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Verma S, Dufort MJ, Olsen TM, Kimmel S, Labuda JC, Scharffenberger S, McGuire AT, Harrison OJ. Antigen-level resolution of commensal-specific B cell responses can be enabled by phage display screening coupled with B cell tetramers. Immunity 2024; 57:1428-1441.e8. [PMID: 38723638 PMCID: PMC11168869 DOI: 10.1016/j.immuni.2024.04.014] [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: 10/12/2023] [Revised: 02/07/2024] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
Induction of commensal-specific immunity contributes to tissue homeostasis, yet the mechanisms underlying induction of commensal-specific B cells remain poorly understood in part due to a lack of tools to identify these cells. Using phage display, we identified segmented filamentous bacteria (SFB) antigens targeted by serum and intestinal antibodies and generated B cell tetramers to track SFB-specific B cells in gut-associated lymphoid tissues. We revealed a compartmentalized response in SFB-specific B cell activation, with a gradient of immunoglobulin A (IgA), IgG1, and IgG2b isotype production along Peyer's patches contrasted by selective production of IgG2b within mesenteric lymph nodes. V(D)J sequencing and monoclonal antibody generation identified somatic hypermutation driven affinity maturation to SFB antigens under homeostatic conditions. Combining phage display and B cell tetramers will enable investigation of the ontogeny and function of commensal-specific B cell responses in tissue immunity, inflammation, and repair.
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Affiliation(s)
- Sheenam Verma
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Matthew J Dufort
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Tayla M Olsen
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Samantha Kimmel
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Jasmine C Labuda
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Sam Scharffenberger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Oliver J Harrison
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Immunology, University of Washington, Seattle, WA, USA.
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2
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Liu J, Jiang G, Zhang H, Zhang H, Jia X, Gan Z, Yu H. Effects of Hibernation on Colonic Epithelial Tissue and Gut Microbiota in Wild Chipmunks ( Tamias sibiricus). Animals (Basel) 2024; 14:1498. [PMID: 38791715 PMCID: PMC11117362 DOI: 10.3390/ani14101498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
The gut microbiota plays a crucial role in the host's metabolic processes. Many studies have shown significant changes in the gut microbiota of mammals during hibernation to adapt to the changes in the external environment, but there is limited research on the colonic epithelial tissue and gut microbiota of the wild chipmunks during hibernation. This study analyzed the diversity, composition, and function of the gut microbiota of the wild chipmunk during hibernation using 16S rRNA gene high-throughput sequencing technology, and further conducted histological analysis of the colon. Histological analysis of the colon showed an increase in goblet cells in the hibernation group, which was an adaptive change to long-term fasting during hibernation. The dominant gut microbial phyla were Bacteroidetes, Firmicutes, and Proteobacteria, and the relative abundance of them changed significantly. The analysis of gut microbiota structural differences indicated that the relative abundance of Helicobacter typhlonius and Mucispirillum schaedleri increased significantly, while unclassified Prevotella-9, unclassified Prevotellaceae-UCG-001, unclassified Prevotellaceae-UCG-003 and other species of Prevotella decreased significantly at the species level. Alpha diversity analysis showed that hibernation increased the diversity and richness of the gut microbiota. Beta diversity analysis revealed significant differences in gut microbiota diversity between the hibernation group and the control group. PICRUSt2 functional prediction analysis of the gut microbiota showed that 15 pathways, such as lipid metabolism, xenobiotics biodegradation and metabolism, amino acid metabolism, environmental adaptation, and neurodegenerative diseases, were significantly enriched in the hibernation group, while 12 pathways, including carbohydrate metabolism, replication and repair, translation, and transcription, were significantly enriched in the control group. It can be seen that during hibernation, the gut microbiota of the wild chipmunk changes towards taxa that are beneficial for reducing carbohydrate consumption, increasing fat consumption, and adapting more strongly to environmental changes in order to better provide energy for the body and ensure normal life activities during hibernation.
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Affiliation(s)
- Juntao Liu
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Guangyu Jiang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Hongrui Zhang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Haiying Zhang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
| | - Xiaoyan Jia
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
| | - Zhenwei Gan
- School of Public Health, Jilin University, Changchun 130021, China;
| | - Huimei Yu
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (J.L.); (G.J.); (H.Z.); (H.Z.); (X.J.)
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3
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Perdijk O, Azzoni R, Marsland BJ. The microbiome: an integral player in immune homeostasis and inflammation in the respiratory tract. Physiol Rev 2024; 104:835-879. [PMID: 38059886 DOI: 10.1152/physrev.00020.2023] [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: 05/02/2023] [Revised: 11/07/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
The last decade of microbiome research has highlighted its fundamental role in systemic immune and metabolic homeostasis. The microbiome plays a prominent role during gestation and into early life, when maternal lifestyle factors shape immune development of the newborn. Breast milk further shapes gut colonization, supporting the development of tolerance to commensal bacteria and harmless antigens while preventing outgrowth of pathogens. Environmental microbial and lifestyle factors that disrupt this process can dysregulate immune homeostasis, predisposing infants to atopic disease and childhood asthma. In health, the low-biomass lung microbiome, together with inhaled environmental microbial constituents, establishes the immunological set point that is necessary to maintain pulmonary immune defense. However, in disease perturbations to immunological and physiological processes allow the upper respiratory tract to act as a reservoir of pathogenic bacteria, which can colonize the diseased lung and cause severe inflammation. Studying these host-microbe interactions in respiratory diseases holds great promise to stratify patients for suitable treatment regimens and biomarker discovery to predict disease progression. Preclinical studies show that commensal gut microbes are in a constant flux of cell division and death, releasing microbial constituents, metabolic by-products, and vesicles that shape the immune system and can protect against respiratory diseases. The next major advances may come from testing and utilizing these microbial factors for clinical benefit and exploiting the predictive power of the microbiome by employing multiomics analysis approaches.
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Affiliation(s)
- Olaf Perdijk
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Rossana Azzoni
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology, School of Translational Science, Monash University, Melbourne, Victoria, Australia
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4
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Cui H, Wang N, Li H, Bian Y, Wen W, Kong X, Wang F. The dynamic shifts of IL-10-producing Th17 and IL-17-producing Treg in health and disease: a crosstalk between ancient "Yin-Yang" theory and modern immunology. Cell Commun Signal 2024; 22:99. [PMID: 38317142 PMCID: PMC10845554 DOI: 10.1186/s12964-024-01505-0] [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: 12/07/2023] [Accepted: 01/28/2024] [Indexed: 02/07/2024] Open
Abstract
The changes in T regulatory cell (Treg) and T helper cell (Th) 17 ratios holds paramount importance in ensuring internal homeostasis and disease progression. Recently, novel subsets of Treg and Th17, namely IL-17-producing Treg and IL-10-producing Th17 have been identified. IL-17-producing Treg and IL-10-producing Th17 are widely considered as the intermediates during Treg/Th17 transformation. These "bi-functional" cells exhibit plasticity and have been demonstrated with important roles in multiple physiological functions and disease processes. Yin and Yang represent opposing aspects of phenomena according to the ancient Chinese philosophy "Yin-Yang" theory. Furthermore, Yin can transform into Yang, and vice versa, under specific conditions. This theory has been widely used to describe the contrasting functions of immune cells and molecules. Therefore, immune-activating populations (Th17, M1 macrophage, etc.) and immune overreaction (inflammation, autoimmunity) can be considered Yang, while immunosuppressive populations (Treg, M2 macrophage, etc.) and immunosuppression (tumor, immunodeficiency) can be considered Yin. However, another important connotation of "Yin-Yang" theory, the conversion between Yin and Yang, has been rarely documented in immune studies. The discovery of IL-17-producing Treg and IL-10-producing Th17 enriches the meaning of "Yin-Yang" theory and further promotes the relationship between ancient "Yin-Yang" theory and modern immunology. Besides, illustrating the functions of IL-17-producing Treg and IL-10-producing Th17 and mechanisms governing their differentiation provides valuable insights into the mechanisms underlying the dynamically changing statement of immune statement in health and diseases.
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Affiliation(s)
- Huantian Cui
- First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Ning Wang
- First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Hanzhou Li
- College of Integrative Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yuhong Bian
- College of Integrative Chinese and Western Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Weibo Wen
- First School of Clinical Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Xiangying Kong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Fudi Wang
- The First Affiliated Hospital, Institute of Translational Medicine, The Second Affiliated Hospital, School of Public Health, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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5
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Abramson J, Dobeš J, Lyu M, Sonnenberg GF. The emerging family of RORγt + antigen-presenting cells. Nat Rev Immunol 2024; 24:64-77. [PMID: 37479834 PMCID: PMC10844842 DOI: 10.1038/s41577-023-00906-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2023] [Indexed: 07/23/2023]
Abstract
Antigen-presenting cells (APCs) are master regulators of the immune response by directly interacting with T cells to orchestrate distinct functional outcomes. Several types of professional APC exist, including conventional dendritic cells, B cells and macrophages, and numerous other cell types have non-classical roles in antigen presentation, such as thymic epithelial cells, endothelial cells and granulocytes. Accumulating evidence indicates the presence of a new family of APCs marked by the lineage-specifying transcription factor retinoic acid receptor-related orphan receptor-γt (RORγt) and demonstrates that these APCs have key roles in shaping immunity, inflammation and tolerance, particularly in the context of host-microorganism interactions. These RORγt+ APCs include subsets of group 3 innate lymphoid cells, extrathymic autoimmune regulator-expressing cells and, potentially, other emerging populations. Here, we summarize the major findings that led to the discovery of these RORγt+ APCs and their associated functions. We discuss discordance in recent reports and identify gaps in our knowledge in this burgeoning field, which has tremendous potential to advance our understanding of fundamental immune concepts.
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Affiliation(s)
- Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jan Dobeš
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Mengze Lyu
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory F Sonnenberg
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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6
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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: 11] [Impact Index Per Article: 11.0] [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.
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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
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7
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Feng S, Wang S, Qu D, Li J, Tian F, Yu L, Zhang H, Zhao J, Chen W, Zhai Q. Species- or genus-dependent immunostimulatory effects of gut-derived potential probiotics. J Genet Genomics 2023; 50:786-794. [PMID: 36356718 DOI: 10.1016/j.jgg.2022.11.001] [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: 07/19/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
The immune regulatory effects of probiotics have been widely recognized to be strain-specific. However, it is unknown if there is a species- or genus-dependent manner. In this study, we use an in vitro mesenteric lymph node (MLN) model to systematically evaluate the immunostimulatory effects of gut-derived potential probiotics. The results exhibit an obvious species or genus consensus immune response pattern. RNA-seq shows that T cell-dependent B cell activation and antibody responses may be inherent to this model. Of the five tested genera, Akkermansia spp. and Clostridium butyrium directly activate the immune response in vitro, as indicated by the secretion of interleukin-10. Bifidobacterium spp. and Bacteroides spp. activate immune response with the help of stimuli (anti-CD3 and anti-CD28 antibodies). Lactobacillus spp. blunt the immune response with or without stimuli. Further investigations show that the cell surface protein of A. muciniphila AH39, which may serve as a T cell receptor cognate antigen, might evoke an in vitro immune activation. In vivo, oral administration of A. muciniphila AH39 influences the proportion of T regulatory cells (Tregs) in MLNs and the spleen under homeostasis in both specific pathogen-free and germ-free mice. All these findings indicate the distinct effects of different genera or species of potential gut-derived probiotics on intestinal and systemic immunity.
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Affiliation(s)
- Saisai Feng
- Institute of Food Sciences, Shanxi Normal University, Taiyuan, Shanxi 030000, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Dingwu Qu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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8
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Wang J, Zhao X, Wan YY. Intricacies of TGF-β signaling in Treg and Th17 cell biology. Cell Mol Immunol 2023; 20:1002-1022. [PMID: 37217798 PMCID: PMC10468540 DOI: 10.1038/s41423-023-01036-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Balanced immunity is pivotal for health and homeostasis. CD4+ helper T (Th) cells are central to the balance between immune tolerance and immune rejection. Th cells adopt distinct functions to maintain tolerance and clear pathogens. Dysregulation of Th cell function often leads to maladies, including autoimmunity, inflammatory disease, cancer, and infection. Regulatory T (Treg) and Th17 cells are critical Th cell types involved in immune tolerance, homeostasis, pathogenicity, and pathogen clearance. It is therefore critical to understand how Treg and Th17 cells are regulated in health and disease. Cytokines are instrumental in directing Treg and Th17 cell function. The evolutionarily conserved TGF-β (transforming growth factor-β) cytokine superfamily is of particular interest because it is central to the biology of both Treg cells that are predominantly immunosuppressive and Th17 cells that can be proinflammatory, pathogenic, and immune regulatory. How TGF-β superfamily members and their intricate signaling pathways regulate Treg and Th17 cell function is a question that has been intensely investigated for two decades. Here, we introduce the fundamental biology of TGF-β superfamily signaling, Treg cells, and Th17 cells and discuss in detail how the TGF-β superfamily contributes to Treg and Th17 cell biology through complex yet ordered and cooperative signaling networks.
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Affiliation(s)
- Junying Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xingqi Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yisong Y Wan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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9
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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.
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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
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10
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Zhao B, Osbelt L, Lesker TR, Wende M, Galvez EJC, Hönicke L, Bublitz A, Greweling-Pils MC, Grassl GA, Neumann-Schaal M, Strowig T. Helicobacter spp. are prevalent in wild mice and protect from lethal Citrobacter rodentium infection in the absence of adaptive immunity. Cell Rep 2023; 42:112549. [PMID: 37245209 DOI: 10.1016/j.celrep.2023.112549] [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: 01/14/2023] [Revised: 03/15/2023] [Accepted: 05/04/2023] [Indexed: 05/30/2023] Open
Abstract
Transfer of the gut microbiota from wild to laboratory mice alters the host's immune status and enhances resistance to infectious and metabolic diseases, but understanding of which microbes and how they promote host fitness is only emerging. Our analysis of metagenomic sequencing data reveals that Helicobacter spp. are enriched in wild compared with specific-pathogen-free (SPF) and conventionally housed mice, with multiple species commonly co-colonizing their hosts. We create laboratory mice harboring three non-SPF Helicobacter spp. to evaluate their effect on mucosal immunity and colonization resistance to the enteropathogen Citrobacter rodentium. Our experiments reveal that Helicobacter spp. interfere with C. rodentium colonization and attenuate C. rodentium-induced gut inflammation in wild-type (WT) mice, even preventing lethal infection in Rag2-/- SPF mice. Further analyses suggest that Helicobacter spp. interfere with tissue attachment of C. rodentium, putatively by reducing the availability of mucus-derived sugars. These results unveil pivotal protective functions of wild mouse microbiota constituents against intestinal infection.
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Affiliation(s)
- Bei Zhao
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging, and Modelling of Neuronal and Inflammatory Processes, Otto von Guericke University, Magdeburg, Germany
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging, and Modelling of Neuronal and Inflammatory Processes, Otto von Guericke University, Magdeburg, Germany
| | - Eric J C Galvez
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Lisa Hönicke
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Arne Bublitz
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Guntram A Grassl
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine (CiiM), A Joint Venture Between the Helmholtz Center for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.
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11
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Cheru N, Hafler DA, Sumida TS. Regulatory T cells in peripheral tissue tolerance and diseases. Front Immunol 2023; 14:1154575. [PMID: 37197653 PMCID: PMC10183596 DOI: 10.3389/fimmu.2023.1154575] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/13/2023] [Indexed: 05/19/2023] Open
Abstract
Maintenance of peripheral tolerance by CD4+Foxp3+ regulatory T cells (Tregs) is essential for regulating autoreactive T cells. The loss of function of Foxp3 leads to autoimmune disease in both animals and humans. An example is the rare, X-linked recessive disorder known as IPEX (Immune Dysregulation, Polyendocrinopathy, Enteropathy X-linked) syndrome. In more common human autoimmune diseases, defects in Treg function are accompanied with aberrant effector cytokines such as IFNγ. It has recently become appreciated that Tregs plays an important role in not only maintaining immune homeostasis but also in establishing the tissue microenvironment and homeostasis of non-lymphoid tissues. Tissue resident Tregs show profiles that are unique to their local environments which are composed of both immune and non-immune cells. Core tissue-residence gene signatures are shared across different tissue Tregs and are crucial to homeostatic regulation and maintaining the tissue Treg pool in a steady state. Through interaction with immunocytes and non-immunocytes, tissue Tregs exert a suppressive function via conventional ways involving contact dependent and independent processes. In addition, tissue resident Tregs communicate with other tissue resident cells which allows Tregs to adopt to their local microenvironment. These bidirectional interactions are dependent on the specific tissue environment. Here, we summarize the recent advancements of tissue Treg studies in both human and mice, and discuss the molecular mechanisms that maintain tissue homeostasis and prevent pathogenesis.
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Affiliation(s)
- Nardos Cheru
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, United States
| | - David A. Hafler
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, United States
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - Tomokazu S. Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States
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12
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Campbell C, Kandalgaonkar MR, Golonka RM, Yeoh BS, Vijay-Kumar M, Saha P. Crosstalk between Gut Microbiota and Host Immunity: Impact on Inflammation and Immunotherapy. Biomedicines 2023; 11:biomedicines11020294. [PMID: 36830830 PMCID: PMC9953403 DOI: 10.3390/biomedicines11020294] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Gut microbes and their metabolites are actively involved in the development and regulation of host immunity, which can influence disease susceptibility. Herein, we review the most recent research advancements in the gut microbiota-immune axis. We discuss in detail how the gut microbiota is a tipping point for neonatal immune development as indicated by newly uncovered phenomenon, such as maternal imprinting, in utero intestinal metabolome, and weaning reaction. We describe how the gut microbiota shapes both innate and adaptive immunity with emphasis on the metabolites short-chain fatty acids and secondary bile acids. We also comprehensively delineate how disruption in the microbiota-immune axis results in immune-mediated diseases, such as gastrointestinal infections, inflammatory bowel diseases, cardiometabolic disorders (e.g., cardiovascular diseases, diabetes, and hypertension), autoimmunity (e.g., rheumatoid arthritis), hypersensitivity (e.g., asthma and allergies), psychological disorders (e.g., anxiety), and cancer (e.g., colorectal and hepatic). We further encompass the role of fecal microbiota transplantation, probiotics, prebiotics, and dietary polyphenols in reshaping the gut microbiota and their therapeutic potential. Continuing, we examine how the gut microbiota modulates immune therapies, including immune checkpoint inhibitors, JAK inhibitors, and anti-TNF therapies. We lastly mention the current challenges in metagenomics, germ-free models, and microbiota recapitulation to a achieve fundamental understanding for how gut microbiota regulates immunity. Altogether, this review proposes improving immunotherapy efficacy from the perspective of microbiome-targeted interventions.
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Affiliation(s)
- Connor Campbell
- Department of Physiology & Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Mrunmayee R. Kandalgaonkar
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Rachel M. Golonka
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Beng San Yeoh
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Matam Vijay-Kumar
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Piu Saha
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
- Correspondence:
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13
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Hackstein CP, Costigan D, Drexhage L, Pearson C, Bullers S, Ilott N, Akther HD, Gu Y, FitzPatrick MEB, Harrison OJ, Garner LC, Mann EH, Pandey S, Friedrich M, Provine NM, Uhlig HH, Marchi E, Powrie F, Klenerman P, Thornton EE. A conserved population of MHC II-restricted, innate-like, commensal-reactive T cells in the gut of humans and mice. Nat Commun 2022; 13:7472. [PMID: 36463279 PMCID: PMC9719512 DOI: 10.1038/s41467-022-35126-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 11/20/2022] [Indexed: 12/05/2022] Open
Abstract
Interactions with commensal microbes shape host immunity on multiple levels and play a pivotal role in human health and disease. Tissue-dwelling, antigen-specific T cells are poised to respond to local insults, making their phenotype important in the relationship between host and microbes. Here we show that MHC-II restricted, commensal-reactive T cells in the colon of both humans and mice acquire transcriptional and functional characteristics associated with innate-like T cells. This cell population is abundant and conserved in the human and murine colon and endowed with polyfunctional effector properties spanning classic Th1- and Th17-cytokines, cytotoxic molecules, and regulators of epithelial homeostasis. T cells with this phenotype are increased in ulcerative colitis patients, and their presence aggravates pathology in dextran sodium sulphate-treated mice, pointing towards a pathogenic role in colitis. Our findings add to the expanding spectrum of innate-like immune cells positioned at the frontline of intestinal immune surveillance, capable of acting as sentinels of microbes and the local cytokine milieu.
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Affiliation(s)
- Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dana Costigan
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Linnea Drexhage
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Claire Pearson
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Samuel Bullers
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Nicholas Ilott
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Hossain Delowar Akther
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yisu Gu
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oliver J Harrison
- Center for Fundamental Immunology, Benaroya Research Institute, 1201 9th Ave, Seattle, WA, 98101, USA
- Department of Immunology, University of Washington, 750 Republican St, Seattle, WA, 98108, USA
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elizabeth H Mann
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Sumeet Pandey
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Matthias Friedrich
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, and Biomedical Research Centre, and Department of Paediatrics, University of Oxford, Oxford, OX39DU, UK
| | - Emanuele Marchi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Emily E Thornton
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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14
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Yi J, Miller AT, Archambault AS, Jones AJ, Bradstreet TR, Bandla S, Hsu YS, Edelson BT, Zhou YW, Fremont DH, Egawa T, Singh N, Wu GF, Hsieh CS. Antigen-specific depletion of CD4 + T cells by CAR T cells reveals distinct roles of higher- and lower-affinity TCRs during autoimmunity. Sci Immunol 2022; 7:eabo0777. [PMID: 36206355 PMCID: PMC9867937 DOI: 10.1126/sciimmunol.abo0777] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Both higher- and lower-affinity self-reactive CD4+ T cells are expanded in autoimmunity; however, their individual contribution to disease remains unclear. We addressed this question using peptide-MHCII chimeric antigen receptor (pMHCII-CAR) T cells to specifically deplete peptide-reactive T cells in mice. Integration of improvements in CAR engineering with TCR repertoire analysis was critical for interrogating in vivo the role of TCR affinity in autoimmunity. Our original MOG35-55 pMHCII-CAR, which targeted only higher-affinity TCRs, could prevent the induction of experimental autoimmune encephalomyelitis (EAE). However, pMHCII-CAR enhancements to pMHCII stability, as well as increased survivability via overexpression of a dominant-negative Fas, were required to target lower-affinity MOG-specific T cells and reverse ongoing clinical EAE. Thus, these data suggest a model in which higher-affinity autoreactive T cells are required to provide the "activation energy" for initiating neuroinflammatory injury, but lower-affinity cells are sufficient to maintain ongoing disease.
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Affiliation(s)
- Jaeu Yi
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA,Co-first authors
| | - Aidan T. Miller
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA,Co-first authors
| | - Angela S. Archambault
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Andrew J. Jones
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA
| | - Tara R. Bradstreet
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sravanthi Bandla
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yu-Sung Hsu
- Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Brian T. Edelson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - You W. Zhou
- Wugen Inc, 4340 Duncan Ave, St Louis MO 63110, USA
| | - Daved H. Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathan Singh
- Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Gregory F. Wu
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA,Correspondence: and
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA,Correspondence: and
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15
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Davar D, Zarour HM. Facts and Hopes for Gut Microbiota Interventions in Cancer Immunotherapy. Clin Cancer Res 2022; 28:4370-4384. [PMID: 35748749 PMCID: PMC9561605 DOI: 10.1158/1078-0432.ccr-21-1129] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 01/07/2023]
Abstract
Immune checkpoint inhibitors (ICI) targeting cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed death 1 (PD-1) proteins transformed the management of advanced cancers. Many tumor-intrinsic factors modulate immunological and clinical responses to such therapies, but ample evidence also implicates the gut microbiome in responses. The gut microbiome, comprising the bacteria, archaea, fungi, and viruses that live in the human digestive tract, is an established determinant of host immunity, but its impact on response to ICI therapy in mice and humans with cancer has only recently been appreciated. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes show promise in mice and humans with cancer. In this review, we discuss the rationale for gut microbiome-based cancer therapies, the results from early-phase clinical trials, and possible future developments.
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Affiliation(s)
- Diwakar Davar
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Hassane M. Zarour
- Department of Medicine and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
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16
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Fraschilla I, Amatullah H, Rahman RU, Jeffrey KL. Immune chromatin reader SP140 regulates microbiota and risk for inflammatory bowel disease. Cell Host Microbe 2022; 30:1370-1381.e5. [PMID: 36130593 PMCID: PMC10266544 DOI: 10.1016/j.chom.2022.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/30/2022] [Accepted: 08/30/2022] [Indexed: 12/25/2022]
Abstract
Inflammatory bowel disease (IBD) is driven by host genetics and environmental factors, including commensal microorganisms. Speckled Protein 140 (SP140) is an immune-restricted chromatin "reader" that is associated with Crohn's disease (CD), multiple sclerosis (MS), and chronic lymphocytic leukemia (CLL). However, the disease-causing mechanisms of SP140 remain undefined. Here, we identify an immune-intrinsic role for SP140 in regulating phagocytic defense responses to prevent the expansion of inflammatory bacteria. Mice harboring altered microbiota due to hematopoietic Sp140 deficiency exhibited severe colitis that was transmissible upon cohousing and ameliorated with antibiotics. Loss of SP140 results in blooms of Proteobacteria, including Helicobacter in Sp140-/- mice and Enterobacteriaceae in humans bearing the CD-associated SP140 loss-of-function variant. Phagocytes from patients with the SP140 loss-of-function variant and Sp140-/- mice exhibited altered antimicrobial defense programs required for control of pathobionts. Thus, mutations within this epigenetic reader may constitute a predisposing event in human diseases provoked by microbiota.
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Affiliation(s)
- Isabella Fraschilla
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Raza-Ur Rahman
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Center for the Study of Inflammatory Bowel Disease, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Massachusetts Institute of Technology Center for Microbiome, Informatics and Therapeutics, Cambridge, MA 02139, USA.
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17
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Pedersen TK, Brown EM, Plichta DR, Johansen J, Twardus SW, Delorey TM, Lau H, Vlamakis H, Moon JJ, Xavier RJ, Graham DB. The CD4 + T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease. Immunity 2022; 55:1909-1923.e6. [PMID: 36115338 PMCID: PMC9890645 DOI: 10.1016/j.immuni.2022.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/19/2022] [Accepted: 08/24/2022] [Indexed: 02/03/2023]
Abstract
Reciprocal interactions between host T helper cells and gut microbiota enforce local immunological tolerance and modulate extra-intestinal immunity. However, our understanding of antigen-specific tolerance to the microbiome is limited. Here, we developed a systematic approach to predict HLA class-II-specific epitopes using the humanized bacteria-originated T cell antigen (hBOTA) algorithm. We identified a diverse set of microbiome epitopes spanning all major taxa that are compatible with presentation by multiple HLA-II alleles. In particular, we uncovered an immunodominant epitope from the TonB-dependent receptor SusC that was universally recognized and ubiquitous among Bacteroidales. In healthy human subjects, SusC-reactive T cell responses were characterized by IL-10-dominant cytokine profiles, whereas in patients with active Crohn's disease, responses were associated with elevated IL-17A. Our results highlight the potential of targeted antigen discovery within the microbiome to reveal principles of tolerance and functional transitions during inflammation.
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Affiliation(s)
- Thomas K Pedersen
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Disease Systems Immunology, Department of Biotechnology and Biomedicine, Section for Protein Science and Biotherapeutics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Eric M Brown
- Infectious Disease and Microbiome Program, The 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
| | - Damian R Plichta
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joachim Johansen
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shaina W Twardus
- Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Toni M Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Helena Lau
- Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hera Vlamakis
- Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James J Moon
- Center for Immunology and Inflammatory Diseases and Division of Pulmonary and Critical Care Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ramnik J Xavier
- Infectious Disease and Microbiome Program, The 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; Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel B Graham
- Infectious Disease and Microbiome Program, The 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; Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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18
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Sequestration of gut pathobionts in intraluminal casts, a mechanism to avoid dysregulated T cell activation by pathobionts. Proc Natl Acad Sci U S A 2022; 119:e2209624119. [PMID: 36201539 PMCID: PMC9565271 DOI: 10.1073/pnas.2209624119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
T cells that express the transcription factor RORγ, regulatory (Treg), or conventional (Th17) are strongly influenced by intestinal symbionts. In a genetic approach to identify mechanisms underlying this influence, we performed a screen for microbial genes implicated, in germfree mice monocolonized with Escherichia coli Nissle. The loss of capsule-synthesis genes impaired clonal expansion and differentiation of intestinal RORγ+ T cells. Mechanistic exploration revealed that the capsule-less mutants remained able to induce species-specific immunoglobulin A (IgA) and were highly IgA-coated. They could still trigger myeloid cells, and more effectively damaged epithelial cells in vitro. Unlike wild-type microbes, capsule-less mutants were mostly engulfed in intraluminal casts, large agglomerates composed of myeloid cells extravasated into the gut lumen. We speculate that sequestration in luminal casts of potentially harmful microbes, favored by IgA binding, reduces the immune system's actual exposure, preserving host-microbe equilibrium. The variable immunostimulation by microbes that has been charted in recent years may not solely be conditioned by triggering molecules or metabolites but also by physical limits to immune system exposure.
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19
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Kedmi R, Najar TA, Mesa KR, Grayson A, Kroehling L, Hao Y, Hao S, Pokrovskii M, Xu M, Talbot J, Wang J, Germino J, Lareau CA, Satpathy AT, Anderson MS, Laufer TM, Aifantis I, Bartleson JM, Allen PM, Paidassi H, Gardner JM, Stoeckius M, Littman DR. A RORγt + cell instructs gut microbiota-specific T reg cell differentiation. Nature 2022; 610:737-743. [PMID: 36071167 PMCID: PMC9908423 DOI: 10.1038/s41586-022-05089-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/08/2022] [Indexed: 01/19/2023]
Abstract
The mutualistic relationship of gut-resident microbiota and the host immune system promotes homeostasis that ensures maintenance of the microbial community and of a largely non-aggressive immune cell compartment1,2. The consequences of disturbing this balance include proximal inflammatory conditions, such as Crohn's disease, and systemic illnesses. This equilibrium is achieved in part through the induction of both effector and suppressor arms of the adaptive immune system. Helicobacter species induce T regulatory (Treg) and T follicular helper (TFH) cells under homeostatic conditions, but induce inflammatory T helper 17 (TH17) cells when induced Treg (iTreg) cells are compromised3,4. How Helicobacter and other gut bacteria direct T cells to adopt distinct functions remains poorly understood. Here we investigated the cells and molecular components required for iTreg cell differentiation. We found that antigen presentation by cells expressing RORγt, rather than by classical dendritic cells, was required and sufficient for induction of Treg cells. These RORγt+ cells-probably type 3 innate lymphoid cells and/or Janus cells5-require the antigen-presentation machinery, the chemokine receptor CCR7 and the TGFβ activator αv integrin. In the absence of any of these factors, there was expansion of pathogenic TH17 cells instead of iTreg cells, induced by CCR7-independent antigen-presenting cells. Thus, intestinal commensal microbes and their products target multiple antigen-presenting cells with pre-determined features suited to directing appropriate T cell differentiation programmes, rather than a common antigen-presenting cell that they endow with appropriate functions.
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Affiliation(s)
- Ranit Kedmi
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Tariq A Najar
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Kailin R Mesa
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Allyssa Grayson
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA
| | - Lina Kroehling
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA
| | - Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Maria Pokrovskii
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Calico Life Sciences, LLC, South San Francisco, CA, USA
| | - Mo Xu
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,National Institute for Biological Sciences, Beijing, China
| | - Jhimmy Talbot
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA.,Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jiaxi Wang
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joe Germino
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA.,Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Terri M Laufer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, C. Michael Crescenz Veterans Administration Medical Center, Philadelphia, PA, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Juliet M Bartleson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,Federation Bio, South San Francisco, CA, USA
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Helena Paidassi
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - James M Gardner
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.,Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Marlon Stoeckius
- Technology Innovation Lab, New York Genome Center, New York, NY, USA.,10X Genomics, Stockholm, Sweden
| | - Dan R Littman
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA. .,Howard Hughes Medical Institute, New York, NY, USA.
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20
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Bousbaine D, Fisch LI, London M, Bhagchandani P, Rezende de Castro TB, Mimee M, Olesen S, Reis BS, VanInsberghe D, Bortolatto J, Poyet M, Cheloha RW, Sidney J, Ling J, Gupta A, Lu TK, Sette A, Alm EJ, Moon JJ, Victora GD, Mucida D, Ploegh HL, Bilate AM. A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes. Science 2022; 377:660-666. [PMID: 35926021 PMCID: PMC9766740 DOI: 10.1126/science.abg5645] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4+ T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota. However, the identity of the microbial antigens recognized by CD4+ T cells that can differentiate into CD4IELs remains unknown. We identified β-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation. In a mouse model of colitis, β-hexosaminidase-specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa.
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Affiliation(s)
- Djenet Bousbaine
- Microbiology Graduate Program, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Laura I Fisch
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Mariya London
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Preksha Bhagchandani
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Tiago B Rezende de Castro
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA.,Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Mark Mimee
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Synthetic Biology Center, MIT, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Scott Olesen
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - David VanInsberghe
- Microbiology Graduate Program, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA.,Department of Civil and Environmental Engineering, MIT, Cambridge, MA, USA
| | - Juliana Bortolatto
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jingjing Ling
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Aaron Gupta
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Timothy K Lu
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Synthetic Biology Center, MIT, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - James J Moon
- Center for Immunology and Inflammatory Diseases and Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, 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
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Angelina M Bilate
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
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21
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Rice TA, Bielecka AA, Nguyen MT, Rosen CE, Song D, Sonnert ND, Yang Y, Cao Y, Khetrapal V, Catanzaro JR, Martin AL, Rashed SA, Leopold SR, Hao L, Yu X, van Dijk D, Ring AM, Flavell RA, de Zoete MR, Palm NW. Interspecies commensal interactions have nonlinear impacts on host immunity. Cell Host Microbe 2022; 30:988-1002.e6. [PMID: 35640610 PMCID: PMC9283318 DOI: 10.1016/j.chom.2022.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/22/2022] [Accepted: 05/04/2022] [Indexed: 02/03/2023]
Abstract
The impacts of individual commensal microbes on immunity and disease can differ dramatically depending on the surrounding microbial context; however, the specific bacterial combinations that dictate divergent immunological outcomes remain largely undefined. Here, we characterize an immunostimulatory Allobaculum species from an inflammatory bowel disease patient that exacerbates colitis in gnotobiotic mice. Allobaculum inversely associates with the taxonomically divergent immunostimulatory species Akkermansia muciniphila in human-microbiota-associated mice and human cohorts. Co-colonization with A. muciniphila ameliorates Allobaculum-induced intestinal epithelial cell activation and colitis in mice, whereas Allobaculum blunts the A.muciniphila-specific systemic antibody response and reprograms the immunological milieu in mesenteric lymph nodes by blocking A.muciniphila-induced dendritic cell activation and T cell expansion. These studies thus identify a pairwise reciprocal interaction between human gut bacteria that dictates divergent immunological outcomes. Furthermore, they establish a generalizable framework to define the contextual cues contributing to the "incomplete penetrance" of microbial impacts on human disease.
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Affiliation(s)
- Tyler A. Rice
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Agata A. Bielecka
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Present address: Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mytien T. Nguyen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Connor E. Rosen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Present address: Arcus Biosciences, Hayward, CA 94545, USA
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicole D. Sonnert
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yi Yang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yiyun Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Varnica Khetrapal
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jason R. Catanzaro
- Section of Pulmonology, Allergy, Immunology, and Sleep Medicine, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anjelica L. Martin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Saleh A. Rashed
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Present address: Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Shana R. Leopold
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Liming Hao
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xuezhu Yu
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - David van Dijk
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Aaron M. Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marcel R. de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Lead Contact: Noah W. Palm:
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22
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van der Veeken J, Campbell C, Pritykin Y, Schizas M, Verter J, Hu W, Wang ZM, Matheis F, Mucida D, Charbonnier LM, Chatila TA, Rudensky AY. Genetic tracing reveals transcription factor Foxp3-dependent and Foxp3-independent functionality of peripherally induced Treg cells. Immunity 2022; 55:1173-1184.e7. [PMID: 35700740 PMCID: PMC9885886 DOI: 10.1016/j.immuni.2022.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/19/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023]
Abstract
Regulatory T (Treg) cells expressing the transcription factor Foxp3 are an essential suppressive T cell lineage of dual origin: Foxp3 induction in thymocytes and mature CD4+ T cells gives rise to thymic (tTreg) and peripheral (pTreg) Treg cells, respectively. While tTreg cells suppress autoimmunity, pTreg cells enforce tolerance to food and commensal microbiota. However, the role of Foxp3 in pTreg cells and the mechanisms supporting their differentiation remain poorly understood. Here, we used genetic tracing to identify microbiota-induced pTreg cells and found that many of their distinguishing features were Foxp3 independent. Lineage-committed, microbiota-dependent pTreg-like cells persisted in the colon in the absence of Foxp3. While Foxp3 was critical for the suppression of a Th17 cell program, colitis, and mastocytosis, pTreg cells suppressed colonic effector T cell expansion in a Foxp3-independent manner. Thus, Foxp3 and the tolerogenic signals that precede and promote its expression independently confer distinct facets of pTreg functionality.
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Affiliation(s)
- Joris van der Veeken
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
| | - Clarissa Campbell
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA,CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics and Computer Science Department, Princeton University, Princeton, NJ, USA
| | - Michail Schizas
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacob Verter
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Hu
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhong-Min Wang
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA,Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanny Matheis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Talal A Chatila
- Division of Immunology, Boston Children’s Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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23
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Yang W, Yu T, Cong Y. CD4+ T cell metabolism, gut microbiota, and autoimmune diseases: Implication in precision medicine of autoimmune diseases. PRECISION CLINICAL MEDICINE 2022; 5:pbac018. [PMID: 35990897 PMCID: PMC9384833 DOI: 10.1093/pcmedi/pbac018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/03/2022] [Indexed: 12/03/2022] Open
Abstract
CD4+ T cells are critical to the development of autoimmune disorders. Glucose, fatty acids, and glutamine metabolisms are the primary metabolic pathways in immune cells, including CD4+ T cells. The distinct metabolic programs in CD4+ T cell subsets are recognized to reflect the bioenergetic requirements, which are compatible with their functional demands. Gut microbiota affects T cell responses by providing a series of antigens and metabolites. Accumulating data indicate that CD4+ T cell metabolic pathways underlie aberrant T cell functions, thereby regulating the pathogenesis of autoimmune disorders, including inflammatory bowel diseases, systemic lupus erythematosus, and rheumatoid arthritis. Here, we summarize the current progress of CD4+ T cell metabolic programs, gut microbiota regulation of T cell metabolism, and T cell metabolic adaptions to autoimmune disorders to shed light on potential metabolic therapeutics for autoimmune diseases.
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Affiliation(s)
- Wenjing Yang
- Department of Microbiology and Immunology, University of Texas Medical Branch , Galveston, TX, 77555 , USA
- Sealy Center for Microbiome Research, University of Texas Medical Branch , Galveston, TX, 77555 , USA
| | - Tianming Yu
- Department of Microbiology and Immunology, University of Texas Medical Branch , Galveston, TX, 77555 , USA
- Sealy Center for Microbiome Research, University of Texas Medical Branch , Galveston, TX, 77555 , USA
| | - Yingzi Cong
- Department of Microbiology and Immunology, University of Texas Medical Branch , Galveston, TX, 77555 , USA
- Sealy Center for Microbiome Research, University of Texas Medical Branch , Galveston, TX, 77555 , USA
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24
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Tomasi M, Caproni E, Benedet M, Zanella I, Giorgetta S, Dalsass M, König E, Gagliardi A, Fantappiè L, Berti A, Tamburini S, Croia L, Di Lascio G, Bellini E, Valensin S, Licata G, Sebastiani G, Dotta F, Armanini F, Cumbo F, Asnicar F, Blanco-Míguez A, Ruggiero E, Segata N, Grandi G, Grandi A. Outer Membrane Vesicles From The Gut Microbiome Contribute to Tumor Immunity by Eliciting Cross-Reactive T Cells. Front Oncol 2022; 12:912639. [PMID: 35847919 PMCID: PMC9281500 DOI: 10.3389/fonc.2022.912639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/20/2022] [Indexed: 12/03/2022] Open
Abstract
A growing body of evidence supports the notion that the gut microbiome plays an important role in cancer immunity. However, the underpinning mechanisms remain to be fully elucidated. One attractive hypothesis envisages that among the T cells elicited by the plethora of microbiome proteins a few exist that incidentally recognize neo-epitopes arising from cancer mutations (“molecular mimicry (MM)” hypothesis). To support MM, the human probiotic Escherichia coli Nissle was engineered with the SIINFEKL epitope (OVA-E.coli Nissle) and orally administered to C57BL/6 mice. The treatment with OVA-E.coli Nissle, but not with wild type E. coli Nissle, induced OVA-specific CD8+ T cells and inhibited the growth of tumors in mice challenged with B16F10 melanoma cells expressing OVA. The microbiome shotgun sequencing and the sequencing of TCRs from T cells recovered from both lamina propria and tumors provide evidence that the main mechanism of tumor inhibition is mediated by the elicitation at the intestinal site of cross-reacting T cells, which subsequently reach the tumor environment. Importantly, the administration of Outer Membrane Vesicles (OMVs) from engineered E. coli Nissle, as well as from E. coli BL21(DE3)ΔompA, carrying cancer-specific T cell epitopes also elicited epitope-specific T cells in the intestine and inhibited tumor growth. Overall, our data strengthen the important role of MM in tumor immunity and assign a novel function of OMVs in host-pathogen interaction. Moreover, our results pave the way to the exploitation of probiotics and OMVs engineered with tumor specific-antigens as personalized mucosal cancer vaccines.
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Affiliation(s)
- Michele Tomasi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Elena Caproni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Benedet
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Toscana Life Sciences Foundation, Siena, Italy
| | - Ilaria Zanella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sebastiano Giorgetta
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Mattia Dalsass
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Enrico König
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Toscana Life Sciences Foundation, Siena, Italy
| | | | | | - Alvise Berti
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Silvia Tamburini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Lorenzo Croia
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Di Lascio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | | | - Giada Licata
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences Foundation, Siena, Italy
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences Foundation, Siena, Italy
| | - Francesco Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- Fondazione Umberto Di Mario, c/o Toscana Life Sciences Foundation, Siena, Italy
- Tuscany Centre for Precision Medicine (CReMeP), Siena, Italy
| | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Aitor Blanco-Míguez
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Eliana Ruggiero
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCSS) Ospedale San Raffaele, Milan, Italy
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Guido Grandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- *Correspondence: Guido Grandi, ; Alberto Grandi,
| | - Alberto Grandi
- Toscana Life Sciences Foundation, Siena, Italy
- BiOMViS Srl, Siena, Italy
- *Correspondence: Guido Grandi, ; Alberto Grandi,
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25
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Melo-González F, Sepúlveda-Alfaro J, Schultz BM, Suazo ID, Boone DL, Kalergis AM, Bueno SM. Distal Consequences of Mucosal Infections in Intestinal and Lung Inflammation. Front Immunol 2022; 13:877533. [PMID: 35572549 PMCID: PMC9095905 DOI: 10.3389/fimmu.2022.877533] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Infectious diseases are one of the leading causes of morbidity and mortality worldwide, affecting high-risk populations such as children and the elderly. Pathogens usually activate local immune responses at the site of infection, resulting in both protective and inflammatory responses, which may lead to local changes in the microbiota, metabolites, and the cytokine environment. Although some pathogens can disseminate and cause systemic disease, increasing evidence suggests that local infections can affect tissues not directly invaded. In particular, diseases occurring at distal mucosal barriers such as the lung and the intestine seem to be linked, as shown by epidemiological studies in humans. These mucosal barriers have bidirectional interactions based mainly on multiple signals derived from the microbiota, which has been termed as the gut-lung axis. However, the effects observed in such distal places are still incompletely understood. Most of the current research focuses on the systemic impact of changes in microbiota and bacterial metabolites during infection, which could further modulate immune responses at distal tissue sites. Here, we describe how the gut microbiota and associated metabolites play key roles in maintaining local homeostasis and preventing enteric infection by direct and indirect mechanisms. Subsequently, we discuss recent murine and human studies linking infectious diseases with changes occurring at distal mucosal barriers, with particular emphasis on bacterial and viral infections affecting the lung and the gastrointestinal tract. Further, we discuss the potential mechanisms by which pathogens may cause such effects, promoting either protection or susceptibility to secondary infection.
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Affiliation(s)
- Felipe Melo-González
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Javiera Sepúlveda-Alfaro
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bárbara M. Schultz
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isidora D. Suazo
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - David L. Boone
- Department of Microbiology and Immunology, Indiana University School of Medicine-South Bend, South Bend, IN, United States
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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26
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Abstract
The immune system employs recognition tools to communicate with its microbial evolutionary partner. Among all the methods of microbial perception, T cells enable the widest spectrum of microbial recognition resolution, ranging from the crudest detection of whole groups of microbes to the finest detection of specific antigens. The application of this recognition capability to the crucial task of combatting infections has been the focus of classical immunology. We now appreciate that the coevolution of the immune system and the microbiota has led to development of a lush immunological decision tree downstream of microbial recognition, of which an inflammatory response is but one branch. In this review we discuss known T cell-microbe interactions in the gut and place them in the context of an algorithmic framework of recognition, context-dependent interpretation, and response circuits across multiple levels of microbial recognition resolution. The malleability of T cells in response to the microbiota presents an opportunity to edit immune response cellularity, identity, and functionality by utilizing microbiota-controlled pathways to promote human health.
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Affiliation(s)
- Ivaylo I Ivanov
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA;
| | - Timur Tuganbaev
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Ashwin N Skelly
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan;
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27
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Abstract
The immune system employs recognition tools to communicate with its microbial evolutionary partner. Among all the methods of microbial perception, T cells enable the widest spectrum of microbial recognition resolution, ranging from the crudest detection of whole groups of microbes to the finest detection of specific antigens. The application of this recognition capability to the crucial task of combatting infections has been the focus of classical immunology. We now appreciate that the coevolution of the immune system and the microbiota has led to development of a lush immunological decision tree downstream of microbial recognition, of which an inflammatory response is but one branch. In this review we discuss known T cell-microbe interactions in the gut and place them in the context of an algorithmic framework of recognition, context-dependent interpretation, and response circuits across multiple levels of microbial recognition resolution. The malleability of T cells in response to the microbiota presents an opportunity to edit immune response cellularity, identity, and functionality by utilizing microbiota-controlled pathways to promote human health. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ivaylo I Ivanov
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA;
| | - Timur Tuganbaev
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Ashwin N Skelly
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan.,RIKEN Center for Integrative Medical Sciences, Yokohama, Japan;
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28
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Bae J, Park K, Kim YM. Commensal Microbiota and Cancer Immunotherapy: Harnessing Commensal Bacteria for Cancer Therapy. Immune Netw 2022; 22:e3. [PMID: 35291651 PMCID: PMC8901697 DOI: 10.4110/in.2022.22.e3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/01/2022] Open
Abstract
Cancer is one of the leading causes of death worldwide and the number of cancer patients is expected to continuously increase in the future. Traditional cancer therapies focus on inhibiting cancer growth while largely ignoring the contribution of the immune system in eliminating cancer cells. Recently, better understanding of immunological mechanisms pertaining to cancer progress has led to development of several immunotherapies, which revolutionized cancer treatment. Nonetheless, only a small proportion of cancer patients respond to immunotherapy and maintain a durable response. Among multiple factors contributing to the variability of immunotherapy response rates, commensal microbiota inhabiting patients have been identified as one of the most critical factors determining the success of immunotherapy. The functional diversity of microbiota differentially affects the host immune system and controls the efficacy of immunotherapy in individual cancer patients. Moreover, clinical studies have demonstrated that changing the gut microbiota composition by fecal microbiota transplantation in patients who failed a previous immunotherapy converts them to responders of the same therapy. Consequently, both academic and industrial researchers are putting extensive efforts to identify and develop specific bacteria or bacteria mixtures for cancer immunotherapy. In this review, we will summarize the immunological roles of commensal microbiota in cancer treatment and give specific examples of bacteria that show anticancer effect when administered as a monotherapy or as an adjuvant agent for immunotherapy. We will also list ongoing clinical trials testing the anticancer effect of commensal bacteria.
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Affiliation(s)
- Jihong Bae
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Kwangcheon Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - You-Me Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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Microbiota-specific T follicular helper cells drive tertiary lymphoid structures and anti-tumor immunity against colorectal cancer. Immunity 2021; 54:2812-2824.e4. [PMID: 34861182 PMCID: PMC8865366 DOI: 10.1016/j.immuni.2021.11.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/19/2021] [Accepted: 11/04/2021] [Indexed: 02/06/2023]
Abstract
The composition of the intestinal microbiota is associated with both the development of tumors and the efficacy of anti-tumor immunity. Here, we examined the impact of microbiota-specific T cells in anti-colorectal cancer (CRC) immunity. Introduction of Helicobacter hepaticus (Hhep) in a mouse model of CRC did not alter the microbial landscape but increased tumor infiltration by cytotoxic lymphocytes and inhibited tumor growth. Anti-tumor immunity was independent of CD8+ T cells but dependent upon CD4+ T cells, B cells, and natural killer (NK) cells. Hhep colonization induced Hhep-specific T follicular helper (Tfh) cells, increased the number of colon Tfh cells, and supported the maturation of Hhep+ tumor-adjacent tertiary lymphoid structures. Tfh cells were necessary for Hhep-mediated tumor control and immune infiltration, and adoptive transfer of Hhep-specific CD4+ T cells to Tfh cell-deficient Bcl6fl/flCd4Cre mice restored anti-tumor immunity. Thus, introduction of immunogenic intestinal bacteria can promote Tfh-associated anti-tumor immunity in the colon, suggesting therapeutic approaches for the treatment of CRC.
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Jeffery R, Ilott NE, Powrie F. Genetic and environmental factors shape the host response to Helicobacter hepaticus: insights into IBD pathogenesis. Curr Opin Microbiol 2021; 65:145-155. [PMID: 34883389 DOI: 10.1016/j.mib.2021.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 11/03/2022]
Abstract
Pathobionts are members of the gut microbiota with the capacity to cause disease when there is malfunctioning intestinal homeostasis. These organisms are thought to be major contributors to the pathogenesis of inflammatory bowel disease (IBD), a group of chronic inflammatory disorders driven by dysregulated responses towards the microbiota. Over two decades have passed since the discovery of Helicobacter hepaticus, a mouse pathobiont which causes colitis in the context of immune deficiency. During this time, we have developed a detailed understanding of the cellular players and cytokine networks which drive H. hepaticus immunopathology. However, we are just beginning to understand the microbial factors that enable H. hepaticus to interact with the host and influence colonic health and disease. Here we review key H. hepaticus-host interactions, their relevance to other exemplar pathobionts and how when maladapted they drive colitis. Further understanding of these pathways may offer new therapeutic approaches for IBD.
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Affiliation(s)
- Rebecca Jeffery
- Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7FY, United Kingdom
| | - Nicholas E Ilott
- Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7FY, United Kingdom
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, Oxford OX3 7FY, United Kingdom.
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31
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Russler-Germain EV, Jung J, Miller AT, Young S, Yi J, Wehmeier A, Fox LE, Monte KJ, Chai JN, Kulkarni DH, Funkhouser-Jones LJ, Wilke G, Durai V, Zinselmeyer BH, Czepielewski RS, Greco S, Murphy KM, Newberry RD, Sibley LD, Hsieh CS. Commensal Cryptosporidium colonization elicits a cDC1-dependent Th1 response that promotes intestinal homeostasis and limits other infections. Immunity 2021; 54:2547-2564.e7. [PMID: 34715017 DOI: 10.1016/j.immuni.2021.10.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 06/01/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022]
Abstract
Cryptosporidium can cause severe diarrhea and morbidity, but many infections are asymptomatic. Here, we studied the immune response to a commensal strain of Cryptosporidium tyzzeri (Ct-STL) serendipitously discovered when conventional type 1 dendritic cell (cDC1)-deficient mice developed cryptosporidiosis. Ct-STL was vertically transmitted without negative health effects in wild-type mice. Yet, Ct-STL provoked profound changes in the intestinal immune system, including induction of an IFN-γ-producing Th1 response. TCR sequencing coupled with in vitro and in vivo analysis of common Th1 TCRs revealed that Ct-STL elicited a dominant antigen-specific Th1 response. In contrast, deficiency in cDC1s skewed the Ct-STL CD4 T cell response toward Th17 and regulatory T cells. Although Ct-STL predominantly colonized the small intestine, colon Th1 responses were enhanced and associated with protection against Citrobacter rodentium infection and exacerbation of dextran sodium sulfate and anti-IL10R-triggered colitis. Thus, Ct-STL represents a commensal pathobiont that elicits Th1-mediated intestinal homeostasis that may reflect asymptomatic human Cryptosporidium infection.
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Affiliation(s)
- Emilie V Russler-Germain
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jisun Jung
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Aidan T Miller
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shannon Young
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jaeu Yi
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alec Wehmeier
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lindsey E Fox
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristen J Monte
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiani N Chai
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Devesha H Kulkarni
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lisa J Funkhouser-Jones
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Georgia Wilke
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vivek Durai
- Department of Pathology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bernd H Zinselmeyer
- Department of Pathology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rafael S Czepielewski
- Department of Pathology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suellen Greco
- Division of Comparative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kenneth M Murphy
- Department of Pathology, Division of Immunobiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rodney D Newberry
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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32
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Muschaweck M, Kopplin L, Ticconi F, Schippers A, Iljazovic A, Gálvez EJC, Abdallah AT, Wagner N, Costa IG, Strowig T, Pabst O. Cognate recognition of microbial antigens defines constricted CD4 + T cell receptor repertoires in the inflamed colon. Immunity 2021; 54:2565-2577.e6. [PMID: 34582747 DOI: 10.1016/j.immuni.2021.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Key aspects of intestinal T cells, including their antigen specificity and their selection by the microbiota and other intestinal antigens, as well as the contribution of individual T cell clones to regulatory and effector functions, remain unresolved. Here we tracked adoptively transferred T cell populations to specify the interrelation of T cell receptor repertoire and the gut antigenic environment. We show that dominant TCRα clonotypes were shared between interferon-γ- and interleukin-17-producing but not regulatory Foxp3+ T cells. Identical TCRα clonotypes accumulated in the colon of different individuals, whereas antibiotics or defined colonization correlated with the expansion of distinct expanded T cell clonotypes. Our results demonstrate key aspects of intestinal CD4+ T cell activation and suggest that few microbial species exert a dominant effect on the intestinal T cell repertoire during colitis. We speculate that dominant proinflammatory T cell clones might provide a therapeutic target in human inflammatory bowel disease.
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Affiliation(s)
- Moritz Muschaweck
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany; Department of Pediatrics, RWTH Aachen University, Aachen, Germany.
| | - Lydia Kopplin
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | - Fabio Ticconi
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany; Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Angela Schippers
- Department of Pediatrics, RWTH Aachen University, Aachen, Germany
| | - Aida Iljazovic
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany
| | - Ali T Abdallah
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, Aachen, Germany
| | - Norbert Wagner
- Department of Pediatrics, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany
| | - Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany.
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33
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Tsou AM, Goettel JA, Bao B, Biswas A, Kang YH, Redhu NS, Peng K, Putzel GG, Saltzman J, Kelly R, Gringauz J, Barends J, Hatazaki M, Frei SM, Emani R, Huang Y, Shen Z, Fox JG, Glickman JN, Horwitz BH, Snapper SB. Utilizing a reductionist model to study host-microbe interactions in intestinal inflammation. MICROBIOME 2021; 9:215. [PMID: 34732258 PMCID: PMC8565002 DOI: 10.1186/s40168-021-01161-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/10/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND The gut microbiome is altered in patients with inflammatory bowel disease, yet how these alterations contribute to intestinal inflammation is poorly understood. Murine models have demonstrated the importance of the microbiome in colitis since colitis fails to develop in many genetically susceptible animal models when re-derived into germ-free environments. We have previously shown that Wiskott-Aldrich syndrome protein (WASP)-deficient mice (Was-/-) develop spontaneous colitis, similar to human patients with loss-of-function mutations in WAS. Furthermore, we showed that the development of colitis in Was-/- mice is Helicobacter dependent. Here, we utilized a reductionist model coupled with multi-omics approaches to study the role of host-microbe interactions in intestinal inflammation. RESULTS Was-/- mice colonized with both altered Schaedler flora (ASF) and Helicobacter developed colitis, while those colonized with either ASF or Helicobacter alone did not. In Was-/- mice, Helicobacter relative abundance was positively correlated with fecal lipocalin-2 (LCN2), a marker of intestinal inflammation. In contrast, WT mice colonized with ASF and Helicobacter were free of inflammation and strikingly, Helicobacter relative abundance was negatively correlated with LCN2. In Was-/- colons, bacteria breach the mucus layer, and the mucosal relative abundance of ASF457 Mucispirillum schaedleri was positively correlated with fecal LCN2. Meta-transcriptomic analyses revealed that ASF457 had higher expression of genes predicted to enhance fitness and immunogenicity in Was-/- compared to WT mice. In contrast, ASF519 Parabacteroides goldsteinii's relative abundance was negatively correlated with LCN2 in Was-/- mice, and transcriptional analyses showed lower expression of genes predicted to facilitate stress adaptation by ASF519 in Was-/-compared to WT mice. CONCLUSIONS These studies indicate that the effect of a microbe on the immune system can be context dependent, with the same bacteria eliciting a tolerogenic response under homeostatic conditions but promoting inflammation in immune-dysregulated hosts. Furthermore, in inflamed environments, some bacteria up-regulate genes that enhance their fitness and immunogenicity, while other bacteria are less able to adapt and decrease in abundance. These findings highlight the importance of studying host-microbe interactions in different contexts and considering how the transcriptional profile and fitness of bacteria may change in different hosts when developing microbiota-based therapeutics. Video abstract.
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Affiliation(s)
- Amy M Tsou
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY, USA.
- Division of Pediatric Gastroenterology and Nutrition, Weill Cornell Medical College, New York, NY, USA.
| | - Jeremy A Goettel
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bin Bao
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Amlan Biswas
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yu Hui Kang
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Naresh S Redhu
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kaiyue Peng
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Department of Gastroenterology, Children's Hospital of Fudan University, Shanghai, China
| | - Gregory G Putzel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY, USA
| | - Jeffrey Saltzman
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Ryan Kelly
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Jordan Gringauz
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Jared Barends
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Mai Hatazaki
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, NY, USA
| | - Sandra M Frei
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Rohini Emani
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ying Huang
- Department of Gastroenterology, Children's Hospital of Fudan University, Shanghai, China
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan N Glickman
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Bruce H Horwitz
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Emergency Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA.
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Schroeter CB, Huntemann N, Bock S, Nelke C, Kremer D, Pfeffer K, Meuth SG, Ruck T. Crosstalk of Microorganisms and Immune Responses in Autoimmune Neuroinflammation: A Focus on Regulatory T Cells. Front Immunol 2021; 12:747143. [PMID: 34691057 PMCID: PMC8529161 DOI: 10.3389/fimmu.2021.747143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/20/2021] [Indexed: 12/22/2022] Open
Abstract
Regulatory T cells (Tregs) are the major determinant of peripheral immune tolerance. Many Treg subsets have been described, however thymus-derived and peripherally induced Tregs remain the most important subpopulations. In multiple sclerosis, a prototypical autoimmune disorder of the central nervous system, Treg dysfunction is a pathogenic hallmark. In contrast, induction of Treg proliferation and enhancement of their function are central immune evasion mechanisms of infectious pathogens. In accordance, Treg expansion is compartmentalized to tissues with high viral replication and prolonged in chronic infections. In friend retrovirus infection, Treg expansion is mainly based on excessive interleukin-2 production by infected effector T cells. Moreover, pathogens seem also to enhance Treg functions as shown in human immunodeficiency virus infection, where Tregs express higher levels of effector molecules such as cytotoxic T-lymphocyte-associated protein 4, CD39 and cAMP and show increased suppressive capacity. Thus, insights into the molecular mechanisms by which intracellular pathogens alter Treg functions might aid to find new therapeutic approaches to target central nervous system autoimmunity. In this review, we summarize the current knowledge of the role of pathogens for Treg function in the context of autoimmune neuroinflammation. We discuss the mechanistic implications for future therapies and provide an outlook for new research directions.
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Affiliation(s)
- Christina B Schroeter
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Niklas Huntemann
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefanie Bock
- Department of Neurology With Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Christopher Nelke
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - David Kremer
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sven G Meuth
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Bhattacharjee A, Burr AHP, Overacre-Delgoffe AE, Tometich JT, Yang D, Huckestein BR, Linehan JL, Spencer SP, Hall JA, Harrison OJ, Morais da Fonseca D, Norton EB, Belkaid Y, Hand TW. Environmental enteric dysfunction induces regulatory T cells that inhibit local CD4+ T cell responses and impair oral vaccine efficacy. Immunity 2021; 54:1745-1757.e7. [PMID: 34348118 DOI: 10.1016/j.immuni.2021.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 04/21/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022]
Abstract
Environmental enteric dysfunction (EED) is a gastrointestinal inflammatory disease caused by malnutrition and chronic infection. EED is associated with stunting in children and reduced efficacy of oral vaccines. To study the mechanisms of oral vaccine failure during EED, we developed a microbiota- and diet-dependent mouse EED model. Analysis of E. coli-labile toxin vaccine-specific CD4+ T cells in these mice revealed impaired CD4+ T cell responses in the small intestine and but not the lymph nodes. EED mice exhibited increased frequencies of small intestine-resident RORγT+FOXP3+ regulatory T (Treg) cells. Targeted deletion of RORγT from Treg cells restored small intestinal vaccine-specific CD4 T cell responses and vaccine-mediated protection upon challenge. However, ablation of RORγT+FOXP3+ Treg cells made mice more susceptible to EED-induced stunting. Our findings provide insight into the poor efficacy of oral vaccines in EED and highlight how RORγT+FOXP3+ Treg cells can regulate intestinal immunity while leaving systemic responses intact.
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Affiliation(s)
- Amrita Bhattacharjee
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA
| | - Ansen H P Burr
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA; Program in Microbiology and Immunology, Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15261, USA
| | - Abigail E Overacre-Delgoffe
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA
| | - Justin T Tometich
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA
| | - Deyi Yang
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA; Central South University, Xiangya School of Medicine, Changsha, PRC
| | - Brydie R Huckestein
- Program in Microbiology and Immunology, Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15261, USA
| | - Jonathan L Linehan
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Sean P Spencer
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Jason A Hall
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Oliver J Harrison
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Denise Morais da Fonseca
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth B Norton
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Timothy W Hand
- R.K. Mellon Institute for Pediatric Research, Pediatrics Department, Infectious Disease Section, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224 USA; Program in Microbiology and Immunology, Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15261, USA.
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36
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Wang J, Zheng S, Yang X, Huazeng B, Cheng Q. Influences of non-IgE-mediated cow's milk protein allergy-associated gut microbial dysbiosis on regulatory T cell-mediated intestinal immune tolerance and homeostasis. Microb Pathog 2021; 158:105020. [PMID: 34089791 DOI: 10.1016/j.micpath.2021.105020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/02/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Gut microbial dysbiosis is closely associated with cow's milk protein allergy (CMPA) during infancy. Recent research has highlighted the crucial role of the commensal microbiota-induced intestinal regulatory T (Treg) cell response in the development of oral tolerance and protection against IgE-mediated food allergies. However, the influences of CMPA (particularly non-IgE-mediated CMPA)-associated microbial dysbiosis on Treg cell-mediated intestinal immune tolerance and homeostasis remain poorly characterized. To investigate this issue, fecal microbiota from infant donors with food protein-induced allergic proctocolitis (FPIAP) associated with cow's milk, which is the most frequent clinical type of non-IgE-mediated gastrointestinal CMPA, and from age-matched healthy controls were transplanted into germ-free mice in this study. Two weeks post fecal microbiota transplantation, the gut microbiome of the recipient mice was analyzed by 16S rRNA gene sequencing, and the intestinal immunological alterations associated with the Treg cell compartment and intestinal immune homeostasis were detected. The specific gut microbial phylotypes that were potentially responsible for the disruption of intestinal immune homeostasis were also analyzed. We observed that the main characteristics of the gut microbiome in infant donors could be stably maintained in recipient mice. We also found that mice colonized with the gut microbiome from infants with cow's milk-induced FPIAP showed significant deficiencies in the accumulation and function of intestinal Treg cells. Furthermore, these mice showed disrupted intestinal immune homeostasis, which was characterized by an overactivated Th2 biased immune response. We further identified two potentially pathogenic genera that contribute to this disruption. Overall, our results highlight a destructive effect of non-IgE-mediated CMPA-associated microbial dysbiosis on intestinal immune tolerance and homeostasis. We believe these findings will help improve our understanding of the gut microbiota-mediated pathogenesis of non-IgE-mediated CMPA in the future.
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Affiliation(s)
- Jinzhi Wang
- Department of Nephrology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatircs, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Shuang Zheng
- Department of Child Health Care, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Xin Yang
- Department of Child Health Care, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Ben Huazeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Qian Cheng
- Department of Child Health Care, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Health and Nutrition, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.
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37
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Knoop KA, McDonald KG, Hsieh CS, Tarr PI, Newberry RD. Regulatory T Cells Developing Peri-Weaning Are Continually Required to Restrain Th2 Systemic Responses Later in Life. Front Immunol 2021; 11:603059. [PMID: 33613522 PMCID: PMC7891039 DOI: 10.3389/fimmu.2020.603059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
Atopic disorders including allergic rhinitis, asthma, food allergy, and dermatitis, are increasingly prevalent in Western societies. These disorders are largely characterized by T helper type 2 (Th2) immune responses to environmental triggers, particularly inhaled and dietary allergens. Exposure to such stimuli during early childhood reduces the frequency of allergies in at-risk children. These allergic responses can be restrained by regulatory T cells (Tregs), particularly Tregs arising in the gut. The unique attributes of how early life exposure to diet and microbes shape the intestinal Treg population is a topic of significant interest. While imprinting during early life promotes the development of a balanced immune system and protects against immunopathology, it remains unclear if Tregs that develop in early life continue to restrain systemic inflammatory responses throughout adulthood. Here, an inducible deletion strategy was used to label Tregs at specified time points with a targeted mechanism to be deleted later. Deletion of the Tregs labeled peri-weaning at day of life 24, but not before weaning at day of life 14, resulted in increased circulating IgE and IL-13, and abrogated induction of tolerance towards new antigens. Thus, Tregs developing peri-weaning, but not before day of life 14 are continually required to restrain allergic responses into adulthood.
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MESH Headings
- Administration, Oral
- Adoptive Transfer
- Age Factors
- Animals
- Animals, Genetically Modified
- Antigens/administration & dosage
- Antigens/immunology
- Cell Communication
- Colon/immunology
- Colon/metabolism
- Cytokines/blood
- Disease Models, Animal
- Hypersensitivity, Delayed/blood
- Hypersensitivity, Delayed/genetics
- Hypersensitivity, Delayed/immunology
- Immune Tolerance
- Immunoglobulin E/blood
- Mice, Inbred C57BL
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- Ovalbumin
- Phenotype
- Signal Transduction
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/transplantation
- Th2 Cells/immunology
- Th2 Cells/metabolism
- Weaning
- Mice
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Affiliation(s)
- Kathryn A. Knoop
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Department of Immunology, Mayo Clinic, Rochester, MN, United States
| | - Keely G. McDonald
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Phillip I. Tarr
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Department of Pediatrics and Molecular Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, United States
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38
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Russler-Germain EV, Yi J, Young S, Nutsch K, Wong HS, Ai TL, Chai JN, Durai V, Kaplan DH, Germain RN, Murphy KM, Hsieh CS. Gut Helicobacter presentation by multiple dendritic cell subsets enables context-specific regulatory T cell generation. eLife 2021; 10:54792. [PMID: 33533717 PMCID: PMC7877908 DOI: 10.7554/elife.54792] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Generation of tolerogenic peripheral regulatory T (pTreg) cells is commonly thought to involve CD103+ gut dendritic cells (DCs), yet their role in commensal-reactive pTreg development is unclear. Using two Helicobacter-specific T cell receptor (TCR) transgenic mouse lines, we found that both CD103+ and CD103- migratory, but not resident, DCs from the colon-draining mesenteric lymph node presented Helicobacter antigens to T cells ex vivo. Loss of most CD103+ migratory DCs in vivo using murine genetic models did not affect the frequency of Helicobacter-specific pTreg cell generation or induce compensatory tolerogenic changes in the remaining CD103- DCs. By contrast, activation in a Th1-promoting niche in vivo blocked Helicobacter-specific pTreg generation. Thus, these data suggest a model where DC-mediated effector T cell differentiation is 'dominant', necessitating that all DC subsets presenting antigen are permissive for pTreg cell induction to maintain gut tolerance.
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Affiliation(s)
- Emilie V Russler-Germain
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, United States
| | - Jaeu Yi
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, United States
| | - Shannon Young
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, United States
| | - Katherine Nutsch
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, United States
| | - Harikesh S Wong
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Teresa L Ai
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, United States
| | - Jiani N Chai
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, United States
| | - Vivek Durai
- Department of Pathology, Division of Immunobiology, Washington University School of Medicine, St. Louis, United States
| | - Daniel H Kaplan
- Department of Dermatology, Department of Immunology, Pittsburgh Center for Pain Research, University of Pittsburgh, Pittsburgh, United States
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Kenneth M Murphy
- Department of Pathology, Division of Immunobiology, Washington University School of Medicine, St. Louis, United States
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, United States
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39
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Arnesen H, Knutsen LE, Hognestad BW, Johansen GM, Bemark M, Pabst O, Storset AK, Boysen P. A Model System for Feralizing Laboratory Mice in Large Farmyard-Like Pens. Front Microbiol 2021; 11:615661. [PMID: 33505381 PMCID: PMC7830425 DOI: 10.3389/fmicb.2020.615661] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022] Open
Abstract
Laboratory mice are typically housed under extremely clean laboratory conditions, far removed from the natural lifestyle of a free-living mouse. There is a risk that this isolation from real-life conditions may lead to poor translatability and misinterpretation of results. We and others have shown that feral mice as well as laboratory mice exposed to naturalistic environments harbor a more diverse gut microbiota and display an activated immunological phenotype compared to hygienic laboratory mice. We here describe a naturalistic indoors housing system for mice, representing a farmyard-type habitat typical for house mice. Large open pens were installed with soil and domestic animal feces, creating a highly diverse microbial environment and providing space and complexity allowing for natural behavior. Laboratory C57BL/6 mice were co-housed in this system together with wild-caught feral mice, included as a source of murine microbionts. We found that mice feralized in this manner displayed a gut microbiota structure similar to their feral cohabitants, such as higher relative content of Firmicutes and enrichment of Proteobacteria. Furthermore, the immunophenotype of feralized mice approached that of feral mice, with elevated levels of memory T-cells and late-stage NK cells compared to laboratory-housed control mice, indicating antigenic experience and immune training. The dietary elements presented in the mouse pens could only moderately explain changes in microbial colonization, and none of the immunological changes. In conclusion, this system enables various types of studies using genetically controlled mice on the background of adaptation to a high diversity microbial environment and a lifestyle natural for the species.
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Affiliation(s)
- Henriette Arnesen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Linn Emilie Knutsen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | | | | | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Immunology and Transfusion Medicine, Gothenburg, Sweden
| | - Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | | | - Preben Boysen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
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40
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Abstract
Mucosal surfaces are distinctive sites exposed to environmental, dietary, and microbial antigens. Particularly in the gut, the host continuously actively adapts via complex interactions between the microbiota and dietary compounds and immune and other tissue cells. Regulatory T cells (Tregs) are critical for tuning the intestinal immune response to self- and non-self-antigens in the intestine. Its importance in intestinal homeostasis is illustrated by the onset of overt inflammation caused by deficiency in Treg generation, function, or stability in the gut. A substantial imbalance in Tregs has been observed in intestinal tissue during pathogenic conditions, when a tightly regulated and equilibrated system becomes dysregulated and leads to unimpeded and chronic immune responses. In this chapter, we compile and critically discuss the current knowledge on the key factors that promote Treg-mediated tolerance in the gut, such as those involved in intestinal Treg differentiation, specificity and suppressive function, and their immunophenotype during health and disease. We also discuss the current state of knowledge on Treg dysregulation in human intestine during pathological states such as inflammatory bowel disease (IBD), necrotizing enterocolitis (NEC), graft-versus-host disease (GVHD), and colorectal cancer (CRC), and how that knowledge is guiding development of Treg-targeted therapies to treat or prevent intestinal disorders.
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41
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Lo BC, Chen GY, Núñez G, Caruso R. Gut microbiota and systemic immunity in health and disease. Int Immunol 2020; 33:197-209. [PMID: 33367688 DOI: 10.1093/intimm/dxaa079] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
The mammalian intestine is colonized by trillions of microorganisms that have co-evolved with the host in a symbiotic relationship. Although the influence of the gut microbiota on intestinal physiology and immunity is well known, mounting evidence suggests a key role for intestinal symbionts in controlling immune cell responses and development outside the gut. Although the underlying mechanisms by which the gut symbionts influence systemic immune responses remain poorly understood, there is evidence for both direct and indirect effects. In addition, the gut microbiota can contribute to immune responses associated with diseases outside the intestine. Understanding the complex interactions between the gut microbiota and the host is thus of fundamental importance to understand both immunity and human health.
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Affiliation(s)
- Bernard C Lo
- Department of Pathology and Rogel Cancer Center, Ann Arbor, MI, USA
| | - Grace Y Chen
- Department of Internal Medicine, the University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, Ann Arbor, MI, USA
| | - Roberta Caruso
- Department of Pathology and Rogel Cancer Center, Ann Arbor, MI, USA
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42
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Jacob EM, Borah A, Pillai SC, Kumar DS. Inflammatory Bowel Disease: The Emergence of New Trends in Lifestyle and Nanomedicine as the Modern Tool for Pharmacotherapy. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2460. [PMID: 33316984 PMCID: PMC7764399 DOI: 10.3390/nano10122460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023]
Abstract
The human intestine, which harbors trillions of symbiotic microorganisms, may enter into dysbiosis when exposed to a genetic defect or environmental stress. The naissance of chronic inflammation due to the battle of the immune system with the trespassing gut bacteria leads to the rise of inflammatory bowel disease (IBD). Though the genes behind the scenes and their link to the disease are still unclear, the onset of IBD occurs in young adults and has expanded from the Western world into the newly industrialized countries. Conventional drug deliveries depend on a daily heavy dosage of immune suppressants or anti-inflammatory drugs targeted for the treatment of two types of IBD, ulcerative colitis (UC) and Crohn's disease (CD), which are often associated with systemic side effects and adverse toxicities. Advances in oral delivery through nanotechnology seek remedies to overcome the drawbacks of these conventional drug delivery systems through improved drug encapsulation and targeted delivery. In this review, we discuss the association of genetic factors, the immune system, the gut microbiome, and environmental factors like diet in the pathogenesis of IBD. We also review the various physiological concerns required for oral delivery to the gastrointestinal tract (GIT) and new strategies in nanotechnology-derived, colon-targeting drug delivery systems.
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Affiliation(s)
| | | | | | - D. Sakthi Kumar
- Bio-Nano Electronics Research Centre, Graduate School of Interdisciplinary New Science, Toyo University, Kawagoe, Saitama 350-8585, Japan; (E.M.J.); (A.B.); (S.C.P.)
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43
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Ge Z, Ge L, Muthupalani S, Feng Y, Fox JG. Male-Dependent Promotion of Colitis in 129 Rag2-/- Mice Co-Infected with Helicobacter pylori and Helicobacter hepaticus. Int J Mol Sci 2020; 21:ijms21238886. [PMID: 33255175 PMCID: PMC7727654 DOI: 10.3390/ijms21238886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/08/2023] Open
Abstract
The prevalence of gastric Helicobacter pylori (Hp) infection is ~50% of the world population. However, how Hp infection influences inflammatory bowel disease in humans is not fully defined. In this study, we examined whether co-infection with Hp influenced Helicobacter hepaticus (Hh)–induced intestinal pathology in Rag2−/− mice. Rag2−/− mice of both sexes were infected with Hh, of which a subgroup was followed by infection with Hp two weeks later. Co-infected males, but not females, had significantly higher total colitis index scores in the colon at both 10 and 21 weeks post-Hh infection (WPI) and developed more severe dysplasia at 21 WPI compared with mono-Hh males. There were no significant differences in colonization levels of gastric Hp and colonic Hh between sexes or time-points. In addition, mRNA levels of colonic Il-1β, Ifnγ, Tnfα, Il-17A, Il-17F, Il-18, and Il-23, which play important roles in the development and function of proinflammatory innate lymphoid cell groups 1 and 3, were significantly up-regulated in the dually infected males compared with mono-Hh males at 21 WPI. These data suggest that concomitant Hp infection enhances the inflammatory responses in the colon of-Hh-infected Rag2−/− males, which results in more severe colitis and dysplasia.
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Affiliation(s)
- Zhongming Ge
- Correspondence: (Z.G.); (J.G.F.); Tel.: +1-(617)-253-5518 (Z.G.); +1-(617)-253-1735 (J.G.F.); Fax: +1-(617)-258-5708 (Z.G. & J.G.F.)
| | | | | | | | - James G. Fox
- Correspondence: (Z.G.); (J.G.F.); Tel.: +1-(617)-253-5518 (Z.G.); +1-(617)-253-1735 (J.G.F.); Fax: +1-(617)-258-5708 (Z.G. & J.G.F.)
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44
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Bertolini TB, Biswas M, Terhorst C, Daniell H, Herzog RW, Piñeros AR. Role of orally induced regulatory T cells in immunotherapy and tolerance. Cell Immunol 2020; 359:104251. [PMID: 33248367 DOI: 10.1016/j.cellimm.2020.104251] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/30/2020] [Accepted: 11/01/2020] [Indexed: 12/24/2022]
Abstract
Oral antigen administration to induce regulatory T cells (Treg) takes advantage of regulatory mechanisms that the gastrointestinal tract utilizes to promote unresponsiveness against food antigens or commensal microorganisms. Recently, antigen-based oral immunotherapies (OITs) have shown efficacy as treatment for food allergy and autoimmune diseases. Similarly, OITs appear to prevent anti-drug antibody responses in replacement therapy for genetic diseases. Intestinal epithelial cells and microbiota possibly condition dendritic cells (DC) toward a tolerogenic phenotype that induces Treg via expression of several mediators, e.g. IL-10, transforming growth factor-β, retinoic acid. Several factors, such as metabolites derived from microbiota or diet, impact the stability and expansion of these induced Treg, which include, but are not limited to, FoxP3+ Treg, LAP+ Treg, and/or Tr1 cells. Here, we review various orally induced Treg, their plasticity and cooperation between the Treg subsets, as well as underlying mechanisms controlling their induction and role in oral tolerance.
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Affiliation(s)
- Thais B Bertolini
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Moanaro Biswas
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cox Terhorst
- Division of Immunology, Beth Israel Deaconess Medical Center (BIDMC), Harvard Medical School, Boston, MA, USA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roland W Herzog
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Annie R Piñeros
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
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45
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Bousbaine D, Ploegh HL. Antigen discovery tools for adaptive immune receptor repertoire research. ACTA ACUST UNITED AC 2020; 24:64-70. [PMID: 33195881 DOI: 10.1016/j.coisb.2020.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The adaptive immune system has evolved to recognize with incredible precision a large diversity of molecules. Innovations in high-throughput sequencing and bioinformatics have accelerated large-scale immune repertoire analyses and given us important insights into the behavior of the adaptive immune system. However, establishing a connection between receptor sequence and its antigen-specificity remains a challenge despite its central role in determining T and B cell fate. We discuss recent large-scale antigen discovery technologies which can be combined with adaptive immune receptor repertoire (AIRR) studies. We highlight important discoveries made using repertoire analyses in the field of host-microbe interactions.
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Affiliation(s)
- Djenet Bousbaine
- Department of Bioengineering and ChEM-H, Stanford University, Stanford CA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston MA, USA
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46
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Rengarajan S, Knoop KA, Rengarajan A, Chai JN, Grajales-Reyes JG, Samineni VK, Russler-Germain EV, Ranganathan P, Fasano A, Sayuk GS, Gereau RW, Kau AL, Knights D, Kashyap PC, Ciorba MA, Newberry RD, Hsieh CS. A Potential Role for Stress-Induced Microbial Alterations in IgA-Associated Irritable Bowel Syndrome with Diarrhea. CELL REPORTS MEDICINE 2020; 1. [PMID: 33196055 PMCID: PMC7659537 DOI: 10.1016/j.xcrm.2020.100124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Stress is a known trigger for flares of inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS); however, this process is not well understood. Here, we find that restraint stress in mice leads to signs of diarrhea, fecal dysbiosis, and a barrier defect via the opening of goblet-cell associated passages. Notably, stress increases host immunity to gut bacteria as assessed by immunoglobulin A (IgA)-bound gut bacteria. Stress-induced microbial changes are necessary and sufficient to elicit these effects. Moreover, similar to mice, many diarrhea-predominant IBS (IBS-D) patients from two cohorts display increased antibacterial immunity as assessed by IgA-bound fecal bacteria. This antibacterial IgA response in IBS-D correlates with somatic symptom severity and was distinct from healthy controls or IBD patients. These findings suggest that stress may play an important role in patients with IgA-associated IBS-D by disrupting the intestinal microbial community that alters gastrointestinal function and host immunity to commensal bacteria. Stress in mice causes diarrhea, dysbiosis, barrier defect, increased antibacterial IgA Stress-induced microbial changes are sufficient to elicit the above effects IBS-D patients from two cohorts display increased and unique antibacterial IgA Antibacterial IgA in IBS-D correlates with patient symptom severity
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Affiliation(s)
- Sunaina Rengarajan
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathryn A Knoop
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Arvind Rengarajan
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiani N Chai
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jose G Grajales-Reyes
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vijay K Samineni
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emilie V Russler-Germain
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Prabha Ranganathan
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessio Fasano
- Center for Celiac Research and Treatment and Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gregory S Sayuk
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Gastroenterology Section, John Cochran Veterans Affairs Medical Center, St. Louis, MO 63125, USA
| | - Robert W Gereau
- Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew L Kau
- Center for Women's Infectious Disease Research and Department of Internal Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dan Knights
- Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Matthew A Ciorba
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rodney D Newberry
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Lead Contact
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47
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Fluckiger A, Daillère R, Sassi M, Sixt BS, Liu P, Loos F, Richard C, Rabu C, Alou MT, Goubet AG, Lemaitre F, Ferrere G, Derosa L, Duong CPM, Messaoudene M, Gagné A, Joubert P, De Sordi L, Debarbieux L, Simon S, Scarlata CM, Ayyoub M, Palermo B, Facciolo F, Boidot R, Wheeler R, Boneca IG, Sztupinszki Z, Papp K, Csabai I, Pasolli E, Segata N, Lopez-Otin C, Szallasi Z, Andre F, Iebba V, Quiniou V, Klatzmann D, Boukhalil J, Khelaifia S, Raoult D, Albiges L, Escudier B, Eggermont A, Mami-Chouaib F, Nistico P, Ghiringhelli F, Routy B, Labarrière N, Cattoir V, Kroemer G, Zitvogel L. Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage. Science 2020; 369:936-942. [PMID: 32820119 DOI: 10.1126/science.aax0701] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 02/28/2020] [Accepted: 06/23/2020] [Indexed: 12/28/2022]
Abstract
Intestinal microbiota have been proposed to induce commensal-specific memory T cells that cross-react with tumor-associated antigens. We identified major histocompatibility complex (MHC) class I-binding epitopes in the tail length tape measure protein (TMP) of a prophage found in the genome of the bacteriophage Enterococcus hirae Mice bearing E. hirae harboring this prophage mounted a TMP-specific H-2Kb-restricted CD8+ T lymphocyte response upon immunotherapy with cyclophosphamide or anti-PD-1 antibodies. Administration of bacterial strains engineered to express the TMP epitope improved immunotherapy in mice. In renal and lung cancer patients, the presence of the enterococcal prophage in stools and expression of a TMP-cross-reactive antigen by tumors correlated with long-term benefit of PD-1 blockade therapy. In melanoma patients, T cell clones recognizing naturally processed cancer antigens that are cross-reactive with microbial peptides were detected.
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Affiliation(s)
- Aurélie Fluckiger
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Romain Daillère
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,everImmune, Gustave Roussy Cancer Center, Villejuif, France
| | - Mohamed Sassi
- Université Rennes 1, Laboratoire de Biochimie Pharmaceutique, Inserm U1230 - UPRES EA 2311, Rennes, France
| | - Barbara Susanne Sixt
- Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, 90187, Umeå, Sweden.,Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France
| | - Peng Liu
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France
| | - Friedemann Loos
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France.,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France
| | - Corentin Richard
- Research Platform in Biological Oncology, Dijon, France.,GIMI Genetic and Immunology Medical Institute, Dijon, France.,University of Burgundy-Franche Comté, Dijon, France
| | - Catherine Rabu
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Maryam Tidjani Alou
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Anne-Gaëlle Goubet
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Fabien Lemaitre
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,everImmune, Gustave Roussy Cancer Center, Villejuif, France
| | - Gladys Ferrere
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Lisa Derosa
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, F-94805, France
| | - Connie P M Duong
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France
| | - Meriem Messaoudene
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada
| | - Andréanne Gagné
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada
| | - Luisa De Sordi
- Bacteriophage, Bacterium, Host Laboratory, Institut Pasteur, F-75015 Paris, France.,Sorbonne Université, Centre de Recherche Saint Antoine, INSERM UMRS_938, Paris, France
| | - Laurent Debarbieux
- Bacteriophage, Bacterium, Host Laboratory, Institut Pasteur, F-75015 Paris, France
| | - Sylvain Simon
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Clara-Maria Scarlata
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Maha Ayyoub
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Belinda Palermo
- Unit of Tumor Immunology and Immunotherapy, Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesco Facciolo
- Thoracic Surgery Unit, Department of Surgical Oncology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Romain Boidot
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges-François Leclerc Anticancer Center, UNICANCER, Dijon, France
| | - Richard Wheeler
- Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France
| | - Ivo Gomperts Boneca
- Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France
| | - Zsofia Sztupinszki
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA
| | - Krisztian Papp
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Carlos Lopez-Otin
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Zoltan Szallasi
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Danish Cancer Society Research Center, Copenhagen, Denmark.,MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Fabrice Andre
- Department of Cancer Medicine, Breast Cancer Committee, Gustave Roussy, Villejuif, France.,INSERM Unit 981, Gustave Roussy, Villejuif, France
| | - Valerio Iebba
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,Department of Medical Sciences, University of Trieste, 34137 Trieste, Italy
| | - Valentin Quiniou
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center in Biotherapy (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), F-75651, Paris, France.,Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), F-75651, Paris, France
| | - David Klatzmann
- AP-HP, Hôpital Pitié-Salpêtrière, Clinical Investigation Center in Biotherapy (CIC-BTi) and Immunology-Inflammation-Infectiology and Dermatology Department (3iD), F-75651, Paris, France.,Sorbonne Université, INSERM, Immunology-Immunopathology-Immunotherapy (i3), F-75651, Paris, France
| | - Jacques Boukhalil
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Saber Khelaifia
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- UMR MEPHI, Aix-Marseille Université, IRD, AP-HM, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Laurence Albiges
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Bernard Escudier
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France.,INSERM U981, GRCC, Villejuif, France
| | - Alexander Eggermont
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.,Princess Maxima Center, CS 3584 Utrecht, the Netherlands
| | - Fathia Mami-Chouaib
- INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Fac. de Médecine - Univ. Paris-Sud, Université Paris-Saclay, 94805, Villejuif, France
| | - Paola Nistico
- Unit of Tumor Immunology and Immunotherapy, Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy.,Thoracic Surgery Unit, Department of Surgical Oncology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Bertrand Routy
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Research Center and Department of Cytology and Pathology, Québec City, Québec, Canada.,Division d'Hémato-Oncologie, Département de Médicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Nathalie Labarrière
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Vincent Cattoir
- Université Rennes 1, Laboratoire de Biochimie Pharmaceutique, Inserm U1230 - UPRES EA 2311, Rennes, France.,CHU de Rennes - Hôpital Ponchaillou, Service de Bactériologie-Hygiène Hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Guido Kroemer
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, France. .,Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.,INSERM U1138, Paris, France.,Université de Paris, Paris, France.,Sorbonne Université, Paris, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Department of Women's and Children's Health, Karolinska University Hospital, 1 Stockholm, Sweden.,Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences, Suzhou, China.,Institut Universitaire de France, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France. .,Institut National de la Santé et de la Recherche Médicale, U1015, Institut Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Villejuif, F-94805, France.,Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences, Suzhou, China
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48
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Innate Lymphoid Cells: Important Regulators of Host-Bacteria Interaction for Border Defense. Microorganisms 2020; 8:microorganisms8091342. [PMID: 32887435 PMCID: PMC7563982 DOI: 10.3390/microorganisms8091342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Innate lymphoid cells (ILCs) are a recently discovered type of innate immune lymphocyte. They include three different groups classified by the nature of the transcription factors required for their development and by the cytokines they produce. ILCs mainly reside in tissues close to the mucosal barrier such as the respiratory and gastrointestinal tracts. Due to their close proximity to the mucosal surface, ILCs are exposed to a variety of both commensal and pathogenic bacteria. Under non-pathological conditions, ILCs have been shown to be important regulators for the maintenance of tissue homeostasis by mutual interactions with the microbiome. Besides these important functions at homeostasis, several studies have also provided emerging evidence that ILCs contribute to defense against pathogenic bacterial infection by responding rapidly to the pathogens as well as orchestrating other immune cells. In this review, we summarize recent advances in our understanding of the interactions of ILCs and bacteria, with special focus on the function of the different ILC subsets in bacterial infections.
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49
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Knoop KA, McDonald KG, Coughlin PE, Kulkarni DH, Gustafsson JK, Rusconi B, John V, Ndao IM, Beigelman A, Good M, Warner BB, Elson CO, Hsieh CS, Hogan SP, Tarr PI, Newberry RD. Synchronization of mothers and offspring promotes tolerance and limits allergy. JCI Insight 2020; 5:137943. [PMID: 32759496 DOI: 10.1172/jci.insight.137943] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Allergic disorders, characterized by Th2 immune responses to environmental substances, are increasingly common in children in Western societies. Multiple studies indicate that breastfeeding, early complementary introduction of food allergens, and antibiotic avoidance in the first year of life reduces allergic outcomes in at-risk children. Why the benefit of these practices is restricted to early life is largely unknown. We identified a preweaning interval during which dietary antigens are assimilated by the colonic immune system. This interval is under maternal control via temporal changes in breast milk, coincides with an influx of naive T cells into the colon, and is followed by the development of a long-lived population of colonic peripherally derived Tregs (pTregs) that can be specific for dietary antigens encountered during this interval. Desynchronization of mothers and offspring produced durable deficits in these pTregs, impaired tolerance to dietary antigens introduced during and after this preweaning interval, and resulted in spontaneous Th2 responses. These effects could be rescued by pTregs from the periweaning colon or by Tregs generated in vitro using periweaning colonic antigen-presenting cells. These findings demonstrate that mothers and their offspring are synchronized for the development of a balanced immune system.
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Affiliation(s)
| | | | | | | | | | - Brigida Rusconi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - I Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Avraham Beigelman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Kipper Institute of Allergy and Immunology, Schneider Children's Medical Center of Israel, Tel Aviv University, Israel
| | - Misty Good
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Charles O Elson
- Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Simon P Hogan
- Mary H. Weiser Food Allergy Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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50
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Zhang S, Cho WJ, Jin AT, Kok LY, Shi Y, Heller DE, Lee YAL, Zhou Y, Xie X, Korzenik JR, Lennerz JK, Traverso G. Heparin-Coated Albumin Nanoparticles for Drug Combination in Targeting Inflamed Intestine. Adv Healthc Mater 2020; 9:e2000536. [PMID: 32597571 PMCID: PMC7482138 DOI: 10.1002/adhm.202000536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Targeting areas of inflammation offers potential therapeutic and diagnostic benefits by maximizing drug and imaging marker on-target effects while minimizing systemic exposure that can be associated with adverse side effects. This strategy is particularly beneficial in the management of inflammatory bowel disease (IBD). Here an inflammation-targeting (IT) approach based on heparin-coated human serum albumin nanoparticles (HEP-HSA NPs) that utilize the increased intestinal permeability and changes in electrostatic interaction at the site of intestinal inflammation is described. Using small-molecule and biologic drugs as a model for drug combination, the HEP-HSA NPs demonstrate the capacity to load both drugs simultaneously; the dual-drug loaded HEP-HSA NPs exhibit a higher anti-inflammatory effect than both of the single-drug loaded NPs in vitro and selectively bind to inflamed intestine after enema administration in vivo in a murine model of colitis. Importantly, analyses of the physicochemical characteristics and targeting capacities of these NPs indicate that HEP coating modulates NP binding to the inflamed intestine, providing a foundation for future IT-NP formulation development.
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Affiliation(s)
- Sufeng Zhang
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Won Joon Cho
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amy T. Jin
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lie Yun Kok
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yunhua Shi
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David E. Heller
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Young-Ah Lucy Lee
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yixuan Zhou
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xi Xie
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joshua R. Korzenik
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jochen K. Lennerz
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Giovanni Traverso
- Dr. S. Zhang, A. T. Jin, Prof. J. R. Korzenik, Prof. G. Traverso Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA. Dr. S. Zhang, W. J. Woo, A. T. Jin, L. Y. Kok, Dr. Y. Shi, D. E. Heller, Y.-A. L. Lee, Y. Zhou, Dr. X. Xie Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Dr. S. Zhang, Prof. J. R. Korzenik, Prof. J. K. Lennerz, Prof. G. Traverso Harvard Medical School, Boston, MA 02115, USA. Prof. J. K. Lennerz Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA. Prof. G. Traverso Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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