are key players in ensuring a peaceful coexistence with microorganisms and food antigens at intestinal borders. Startling new information has appeared in recent years on their diversity, the importance of the transcription factor FOXP3, how T cell receptors influence their fate and the unexpected and varied cellular partners that influence Treg cell homeostatic setpoints. We also revisit some tenets, maintained by the echo chambers of Reviews, that rest on uncertain foundations or are a subject of debate.
Collapse
Affiliation(s)
| | - Alvin Pratama
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Yangyang Zhu
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Olivia Venezia
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Esen Sefik
- Department of Immunology, Yale University, New Haven, CT, USA
| | - Chrysothemis Brown
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Paediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | |
Collapse
|
19
|
López-Fandiño R, Molina E, Lozano-Ojalvo D. Intestinal factors promoting the development of RORγt + cells and oral tolerance. Front Immunol 2023; 14:1294292. [PMID: 37936708 PMCID: PMC10626553 DOI: 10.3389/fimmu.2023.1294292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
The gastrointestinal tract has to harmonize the two seemingly opposite functions of fulfilling nutritional needs and avoiding the entry of pathogens, toxins and agents that can cause physical damage. This balance requires a constant adjustment of absorptive and defending functions by sensing environmental changes or noxious substances and initiating adaptive or protective mechanisms against them through a complex network of receptors integrated with the central nervous system that communicate with cells of the innate and adaptive immune system. Effective homeostatic processes at barrier sites take the responsibility for oral tolerance, which protects from adverse reactions to food that cause allergic diseases. During a very specific time interval in early life, the establishment of a stable microbiota in the large intestine is sufficient to prevent pathological events in adulthood towards a much larger bacterial community and provide tolerance towards diverse food antigens encountered later in life. The beneficial effects of the microbiome are mainly exerted by innate and adaptive cells that express the transcription factor RORγt, in whose generation, mediated by different bacterial metabolites, retinoic acid signalling plays a predominant role. In addition, recent investigations indicate that food antigens also contribute, analogously to microbial-derived signals, to educating innate immune cells and instructing the development and function of RORγt+ cells in the small intestine, complementing and expanding the tolerogenic effect of the microbiome in the colon. This review addresses the mechanisms through which microbiota-produced metabolites and dietary antigens maintain intestinal homeostasis, highlighting the complementarity and redundancy between their functions.
Collapse
Affiliation(s)
- Rosina López-Fandiño
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, Madrid, Spain
| | | | | |
Collapse
|
20
|
White Z, Cabrera I, Kapustka I, Sano T. Microbiota as key factors in inflammatory bowel disease. Front Microbiol 2023; 14:1155388. [PMID: 37901813 PMCID: PMC10611514 DOI: 10.3389/fmicb.2023.1155388] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/07/2023] [Indexed: 10/31/2023] Open
Abstract
Inflammatory Bowel Disease (IBD) is characterized by prolonged inflammation of the gastrointestinal tract, which is thought to occur due to dysregulation of the immune system allowing the host's cells to attack the GI tract and cause chronic inflammation. IBD can be caused by numerous factors such as genetics, gut microbiota, and environmental influences. In recent years, emphasis on commensal bacteria as a critical player in IBD has been at the forefront of new research. Each individual harbors a unique bacterial community that is influenced by diet, environment, and sanitary conditions. Importantly, it has been shown that there is a complex relationship among the microbiome, activation of the immune system, and autoimmune disorders. Studies have shown that not only does the microbiome possess pathogenic roles in the progression of IBD, but it can also play a protective role in mediating tissue damage. Therefore, to improve current IBD treatments, understanding not only the role of harmful bacteria but also the beneficial bacteria could lead to attractive new drug targets. Due to the considerable diversity of the microbiome, it has been challenging to characterize how particular microorganisms interact with the host and other microbiota. Fortunately, with the emergence of next-generation sequencing and the increased prevalence of germ-free animal models there has been significant advancement in microbiome studies. By utilizing human IBD studies and IBD mouse models focused on intraepithelial lymphocytes and innate lymphoid cells, this review will explore the multifaceted roles the microbiota plays in influencing the immune system in IBD.
Collapse
Affiliation(s)
| | | | | | - Teruyuki Sano
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| |
Collapse
|
21
|
Lu S, Zou W, Chen X, Sun G, Cidan Y, Almutairi MH, Dunzhu L, Nazar M, Mehmood K, Zhu Y, Basang W, Li K. Effects of Cryptosporidium parvum infection on intestinal fungal microbiota in yaks (Bos grunniens). Microb Pathog 2023; 183:106322. [PMID: 37633503 DOI: 10.1016/j.micpath.2023.106322] [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: 05/25/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
During the last decade, researchers had started to focus on the relationship between intestinal parasitic infection and variation of intestinal microflora. Cryptosporidium is a widely known opportunistic and zoonotic pathogen. Several studies have shown that Cryptosporidium infection has impact to alter the gut microflora. However, there are only few studies referring to the fungal microflora changes in response to Cryptosporidium infection in highland ruminants. Therefore, the present study was performed for exploring the alternations of intestinal fungal microbiota in yaks after exposure to Cryptosporidium infection. In present study, Amplicon sequencing of ITS regions was used to study the variations of fungal microflora in yaks. After filtering the raw data, over 45 000 and 62 000 clean data were obtained in uninfected and infected yaks, respectively. By using alpha diversity analysis, it was found that there is no significant difference in the richness and evenness when positive samples were compared with negative ones, whereas intestinal fungal communities in different taxa in yaks were changed. The results of present study depicted that 2-phyla and 21-genera in the infected animals had significantly (P < 0.05) changed. These genera were Septoria, Coniothyrium, Cleistothelebolus, Bensingtonia, Cystobasidium, Filobasidium, Coprotus, Carex, Blumeria, Coprinellus, Leucosporidium, Phialophora, Isolepis, Ascobolus, Thecaphora, Mortierella, Urocystis, Symmetrospora and Lasiobolus. In addition, we found variations in 28 enzymes suggesting that the function of microbiota was also affected. It is concluded that there are drastic changes in the fungal microflora and microbiota functions after exposure to Cryptosporidium infection in yak. Our results help to focus on the prompt way for the development of new therapies to control Cryptosporidiosis.
Collapse
Affiliation(s)
- Sijia Lu
- Institute of Traditional Chinese Veterinary Medicine & MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Wen Zou
- Institute of Traditional Chinese Veterinary Medicine & MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xiushuang Chen
- Institute of Traditional Chinese Veterinary Medicine & MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Guangming Sun
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Yangji Cidan
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Mikhlid H Almutairi
- Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451, Riyadh, Saudi Arabia
| | - Luosang Dunzhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China
| | - Mudassar Nazar
- University of Agriculture Faisalabad, Sub-Campus, Burewala, 61010, Pakistan
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, 63100, Pakistan
| | - Yanbin Zhu
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China.
| | - Wangdui Basang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agriculture and Animal Husbandry Science, Lhasa, 850009, China.
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine & MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, PR China.
| |
Collapse
|
22
|
Nagashima K, Zhao A, Atabakhsh K, Bae M, Blum JE, Weakley A, Jain S, Meng X, Cheng AG, Wang M, Higginbottom S, Dimas A, Murugkar P, Sattely ES, Moon JJ, Balskus EP, Fischbach MA. Mapping the T cell repertoire to a complex gut bacterial community. Nature 2023; 621:162-170. [PMID: 37587342 PMCID: PMC10948025 DOI: 10.1038/s41586-023-06431-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/13/2023] [Indexed: 08/18/2023]
Abstract
Certain bacterial strains from the microbiome induce a potent, antigen-specific T cell response1-5. However, the specificity of microbiome-induced T cells has not been explored at the strain level across the gut community. Here, we colonize germ-free mice with complex defined communities (roughly 100 bacterial strains) and profile T cell responses to each strain. The pattern of responses suggests that many T cells in the gut repertoire recognize several bacterial strains from the community. We constructed T cell hybridomas from 92 T cell receptor (TCR) clonotypes; by screening every strain in the community against each hybridoma, we find that nearly all the bacteria-specific TCRs show a one-to-many TCR-to-strain relationship, including 13 abundant TCR clonotypes that each recognize 18 Firmicutes. By screening three pooled bacterial genomic libraries, we discover that these 13 clonotypes share a single target: a conserved substrate-binding protein from an ATP-binding cassette transport system. Peripheral regulatory T cells and T helper 17 cells specific for an epitope from this protein are abundant in community-colonized and specific pathogen-free mice. Our work reveals that T cell recognition of commensals is focused on widely conserved, highly expressed cell-surface antigens, opening the door to new therapeutic strategies in which colonist-specific immune responses are rationally altered or redirected.
Collapse
Affiliation(s)
- Kazuki Nagashima
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Aishan Zhao
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Katayoon Atabakhsh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Minwoo Bae
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jamie E Blum
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Allison Weakley
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sunit Jain
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Xiandong Meng
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Alice G Cheng
- Department of Gastroenterology, Stanford School of Medicine, Stanford, CA, USA
| | - Min Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Steven Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Alex Dimas
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
| | | | - Elizabeth S Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - James J Moon
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- ChEM-H Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
23
|
Yan Y, Lei Y, Qu Y, Fan Z, Zhang T, Xu Y, Du Q, Brugger D, Chen Y, Zhang K, Zhang E. Bacteroides uniformis-induced perturbations in colonic microbiota and bile acid levels inhibit TH17 differentiation and ameliorate colitis developments. NPJ Biofilms Microbiomes 2023; 9:56. [PMID: 37580334 PMCID: PMC10425470 DOI: 10.1038/s41522-023-00420-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/14/2023] [Indexed: 08/16/2023] Open
Abstract
Inflammatory bowel disease (IBD) is associated with gut dysbiosis and can lead to colitis-associated malignancies. Bacteroides uniformis (Bu) regulates animal intestinal homeostasis; however, the mechanism by which it alleviates colitis in mice remains unknown. We investigated the effects of B. uniformis JCM5828 and its metabolites on female C57BL/6J mice with dextran sulfate sodium salt (DSS) induced colitis. Treatment with Bu considerably alleviated colitis progression and restored the mechanical and immune barrier protein expression. Additionally, Bu increased the abundance of the symbiotic bacteria Bifidobacterium and Lactobacillus vaginalis while decreasing that of pathogenic Escherichia-Shigella, and modulated intestinal bile acid metabolism. Bu largely regulated the expression of key regulatory proteins of the NF-κB and mitogen-activated protein kinase (MAPK) signaling pathways in colonic tissues and the differentiation of TH17 cells. However, Bu could not directly inhibit TH17 cell differentiation in vitro; it modulated the process in the lamina propria by participating in bile acid metabolism and regulating key metabolites (alpha-muricholic, hyodeoxycholic, and isolithocholic acid), thereby modulating the intestinal immune response. Our findings suggest that Bu or bile acid supplements are potential therapies for colitis and other diseases associated with intestinal barrier dysfunction.
Collapse
Affiliation(s)
- YiTing Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yu Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ying Qu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhen Fan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ting Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangbin Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Qian Du
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Daniel Brugger
- Institute of Animal Nutrition and Dietetics, Vetsuisse-Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ke Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Enping Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
24
|
Lockhart A, Reed A, Rezende de Castro T, Herman C, Campos Canesso MC, Mucida D. Dietary protein shapes the profile and repertoire of intestinal CD4+ T cells. J Exp Med 2023; 220:214115. [PMID: 37191720 DOI: 10.1084/jem.20221816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 04/11/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
The intestinal immune system must tolerate food antigens to avoid allergy, a process requiring CD4+ T cells. Combining antigenically defined diets with gnotobiotic models, we show that food and microbiota distinctly influence the profile and T cell receptor repertoire of intestinal CD4+ T cells. Independent of the microbiota, dietary proteins contributed to accumulation and clonal selection of antigen-experienced CD4+ T cells at the intestinal epithelium, imprinting a tissue-specialized transcriptional program including cytotoxic genes on both conventional and regulatory CD4+ T cells (Tregs). This steady state CD4+ T cell response to food was disrupted by inflammatory challenge, and protection against food allergy in this context was associated with Treg clonal expansion and decreased proinflammatory gene expression. Finally, we identified both steady-state epithelium-adapted CD4+ T cells and tolerance-induced Tregs that recognize dietary antigens, suggesting that both cell types may be critical for preventing inappropriate immune responses to food.
Collapse
Affiliation(s)
- Ainsley Lockhart
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
| | - Aubrey Reed
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
| | | | - Calvin Herman
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
| | | | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University , New York, NY, USA
| |
Collapse
|
25
|
D'Adamo GL, Chonwerawong M, Gearing LJ, Marcelino VR, Gould JA, Rutten EL, Solari SM, Khoo PWR, Wilson TJ, Thomason T, Gulliver EL, Hertzog PJ, Giles EM, Forster SC. Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease. Cell Rep Med 2023; 4:101124. [PMID: 37467722 PMCID: PMC10394256 DOI: 10.1016/j.xcrm.2023.101124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/19/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade-specific metagenomic analysis identifies key, functionally distinct Enterococcus clades associated with either IBD or health. Strain-specific in vitro validation demonstrates differences in cell cytotoxicity and inflammatory signaling in intestinal epithelial cells, consistent with the colonic mucosa-specific response measured in patients with IBD. This demonstrates the importance of strain-specific phenotypes and consideration of anatomical sites in exploring the dysregulated host-bacterial interactions in IBD.
Collapse
Affiliation(s)
- Gemma L D'Adamo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Jodee A Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Rutten
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Sean M Solari
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Patricia W R Khoo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia
| | - Trevor J Wilson
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; MHTP Medical Genomics Facility, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Tamblyn Thomason
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Gulliver
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Edward M Giles
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia.
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia.
| |
Collapse
|
26
|
Song X, Zhang H, Zhang Y, Goh B, Bao B, Mello SS, Sun X, Zheng W, Gazzaniga FS, Wu M, Qu F, Yin Q, Gilmore MS, Oh SF, Kasper DL. Gut microbial fatty acid isomerization modulates intraepithelial T cells. Nature 2023; 619:837-843. [PMID: 37380774 DOI: 10.1038/s41586-023-06265-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
The human gut microbiome constantly converts natural products derived from the host and diet into numerous bioactive metabolites1-3. Dietary fats are essential micronutrients that undergo lipolysis to release free fatty acids (FAs) for absorption in the small intestine4. Gut commensal bacteria modify some unsaturated FAs-for example, linoleic acid (LA)-into various intestinal FA isomers that regulate host metabolism and have anticarcinogenic properties5. However, little is known about how this diet-microorganism FA isomerization network affects the mucosal immune system of the host. Here we report that both dietary factors and microbial factors influence the level of gut LA isomers (conjugated LAs (CLAs)) and that CLAs in turn modulate a distinct population of CD4+ intraepithelial lymphocytes (IELs) that express CD8αα in the small intestine. Genetic abolition of FA isomerization pathways in individual gut symbionts significantly decreases the number of CD4+CD8αα+ IELs in gnotobiotic mice. Restoration of CLAs increases CD4+CD8αα+ IEL levels in the presence of the transcription factor hepatocyte nuclear factor 4γ (HNF4γ). Mechanistically, HNF4γ facilitates CD4+CD8αα+ IEL development by modulating interleukin-18 signalling. In mice, specific deletion of HNF4γ in T cells leads to early mortality from infection by intestinal pathogens. Our data reveal a new role for bacterial FA metabolic pathways in the control of host intraepithelial immunological homeostasis by modulating the relative number of CD4+ T cells that were CD4+CD8αα+.
Collapse
Affiliation(s)
- Xinyang Song
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Haohao Zhang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yanbo Zhang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Byoungsook Goh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bin Bao
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Suelen S Mello
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Ximei Sun
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Wen Zheng
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca S Gazzaniga
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Mass General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Meng Wu
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Fangfang Qu
- Department of Computer Science, Tufts University, Medford, MA, USA
| | - Qiangzong Yin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michael S Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Sungwhan F Oh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dennis L Kasper
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
27
|
Graham DB, Xavier RJ. Conditioning of the immune system by the microbiome. Trends Immunol 2023; 44:499-511. [PMID: 37236891 DOI: 10.1016/j.it.2023.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023]
Abstract
The human intestinal microbiome has coevolved with its host to establish a stable homeostatic relationship with hallmark features of mutualistic symbioses, yet the mechanistic underpinnings of host-microbiome interactions are incompletely understood. Thus, it is an opportune time to conceive a common framework for microbiome-mediated regulation of immune function. We propose the term conditioned immunity to describe the multifaceted mechanisms by which the microbiome modulates immunity. In this regard, microbial colonization is a conditioning exposure that has durable effects on immune function through the action of secondary metabolites, foreign molecular patterns, and antigens. Here, we discuss how spatial niches impact host exposure to microbial products at the level of dose and timing, which elicit diverse conditioned responses.
Collapse
Affiliation(s)
- Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| |
Collapse
|
28
|
Abstract
The incomplete removal of T cells that are reactive against self-proteins during their differentiation in the thymus requires mechanisms of tolerance that prevent their effector function within the periphery. A further challenge is imposed by the need to establish tolerance to the holobiont self, which comprises a highly complex community of commensal microorganisms. Here, we review recent advances in the investigation of peripheral T cell tolerance, focusing on new insights into mechanisms of tolerance to the gut microbiota, including tolerogenic antigen-presenting cell types and immunomodulatory lymphocytes, and their layered ontogeny that underlies developmental windows for establishing intestinal tolerance. While emphasizing the intestine as a model tissue for studying peripheral T cell tolerance, we highlight overlapping and distinct pathways that underlie tolerance to self-antigens versus commensal antigens within a broader framework for immune tolerance.
Collapse
|
29
|
Weingarden AR, Treiger O, Ulsh L, Limketkai B, Goldenberg D, Okafor P, Sonu I, Stollman N, Neshatian L. Delivery of Fecal Material to Terminal Ileum Is Associated with Long-Term Success of Fecal Microbiota Transplantation. Dig Dis Sci 2023; 68:2006-2014. [PMID: 36372864 PMCID: PMC10994768 DOI: 10.1007/s10620-022-07761-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/03/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent Clostridioides difficile infection (CDI). However, 10-20% of patients still fail to recover following FMT. There is a need to understand why these failures occur and if there are modifiable factors that can be addressed by clinicians performing FMT. AIMS We sought to identify factors related to the FMT procedure itself which could impact FMT outcomes. We also aimed to identify patient demographics which might be associated with FMT outcomes and whether any factors were associated with early FMT failure compared to late CDI recurrence. METHODS We performed a retrospective multicenter cohort analysis of FMT procedures between October 2005 and November 2020. We collected data on patient demographics, details of the FMT procedure, and procedure outcomes. Using univariate and multivariate regression, we evaluated whether these factors were associated with long-term FMT success, early FMT failure (less than 60 days following procedure), or late CDI recurrence (more than 60 days following procedure). RESULTS Long-term success of FMT was strongly correlated with any delivery of stool to the terminal ileum (Odds Ratio [OR] 4.83, 95% confidence interval [CI] 1.359-17.167) and underlying neurologic disease (OR 8.012, 95% CI 1.041-61.684). Lower bowel prep quality was significantly associated with both early FMT failure (p = 0.034) and late CDI recurrence (p = 0.050). CONCLUSIONS Delivery of stool to the terminal ileum is significantly associated with long-term success following FMT. This is a relatively safe practice which could easily be incorporated into the standard of care for colonoscopic FMT.
Collapse
Affiliation(s)
- Alexa R Weingarden
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford University, 420 Broadway Street Pavilion D, 2nd Floor, Redwood City, CA, 94063, USA.
| | - Olivia Treiger
- Division of Gastroenterology, Alta Bates Summit Medical Center, East Bay Center for Digestive Health, 300 Frank H Ogawa Plaza #450, Oakland, CA, 94612, USA
| | - Lauren Ulsh
- Department of Medicine, Stanford University, 300 Pasteur Drive, S102, Stanford, CA, 94304, USA
| | - Berkeley Limketkai
- Division of Digestive Diseases, David Geffen School of Medicine at University of California Los Angeles, Westwood Digestive Diseases, 100 Medical Plaza, Suite 345, Los Angeles, CA, 90024, USA
| | - David Goldenberg
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford University, 420 Broadway Street Pavilion D, 2nd Floor, Redwood City, CA, 94063, USA
| | - Philip Okafor
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford University, 420 Broadway Street Pavilion D, 2nd Floor, Redwood City, CA, 94063, USA
| | - Irene Sonu
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford University, 420 Broadway Street Pavilion D, 2nd Floor, Redwood City, CA, 94063, USA
| | - Neil Stollman
- Department of Medicine, Stanford University, 300 Pasteur Drive, S102, Stanford, CA, 94304, USA
| | - Leila Neshatian
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford University, 420 Broadway Street Pavilion D, 2nd Floor, Redwood City, CA, 94063, USA
| |
Collapse
|
30
|
Chen YE, Bousbaine D, Veinbachs A, Atabakhsh K, Dimas A, Yu VK, Zhao A, Enright NJ, Nagashima K, Belkaid Y, Fischbach MA. Engineered skin bacteria induce antitumor T cell responses against melanoma. Science 2023; 380:203-210. [PMID: 37053311 DOI: 10.1126/science.abp9563] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Certain bacterial colonists induce a highly specific T cell response. A hallmark of this encounter is that adaptive immunity develops preemptively, in the absence of an infection. However, the functional properties of colonist-induced T cells are not well defined, limiting our ability to understand anticommensal immunity and harness it therapeutically. We addressed both challenges by engineering the skin bacterium Staphylococcus epidermidis to express tumor antigens anchored to secreted or cell-surface proteins. Upon colonization, engineered S. epidermidis elicits tumor-specific T cells that circulate, infiltrate local and metastatic lesions, and exert cytotoxic activity. Thus, the immune response to a skin colonist can promote cellular immunity at a distal site and can be redirected against a target of therapeutic interest by expressing a target-derived antigen in a commensal.
Collapse
Affiliation(s)
- Y Erin Chen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Dermatology Service, San Francisco Veterans Administration Health Care System, San Francisco, CA 94121, USA
| | - Djenet Bousbaine
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Alessandra Veinbachs
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Katayoon Atabakhsh
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Alex Dimas
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Victor K Yu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Aishan Zhao
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nora J Enright
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Kazuki Nagashima
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, Stanford, CA 94305, USA
| |
Collapse
|
31
|
Lockhart A, Reed A, de Castro TR, Herman C, Canesso MCC, Mucida D. Dietary protein shapes the profile and repertoire of intestinal CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536475. [PMID: 37090529 PMCID: PMC10120666 DOI: 10.1101/2023.04.11.536475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The intestinal immune system must tolerate food antigens to avoid allergy, a process requiring CD4 + T cells. Combining antigenically defined diets with gnotobiotic models, we show that food and microbiota distinctly influence the profile and T cell receptor repertoire of intestinal CD4 + T cells. Independent of the microbiota, dietary proteins contributed to accumulation and clonal selection of antigen-experienced CD4 + T cells at the intestinal epithelium, imprinting a tissue specialized transcriptional program including cytotoxic genes on both conventional and regulatory CD4 + T cells (Tregs). This steady state CD4 + T cell response to food was disrupted by inflammatory challenge, and protection against food allergy in this context was associated with Treg clonal expansion and decreased pro-inflammatory gene expression. Finally, we identified both steady state epithelium-adapted CD4 + T cells and tolerance-induced Tregs that recognize dietary antigens, suggesting that both cell types may be critical for preventing inappropriate immune responses to food.
Collapse
|
32
|
Sun W, Chen Y, Wang L, Wang Z, Liu S, Zhang M, Liu Y, Li Q, Zhang H. Gram-scale preparation of quercetin supramolecular nanoribbons for intestinal inflammatory diseases by oral administration. Biomaterials 2023; 295:122039. [PMID: 36791522 DOI: 10.1016/j.biomaterials.2023.122039] [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: 09/14/2022] [Revised: 01/20/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023]
Abstract
Gastrointestinal (GI) tract, which possesses the largest surface area of mucosa in the body, is easily suffered from inflammatory damages under the exposure of external stimulations. Excessive reactive oxygen species (ROS) production and continuous oxidative stress in intestines can elicit local mucosal injury, accelerate mucosal ulceration, and amplify the inflammatory response. Thereby, antioxidant therapy is a potential strategy against intestinal inflammatory diseases. Herein, we demonstrate the gram-scale preparation of quercetin supramolecular nanoribbons (SNRs) by using free quercetin molecules as the sole building block for preventing and treating intestinal inflammatory diseases. Unlike current clinical medicines, which mainly confront with poor response and severe adverse effects via bloodstream delivery, our quercetin SNRs possess an excellent antioxidant activity in the harsh environments of GI tract, a relative long retention time in GI tract, an admirable metabolism in GI tract without burdening other organs, and a specific adhesion to the inflamed intestinal epithelium via electrostatic interactions. These advantages strongly guarantee the applications of quercetin SNRs as oral medicines for intestinal inflammatory diseases. After establishing the models of intestinal inflammatory diseases caused by irradiation and drug stimulations, our quercetin SNRs exhibit the promising protective and therapeutic effects for radiation-induced acute enteritis and dextran sulfate sodium (DSS)-induced acute colitis. Because the super easy and fast preparation procedure and the nearly 100% loading capacity of quercetin SNRs, the current work provides a supramolecular nanomedicine with great clinical translation potential against intestinal inflammatory diseases.
Collapse
Affiliation(s)
- Wei Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Yingxuan Chen
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130021, PR China
| | - Liang Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Ze Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Shuwei Liu
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun, 130021, PR China
| | - Mengzhu Zhang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130021, PR China
| | - Yi Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China.
| | - Quanshun Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130021, PR China.
| | - Hao Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China; Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun, 130021, PR China; Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| |
Collapse
|
33
|
Bhuyan ZA, Rahman MA, Maradana MR, Mehdi AM, Bergot AS, Simone D, El-Kurdi M, Garrido-Mesa J, Cai CBB, Cameron AJ, Hanson AL, Nel HJ, Kenna T, Leo P, Rehaume L, Brown MA, Ciccia F, Thomas R. Genetically encoded Runx3 and CD4 + intestinal epithelial lymphocyte deficiencies link SKG mouse and human predisposition to spondyloarthropathy. Clin Immunol 2023; 247:109220. [PMID: 36596403 DOI: 10.1016/j.clim.2022.109220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 01/02/2023]
Abstract
Disturbances in immune regulation, intestinal dysbiosis and inflammation characterize ankylosing spondylitis (AS), which is associated with RUNX3 loss-of-function variants. ZAP70W163C mutant (SKG) mice have reduced ZAP70 signaling, spondyloarthritis and ileitis. In small intestine, Foxp3+ regulatory T cells (Treg) and CD4+CD8αα+TCRαβ+ intraepithelial lymphocytes (CD4-IEL) control inflammation. TGF-β and retinoic acid (RA)-producing dendritic cells and MHC-class II+ intestinal epithelial cells (IEC) are required for Treg and CD4-IEL differentiation from CD4+ conventional or Treg precursors, with upregulation of Runx3 and suppression of ThPOK. We show in SKG mouse ileum, that ZAP70W163C or ZAP70 inhibition prevented CD4-IEL but not Treg differentiation, dysregulating Runx3 and ThPOK. TGF-β/RA-mediated CD4-IEL development, T-cell IFN-γ production, MHC class-II+ IEC, tissue-resident memory T-cell and Runx3-regulated genes were reduced. In AS intestine, CD4-IEL were decreased, while in AS blood CD4+CD8+ T cells were reduced and Treg increased. Thus, genetically-encoded TCR signaling dysfunction links intestinal T-cell immunodeficiency in mouse and human spondyloarthropathy.
Collapse
Affiliation(s)
- Zaied Ahmed Bhuyan
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - M Arifur Rahman
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Muralidhara Rao Maradana
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Ahmed M Mehdi
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Anne-Sophie Bergot
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Davide Simone
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Marya El-Kurdi
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Cheng Bang Benjamin Cai
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Amy J Cameron
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Aimee L Hanson
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Hendrik J Nel
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Tony Kenna
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Paul Leo
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Linda Rehaume
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Genomics England Ltd, Charterhouse Square, London, United Kingdom
| | - Francesco Ciccia
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Ranjeny Thomas
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.
| |
Collapse
|
34
|
Wang Y, Jenq RR, Wargo JA, Watowich SS. Microbiome influencers of checkpoint blockade-associated toxicity. J Exp Med 2023; 220:213796. [PMID: 36622383 PMCID: PMC9836236 DOI: 10.1084/jem.20220948] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Immunotherapy has greatly improved cancer outcomes, yet variability in response and off-target tissue damage can occur with these treatments, including immune checkpoint inhibitors (ICIs). Multiple lines of evidence indicate the host microbiome influences ICI response and risk of immune-related adverse events (irAEs). As the microbiome is modifiable, these advances indicate the potential to manipulate microbiome components to increase ICI success. We discuss microbiome features associated with ICI response, with focus on bacterial taxa and potential immune mechanisms involved in irAEs, and the overall goal of driving novel approaches to manipulate the microbiome to improve ICI efficacy while avoiding irAE risk.
Collapse
Affiliation(s)
- Yinghong Wang
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Platform for Innovative Microbiome and Translational Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer A. Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Platform for Innovative Microbiome and Translational Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie S. Watowich
- Platform for Innovative Microbiome and Translational Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
35
|
SpPdp11 Administration in Diet Modified the Transcriptomic Response and Its Microbiota Associated in Mechanically Induced Wound Sparus aurata Skin. Animals (Basel) 2023; 13:ani13020193. [PMID: 36670734 PMCID: PMC9854838 DOI: 10.3390/ani13020193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Skin lesions are a frequent fact associated with intensive conditions affecting farmed fish. Knowing that the use of probiotics can improve fish skin health, SpPdp11 dietary administration has demonstrated beneficial effects for farmed fish, so its potential on the skin needs to be studied more deeply. The wounded specimens that received the diet with SpPdp11 showed a decrease in the abundance of Enterobacteriaceae, Photobacterium and Achromobacter related to bacterial biofilm formation, as well as the overexpression of genes involved in signaling mechanisms (itpr3), cell migration and differentiation (panxa, ttbk1a, smpd3, vamp5); and repression of genes related to cell proliferation (vstm4a, areg), consistent with a more efficient skin healing processes than that observed in the wounded control group. In addition, among the groups of damaged skin with different diets, Achromobacter, f_Ruminococcaceae, p_Bacteroidetes, Fluviicola and Flavobacterium genera with significant differences showed positive correlations with genes related to cell migration and negative correlations with inflammation and cell proliferation and may be the target of future studies.
Collapse
|
36
|
Zhou T, Xu W, Wang Q, Jiang C, Li H, Chao Y, Sun Y, A L. The effect of the "Oral-Gut" axis on periodontitis in inflammatory bowel disease: A review of microbe and immune mechanism associations. Front Cell Infect Microbiol 2023; 13:1132420. [PMID: 36923589 PMCID: PMC10008960 DOI: 10.3389/fcimb.2023.1132420] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/31/2023] [Indexed: 03/02/2023] Open
Abstract
Periodontitis and inflammatory bowel diseases (IBD) are inflammatory diseases of the gastrointestinal tract that share common features of microbial-induced ecological dysregulation and host immune inflammatory response. The close relationship between periodontitis and IBD is characterized by a higher prevalence of IBD in patients with periodontitis and a higher prevalence and severity of periodontitis in patients with IBD, indicating that periodontitis and IBD are different from the traditional independent diseases and form an "Oral-Gut" axis between the two, which affect each other and thus form a vicious circle. However, the specific mechanisms leading to the association between the two are not fully understood. In this article, we describe the interconnection between periodontitis and IBD in terms of microbial pathogenesis and immune dysregulation, including the ectopic colonization of the gut by pathogenic bacteria associated with periodontitis that promotes inflammation in the gut by activating the host immune response, and the alteration of the oral microbiota due to IBD that affects the periodontal inflammatory response. Among the microbial factors, pathogenic bacteria such as Klebsiella, Porphyromonas gingivalis and Fusobacterium nucleatum may act as the microbial bridge between periodontitis and IBD, while among the immune mechanisms, Th17 cell responses and the secreted pro-inflammatory factors IL-1β, IL-6 and TNF-α play a key role in the development of both diseases. This suggests that in future studies, we can look for targets in the "Oral-Gut" axis to control and intervene in periodontal inflammation by regulating periodontal or intestinal flora through immunological methods.
Collapse
Affiliation(s)
- Tianyu Zhou
- Department of Oral Implantology, School and Hospital of Stomatology, Jilin University, Changchun, China
| | - Wenzhou Xu
- Department of Periodontology, School and Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Sciences and Technology for Stomatology Nanoengineering, Changchun, China
| | - Qiqi Wang
- Department of Periodontology, School and Hospital of Stomatology, Jilin University, Changchun, China
| | - Cong Jiang
- Department of Oral Implantology, School and Hospital of Stomatology, Jilin University, Changchun, China
| | - Hongyan Li
- Department of Periodontology, School and Hospital of Stomatology, Jilin University, Changchun, China
| | - Yang Chao
- Department of Gastroendoscopy, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yue Sun
- Department of Oral Implantology, School and Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Sciences and Technology for Stomatology Nanoengineering, Changchun, China
- *Correspondence: Yue Sun, ; Lan A,
| | - Lan A
- Department of Oral Implantology, School and Hospital of Stomatology, Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Sciences and Technology for Stomatology Nanoengineering, Changchun, China
- *Correspondence: Yue Sun, ; Lan A,
| |
Collapse
|
37
|
Jotereau F, Alameddine J, Teusan R, Pédron A, Jouand N, Altare F, Godefroy E. Human gut microbiota-reactive DP8α regulatory T cells, signature and related emerging functions. Front Immunol 2022; 13:1026994. [PMID: 36479125 PMCID: PMC9720269 DOI: 10.3389/fimmu.2022.1026994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
In mice, microbiota-induced Tregs both maintain intestinal homeostasis and provide resistance to immuno-pathologies in the adult. Identifying their human functional counterpart therefore represents an important goal. We discovered, in the human colonic lamina propria and blood, a FoxP3-negative IL-10-secreting Treg subset, which co-expresses CD4 and CD8α (hence named DP8α) and displays a TCR-reactivity against Faecalibacterium prausnitzii, indicating a role for this symbiotic bacterium in their induction. Moreover, supporting their role in intestinal homeostasis, we previously reported both their drastic decrease in IBD patients and their protective role in vivo against intestinal inflammation, in mice. Here, we aimed at identifying the genomic, phenotypic and functional signatures of these microbiota-induced Tregs, towards delineating their physiological role(s) and clinical potential. Human F. prausnitzii-reactive DP8α Treg clones were derived from both the colonic lamina propria and blood. RNA-sequencing, flow cytometry and functional assays were performed to characterize their response upon activation and compare them to donor- and tissue-matched FoxP3+ Treg clones. DP8α Tregs exhibited a unique mixed Tr1-like/cytotoxic CD4+ T cell-profile and shared the RORγt and MAF master genes with mouse gut microbiota-induced FoxP3+ Tregs. We revealed their potent cytotoxic, chemotactic and IgA-promoting abilities, which were confirmed using in vitro assays. Therefore, besides their induction by a Clostridium bacterium, DP8α Tregs also partake master genes with mouse microbiota-induced Tregs. The present identification of their complete signature and novel functional properties, should be key in delineating the in vivo roles and therapeutic applications of these unique human microbiota-induced Tregs through their study in pathological contexts, particularly in inflammatory bowel diseases.
Collapse
Affiliation(s)
- Francine Jotereau
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France,*Correspondence: Emmanuelle Godefroy, ; Francine Jotereau, ; Frédéric Altare,
| | - Joudy Alameddine
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France
| | - Raluca Teusan
- Nantes Université, CHU Nantes, INSERM, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes, France
| | - Annabelle Pédron
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France
| | - Nicolas Jouand
- Cytocell, BioCore, Nantes Université UMS 3556, Inserm US016, CNRS UAR 3556, CHU Nantes, SFR Santé François BONAMY, Nantes, France
| | - Frédéric Altare
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France,*Correspondence: Emmanuelle Godefroy, ; Francine Jotereau, ; Frédéric Altare,
| | - Emmanuelle Godefroy
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France,*Correspondence: Emmanuelle Godefroy, ; Francine Jotereau, ; Frédéric Altare,
| |
Collapse
|
38
|
Cervantes-Barragan L, Colonna M. A microbiota-derived antigen drives CD4 + intraepithelial lymphocyte (CD4IEL) development. Trends Immunol 2022; 43:858-860. [PMID: 36243620 DOI: 10.1016/j.it.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 01/12/2023]
Abstract
CD4+ intraepithelial lymphocytes (CD4IEL) are tissue-resident T cells with cytotoxic and regulatory properties; together with peripheral regulatory T cells, they control intestinal inflammation. Recently, Bousbaine and colleagues identified a microbiota-derived conserved antigen that induces CD4IEL differentiation and promotes their regulatory function, attenuating the severity of murine colitis.
Collapse
Affiliation(s)
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| |
Collapse
|
39
|
Help from commensals: β-hex to regulate gut immunity. Cell Host Microbe 2022; 30:1349-1351. [DOI: 10.1016/j.chom.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
40
|
Shenoy MK, Koch MA. Twice the tolerance. Science 2022; 377:575-576. [PMID: 35926048 DOI: 10.1126/science.add7145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A gut microbiota-derived antigen elicits distinct subsets of regulatory T cells to suppress inflammation in mice.
Collapse
Affiliation(s)
- Meera K Shenoy
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Meghan A Koch
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.,Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| |
Collapse
|