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Davis EC, Castagna VP, Sela DA, Hillard MA, Lindberg S, Mantis NJ, Seppo AE, Järvinen KM. Gut microbiome and breast-feeding: Implications for early immune development. J Allergy Clin Immunol 2022; 150:523-534. [PMID: 36075638 PMCID: PMC9463492 DOI: 10.1016/j.jaci.2022.07.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022]
Abstract
Establishment of the gut microbiome during early life is a complex process with lasting implications for an individual's health. Several factors influence microbial assembly; however, breast-feeding is recognized as one of the most influential drivers of gut microbiome composition during infancy, with potential implications for function. Differences in gut microbial communities between breast-fed and formula-fed infants have been consistently observed and are hypothesized to partially mediate the relationships between breast-feeding and decreased risk for numerous communicable and noncommunicable diseases in early life. Despite decades of research on the gut microbiome of breast-fed infants, there are large scientific gaps in understanding how human milk has evolved to support microbial and immune development. This review will summarize the evidence on how breast-feeding broadly affects the composition and function of the early-life gut microbiome and discuss mechanisms by which specific human milk components shape intestinal bacterial colonization, succession, and function.
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Affiliation(s)
- Erin C Davis
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY
| | | | - David A Sela
- Department of Food Science, University of Massachusetts Amherst, Amherst, Mass; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Mass; Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, Mass
| | - Margaret A Hillard
- Department of Food Science, University of Massachusetts Amherst, Amherst, Mass; Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, Mass
| | - Samantha Lindberg
- Department of Biomedical Sciences, University of Albany, Rensselaer, NY
| | - Nicholas J Mantis
- Division of Infectious Diseases, New York State Department of Health, Albany, NY
| | - Antti E Seppo
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY
| | - Kirsi M Järvinen
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY; Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY; Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY.
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52
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Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Reference-based comparison of adaptive immune receptor repertoires. CELL REPORTS METHODS 2022; 2:100269. [PMID: 36046619 PMCID: PMC9421535 DOI: 10.1016/j.crmeth.2022.100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
B and T cell receptor (immune) repertoires can represent an individual's immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a limited number of parameters. Here, we introduce immuneREF: a quantitative multidimensional measure of adaptive immune repertoire (and transcriptome) similarity that allows interpretation of immune repertoire variation by relying on both repertoire features and cross-referencing of simulated and experimental datasets. To quantify immune repertoire similarity landscapes across health and disease, we applied immuneREF to >2,400 datasets from individuals with varying immune states (healthy, [autoimmune] disease, and infection). We discovered, in contrast to the current paradigm, that blood-derived immune repertoires of healthy and diseased individuals are highly similar for certain immune states, suggesting that repertoire changes to immune perturbations are less pronounced than previously thought. In conclusion, immuneREF enables the population-wide study of adaptive immune response similarity across immune states.
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Affiliation(s)
- Cédric R. Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Teresa Rubio
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
| | - Longlong Wang
- BGI-Shenzhen, Shenzhen, China
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Philippe A. Robert
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Igor Snapkov
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | - Marieke L. Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sonia Tarazona
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Valencia, Spain
| | - Geir K. Sandve
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
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53
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Vujkovic-Cvijin I, Welles HC, Ha CWY, Huq L, Mistry S, Brenchley JM, Trinchieri G, Devkota S, Belkaid Y. The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces. Sci Transl Med 2022; 14:eabl3927. [PMID: 35976997 PMCID: PMC9741845 DOI: 10.1126/scitranslmed.abl3927] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Unique gut microbiota compositions have been associated with inflammatory diseases, but identifying gut bacterial functions linked to immune activation in humans remains challenging. Translocation of pathogens from mucosal surfaces into peripheral tissues can elicit immune activation, although whether and which gut commensal bacteria translocate in inflammatory diseases is difficult to assess. We report that a subset of commensal gut microbiota constituents that translocate across the gut barrier in mice and humans are associated with heightened systemic immunoglobulin G (IgG) responses. We present a modified high-throughput, culture-independent approach to quantify systemic IgG against gut commensal bacteria in human serum samples without the need for paired stool samples. Using this approach, we highlight several commensal bacterial species that elicit elevated IgG responses in patients with inflammatory bowel disease (IBD) including taxa within the clades Collinsella, Bifidobacterium, Lachnospiraceae, and Ruminococcaceae. These and other taxa identified as translocating bacteria or targets of systemic immunity in IBD concomitantly exhibited heightened transcriptional activity and growth rates in IBD patient gut microbiomes. Our approach represents a complementary tool to illuminate interactions between the host and its gut microbiota and may provide an additional method to identify microbes linked to inflammatory disease.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Hugh C. Welles
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Connie W. Y. Ha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lutfi Huq
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Shreni Mistry
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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54
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Lee H, Yoo DK, Han J, Kim KH, Noh J, Lee Y, Lee E, Kwon S, Chung J. Optimization of peripheral blood volume for in silico reconstitution of the human B cell receptor repertoire. FEBS Open Bio 2022; 12:1634-1643. [PMID: 35866358 PMCID: PMC9433817 DOI: 10.1002/2211-5463.13467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022] Open
Abstract
B cells recognize antigens via membrane‐expressed B‐cell receptors (BCR) and antibodies. Similar human BCR sequences are frequently found at a significantly higher frequency than that theoretically calculated. Patients infected with SARS‐CoV2 and HIV or with autoimmune diseases share very similar BCRs. Therefore, in silico reconstitution of BCR repertoires and identification of stereotypical BCR sequences related to human pathology have diagnostic potential. Furthermore, monitoring changes of clinically significant BCR sequences and isotype conversion has prognostic potential. For BCR repertoire analysis, peripheral blood (PB) is the most convenient source. However, the optimal human PB volume for in silico reconstitution of the BCR repertoire has not been studied in detail. Here, we sampled 5, 10, and 20 mL PB from the left arm and 40 mL PB from the right arm of two volunteers, reconstituted in silico PB BCR repertoires, and compared their composition. In both volunteers, PB sampling over 20 mL resulted in slight increases in functional unique sequences (FUSs) or almost no increase in repertoire diversity. All FUSs with a frequency above 0.08% or 0.03% in the 40 mL PB BCR repertoire were detected even in the 5 mL PB BCR repertoire from each volunteer. FUSs with a higher frequency were more likely to be found in BCR repertoires from reduced PB volume, and those coexisting in two repertoires showed a statistically significant correlation in frequency irrespective of sampled anatomical site. The correlation was more significant in higher‐frequency FUSs. These observations support the potential of BCR repertoire analysis for diagnosis.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jerome Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Ki Hyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Korea.,BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul, 08826, Korea.,Bio-MAX Institute, Seoul National University, Seoul, 08826, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
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55
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Perruzza L, Strati F, Raneri M, Li H, Gargari G, Rezzonico-Jost T, Palatella M, Kwee I, Morone D, Seehusen F, Sonego P, Donati C, Franceschi P, Macpherson AJ, Guglielmetti S, Greiff V, Grassi F. Apyrase-mediated amplification of secretory IgA promotes intestinal homeostasis. Cell Rep 2022; 40:111112. [PMID: 35858559 DOI: 10.1016/j.celrep.2022.111112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/15/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
Secretory immunoglobulin A (SIgA) interaction with commensal bacteria conditions microbiota composition and function. However, mechanisms regulating reciprocal control of microbiota and SIgA are not defined. Bacteria-derived adenosine triphosphate (ATP) limits T follicular helper (Tfh) cells in the Peyer's patches (PPs) via P2X7 receptor (P2X7R) and thereby SIgA generation. Here we show that hydrolysis of extracellular ATP (eATP) by apyrase results in amplification of the SIgA repertoire. The enhanced breadth of SIgA in mice colonized with apyrase-releasing Escherichia coli influences topographical distribution of bacteria and expression of genes involved in metabolic versus immune functions in the intestinal epithelium. SIgA-mediated conditioning of bacteria and enterocyte function is reflected by differences in nutrient absorption in mice colonized with apyrase-expressing bacteria. Apyrase-induced SIgA improves intestinal homeostasis and attenuates barrier impairment and susceptibility to infection by enteric pathogens in antibiotic-induced dysbiosis. Therefore, amplification of SIgA by apyrase can be leveraged to restore intestinal fitness in dysbiotic conditions.
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Affiliation(s)
- Lisa Perruzza
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Francesco Strati
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Matteo Raneri
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Hai Li
- Maurice Müller Laboratories, Department of Biomedical Research, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern 3010, Switzerland
| | - Giorgio Gargari
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan 20133, Italy
| | - Tanja Rezzonico-Jost
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Martina Palatella
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Ivo Kwee
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Diego Morone
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Frauke Seehusen
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Paolo Sonego
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN) 38098, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN) 38098, Italy
| | - Pietro Franceschi
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN) 38098, Italy
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department of Biomedical Research, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern 3010, Switzerland
| | - Simone Guglielmetti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan 20133, Italy
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo 0372, Norway
| | - Fabio Grassi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland.
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56
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Gilboa A, Hope R, Ben Simon S, Polak P, Koren O, Yaari G. Ontogeny of the B Cell Receptor Repertoire and Microbiome in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2713-2725. [PMID: 35623663 DOI: 10.4049/jimmunol.2100955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
The immune system matures throughout childhood to achieve full functionality in protecting our bodies against threats. The immune system has a strong reciprocal symbiosis with the host bacterial population and the two systems co-develop, shaping each other. Despite their fundamental role in health physiology, the ontogeny of these systems is poorly characterized. In this study, we investigated the development of the BCR repertoire by analyzing high-throughput sequencing of their receptors in several time points of young C57BL/6J mice. In parallel, we explored the development of the gut microbiome. We discovered that the gut IgA repertoires change from birth to adolescence, including an increase in CDR3 lengths and somatic hypermutation levels. This contrasts with the spleen IgM repertoires that remain stable and distinct from the IgA repertoires in the gut. We also discovered that large clones that germinate in the gut are initially confined to a specific gut compartment, then expand to nearby compartments and later on expand also to the spleen and remain there. Finally, we explored the associations between diversity indices of the B cell repertoires and the microbiome, as well as associations between bacterial and BCR clusters. Our results shed light on the ontogeny of the adaptive immune system and the microbiome, providing a baseline for future research.
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Affiliation(s)
- Amit Gilboa
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
| | - Ronen Hope
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Shira Ben Simon
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Pazit Polak
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Gur Yaari
- Bioengineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel;
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel; and
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57
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Bourgonje AR, Roo-Brand G, Lisotto P, Sadaghian Sadabad M, Reitsema RD, de Goffau MC, Faber KN, Dijkstra G, Harmsen HJM. Patients With Inflammatory Bowel Disease Show IgG Immune Responses Towards Specific Intestinal Bacterial Genera. Front Immunol 2022; 13:842911. [PMID: 35693832 PMCID: PMC9174456 DOI: 10.3389/fimmu.2022.842911] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/25/2022] [Indexed: 12/26/2022] Open
Abstract
Introduction Inflammatory bowel disease (IBD) is characterized by a disturbed gut microbiota composition. Patients with IBD have both elevated mucosal and serum levels of IgG-antibodies directed against bacterial antigens, including flagellins. In this study, we aimed to determine to which intestinal bacteria the humoral immune response is directed to in patients with IBD. Methods Fecal and serum samples were collected from patients with IBD (n=55) and age- and sex-matched healthy controls (n=55). Fecal samples were incubated with autologous serum and IgG-coated fractions were isolated by magnetic-activated cell sorting (MACS) and its efficiency was assessed by flow cytometry. The bacterial composition of both untreated and IgG-coated fecal samples was determined by 16S rRNA-gene Illumina sequencing. Results IgG-coated fecal samples were characterized by significantly lower microbial diversity compared to the fecal microbiome. Both in patients with IBD and controls, serum IgG responses were primarily directed to Streptococcus, Lactobacillus, Lactococcus, Enterococcus, Veillonella and Enterobacteriaceae, as well as against specific Lachnospiraceae bacteria, including Coprococcus and Dorea (all P<0.001), and to Ruminococcus gnavus-like bacteria (P<0.05). In contrast, serological IgG responses against typical commensal, anaerobic and colonic microbial species were rather low, e.g. to the Lachnospiraceae members Roseburia and Blautia, to Faecalibacterium, as well as to Bacteroides. Patients with IBD showed more IgG-coating of Streptococcus, Lactobacillus, and Lactococcus bacteria compared to healthy controls (all P<0.05). No differences in IgG-coated bacterial fractions were observed between Crohn's disease and ulcerative colitis, between active or non-active disease, nor between different disease locations. Conclusion The IgG immune response is specifically targeted at distinct intestinal bacterial genera that are typically associated with the small intestinal microbiota, whereas responses against more colonic-type commensals are lower, which was particularly the case for patients with IBD. These findings may be indicative of a strong immunological exposure to potentially pathogenic intestinal bacteria in concordance with relative immune tolerance against commensal bacteria.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Geesje Roo-Brand
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paola Lisotto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mehdi Sadaghian Sadabad
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rosanne D Reitsema
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marcus C de Goffau
- Department of Vascular Medicine, University of Amsterdam, Amsterdam University Medical Center, Amsterdam, Netherlands.,Wellcome Genome Campus, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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58
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Abstract
High-throughput sequencing for B cell receptor (BCR) repertoire provides useful insights for the adaptive immune system. With the continuous development of the BCR-seq technology, many efforts have been made to develop methods for analyzing the ever-increasing BCR repertoire data. In this review, we comprehensively outline different BCR repertoire library preparation protocols and summarize three major steps of BCR-seq data analysis, i. e., V(D)J sequence annotation, clonal phylogenetic inference, and BCR repertoire profiling and mining. Different from other reviews in this field, we emphasize background intuition and the statistical principle of each method to help biologists better understand it. Finally, we discuss data mining problems for BCR-seq data and with a highlight on recently emerging multiple-sample analysis.
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59
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Choden T, Cohen NA. The gut microbiome and the immune system. EXPLORATION OF MEDICINE 2022. [DOI: 10.37349/emed.2022.00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The human body contains trillions of microbes which generally live in symbiosis with the host. The interaction of the gut microbiome with elements of the host immune system has far-reaching effects in the development of normal gut and systemic immune responses. Disturbances to this intricate relationship may be responsible for a multitude of gastrointestinal and systemic immune mediated diseases. This review describes the development of the gut microbiome and its interaction with host immune cells in both health and disease states.
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Affiliation(s)
- Tenzin Choden
- Section of Gastroenterology, Hepatology and Nutrition, University of Chicago Medicine, Chicago, IL 60637, USA
| | - Nathaniel Aviv Cohen
- Section of Gastroenterology, Hepatology and Nutrition, University of Chicago Medicine, Chicago, IL 60637, USA; Inflammatory Bowel Disease Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center, Tel Aviv 6423906, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
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60
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Zhang L, Xu Z, Mak JWY, Chow KM, Lui G, Li TCM, Wong CK, Chan PKS, Ching JYL, Fujiwara Y, Chan FKL, Ng SC. Gut microbiota-derived synbiotic formula (SIM01) as a novel adjuvant therapy for COVID-19: An open-label pilot study. J Gastroenterol Hepatol 2022; 37:823-831. [PMID: 35170078 PMCID: PMC9115073 DOI: 10.1111/jgh.15796] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIM Gut dysbiosis is associated with immune dysfunction and severity of COVID-19. Whether targeting dysbiosis will improve outcomes of COVID-19 is unknown. This study aimed to assess the effects of a novel gut microbiota-derived synbiotic formula (SIM01) as an adjuvant therapy on immunological responses and changes in gut microbiota of hospitalized COVID-19 patients. METHODS This was an open-label, proof-of-concept study. Consecutive COVID-19 patients admitted to an infectious disease referral center in Hong Kong were given a novel formula of Bifidobacteria strains, galactooligosaccharides, xylooligosaccharide, and resistant dextrin (SIM01). The latter was derived from metagenomic databases of COVID-19 patients and healthy population. COVID-19 patients who were admitted under another independent infectious disease team during the same period without receiving SIM01 acted as controls. All patients received standard treatments for COVID-19 according to the hospital protocol. We assessed antibody response, plasma proinflammatory markers, nasopharyngeal SARS-CoV-2 viral load, and fecal microbiota profile from admission up to week 5. RESULTS Twenty-five consecutive COVID-19 patients received SIM01 for 28 days; 30 patients who did not receive the formula acted as controls. Significantly more patients receiving SIM01 than controls developed SARS-CoV-2 IgG antibody (88% vs 63.3%; P = 0.037) by Day 16. One (4%) and 8 patients (26.7%) in the SIM01 and control group, respectively, failed to develop positive IgG antibody upon discharge. At week 5, plasma levels of interleukin (IL)-6, monocyte chemoattractant protein-1 (MCP-1), macrophage colony-stimulating factor (M-CSF), tumor necrosis factor (TNF-α), and IL-1RA reduced significantly in the SIM01 but not in the control group. There was a significant negative correlation of nasopharyngeal SARS-CoV-2 viral load and SIM01 intervention. Metagenomic analysis showed that bacterial species in SIM01 formula were found in greater abundance leading to enrichment of commensal bacteria and suppression of opportunistic pathogens in COVID-19 patients by week 4 and week 5. CONCLUSIONS This proof-of-concept study suggested that the use of a novel gut microbiota-derived synbiotic formula, SIM01, hastened antibody formation against SARS-CoV-2, reduced nasopharyngeal viral load, reduced pro-inflammatory immune markers, and restored gut dysbiosis in hospitalised COVID-19 patients.
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Affiliation(s)
- Lin Zhang
- Microbiota I‐Center (MagIC)The Chinese University of Hong KongHong Kong SARChina,Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina,State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Zhilu Xu
- Microbiota I‐Center (MagIC)The Chinese University of Hong KongHong Kong SARChina,Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina,State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Joyce W Y Mak
- Microbiota I‐Center (MagIC)The Chinese University of Hong KongHong Kong SARChina,Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina,State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Kai Ming Chow
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Grace Lui
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina,Stanley Ho Centre for Emerging Infectious Diseases, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Timothy C M Li
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Chun Kwok Wong
- Department of Chemical Pathology, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Paul K S Chan
- Department of Microbiology, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Jessica Y L Ching
- Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Yasuhiro Fujiwara
- Department of GastroenterologyOsaka City University Graduate School of MedicineOsakaJapan
| | - Francis K L Chan
- Microbiota I‐Center (MagIC)The Chinese University of Hong KongHong Kong SARChina,Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina,State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
| | - Siew C Ng
- Microbiota I‐Center (MagIC)The Chinese University of Hong KongHong Kong SARChina,Department of Medicine and Therapeutics, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina,State Key Laboratory of Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, Faculty of MedicineThe Chinese University of Hong KongHong Kong SARChina
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Bourgonje AR, Vogl T, Segal E, Weersma RK. Antibody signatures in inflammatory bowel disease: current developments and future applications. Trends Mol Med 2022; 28:693-705. [DOI: 10.1016/j.molmed.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 11/25/2022]
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Long-distance relationships - regulation of systemic host defense against infections by the gut microbiota. Mucosal Immunol 2022; 15:809-818. [PMID: 35732817 DOI: 10.1038/s41385-022-00539-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/29/2022] [Accepted: 06/04/2022] [Indexed: 02/04/2023]
Abstract
Despite compartmentalization within the lumen of the gastrointestinal tract, the gut microbiota has a far-reaching influence on immune cell development and function throughout the body. This long-distance relationship is crucial for immune homeostasis, including effective host defense against invading pathogens that cause systemic infections. Herein, we review new insights into how commensal microbes that are spatially restricted to the gut lumen can engage in long-distance relationships with innate and adaptive immune cells at systemic sites to fortify host defenses against infections. In addition, we explore the consequences of intestinal dysbiosis on impaired host defense and immune-mediated pathology during infections, including emerging evidence linking dysbiosis with aberrant systemic inflammation and immune-mediated organ damage in sepsis. As such, therapeutic modification of the gut microbiota is an emerging target for interventions to prevent and/or treat systemic infections and sepsis by harnessing the long-distance relationships between gut microbes and systemic immunity.
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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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64
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Fragoso-Saavedra M, Ramírez-Estudillo C, Peláez-González DL, Ramos-Flores JO, Torres-Franco G, Núñez-Muñoz L, Marcelino-Pérez G, Segura-Covarrubias MG, González-González R, Ruiz-Medrano R, Xoconostle-Cázares B, Gayosso-Vázquez A, Reyes-Maya S, Ramírez-Andoney V, Alonso-Morales RA, Vega-López MA. Combined Subcutaneous-Intranasal Immunization With Epitope-Based Antigens Elicits Binding and Neutralizing Antibody Responses in Serum and Mucosae Against PRRSV-2 and SARS-CoV-2. Front Immunol 2022; 13:848054. [PMID: 35432364 PMCID: PMC9008747 DOI: 10.3389/fimmu.2022.848054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022] Open
Abstract
New vaccine design approaches, platforms, and immunization strategies might foster antiviral mucosal effector and memory responses to reduce asymptomatic infection and transmission in vaccinated individuals. Here, we investigated a combined parenteral and mucosal immunization scheme to induce local and serum antibody responses, employing the epitope-based antigens 3BT and NG19m. These antigens target the important emerging and re-emerging viruses PRRSV-2 and SARS-CoV-2, respectively. We assessed two versions of the 3BT protein, which contains conserved epitopes from the GP5 envelope protein of PRRSV-2: soluble and expressed by the recombinant baculovirus BacDual-3BT. On the other hand, NG19m, comprising the receptor-binding motif of the S protein of SARS-CoV-2, was evaluated as a soluble recombinant protein only. Vietnamese mini-pigs were immunized employing different inoculation routes: subcutaneous, intranasal, or a combination of both (s.c.-i.n.). Animals produced antigen-binding and neut1ralizing antibodies in serum and mucosal fluids, with varying patterns of concentration and activity, depending on the antigen and the immunization schedule. Soluble 3BT was a potent immunogen to elicit binding and neutralizing antibodies in serum, nasal mucus, and vaginal swabs. The vectored immunogen BacDual-3BT induced binding antibodies in serum and mucosae, but PRRSV-2 neutralizing activity was found in nasal mucus exclusively when administered intranasally. NG19m promoted serum and mucosal binding antibodies, which showed differing neutralizing activity. Only serum samples from subcutaneously immunized animals inhibited RBD-ACE2 interaction, while mini-pigs inoculated intranasally or via the combined s.c.-i.n. scheme produced subtle neutralizing humoral responses in the upper and lower respiratory mucosae. Our results show that intranasal immunization, alone or combined with subcutaneous delivery of epitope-based antigens, generates local and systemic binding and neutralizing antibodies. Further investigation is needed to evaluate the capability of the induced responses to prevent infection and reduce transmission.
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Affiliation(s)
- Mario Fragoso-Saavedra
- Laboratorio de Inmunobiología de las Mucosas, Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Carmen Ramírez-Estudillo
- Laboratorio de Inmunobiología de las Mucosas, Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Diana L Peláez-González
- Unidad de Producción y Experimentación de Animales de Laboratorio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Jorge O Ramos-Flores
- Unidad de Producción y Experimentación de Animales de Laboratorio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Gustavo Torres-Franco
- Unidad de Producción y Experimentación de Animales de Laboratorio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Leandro Núñez-Muñoz
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Gabriel Marcelino-Pérez
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María G Segura-Covarrubias
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Rogelio González-González
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Roberto Ruiz-Medrano
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Beatriz Xoconostle-Cázares
- Laboratorio de Biología Molecular de Plantas, Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Amanda Gayosso-Vázquez
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Silvia Reyes-Maya
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Vianey Ramírez-Andoney
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rogelio A Alonso-Morales
- Laboratorio de Genética Molecular, Departamento de Genética y Bioestadística, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Marco A Vega-López
- Laboratorio de Inmunobiología de las Mucosas, Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
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Low L, Suleiman K, Shamdas M, Bassilious K, Poonit N, Rossiter AE, Acharjee A, Loman N, Murray PI, Wallace GR, Rauz S. Gut Dysbiosis in Ocular Mucous Membrane Pemphigoid. Front Cell Infect Microbiol 2022; 12:780354. [PMID: 35493740 PMCID: PMC9046938 DOI: 10.3389/fcimb.2022.780354] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/16/2022] [Indexed: 12/27/2022] Open
Abstract
Mucous Membrane Pemphigoid is an orphan multi-system autoimmune scarring disease involving mucosal sites, including the ocular surface (OcMMP) and gut. Loss of tolerance to epithelial basement membrane proteins and generation of autoreactive T cell and/or autoantibodies are central to the disease process. The gut microbiome plays a critical role in the development of the immune system. Alteration in the gut microbiome (gut dysbiosis) affects the generation of autoreactive T cells and B cell autoantibody repertoire in several autoimmune conditions. This study examines the relationship between gut microbiome diversity and ocular inflammation in patients with OcMMP by comparing OcMMP gut microbiome profiles with healthy controls. DNA was extracted from faecal samples (49 OcMMP patients, 40 healthy controls), amplified for the V4 region of the 16S rRNA gene and sequenced using Illumina Miseq platform. Sequencing reads were processed using the bioinformatics pipeline available in the mothur v.1.44.1 software. After adjusting for participant factors in the multivariable model (age, gender, BMI, diet, proton pump inhibitor use), OcMMP cohort was found to be associated with lower number of operational taxonomic units (OTUs) and Shannon Diversity Index when compared to healthy controls. Within the OcMMP cohort, the number of OTUs were found to be significantly correlated with both the bulbar conjunctival inflammation score (p=0.03) and the current use of systemic immunotherapy (p=0.02). The linear discriminant analysis effect size scores indicated that Streptococcus and Lachnoclostridium were enriched in OcMMP patients whilst Oxalobacter, Clostridia uncultured genus-level group (UCG) 014, Christensenellaceae R-7 group and butyrate-producing bacteria such as Ruminococcus, Lachnospiraceae, Coprococcus, Roseburia, Oscillospiraceae UCG 003, 005, NK4A214 group were enriched in healthy controls (Log10 LDA score < 2, FDR-adjusted p <0.05). In conclusion, OcMMP patients have gut dysbiosis correlating with bulbar conjunctival inflammation and the use of systemic immunotherapies. This provides a framework for future longitudinal deep phenotyping studies on the role of the gut microbiome in the pathogenesis of OcMMP.
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Affiliation(s)
- Liying Low
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Kusy Suleiman
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Mohith Shamdas
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Kerolos Bassilious
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham National Health Service (NHS) Trust, Birmingham, United Kingdom
| | - Natraj Poonit
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham National Health Service (NHS) Trust, Birmingham, United Kingdom
| | - Amanda E. Rossiter
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Animesh Acharjee
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
- Institute of Translational Medicine, University Hospitals Birmingham National Health Service (NHS), Foundation Trust, Birmingham, United Kingdom
- National Institute for Health Research (NIHR) Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham, United Kingdom
| | - Nicholas Loman
- Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Philip I. Murray
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham National Health Service (NHS) Trust, Birmingham, United Kingdom
| | - Graham R. Wallace
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Saaeha Rauz
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham National Health Service (NHS) Trust, Birmingham, United Kingdom
- *Correspondence: Saaeha Rauz,
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66
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Severyn CJ, Siranosian BA, Kong STJ, Moreno A, Li MM, Chen N, Duncan CN, Margossian SP, Lehmann LE, Sun S, Andermann TM, Birbrayer O, Silverstein S, Reynolds CG, Kim S, Banaei N, Ritz J, Fodor AA, London WB, Bhatt AS, Whangbo JS. Microbiota dynamics in a randomized trial of gut decontamination during allogeneic hematopoietic cell transplantation. JCI Insight 2022; 7:e154344. [PMID: 35239511 PMCID: PMC9057614 DOI: 10.1172/jci.insight.154344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUNDGut decontamination (GD) can decrease the incidence and severity of acute graft-versus-host disease (aGVHD) in murine models of allogeneic hematopoietic cell transplantation (HCT). In this pilot study, we examined the impact of GD on gut microbiome composition and the incidence of aGVHD in HCT patients.METHODSWe randomized 20 patients undergoing allogeneic HCT to receive (GD) or not receive (no-GD) oral vancomycin-polymyxin B from day -5 through neutrophil engraftment. We evaluated shotgun metagenomic sequencing of serial stool samples to compare the composition and diversity of the gut microbiome between study arms. We assessed clinical outcomes in the 2 arms and performed strain-specific analyses of pathogens that caused bloodstream infections (BSI).RESULTSThe 2 arms did not differ in the predefined primary outcome of Shannon diversity of the gut microbiome at 2 weeks post-HCT (genus, P = 0.8; species, P = 0.44) or aGVHD incidence (P = 0.58). Immune reconstitution of T cell and B cell subsets was similar between groups. Five patients in the no-GD arm had 8 BSI episodes versus 1 episode in the GD arm (P = 0.09). The BSI-causing pathogens were traceable to the gut in 7 of 8 BSI episodes in the no-GD arm, including Staphylococcus species.CONCLUSIONWhile GD did not differentially affect Shannon diversity or clinical outcomes, our findings suggest that GD may protect against gut-derived BSI in HCT patients by decreasing the prevalence or abundance of gut pathogens.TRIAL REGISTRATIONClinicalTrials.gov NCT02641236.FUNDINGNIH, Damon Runyon Cancer Research Foundation, V Foundation, Sloan Foundation, Emerson Collective, and Stanford Maternal & Child Health Research Institute.
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Affiliation(s)
- Christopher J. Severyn
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Division of Pediatric Stem Cell Transplant and Regenerative Medicine
| | | | | | - Angel Moreno
- Department of Pathology, Stanford University, Palo Alto, California, USA
| | - Michelle M. Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nan Chen
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Christine N. Duncan
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Steven P. Margossian
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Leslie E. Lehmann
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Shan Sun
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Tessa M. Andermann
- Department of Medicine, Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Olga Birbrayer
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Carol G. Reynolds
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Soomin Kim
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University, Palo Alto, California, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Palo Alto, California, USA
| | - Jerome Ritz
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Wendy B. London
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ami S. Bhatt
- Departments of Genetics and Medicine, Division of Hematology
| | - Jennifer S. Whangbo
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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67
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Bonami RH, Thurman CE, Verma S, Westlake CS, Nyhoff LE, Barron BB, Reboldi A, Kendall PL. Bruton's Tyrosine Kinase Supports Gut Mucosal Immunity and Commensal Microbiome Recognition in Autoimmune Arthritis. Front Immunol 2022; 13:748284. [PMID: 35422819 PMCID: PMC9002138 DOI: 10.3389/fimmu.2022.748284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/02/2022] [Indexed: 11/19/2022] Open
Abstract
Bruton's tyrosine kinase (Btk) deficiency preferentially eliminates autoreactive B cells while sparing normal humoral responses, but has not been studied in mucosal immunity. Commensal microbes and intact BTK signaling have been independently shown to be essential for arthritis development in K/BxN mice. Here, we examine how BTK-mediated signaling interfaces with the gut microbiome. Btk-deficient K/BxN mice were found to have small Peyer's Patches with reduced germinal center and IgA class-switched B cells. IgA-switched plasma cells in small intestines were reduced, especially in villi of Btk-deficient mice. IgH CDR3 sequencing showed similar V gene diversity and somatic hypermutation frequency despite Btk deficiency but showed reduced CDR3 amino acid polarity, suggesting potential qualitative differences in the gut plasma cell repertoire. Small intestinal IgA was low and IgA coating of commensal bacteria was reduced. IgA-seq showed a shift in small intestinal microbes that are normally IgA-coated into the uncoated fraction in Btk-deficient mice. Overall, this study shows that BTK supports normal intestinal IgA development in response to commensals. This manuscript was previously published as a preprint at: https://www.biorxiv.org/content/10.1101/2021.03.10.434762v2.
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Affiliation(s)
- Rachel H. Bonami
- Department of Medicine, Division of Rheumatology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation (VI4), Nashville, TN, United States
| | - Christina E. Thurman
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Sonam Verma
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Camille S. Westlake
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lindsay E. Nyhoff
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bridgette B. Barron
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Andrea Reboldi
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Peggy L. Kendall
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation (VI4), Nashville, TN, United States
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Medicine, Division of Allergy and Immunology, Washington University School of Medicine, St. Louis, MO, United States
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68
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Tesei D, Jewczynko A, Lynch AM, Urbaniak C. Understanding the Complexities and Changes of the Astronaut Microbiome for Successful Long-Duration Space Missions. Life (Basel) 2022; 12:life12040495. [PMID: 35454986 PMCID: PMC9031868 DOI: 10.3390/life12040495] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
During space missions, astronauts are faced with a variety of challenges that are unique to spaceflight and that have been known to cause physiological changes in humans over a period of time. Several of these changes occur at the microbiome level, a complex ensemble of microbial communities residing in various anatomic sites of the human body, with a pivotal role in regulating the health and behavior of the host. The microbiome is essential for day-to-day physiological activities, and alterations in microbiome composition and function have been linked to various human diseases. For these reasons, understanding the impact of spaceflight and space conditions on the microbiome of astronauts is important to assess significant health risks that can emerge during long-term missions and to develop countermeasures. Here, we review various conditions that are caused by long-term space exploration and discuss the role of the microbiome in promoting or ameliorating these conditions, as well as space-related factors that impact microbiome composition. The topics explored pertain to microgravity, radiation, immunity, bone health, cognitive function, gender differences and pharmacomicrobiomics. Connections are made between the trifecta of spaceflight, the host and the microbiome, and the significance of these interactions for successful long-term space missions.
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Affiliation(s)
- Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
| | - Anna Jewczynko
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Anne M. Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Camilla Urbaniak
- ZIN Technologies Inc., Middleburg Heights, OH 44130, USA
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
- Correspondence:
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69
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Yang M, Zheng X, Wu Y, Zhang R, Yang Q, Yu Z, Liu J, Zha B, Gong Q, Yang B, Sun B, Zeng M. Preliminary Observation of the Changes in the Intestinal Flora of Patients With Graves’ Disease Before and After Methimazole Treatment. Front Cell Infect Microbiol 2022; 12:794711. [PMID: 35402292 PMCID: PMC8989835 DOI: 10.3389/fcimb.2022.794711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 11/23/2022] Open
Abstract
Immune dysfunction caused by environmental factors plays an important role in the development of Graves’ disease (GD), and environmental factors are closely related to the intestinal flora. Our previous study showed significant changes in the intestinal flora in GD patients compared with healthy volunteers. This study analyzed the relationships between changes in the intestinal flora, thyroid function and relevant thyroid antibodies in GD patients before and after methimazole treatment. The subjects were divided into the UGD group (18 newly diagnosed GD patients), the TGD group (10 GD patients with normal or approximately normal thyroid function after methimazole treatment) and the NC group (11 healthy volunteers). Their fresh stool samples were sent for 16S rRNA gene amplification and Illumina platform sequencing. The correlations of the relative abundance of Bifidobacterium with the levels of TRAb, TgAb and TPOAb in the NC group and the UGD group were analyzed. A total of 1,562,445 high-quality sequences were obtained. In the UGD group, the abundances of Bifidobacterium and Collinsella were higher than that in the NC group; Bacteroides abundance in the TGD group was higher than that in the NC group, while Prevotella and Dialister abundances were lower than that in the NC group; Prevotella and Collinsella abundances in the UGD group were higher than that in the TGD group. The predominant abundance distribution of Bifidobacteriaceae in the UGD group at the family level was superior to that in the NC group. The abundance of Bifidobacterium was positively correlated with the levels of TRAb, TgAb, and TPOAb. The biological diversity of the intestinal flora was reduced in GD patients. After methimazole treatment, the composition of the intestinal flora was significantly altered. The change in Bifidobacterium abundance was positively correlated with TRAb, TgAb and TPOAb, suggesting that it might be related to the immune mechanism of GD. The results of this study may deepen our understanding of the pathogenesis of GD and provide a new idea for the treatment of GD.
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Affiliation(s)
- Mengxue Yang
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
- *Correspondence: Mengxue Yang,
| | - Xiaodi Zheng
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yueyue Wu
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Rui Zhang
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Qian Yang
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Zhiyan Yu
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Jun Liu
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Bingbing Zha
- Department of Endocrinology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology of the Ministry of Education, Zunyi Medical University, Zunyi, China
- Joint International Research Laboratory of Ethnomedicine of the Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Bo Yang
- Department of Endocrinology, Zunyi Medical University, Zunyi, China
| | - Bowen Sun
- Department of Endocrinology, Zunyi Medical University, Zunyi, China
| | - Miao Zeng
- Department of Infectious Diseases I, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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70
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Li Y, Ye Z, Zhu J, Fang S, Meng L, Zhou C. Effects of Gut Microbiota on Host Adaptive Immunity Under Immune Homeostasis and Tumor Pathology State. Front Immunol 2022; 13:844335. [PMID: 35355998 PMCID: PMC8960063 DOI: 10.3389/fimmu.2022.844335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota stimulate and shape the body’s adaptive immune response through bacterial components and its active metabolites, which orchestrates the formation and maintenance of the body’s immune homeostasis. In addition, the imbalances in microbiota-adaptive immunity contribute to the development of tumor and the antitumor efficiency of a series of antitumor therapies at the preclinical and clinical levels. Regardless of significant results, the regulation of gut microbiota on adaptive immunity in immune homeostasis and tumors needs a more thorough understanding. Herein, we highlighted the comprehensive knowledge, status, and limitations in the mechanism of microbiome interaction with adaptive immunity and put forward the prospect of how to translate these insights in inhibiting tumor progression and enhancing the efficacy of antitumor interventions.
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Affiliation(s)
- Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zixuan Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Jianguo Zhu
- Research and Development Department,Wecare-bio Probiotics Co., Ltd., Suzhou, China
| | - Shuguang Fang
- Research and Development Department,Wecare-bio Probiotics Co., Ltd., Suzhou, China
| | - Lijuan Meng
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Chen Zhou, ; Lijuan Meng,
| | - Chen Zhou
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Chen Zhou, ; Lijuan Meng,
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71
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Kong F, Fang C, Zhang Y, Duan L, Du D, Xu G, Li X, Li H, Yin Y, Xu H, Zhang K. Abundance and Metabolism Disruptions of Intratumoral Microbiota by Chemical and Physical Actions Unfreeze Tumor Treatment Resistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105523. [PMID: 35037431 PMCID: PMC8895135 DOI: 10.1002/advs.202105523] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/17/2021] [Indexed: 12/19/2022]
Abstract
Intratumoral or intestinal microbiota correlates with tumorigenesis and progression, and microbiota regulation for reinforcing various anti-tumor approaches is of significant importance, which, however, suffers from no precise regulation method and unclear underlying mechanism. Herein, a microbiome metabolism-engineered phototherapy strategy is established, wherein Nb2 C/Au nanocomposite and the corresponding phototherapy are harnessed to realize "chemical" and "physical" bacterial regulations. Flora analysis and mass spectrometry (MS) and metabonomics combined tests demonstrate that the synergistic microbiota regulations can alter the abundance, diversity of intratumoral microbiome, and disrupt metabolic pathways of microbiome and tumor microenvironment, wherein the differential singling pathways and biosynthetic necessities or metabolites that can affect tumor progression are identified. As well, anti-TNFα is introduced to unite with bacterial regulation to synergistically mitigate bacterial-induced inflammation, which, along with the metabolism disruptions of intratumoral microbiota and tumor microenvironment, unfreezes tumor resistance and harvests significantly-intensified phototherapy-based anti-tumor outcomes against 4T1 and CT26 tumors. The clear underlying principles of microbiome-regulated tumorigenesis and the established microbiome metabolism regulation method provide distinctive insights into tumor therapy, and can be also extended to other gut microbiome-associated lesions interference.
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Affiliation(s)
- Fanlei Kong
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
- Department of Medical UltrasoundAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineNo. 261 Huansha RoadHangzhou310006P. R. China
| | - Chao Fang
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
- Department of Medical Ultrasound and Department of RadiologyGuangxi Medical University Cancer Hospitaland Guangxi Key Laboratory of Bio‐targeting TheranosticsGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Yan Zhang
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Lixia Duan
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
- Department of Medical Ultrasound and Department of RadiologyGuangxi Medical University Cancer Hospitaland Guangxi Key Laboratory of Bio‐targeting TheranosticsGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
| | - Dou Du
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Guang Xu
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Xiaolong Li
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Hongyan Li
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Yifei Yin
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Huixiong Xu
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
| | - Kun Zhang
- Department of Medical Ultrasound and Central LaboratoryUltrasound Research and Education InstituteShanghai Tenth People's HospitalTongji University School of MedicineNo. 301 Yan‐chang‐zhong RoadShanghai200072P. R. China
- Department of Medical Ultrasound and Department of RadiologyGuangxi Medical University Cancer Hospitaland Guangxi Key Laboratory of Bio‐targeting TheranosticsGuangxi Medical UniversityNo. 71 Hedi RoadNanning530021P. R. China
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Luo K, Chen Y, Wang F. Shrimp Plasma MANF Works as an Invertebrate Anti-Inflammatory Factor via a Conserved Receptor Tyrosine Phosphatase. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1214-1223. [PMID: 35149533 DOI: 10.4049/jimmunol.2100595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
For a long time, how anti-inflammatory factors evolved was largely unknown. In this study, we chose a marine invertebrate, Litopenaeus vannamei, as a model and identified that shrimp mesencephalic astrocyte-derived neurotrophic factor (MANF) was an LPS-induced plasma protein, which exerted its anti-inflammatory roles on shrimp hemocytes by suppressing ERK phosphorylation and Dorsal expression. In addition, we demonstrated that shrimp MANF could be associated with a receptor protein tyrosine phosphatase (RPTP) to mediate negative regulation of ERK activation and Dorsal expression. More interestingly, shrimp RPTP-S overexpression in 293T cells could switch shrimp and human MANF-mediated ERK pathway activation to inhibition. In general, our results indicate that this conserved RPTP is the key component for extracellular MANF-mediated ERK pathway inhibition, which gives a possible explanation about why this neurotropic factor could both protect neuron cells from apoptosis and inhibit immune cell M1 activation in various species.
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Affiliation(s)
- Kaiwen Luo
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Yaohui Chen
- Department of Biology, College of Science, Shantou University, Shantou, China
| | - Fan Wang
- Department of Biology, College of Science, Shantou University, Shantou, China;
- Institute of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China; and
- Shantou University-University Malaysia Terengganu Joint Shellfish Research Laboratory, Shantou University, Shantou, China
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73
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Wu Y, Nie C, Luo R, Qi F, Bai X, Chen H, Niu J, Chen C, Zhang W. Effects of Multispecies Probiotic on Intestinal Microbiota and Mucosal Barrier Function of Neonatal Calves Infected With E. coli K99. Front Microbiol 2022; 12:813245. [PMID: 35154038 PMCID: PMC8826468 DOI: 10.3389/fmicb.2021.813245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Altered gut microbiota are implicated in inflammatory neonatal calf diarrhea caused by E. coli K99. Beneficial probiotics are used to modulate gut microbiota. However, factors that mediate host-microbe interactions remain unclear. We evaluated the effects of a combination of multispecies probiotics (MSP) on growth, intestinal epithelial development, intestinal immune function and microbiota of neonatal calves infected with E. coli K99. Twelve newborn calves were randomly assigned as follows: C (control, without MSP); D (E. coli O78:K99 + gentamycin); and P (E. coli O78:K99 + supplemental MSP). All groups were studied for 21 d. MSP supplementation significantly (i) changed fungal Chao1 and Shannon indices of the intestine compared with group D; (ii) reduced the relative abundance of Bacteroides and Actinobacteria, while increasing Bifidobacteria, Ascomycetes, and Saccharomyces, compared with groups C and D; (iii) improved duodenal and jejunal mucosal SIgA and total Short Chain Fatty Acids (SCFA) concentrations compared with group D; (iv) increased relative ZO-1 and occludin mRNA expression in jejunal mucosa compared with group D; and (v) enhanced intestinal energy metabolism and defense mechanisms of calves by reducing HSP90 expression in E. coli K99, thereby alleviating the inflammatory response and promoting recovery of mucosal function. Our research may provide direct theoretical support for future applications of MSP in ruminant production.
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Affiliation(s)
- Yanyan Wu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Cunxi Nie
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Ruiqing Luo
- Xinjiang Tianshan Junken Animal Husbandry Co., Ltd., Shihezi, China
| | - Fenghua Qi
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xue Bai
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Hongli Chen
- Xinjiang Tianshan Junken Animal Husbandry Co., Ltd., Shihezi, China
| | - Junli Niu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Chen Chen
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Wenju Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
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74
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Han X, Guo J, Qin Y, Huang W, You Y, Zhan J. Dietary regulation of the SIgA-gut microbiota interaction. Crit Rev Food Sci Nutr 2022; 63:6379-6392. [PMID: 35125055 DOI: 10.1080/10408398.2022.2031097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Gut microbiota (GM) is essential for host health, and changes in the GM are related to the development of various diseases. Recently, secretory immunoglobulin A (SIgA), the most abundant immunoglobulin isotype in the intestinal mucosa, has been found to play an essential role in controlling GM. SIgA dysfunction can lead to changes in the GM and is associated with the development of various GM-related diseases. Although in early stage, recent studies have shown that assorted dietary interventions, including vitamins, amino acids, fatty acids, polyphenols, oligo/polysaccharides, and probiotics, can influence the intestinal SIgA response and SIgA-GM interaction. Dietary intervention can enhance the SIgA response by directly regulating it (from top to bottom) or by regulating the GM structure or gene expression (from bottom to top). Furthermore, intensive studies involving the particular influence of dietary intervention on SIgA-binding to the GM and SIgA repertoire and the precise regulation of the SIgA response via dietary intervention are still exceedingly scarce and merit further consideration. This review summarizes the existing knowledge and (possible) mechanisms of the influence of dietary intervention on the SIgA-GM interaction. Key issues are considered, and the approaches in addressing these issues in future studies are also discussed.
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Affiliation(s)
- Xue Han
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing
| | - Jielong Guo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yue Qin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Weidong Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yilin You
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jicheng Zhan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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75
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Fleming A, Castro‐Dopico T, Clatworthy MR. B cell class switching in intestinal immunity in health and disease. Scand J Immunol 2022; 95:e13139. [PMID: 34978077 PMCID: PMC9285483 DOI: 10.1111/sji.13139] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022]
Abstract
The gastrointestinal tract is colonized by trillions of commensal microorganisms that collectively form the microbiome and make essential contributions to organism homeostasis. The intestinal immune system must tolerate these beneficial commensals, whilst preventing pathogenic organisms from systemic spread. Humoral immunity plays a key role in this process, with large quantities of immunoglobulin (Ig)A secreted into the lumen on a daily basis, regulating the microbiome and preventing bacteria from encroaching on the epithelium. However, there is an increasing appreciation of the role of IgG antibodies in intestinal immunity, including beneficial effects in neonatal immune development, pathogen and tumour resistance, but also of pathological effects in driving chronic inflammation in inflammatory bowel disease (IBD). These antibody isotypes differ in effector function, with IgG exhibiting more proinflammatory capabilities compared with IgA. Therefore, the process that leads to the generation of different antibody isotypes, class-switch recombination (CSR), requires careful regulation and is orchestrated by the immunological cues generated by the prevalent local challenge. In general, an initiating signal such as CD40 ligation on B cells leads to the induction of activation-induced cytidine deaminase (AID), but a second cytokine-mediated signal determines which Ig heavy chain is expressed. Whilst the cytokines driving intestinal IgA responses are well-studied, there is less clarity on how IgG responses are generated in the intestine, and how these cues might become dysfunctional in IBD. Here, we review the key mechanisms regulating class switching to IgA vs IgG in the intestine, processes that could be therapeutically manipulated in infection and IBD.
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Affiliation(s)
- Aaron Fleming
- Molecular Immunity UnitDepartment of MedicineCambridge Institute of Therapeutic Immunology and Infectious DiseasesUniversity of CambridgeCambridgeUK
| | - Tomas Castro‐Dopico
- Molecular Immunity UnitDepartment of MedicineCambridge Institute of Therapeutic Immunology and Infectious DiseasesUniversity of CambridgeCambridgeUK
- The Francis Crick InstituteLondonUK
| | - Menna R. Clatworthy
- Molecular Immunity UnitDepartment of MedicineCambridge Institute of Therapeutic Immunology and Infectious DiseasesUniversity of CambridgeCambridgeUK
- Cellular GeneticsWellcome Trust Sanger InstituteHinxtonUK
- NIHR Cambridge Biomedical Research CentreCambridgeUK
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76
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Doré E, Joly-Beauparlant C, Morozumi S, Mathieu A, Lévesque T, Allaeys I, Duchez AC, Cloutier N, Leclercq M, Bodein A, Payré C, Martin C, Petit-Paitel A, Gelb MH, Rangachari M, Murakami M, Davidovic L, Flamand N, Arita M, Lambeau G, Droit A, Boilard E. The interaction of secreted phospholipase A2-IIA with the microbiota alters its lipidome and promotes inflammation. JCI Insight 2022; 7:152638. [PMID: 35076027 PMCID: PMC8855825 DOI: 10.1172/jci.insight.152638] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
Secreted phospholipase A2-IIA (sPLA2-IIA) hydrolyzes phospholipids to liberate lysophospholipids and fatty acids. Given its poor activity toward eukaryotic cell membranes, its role in the generation of proinflammatory lipid mediators is unclear. Conversely, sPLA2-IIA efficiently hydrolyzes bacterial membranes. Here, we show that sPLA2-IIA affects the immune system by acting on the intestinal microbial flora. Using mice overexpressing transgene-driven human sPLA2-IIA, we found that the intestinal microbiota was critical for both induction of an immune phenotype and promotion of inflammatory arthritis. The expression of sPLA2-IIA led to alterations of the intestinal microbiota composition, but housing in a more stringent pathogen-free facility revealed that its expression could affect the immune system in the absence of changes to the composition of this flora. In contrast, untargeted lipidomic analysis focusing on bacteria-derived lipid mediators revealed that sPLA2-IIA could profoundly alter the fecal lipidome. The data suggest that a singular protein, sPLA2-IIA, produces systemic effects on the immune system through its activity on the microbiota and its lipidome.
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Affiliation(s)
- Etienne Doré
- CHU de Québec-Université Laval Research Center, Department of Microbiology, Infectiology and Immunology, Quebec City, Quebec, Canada
- ARThrite Research Center, University Laval, Quebec City, Quebec, Canada
| | - Charles Joly-Beauparlant
- CHU de Québec-Université Laval Research Center, Endocrinology and Nephrology Axis, Quebec City, Quebec, Canada
| | - Satoshi Morozumi
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Alban Mathieu
- CHU de Québec-Université Laval Research Center, Endocrinology and Nephrology Axis, Quebec City, Quebec, Canada
| | - Tania Lévesque
- CHU de Québec-Université Laval Research Center, Department of Microbiology, Infectiology and Immunology, Quebec City, Quebec, Canada
- ARThrite Research Center, University Laval, Quebec City, Quebec, Canada
| | - Isabelle Allaeys
- CHU de Québec-Université Laval Research Center, Department of Microbiology, Infectiology and Immunology, Quebec City, Quebec, Canada
- ARThrite Research Center, University Laval, Quebec City, Quebec, Canada
| | - Anne-Claire Duchez
- CHU de Québec-Université Laval Research Center, Department of Microbiology, Infectiology and Immunology, Quebec City, Quebec, Canada
| | - Nathalie Cloutier
- CHU de Québec-Université Laval Research Center, Department of Microbiology, Infectiology and Immunology, Quebec City, Quebec, Canada
| | - Mickaël Leclercq
- CHU de Québec-Université Laval Research Center, Endocrinology and Nephrology Axis, Quebec City, Quebec, Canada
| | - Antoine Bodein
- CHU de Québec-Université Laval Research Center, Endocrinology and Nephrology Axis, Quebec City, Quebec, Canada
| | - Christine Payré
- Côte d’Azur University, The French National Centre for Scientific Research, Institute of Molecular and Cellular Pharmacology, UMR7275, Valbonne Sophia Antipolis, France
| | - Cyril Martin
- The Research Center of the University Institute of Cardiology and Pneumology of Quebec, Quebec City, Quebec, Canada
| | - Agnes Petit-Paitel
- Côte d’Azur University, The French National Centre for Scientific Research, Institute of Molecular and Cellular Pharmacology, UMR7275, Valbonne Sophia Antipolis, France
| | - Michael H. Gelb
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Manu Rangachari
- CHU de Québec-Université Laval Research Center, Neurosciences Axis, Quebec City, Quebec, Canada
| | - Makoto Murakami
- Laboratory of Microenvironmental and Metabolic Health Science, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Laetitia Davidovic
- Côte d’Azur University, The French National Centre for Scientific Research, Institute of Molecular and Cellular Pharmacology, UMR7275, Valbonne Sophia Antipolis, France
| | - Nicolas Flamand
- ARThrite Research Center, University Laval, Quebec City, Quebec, Canada
- The Research Center of the University Institute of Cardiology and Pneumology of Quebec, Quebec City, Quebec, Canada
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama-City University, Yokohama, Japan
| | - Gérard Lambeau
- Côte d’Azur University, The French National Centre for Scientific Research, Institute of Molecular and Cellular Pharmacology, UMR7275, Valbonne Sophia Antipolis, France
| | - Arnaud Droit
- CHU de Québec-Université Laval Research Center, Endocrinology and Nephrology Axis, Quebec City, Quebec, Canada
| | - Eric Boilard
- CHU de Québec-Université Laval Research Center, Department of Microbiology, Infectiology and Immunology, Quebec City, Quebec, Canada
- ARThrite Research Center, University Laval, Quebec City, Quebec, Canada
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77
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Microbiota in relation to cancer. Cancer 2022. [DOI: 10.1016/b978-0-323-91904-3.00007-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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78
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Anisman H, Kusnecov AW. Microbiota and health. Cancer 2022. [DOI: 10.1016/b978-0-323-91904-3.00003-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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79
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Connor RI, Brickley EB, Wieland-Alter WF, Ackerman ME, Weiner JA, Modlin JF, Bandyopadhyay AS, Wright PF. Mucosal immunity to poliovirus. Mucosal Immunol 2022; 15:1-9. [PMID: 34239028 PMCID: PMC8732262 DOI: 10.1038/s41385-021-00428-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/26/2021] [Accepted: 06/14/2021] [Indexed: 02/04/2023]
Abstract
A cornerstone of the global initiative to eradicate polio is the widespread use of live and inactivated poliovirus vaccines in extensive public health campaigns designed to prevent the development of paralytic disease and interrupt transmission of the virus. Central to these efforts is the goal of inducing mucosal immunity able to limit virus replication in the intestine. Recent clinical trials have evaluated new combined regimens of poliovirus vaccines, and demonstrated clear differences in their ability to restrict virus shedding in stool after oral challenge with live virus. Analyses of mucosal immunity accompanying these trials support a critical role for enteric neutralizing IgA in limiting the magnitude and duration of virus shedding. This review summarizes key findings in vaccine-induced intestinal immunity to poliovirus in infants, older children, and adults. The impact of immunization on development and maintenance of protective immunity to poliovirus and the implications for global eradication are discussed.
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Affiliation(s)
- Ruth I Connor
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Elizabeth B Brickley
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Margaret E Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Joshua A Weiner
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | | | | | - Peter F Wright
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA.
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80
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Lynn DJ, Benson SC, Lynn MA, Pulendran B. Modulation of immune responses to vaccination by the microbiota: implications and potential mechanisms. Nat Rev Immunol 2022; 22:33-46. [PMID: 34002068 PMCID: PMC8127454 DOI: 10.1038/s41577-021-00554-7] [Citation(s) in RCA: 124] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 02/05/2023]
Abstract
The need for highly effective vaccines that induce robust and long-lasting immunity has never been more apparent. However, for reasons that are still poorly understood, immune responses to vaccination are highly variable between different individuals and different populations. Furthermore, vaccine immunogenicity is frequently suboptimal in the very populations who are at most risk from infectious disease, including infants, the elderly, and those living in low-income and middle-income countries. Although many factors have the potential to influence vaccine immunogenicity and therefore vaccine effectiveness, increasing evidence from clinical studies and animal models now suggests that the composition and function of the gut microbiota are crucial factors modulating immune responses to vaccination. In this Review, we synthesize this evidence, discuss the immunological mechanisms that potentially mediate these effects and consider the potential of microbiota-targeted interventions to optimize vaccine effectiveness.
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Affiliation(s)
- David J Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia.
| | - Saoirse C Benson
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Miriam A Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Bali Pulendran
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
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81
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Zhang L, Chu CQ. Gut Microbiota-Medication Interaction in Rheumatic Diseases. Front Immunol 2021; 12:796865. [PMID: 34925383 PMCID: PMC8678121 DOI: 10.3389/fimmu.2021.796865] [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: 10/17/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023] Open
Abstract
Besides its contribution to the development of rheumatic diseases, the gut microbiota interact with anti-rheumatic drugs. The intestinal microbiota can directly metabolize many drugs and indirectly change drug metabolism through a complex multi-dimensional interaction with the host, thus affecting individual response to drug therapy and adverse effects. The focus of the current review is to address recent advances and important progress in our understanding of how the gut microbiota interact with anti-rheumatic drugs and provide perspectives on promoting precision treatment, drug discovery, and better therapy for rheumatic diseases.
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Affiliation(s)
- Lingshu Zhang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China.,Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, OR, United States
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, OR, United States.,Section of Rheumatology, Veterans Affairs (VA) Portland Healthcare System, Portland, OR, United States
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82
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Roy K, Agarwal S, Banerjee R, Paul MK, Purbey PK. COVID-19 and gut immunomodulation. World J Gastroenterol 2021; 27:7925-7942. [PMID: 35046621 PMCID: PMC8678818 DOI: 10.3748/wjg.v27.i46.7925] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/09/2021] [Accepted: 11/29/2021] [Indexed: 02/06/2023] Open
Abstract
The disease coronavirus disease 2019 (COVID-19) is a severe respiratory illness that has emerged as a devastating health problem worldwide. The disease outcome is heterogeneous, and severity is likely dependent on the immunity of infected individuals and comorbidities. Although symptoms of the disease are primarily associated with respiratory problems, additional infection or failure of other vital organs are being reported. Emerging reports suggest a quite common co-existence of gastrointestinal (GI) tract symptoms in addition to respiratory symptoms in many COVID-19 patients, and some patients show just the GI symptoms. The possible cause of the GI symptoms could be due to direct infection of the epithelial cells of the gut, which is supported by the fact that (1) The intestinal epithelium expresses a high level of angiotensin-converting enzyme-2 and transmembrane protease serine 2 protein that are required for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry into the cells; (2) About half of the severe COVID-19 patients show viral RNA in their feces and various parts of the GI tract; and (3) SARS-CoV-2 can directly infect gut epithelial cells in vitro (gut epithelial cells and organoids) and in vivo (rhesus monkey). The GI tract seems to be a site of active innate and adaptive immune responses to SARS-CoV-2 as clinically, stool samples of COVID-19 patients possess proinflammatory cytokines (interleukin 8), calprotectin (neutrophils activity), and immunoglobulin A antibodies. In addition to direct immune activation by the virus, impairment of GI epithelium integrity can evoke immune response under the influence of systemic cytokines, hypoxia, and changes in gut microbiota (dysbiosis) due to infection of the respiratory system, which is confirmed by the observation that not all of the GI symptomatic patients are viral RNA positive. This review comprehensively summarizes the possible GI immunomodulation by SARS-CoV-2 that could lead to GI symptoms, their association with disease severity, and potential therapeutic interventions.
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Affiliation(s)
- Koushik Roy
- Microbiology and Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT 84112, United States
| | - Sidra Agarwal
- Department of Gastroenterology, Shadan Institute of Medical Sciences, Peeramcheru 500086, Telangana, India
| | - Rajib Banerjee
- Department of Electronics and Communication Engineering, Dr. B. C. Roy Engineering College, Durgapur 713206, West Bengal, India
| | - Manash K Paul
- Division of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, United States
| | - Prabhat K Purbey
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, United States
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83
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Rochereau N, Michaud E, Waeckel L, Killian M, Gayet R, Goguyer-Deschaumes R, Roblin X, Biolley G, Corthésy B, Paul S. Essential role of TOSO/FAIM3 in intestinal IgM reverse transcytosis. Cell Rep 2021; 37:110006. [PMID: 34788614 DOI: 10.1016/j.celrep.2021.110006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 05/17/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Secretory immunoglobulin A (SIgA) can travel to and from the lumen and transport antigen to subepithelial cells. However, IgM can also multimerize into functional secretory component-bound immunoglobulin. While it is already known that both SIgA and SIgM undergo transcytosis to be secreted at the mucosal surface, only SIgA has been shown to perform retrotranscytosis through microfold cells (M cells) of the Peyer's patch. Here, we investigate whether SIgM could also be taken up by M cells via retrotranscytosis. This transport involves FcμR binding at the apical membrane of M cells. We then demonstrate that SIgM can be exploited by SIgM-p24 (HIV-capsid protein) complexes during immunization in the nasal- or gut-associated lymphoid tissue (NALT or GALT), conferring efficient immune responses against p24. Our data demonstrate a mucosal function of SIgM, which could play a role in the regulation of mucosal immunity.
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Affiliation(s)
- Nicolas Rochereau
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France
| | - Eva Michaud
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France
| | - Louis Waeckel
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France
| | - Martin Killian
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France
| | - Rémi Gayet
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France
| | - Roman Goguyer-Deschaumes
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France
| | - Xavier Roblin
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France
| | - Gilles Biolley
- R&D Laboratory of the Division of Immunology and Allergy, CHUV, Centre des Laboratoires d'Epalinges, 1066 Epalinges, Switzerland
| | - Blaise Corthésy
- R&D Laboratory of the Division of Immunology and Allergy, CHUV, Centre des Laboratoires d'Epalinges, 1066 Epalinges, Switzerland
| | - Stéphane Paul
- Centre International de Recherche en Infectiologie (CIRI), Team GIMAP, Université de Lyon, Université Claude Bernard Lyon 1, INSERM, U1111, CNRS, UMR530, CIC 1408 Vaccinology, 42023 Saint-Etienne, France.
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84
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Campillo-Gimenez L, Rios-Covian D, Rivera-Nieves J, Kiyono H, Chu H, Ernst PB. Microbial-Driven Immunological Memory and Its Potential Role in Microbiome Editing for the Prevention of Colorectal Cancer. Front Cell Infect Microbiol 2021; 11:752304. [PMID: 34869061 PMCID: PMC8633303 DOI: 10.3389/fcimb.2021.752304] [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: 08/02/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Over the last several years, many advances have been made in understanding the role of bacteria in the pathogenesis of gastrointestinal cancers. Beginning with Helicobacter pylori being recognized as the first bacterial carcinogen and the causative agent of most gastric cancers, more recent studies have examined the role of enteric microbes in colorectal cancer. In the digestive tract, these communities are numerous and have a complex interrelationship with local immune/inflammatory responses that impact the health of the host. As modifying the microbiome in the stomach has decreased the risk of gastric cancer, modifying the distal microbiome may decrease the risk of colorectal cancers. To date, very few studies have considered the notion that mucosal lymphocyte-dependent immune memory may confound attempts to change the microbial components in these communities. The goal of this review is to consider some of the factors impacting host-microbial interactions that affect colorectal cancer and raise questions about how immune memory responses to the local microbial consortium affect any attempt to modify the composition of the intestinal microbiome.
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Affiliation(s)
- Laure Campillo-Gimenez
- Department of Pathology, University of California San Diego, San Diego, CA, United States
| | - David Rios-Covian
- Department of Pathology, University of California San Diego, San Diego, CA, United States
| | - Jesus Rivera-Nieves
- Department of Medicine, Division of Gastroenterology, University of California San Diego, San Diego, CA, United States
- San Diego Veterans Affairs (VA) Medical Center, San Diego, CA, United States
| | - Hiroshi Kiyono
- Department of Medicine, Division of Gastroenterology, University of California San Diego, San Diego, CA, United States
- CU-UCSD, Center for Mucosal Immunology, Allergy and Vaccine Development, University of California San Diego, San Diego, CA, United States
- Future Medicine Education and Research Organization, Chiba University, Chiba, Japan
| | - Hiutung Chu
- Department of Pathology, University of California San Diego, San Diego, CA, United States
- CU-UCSD, Center for Mucosal Immunology, Allergy and Vaccine Development, University of California San Diego, San Diego, CA, United States
| | - Peter B. Ernst
- Department of Pathology, University of California San Diego, San Diego, CA, United States
- San Diego Veterans Affairs (VA) Medical Center, San Diego, CA, United States
- CU-UCSD, Center for Mucosal Immunology, Allergy and Vaccine Development, University of California San Diego, San Diego, CA, United States
- Division of Comparative Pathology and Medicine, University of California San Diego, San Diego, CA, United States
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85
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Parallelism of intestinal secretory IgA shapes functional microbial fitness. Nature 2021; 598:657-661. [PMID: 34646015 DOI: 10.1038/s41586-021-03973-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022]
Abstract
Dimeric IgA secreted across mucous membranes in response to nonpathogenic taxa of the microbiota accounts for most antibody production in mammals. Diverse binding specificities can be detected within the polyclonal mucosal IgA antibody response1-10, but limited monoclonal hybridomas have been studied to relate antigen specificity or polyreactive binding to functional effects on microbial physiology in vivo11-17. Here we use recombinant dimeric monoclonal IgAs (mIgAs) to finely map the intestinal plasma cell response to microbial colonization with a single microorganism in mice. We identify a range of antigen-specific mIgA molecules targeting defined surface and nonsurface membrane antigens. Secretion of individual dimeric mIgAs targeting different antigens in vivo showed distinct alterations in the function and metabolism of intestinal bacteria, largely through specific binding. Even in cases in which the same microbial antigen is targeted, microbial metabolic alterations differed depending on IgA epitope specificity. By contrast, bacterial surface coating generally reduced motility and limited bile acid toxicity. The overall intestinal IgA response to a single microbe therefore contains parallel components with distinct effects on microbial carbon-source uptake, bacteriophage susceptibility, motility and membrane integrity.
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86
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Cheng J, Yuan Y, Zhao F, Chen J, Chen P, Li Y, Yan X, Luo C, Shu D, Qu H, Ji J. Thymic T-Cell Production Is Associated With Changes in the Gut Microbiota in Young Chicks. Front Immunol 2021; 12:700603. [PMID: 34566959 PMCID: PMC8461177 DOI: 10.3389/fimmu.2021.700603] [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: 04/27/2021] [Accepted: 08/20/2021] [Indexed: 02/02/2023] Open
Abstract
Increasing studies show that gut microbiota play a central role in immunity, although the impact of the microbiota on mediation of thymic T cells throughout life is not well understood. Chickens have been shown to be a valuable model for studying basic immunology. Here, we show that changes in the gut microbiota are associated with the development of thymic T cells in young chickens. Our results showed that T-cell numbers in newborn chicks sharply increased from day 0 and peaked at day 49. Interestingly, the α-diversity score pattern of change in gut microbiota also increased after day 0 and continued to increase until day 49. We found that early antibiotic treatment resulted in a dramatic reduction in gut alpha diversity: principal component analysis (PCA) showed that antibiotic treatment resulted in a different cluster from the controls on days 9 and 49. In the antibiotic-treated chickens, we identified eight significantly different (p < 0.05) microbes at the phylum level and 14 significantly different (p < 0.05) microbes at the genus level, compared with the controls. Importantly, we found that antibiotic treatment led to a decreased percentage and number of T cells in the thymus when measured at days 9 and 49, as evaluated by flow cytometry. Collectively, our data suggest that intestinal microbiota may be involved in the regulation of T cells in birds, presenting the possibility that interventions that actively modify the gut microbiota in early life may accelerate the maturation of humoral immunity, with resulting anti-inflammatory effects against different pathogens.
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Affiliation(s)
- Jiaheng Cheng
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yushan Yuan
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Fang Zhao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Peng Chen
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ying Li
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xia Yan
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dingming Shu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Qu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jian Ji
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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87
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The role of microbiota in respiratory health and diseases, particularly in tuberculosis. Biomed Pharmacother 2021; 143:112108. [PMID: 34560539 DOI: 10.1016/j.biopha.2021.112108] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022] Open
Abstract
Trillions of beneficial and hostile microorganisms live in the human respiratory and gastrointestinal tracts, which act as gatekeepers in maintaining human health, i.e., protecting the body from pathogens by colonizing mucosal surfaces with microbiota-derived antimicrobial metabolites such as short-chain fatty acids or host-derived cytokines and chemokines. It is widely accepted that the microbiome interacts with each other and with the host in a mutually beneficial relationship. Microbiota in the respiratory tract may also play a crucial role in immune homeostasis, maturation, and maintenance of respiratory physiology. Anti-TB antibiotics may cause dysbiosis in the lung and intestinal microbiota, affecting colonization resistance and making the host more susceptible to Mycobacterium tuberculosis (M. tuberculosis) infection. This review discusses recent advances in our understanding of the lung microbiota composition, the lungs and intestinal microbiota related to respiratory health and diseases, microbiome sequencing and analysis, the bloodstream, and the lymphatic system that underpin the gut-lung axis in M. tuberculosis-infected humans and animals. We also discuss the gut-lung axis interactions with the immune system, the role of the microbiome in TB pathogenesis, and the impact of anti-TB antibiotic therapy on the microbiota in animals, humans, and drug-resistant TB individuals.
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88
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Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol 2021; 40:463-481. [PMID: 34535228 DOI: 10.1016/j.tibtech.2021.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.
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89
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Beutgen VM, Schmelter C, Pfeiffer N, Grus FH. Contribution of the Commensal Microflora to the Immunological Homeostasis and the Importance of Immune-Related Drug Development for Clinical Applications. Int J Mol Sci 2021; 22:8896. [PMID: 34445599 PMCID: PMC8396286 DOI: 10.3390/ijms22168896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Not long ago, self-reactive immune activity was considered as pathological trait. A paradigm shift has now led to the recognition of autoimmune processes as part of natural maintenance of molecular homeostasis. The immune system is assigned further roles beneath the defense against pathogenic organisms. Regarding the humoral immune system, the investigation of natural autoantibodies that are frequently found in healthy individuals has led to further hypotheses involving natural autoimmunity in other processes as the clearing of cellular debris or decrease in inflammatory processes. However, their role and origin have not been entirely clarified, but accumulating evidence links their formation to immune reactions against the gut microbiome. Antibodies targeting highly conserved proteins of the commensal microflora are suggested to show self-reactive properties, following the paradigm of the molecular mimicry. Here, we discuss recent findings, which demonstrate potential links of the commensal microflora to the immunological homeostasis and highlight the possible implications for various diseases. Furthermore, specific components of the immune system, especially antibodies, have become a focus of attention for the medical management of various diseases and provide attractive treatment options in the future. Nevertheless, the development and optimization of such macromolecules still represents a very time-consuming task, shifting the need to more medical agents with simple structural properties and low manufacturing costs. Synthesizing only the biologically active sites of antibodies has become of great interest for the pharmaceutical industry and offers a wide range of therapeutic application areas as it will be discussed in the present review article.
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Affiliation(s)
| | | | | | - Franz H. Grus
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center, 55131 Mainz, Germany; (V.M.B.); (C.S.); (N.P.)
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90
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Wang S, Ma J, Ji Q, Liu Q. Evaluation of an attenuated Listeria monocytogenes as a vaccine vector to control Helicobacter pylori infection. Immunol Lett 2021; 238:68-74. [PMID: 34363896 DOI: 10.1016/j.imlet.2021.07.010] [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: 06/09/2021] [Accepted: 07/29/2021] [Indexed: 12/01/2022]
Abstract
The increasing resistance of Helicobacter pylori (H. pylori) to antibiotics has limited the efficacy of antibiotic therapy in the treatment of H. pylori-associated gastric diseases. The vaccine as an alternative method is becoming a safe and effective way to address this problem. In previous studies, live vector vaccines have proved to be effective in controlling H. pylori infection. Attenuated Listeria monocytogenes (L. monocytogenes) is a potential candidate vector applied in clinical trials, which can deliver foreign antigens and induce a broad immune response. To further explore the effectiveness of L. monocytogenes as a vaccine vector against H. pylori, attenuated L. monocytogenes-based vaccine EGDeΔactA/inlB(EGDeAB)-MECU was constructed to secrete a multi-epitope chimeric antigen (MECU) containing multiple B cell epitopes from H. pylori antigens. EGDeAB-MECU could secrete MECU stably. After immunized by gavage and intravenous injection, both EGDeAB and EGDeAB-MECU could significantly decrease gastric H. pylori colonization and induce a high level of specific antibodies against H. pylori. In conclusion, attenuated L. monocytogenes had an immunotherapeutic effect on H. pylori-infected mice, indicating its further development as a promising candidate vaccine vector for the H. pylori vaccine.
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Affiliation(s)
- Shuying Wang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Junfei Ma
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Qianyu Ji
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Qing Liu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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91
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Salinas I, Fernández-Montero Á, Ding Y, Sunyer JO. Mucosal immunoglobulins of teleost fish: A decade of advances. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 121:104079. [PMID: 33785432 PMCID: PMC8177558 DOI: 10.1016/j.dci.2021.104079] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
Immunoglobulins (Igs) are complex glycoproteins that play critical functions in innate and adaptive immunity of all jawed vertebrates. Given the unique characteristics of mucosal barriers, secretory Igs (sIgs) have specialized to maintain homeostasis and keep pathogens at bay at mucosal tissues from fish to mammals. In teleost fish, the three main IgH isotypes, IgM, IgD and IgT/Z can be found in different proportions at the mucosal secretions of the skin, gills, gut, nasal, buccal, and pharyngeal mucosae. Similar to the role of mammalian IgA, IgT plays a predominant role in fish mucosal immunity. Recent studies in IgT have illuminated the primordial role of sIgs in both microbiota homeostasis and pathogen control at mucosal sites. Ten years ago, IgT was discovered to be an immunoglobulin class specialized in mucosal immunity. Aiming at this 10-year anniversary, the goal of this review is to summarize the current status of the field of fish Igs since that discovery, while identifying knowledge gaps and future avenues that will move the field forward in both basic and applied science areas.
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Affiliation(s)
- Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Álvaro Fernández-Montero
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yang Ding
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - J Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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92
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Abstract
IgA mediates microbial homeostasis at the intestinal mucosa. Within the gut, IgA acts in a context-dependent manner to both prevent and promote bacterial colonization and to influence bacterial gene expression, thus providing exquisite control of the microbiota. IgA-microbiota interactions are highly diverse across individuals and populations, yet the factors driving this variation remain poorly understood. In this Review, we summarize evidence for the host, bacterial and environmental factors that influence IgA-microbiota interactions. Recent advances have helped to clarify the antigenic specificity and immune selection of intestinal IgA and have highlighted the importance of microbial glycan recognition. Furthermore, emerging evidence suggests that diet and nutrition play an important role in shaping IgA recognition of the microbiota. IgA-microbiota interactions are disrupted during both overnutrition and undernutrition and may be altered dynamically in response to diet, with potential implications for host health. We situate this research in the context of outstanding questions and future directions in order to better understand the fascinating paradigm of IgA-microbiota homeostasis.
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93
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Bemark M, Angeletti D. Know your enemy or find your friend?-Induction of IgA at mucosal surfaces. Immunol Rev 2021; 303:83-102. [PMID: 34331314 PMCID: PMC7612940 DOI: 10.1111/imr.13014] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022]
Abstract
Most antibodies produced in the body are of the IgA class. The dominant cell population producing them are plasma cells within the lamina propria of the gastrointestinal tract, but many IgA-producing cells are also found in the airways, within mammary tissues, the urogenital tract and inside the bone marrow. Most IgA antibodies are transported into the lumen by epithelial cells as part of the mucosal secretions, but they are also present in serum and other body fluids. A large part of the commensal microbiota in the gut is covered with IgA antibodies, and it has been demonstrated that this plays a role in maintaining a healthy balance between the host and the bacteria. However, IgA antibodies also play important roles in neutralizing pathogens in the gastrointestinal tract and the upper airways. The distinction between the two roles of IgA - protective and balance-maintaining - not only has implications on function but also on how the production is regulated. Here, we discuss these issues with a special focus on gut and airways.
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Affiliation(s)
- Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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94
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Bouferraa Y, Chedid A, Amhaz G, El Lakkiss A, Mukherji D, Temraz S, Shamseddine A. The Role of Gut Microbiota in Overcoming Resistance to Checkpoint Inhibitors in Cancer Patients: Mechanisms and Challenges. Int J Mol Sci 2021; 22:ijms22158036. [PMID: 34360802 PMCID: PMC8347208 DOI: 10.3390/ijms22158036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
The introduction of immune checkpoint inhibitors has constituted a major revolution in the treatment of patients with cancer. In contrast with the traditional cytotoxic therapies that directly kill tumor cells, this treatment modality enhances the ability of the host’s immune system to recognize and target cancerous cells. While immune checkpoint inhibitors have been effective across multiple cancer types, overcoming resistance remains a key area of ongoing research. The gut microbiota and its role in cancer immunosurveillance have recently become a major field of study. Gut microbiota has been shown to have direct and systemic effects on cancer pathogenesis and hosts anti-tumor immune response. Many studies have also shown that the host microbiota profile plays an essential role in the response to immunotherapy, especially immune checkpoint inhibitors. As such, modulating this microbial environment has offered a potential path to overcome the resistance to immune checkpoint inhibitors. In this review, we will talk about the role of microbiota in cancer pathogenesis and immune-system activity. We will also discuss preclinical and clinical studies that have increased our understanding about the roles and the mechanisms through which microbiota influences the response to treatment with immune checkpoint inhibitors.
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95
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Tuganbaev T, Honda K. Non-zero-sum microbiome immune system interactions. Eur J Immunol 2021; 51:2120-2136. [PMID: 34242413 PMCID: PMC8457126 DOI: 10.1002/eji.202049065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/01/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022]
Abstract
Fundamental asymmetries between the host and its microbiome in enzymatic activities and nutrient storage capabilities have promoted mutualistic adaptations on both sides. As a result, the enteric immune system has evolved so as not to cause a zero‐sum sterilization of non‐self, but rather achieve a non‐zero‐sum self‐reinforcing cooperation with its evolutionary partner the microbiome. In this review, we attempt to integrate the accumulated knowledge of immune—microbiome interactions into an evolutionary framework and trace the pattern of positive immune—microbiome feedback loops across epithelial, enteric nervous system, innate, and adaptive immune circuits. Indeed, the immune system requires commensal signals for its development and function, and reciprocally protects the microbiome from nutrient shortage and pathogen outgrowth. In turn, a healthy microbiome is the result of immune system curatorship as well as microbial ecology. The paradigms of host–microbiome asymmetry and the cooperative nature of their interactions identified in the gut are applicable across all tissues influenced by microbial activities. Incorporation of immune system influences into models of microbiome ecology will be a step forward toward defining what constitutes a healthy human microbiome and guide discoveries of novel host–microbiome mutualistic adaptations that may be harnessed for the promotion of human health.
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Affiliation(s)
- Timur Tuganbaev
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - 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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96
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Guo X, Chen Z, Xing Y. Immune-mediated uveitis and lifestyle factors: A review. Ophthalmic Res 2021; 64:687-695. [PMID: 34348329 DOI: 10.1159/000518496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 06/14/2021] [Indexed: 11/19/2022]
Affiliation(s)
- Xiaoyu Guo
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China,
| | - Zhen Chen
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
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97
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Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota. Nat Med 2021; 27:1442-1450. [PMID: 34282338 DOI: 10.1038/s41591-021-01409-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
Serum antibodies can recognize both pathogens and commensal gut microbiota. However, our current understanding of antibody repertoires is largely based on DNA sequencing of the corresponding B-cell receptor genes, and actual bacterial antigen targets remain incompletely characterized. Here we have profiled the serum antibody responses of 997 healthy individuals against 244,000 rationally selected peptide antigens derived from gut microbiota and pathogenic and probiotic bacteria. Leveraging phage immunoprecipitation sequencing (PhIP-Seq) based on phage-displayed synthetic oligo libraries, we detect a wide breadth of individual-specific as well as shared antibody responses against microbiota that associate with age and gender. We also demonstrate that these antibody epitope repertoires are more longitudinally stable than gut microbiome species abundances. Serum samples of more than 200 individuals collected five years apart could be accurately matched and could serve as an immunologic fingerprint. Overall, our results suggest that systemic antibody responses provide a non-redundant layer of information about microbiota beyond gut microbial species composition.
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98
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Arulraj T, Binder SC, Robert PA, Meyer-Hermann M. Germinal Centre Shutdown. Front Immunol 2021; 12:705240. [PMID: 34305944 PMCID: PMC8293096 DOI: 10.3389/fimmu.2021.705240] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022] Open
Abstract
Germinal Centres (GCs) are transient structures in secondary lymphoid organs, where affinity maturation of B cells takes place following an infection. While GCs are responsible for protective antibody responses, dysregulated GC reactions are associated with autoimmune disease and B cell lymphoma. Typically, ‘normal’ GCs persist for a limited period of time and eventually undergo shutdown. In this review, we focus on an important but unanswered question – what causes the natural termination of the GC reaction? In murine experiments, lack of antigen, absence or constitutive T cell help leads to premature termination of the GC reaction. Consequently, our present understanding is limited to the idea that GCs are terminated due to a decrease in antigen access or changes in the nature of T cell help. However, there is no direct evidence on which biological signals are primarily responsible for natural termination of GCs and a mechanistic understanding is clearly lacking. We discuss the present understanding of the GC shutdown, from factors impacting GC dynamics to changes in cellular interactions/dynamics during the GC lifetime. We also address potential missing links and remaining questions in GC biology, to facilitate further studies to promote a better understanding of GC shutdown in infection and immune dysregulation.
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Affiliation(s)
- Theinmozhi Arulraj
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian C Binder
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Philippe A Robert
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Immunology, University of Oslo, Oslo, Norway
| | - Michael Meyer-Hermann
- Department of Systems Immunology, Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
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99
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Ma J, Ji Q, Wang S, Qiu J, Liu Q. Identification and evaluation of a panel of strong constitutive promoters in Listeria monocytogenes for improving the expression of foreign antigens. Appl Microbiol Biotechnol 2021; 105:5135-5145. [PMID: 34086117 PMCID: PMC8175932 DOI: 10.1007/s00253-021-11374-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/10/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022]
Abstract
Attenuated Listeria monocytogenes could be a potential vaccine vector for the immunotherapy of tumors or pathogens. However, the lack of reliable promoters has limited its ability to express foreign antigens. In the present study, 21 promoters were identified from Listeria monocytogenes through RNA-seq analysis under two pH conditions of pH 7.4 and pH 5.5. Based on the constructed fluorescence report system, 7 constitutive promoters exhibited higher strength than Phelp (1.8-fold to 5.4-fold), a previously reported strong promoter. Furthermore, the selected 5 constitutive promoters exhibited higher UreB production activity than Phelp (1.1-fold to 8.3-fold). Notably, a well-characterized constitutive promoter P18 was found with the highest activity of fluorescence intensity and UreB production. In summary, the study provides a panel of strong constitutive promoters for Listeria monocytogenes and offers a theoretical basis for mining constitutive promoters in other organisms. KEY POINTS: • Twenty-one promoters were identified from L. monocytogenes through RNA-seq. • Fluorescent tracer of L. monocytogenes (P18) was performed in vitro and in vivo. • A well-characterized constitutive promoter P18 could improve the expression level of a foreign antigen UreB in L. monocytogenes.
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Affiliation(s)
- Junfei Ma
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Qianyu Ji
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Shuying Wang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Jingxuan Qiu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Qing Liu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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100
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Pagan JD, Vlamakis H, Gaca A, Xavier RJ, Anthony RM. Modulating T Follicular Cells In Vivo Enhances Antigen-Specific Humoral Immunity. THE JOURNAL OF IMMUNOLOGY 2021; 206:2583-2595. [PMID: 34011521 DOI: 10.4049/jimmunol.2001434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/22/2021] [Indexed: 11/19/2022]
Abstract
Generation of high-affinity IgG is essential for defense against infections and cancer, which is the intended consequence of many vaccines, but can cause autoimmune and inflammatory diseases when inappropriately directed against self. The interplay of T follicular helper (TFH) cells and T follicular regulatory (TFR) cells is critical for the production of high-affinity IgG of a specific subclass. In this study, we sought to improve Ag-specific IgG responses with two interventions intended to transiently diminish TFR cell influence. First, adult mice were administered an antibiotic mixture (ABX) for an extended period to deplete the immunoregulatory intestinal microbiota. This intriguingly increased TFH cell and reduced TFR cell numbers. 2,4,6-Trinitrophenyl hapten conjugated to keyhole limpet hemocyanin immunization resulted in higher affinity 2,4,6-trinitrophenyl hapten-specific IgG1 in ABX mice compared with controls. In a model of IgG-driven inflammatory nephritis, ABX mice had significantly worse nephritis accompanied by higher affinity Ag-specific IgG2b and enriched TFH cells compared with controls. Second, we sought to functionally manipulate TFH and TFR cells, which both express the checkpoint inhibitory molecule, PD-1, by administration of anti-PD-1 during immunization. This intervention enhanced the affinity of Ag-specific IgG of the appropriate subclass and increased in TFH cells following 2,4,6-trinitrophenyl hapten conjugated to keyhole limpet hemocyanin immunization and nephritis induction. These results suggest that altering TFH and TFR cell ratios during immunization is an appealing strategy to qualitatively improve Ag- and subclass-specific IgG responses.
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Affiliation(s)
- Jose D Pagan
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA
| | - Hera Vlamakis
- Broad Immunology, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA; and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA
| | - Anthony Gaca
- Broad Immunology, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA; and
| | - Ramnik J Xavier
- Broad Immunology, Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA; and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA;
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