1
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Li TT, Chen X, Huo D, Arifuzzaman M, Qiao S, Jin WB, Shi H, Li XV, Iliev ID, Artis D, Guo CJ. Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology. Cell Host Microbe 2024:S1931-3128(24)00121-5. [PMID: 38657606 DOI: 10.1016/j.chom.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
The intestine and liver are thought to metabolize dietary nutrients and regulate host nutrient homeostasis. Here, we find that the gut microbiota also reshapes the host amino acid (aa) landscape via efficiently metabolizing intestinal aa. To identify the responsible microbes/genes, we developed a metabolomics-based assay to screen 104 commensals and identified candidates that efficiently utilize aa. Using genetics, we identified multiple responsible metabolic genes in phylogenetically diverse microbes. By colonizing germ-free mice with the wild-type strain and their isogenic mutant deficient in individual aa-metabolizing genes, we found that these genes regulate the availability of gut and circulatory aa. Notably, microbiota genes for branched-chain amino acids (BCAAs) and tryptophan metabolism indirectly affect host glucose homeostasis via peripheral serotonin. Collectively, at single-gene level, this work characterizes a microbiota-encoded metabolic activity that affects host nutrient homeostasis and provides a roadmap to interrogate microbiota-dependent activity to improve human health.
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Affiliation(s)
- Ting-Ting Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xi Chen
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Da Huo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Mohammad Arifuzzaman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Shanshan Qiao
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Huiqing Shi
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xin V Li
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Friedman Center for Nutrition and Inflammation, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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2
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Galloway-Peña J, Iliev ID, McAllister F. Fungi in cancer. Nat Rev Cancer 2024:10.1038/s41568-024-00665-y. [PMID: 38347100 DOI: 10.1038/s41568-024-00665-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/29/2023] [Indexed: 02/18/2024]
Affiliation(s)
- Jessica Galloway-Peña
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
| | - Iliyan D Iliev
- Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Austin, TX, USA.
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Austin, TX, USA.
- Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Austin, TX, USA.
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Austin, TX, USA.
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3
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Kusakabe T, Lin WY, Cheong JG, Singh G, Ravishankar A, Yeung ST, Mesko M, DeCelie MB, Carriche G, Zhao Z, Rand S, Doron I, Putzel GG, Worgall S, Cushing M, Westblade L, Inghirami G, Parkhurst CN, Guo CJ, Schotsaert M, García-Sastre A, Josefowicz SZ, Salvatore M, Iliev ID. Fungal microbiota sustains lasting immune activation of neutrophils and their progenitors in severe COVID-19. Nat Immunol 2023; 24:1879-1889. [PMID: 37872315 PMCID: PMC10805066 DOI: 10.1038/s41590-023-01637-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Gastrointestinal fungal dysbiosis is a hallmark of several diseases marked by systemic immune activation. Whether persistent pathobiont colonization during immune alterations and impaired gut barrier function has a durable impact on host immunity is unknown. We found that elevated levels of Candida albicans immunoglobulin G (IgG) antibodies marked patients with severe COVID-19 (sCOVID-19) who had intestinal Candida overgrowth, mycobiota dysbiosis and systemic neutrophilia. Analysis of hematopoietic stem cell progenitors in sCOVID-19 revealed transcriptional changes in antifungal immunity pathways and reprogramming of granulocyte myeloid progenitors (GMPs) for up to a year. Mice colonized with C. albicans patient isolates experienced increased lung neutrophilia and pulmonary NETosis during severe acute respiratory syndrome coronavirus-2 infection, which were partially resolved with antifungal treatment or by interleukin-6 receptor blockade. sCOVID-19 patients treated with tocilizumab experienced sustained reductions in C. albicans IgG antibodies titers and GMP transcriptional changes. These findings suggest that gut fungal pathobionts may contribute to immune activation during inflammatory diseases, offering potential mycobiota-immune therapeutic strategies for sCOVID-19 with prolonged symptoms.
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Affiliation(s)
- Takato Kusakabe
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Woan-Yu Lin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
| | - Jin-Gyu Cheong
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Stephen T Yeung
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- Department of Microbiology, New York University, Langone Health, New York City, NY, USA
| | - Marissa Mesko
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Meghan Bialt DeCelie
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Guilhermina Carriche
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Sophie Rand
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Itai Doron
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Gregory G Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Stefan Worgall
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pediatrics, Weill Cornell Medicine, New York City, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Christopher N Parkhurst
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Chun-Jun Guo
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York City, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai New York, New York City, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Steven Z Josefowicz
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Mirella Salvatore
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Iliyan D Iliev
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA.
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York City, NY, USA.
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4
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Martini GR, Tikhonova E, Rosati E, DeCelie MB, Sievers LK, Tran F, Lessing M, Bergfeld A, Hinz S, Nikolaus S, Kümpers J, Matysiak A, Hofmann P, Saggau C, Schneiders S, Kamps AK, Jacobs G, Lieb W, Maul J, Siegmund B, Seegers B, Hinrichsen H, Oberg HH, Wesch D, Bereswill S, Heimesaat MM, Rupp J, Kniemeyer O, Brakhage AA, Brunke S, Hube B, Aden K, Franke A, Iliev ID, Scheffold A, Schreiber S, Bacher P. Selection of cross-reactive T cells by commensal and food-derived yeasts drives cytotoxic T H1 cell responses in Crohn's disease. Nat Med 2023; 29:2602-2614. [PMID: 37749331 PMCID: PMC10579100 DOI: 10.1038/s41591-023-02556-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023]
Abstract
Aberrant CD4+ T cell reactivity against intestinal microorganisms is considered to drive mucosal inflammation in inflammatory bowel diseases. The disease-relevant microbial species and the corresponding microorganism-specific, pathogenic T cell phenotypes remain largely unknown. In the present study, we identified common gut commensal and food-derived yeasts, as direct activators of altered CD4+ T cell reactions in patients with Crohn's disease (CD). Yeast-responsive CD4+ T cells in CD display a cytotoxic T helper cell (TH1 cell) phenotype and show selective expansion of T cell clones that are highly cross-reactive to several commensal, as well as food-derived, fungal species. This indicates cross-reactive T cell selection by repeated encounter with conserved fungal antigens in the context of chronic intestinal disease. Our results highlighted a role of yeasts as drivers of aberrant CD4+ T cell reactivity in patients with CD and suggest that both gut-resident fungal commensals and daily dietary intake of yeasts might contribute to chronic activation of inflammatory CD4+ T cell responses in patients with CD.
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Affiliation(s)
- Gabriela Rios Martini
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ekaterina Tikhonova
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Elisa Rosati
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Meghan Bialt DeCelie
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Laura Katharina Sievers
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Matthias Lessing
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Arne Bergfeld
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Sophia Hinz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Julia Kümpers
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Anna Matysiak
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Philipp Hofmann
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stephan Schneiders
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Ann-Kristin Kamps
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Gunnar Jacobs
- Institute of Epidemiology, Christian-Albrechts-University of Kiel and popgen Biobank, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel and popgen Biobank, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jochen Maul
- Gastroenterologie am Bayerischen Platz, Berlin, Germany
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | | | | | - Hans-Heinrich Oberg
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Daniela Wesch
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stefan Bereswill
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Markus M Heimesaat
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
- Friedrich Schiller Universität, Jena, Germany
| | - Sascha Brunke
- Institute of Microbiology, Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Bernhard Hube
- Friedrich Schiller Universität, Jena, Germany
- Institute of Microbiology, Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute, Jena, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
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5
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Awasthi D, Chopra S, Cho BA, Emmanuelli A, Sandoval TA, Hwang SM, Chae CS, Salvagno C, Tan C, Vasquez-Urbina L, Fernandez Rodriguez JJ, Santagostino SF, Iwawaki T, Romero-Sandoval EA, Crespo MS, Morales DK, Iliev ID, Hohl TM, Cubillos-Ruiz JR. Inflammatory ER stress responses dictate the immunopathogenic progression of systemic candidiasis. J Clin Invest 2023; 133:e167359. [PMID: 37432737 PMCID: PMC10471176 DOI: 10.1172/jci167359] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Recognition of pathogen-associated molecular patterns can trigger the inositol-requiring enzyme 1 α (IRE1α) arm of the endoplasmic reticulum (ER) stress response in innate immune cells. This process maintains ER homeostasis and also coordinates diverse immunomodulatory programs during bacterial and viral infections. However, the role of innate IRE1α signaling in response to fungal pathogens remains elusive. Here, we report that systemic infection with the human opportunistic fungal pathogen Candida albicans induced proinflammatory IRE1α hyperactivation in myeloid cells that led to fatal kidney immunopathology. Mechanistically, simultaneous activation of the TLR/IL-1R adaptor protein MyD88 and the C-type lectin receptor dectin-1 by C. albicans induced NADPH oxidase-driven generation of ROS, which caused ER stress and IRE1α-dependent overexpression of key inflammatory mediators such as IL-1β, IL-6, chemokine (C-C motif) ligand 5 (CCL5), prostaglandin E2 (PGE2), and TNF-α. Selective ablation of IRE1α in leukocytes, or treatment with an IRE1α pharmacological inhibitor, mitigated kidney inflammation and prolonged the survival of mice with systemic C. albicans infection. Therefore, controlling IRE1α hyperactivation may be useful for impeding the immunopathogenic progression of disseminated candidiasis.
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Affiliation(s)
| | - Sahil Chopra
- Department of Obstetrics and Gynecology, and
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Byuri A. Cho
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Emmanuelli
- Department of Obstetrics and Gynecology, and
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| | | | | | | | | | - Chen Tan
- Department of Obstetrics and Gynecology, and
| | | | - Jose J. Fernandez Rodriguez
- Unit of Excellence, Institute of Biology and Molecular Genetics, CSIC–Universidad de Valladolid, Valladolid, Spain
| | - Sara F. Santagostino
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, and Weill Cornell Medicine, New York, New York, USA
| | - Takao Iwawaki
- Division of Cell Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
| | - E. Alfonso Romero-Sandoval
- Department of Anesthesiology, Pain Mechanisms Laboratory, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Mariano Sanchez Crespo
- Unit of Excellence, Institute of Biology and Molecular Genetics, CSIC–Universidad de Valladolid, Valladolid, Spain
| | | | - Iliyan D. Iliev
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
- Department of Medicine and
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, New York, USA
| | - Tobias M. Hohl
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, and
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
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6
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Jans M, Kolata M, Blancke G, Ciers M, Dohlman AB, Kusakabe T, Sze M, Thiran A, Berx G, Tejpar S, van Loo G, Iliev ID, Remaut H, Vereecke L. Colibactin-induced genotoxicity and colorectal cancer exacerbation critically depends on adhesin-mediated epithelial binding. bioRxiv 2023:2023.08.16.553526. [PMID: 37645947 PMCID: PMC10462063 DOI: 10.1101/2023.08.16.553526] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Various bacteria are suggested to contribute to colorectal cancer (CRC) development, including pks+ E. coli which produce the genotoxin colibactin that induces characteristic mutational signatures in host epithelial cells. It remains unclear how the highly unstable colibactin molecule is able to access host epithelial cells and its DNA to cause harm. Using the microbiota-dependent ZEB2-transgenic mouse model of invasive CRC, we found that pks+ E. coli drives CRC exacerbation and tissue invasion in a colibactin-dependent manner. Using isogenic mutant strains, we further demonstrate that CRC exacerbation critically depends on expression of the E. coli type-1 pilus adhesin FimH and the F9-pilus adhesin FmlH. Blocking bacterial adhesion using a pharmacological FimH inhibitor attenuates colibactin-mediated genotoxicity and CRC exacerbation. Together, we show that the oncogenic potential of pks+ E. coli critically depends on bacterial adhesion to host epithelial cells and is critically mediated by specific bacterial adhesins. Adhesin-mediated epithelial binding subsequently allows production of the genotoxin colibactin in close proximity to host epithelial cells, which promotes DNA damage and drives CRC development. These findings present promising therapeutic avenues for the development of anti-adhesive therapies aiming at mitigating colibactin-induced DNA damage and inhibiting the initiation and progression of CRC, particularly in individuals at risk for developing CRC.
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7
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Lin WY, Iliev ID. Gut epithelium modulates fungal pathogenesis. Science 2023; 381:483-484. [PMID: 37535732 PMCID: PMC10790205 DOI: 10.1126/science.adj1240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Specialized epithelium secretes an antifungal peptide.
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Affiliation(s)
- Woan-Yu Lin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Iliyan D Iliev
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
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8
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Doron I, Kusakabe T, Iliev ID. Immunoglobulins at the interface of the gut mycobiota and anti-fungal immunity. Semin Immunol 2023; 67:101757. [PMID: 37003056 PMCID: PMC10192079 DOI: 10.1016/j.smim.2023.101757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The dynamic and complex community of microbes that colonizes the intestines is composed of bacteria, fungi, and viruses. At the mucosal surfaces, immunoglobulins play a key role in protection against bacterial and fungal pathogens, and their toxins. Secretory immunoglobulin A (sIgA) is the most abundantly produced antibody at the mucosal surfaces, while Immunoglobulin G (IgG) isotypes play a critical role in systemic protection. IgA and IgG antibodies with reactivity to commensal fungi play an important role in shaping the mycobiota and host antifungal immunity. In this article, we review the latest evidence that establishes a connection between commensal fungi and B cell-mediated antifungal immunity as an additional layer of protection against fungal infections and inflammation.
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Affiliation(s)
- Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Takato Kusakabe
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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9
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Iliev ID, Lin WY, Gaffen SL. When IL-17 gets on your nerves. Cell 2023; 186:466-468. [PMID: 36736299 PMCID: PMC10967262 DOI: 10.1016/j.cell.2022.12.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 02/05/2023]
Abstract
Microbiota-induced IL-17 production mediates CNS processes and animal behavior. However, its role on the peripheral nervous system (PNS) remains largely unknown. Enamorado et al. demonstrate that commensal-specific Th17 cells are recalled following tissue injury to support local nerve regeneration, a process orchestrated by IL-17 signaling on peripheral neurons.
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Affiliation(s)
- Iliyan D Iliev
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
| | - Woan-Yu Lin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sarah L Gaffen
- Division of Rheumatology & Clinical Immunology, Department of Medicine University of Pittsburgh, Pittsburgh, PA, USA.
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10
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Case NT, Berman J, Blehert DS, Cramer RA, Cuomo C, Currie CR, Ene IV, Fisher MC, Fritz-Laylin LK, Gerstein AC, Glass NL, Gow NAR, Gurr SJ, Hittinger CT, Hohl TM, Iliev ID, James TY, Jin H, Klein BS, Kronstad JW, Lorch JM, McGovern V, Mitchell AP, Segre JA, Shapiro RS, Sheppard DC, Sil A, Stajich JE, Stukenbrock EE, Taylor JW, Thompson D, Wright GD, Heitman J, Cowen LE. The future of fungi: threats and opportunities. G3 (Bethesda) 2022; 12:jkac224. [PMID: 36179219 PMCID: PMC9635647 DOI: 10.1093/g3journal/jkac224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/12/2022] [Indexed: 01/13/2023]
Abstract
The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.
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Affiliation(s)
- Nicola T Case
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Judith Berman
- Shmunis School of Biomedical and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - David S Blehert
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | - Robert A Cramer
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Christina Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Iuliana V Ene
- Department of Mycology, Institut Pasteur, Université de Paris, Paris 75015, France
| | - Matthew C Fisher
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London W2 1PG, UK
| | | | - Aleeza C Gerstein
- Department of Microbiology and Department of Statistics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
| | - Neil A R Gow
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Sarah J Gurr
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, and Immunology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Iliyan D Iliev
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Bruce S Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Internal Medicine, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jeffrey M Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI 53711, USA
| | | | - Aaron P Mitchell
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Donald C Sheppard
- McGill Interdisciplinary Initiative in Infection and Immunology, Departments of Medicine, Microbiology & Immunology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94117, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California—Riverside, Riverside, CA 92507, USA
| | - Eva E Stukenbrock
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Environmental Genomics, Christian-Albrechts University, Kiel 24118, Germany
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California—Berkeley, Berkeley, CA 94720, USA
| | | | - Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Medicine, and Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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11
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Dohlman AB, Klug J, Mesko M, Gao IH, Lipkin SM, Shen X, Iliev ID. A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors. Cell 2022; 185:3807-3822.e12. [PMID: 36179671 PMCID: PMC9564002 DOI: 10.1016/j.cell.2022.09.015] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 01/26/2023]
Abstract
Fungal microorganisms (mycobiota) comprise a small but immunoreactive component of the human microbiome, yet little is known about their role in human cancers. Pan-cancer analysis of multiple body sites revealed tumor-associated mycobiomes at up to 1 fungal cell per 104 tumor cells. In lung cancer, Blastomyces was associated with tumor tissues. In stomach cancers, high rates of Candida were linked to the expression of pro-inflammatory immune pathways, while in colon cancers Candida was predictive of metastatic disease and attenuated cellular adhesions. Across multiple GI sites, several Candida species were enriched in tumor samples and tumor-associated Candida DNA was predictive of decreased survival. The presence of Candida in human GI tumors was confirmed by external ITS sequencing of tumor samples and by culture-dependent analysis in an independent cohort. These data implicate the mycobiota in the pathogenesis of GI cancers and suggest that tumor-associated fungal DNA may serve as diagnostic or prognostic biomarkers.
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Affiliation(s)
- Anders B Dohlman
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA.
| | - Jared Klug
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Marissa Mesko
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iris H Gao
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Steven M Lipkin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA; Terasaki Institute, Los Angeles, CA 90024, USA
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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12
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Li XV, Leonardi I, Putzel GG, Semon A, Fiers WD, Kusakabe T, Lin WY, Gao IH, Doron I, Gutierrez-Guerrero A, DeCelie MB, Carriche GM, Mesko M, Yang C, Naglik JR, Hube B, Scherl EJ, Iliev ID. Author Correction: Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature 2022; 608:E21. [PMID: 35859182 DOI: 10.1038/s41586-022-05102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory G Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - William D Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Takato Kusakabe
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Woan-Yu Lin
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Iris H Gao
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alejandra Gutierrez-Guerrero
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Meghan B DeCelie
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Guilhermina M Carriche
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marissa Mesko
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Chen Yang
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Julian R Naglik
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany.,Institute of Microbiology, FriedrichSchiller University, Jena, Germany
| | - Ellen J Scherl
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.,The Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA. .,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA. .,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA. .,Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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13
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Leonardi I, Gao IH, Lin WY, Allen M, Li XV, Fiers WD, De Celie MB, Putzel GG, Yantiss RK, Johncilla M, Colak D, Iliev ID. Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity. Cell 2022; 185:831-846.e14. [PMID: 35176228 PMCID: PMC8897247 DOI: 10.1016/j.cell.2022.01.017] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 11/30/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
Fungal communities (the mycobiota) are an integral part of the gut microbiota, and the disruption of their integrity contributes to local and gut-distal pathologies. Yet, the mechanisms by which intestinal fungi promote homeostasis remain unclear. We characterized the mycobiota biogeography along the gastrointestinal tract and identified a subset of fungi associated with the intestinal mucosa of mice and humans. Mucosa-associated fungi (MAF) reinforced intestinal epithelial function and protected mice against intestinal injury and bacterial infection. Notably, intestinal colonization with a defined consortium of MAF promoted social behavior in mice. The gut-local effects on barrier function were dependent on IL-22 production by CD4+ T helper cells, whereas the effects on social behavior were mediated through IL-17R-dependent signaling in neurons. Thus, the spatial organization of the gut mycobiota is associated with host-protective immunity and epithelial barrier function and might be a driver of the neuroimmune modulation of mouse behavior through complementary Type 17 immune mechanisms.
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Affiliation(s)
- Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iris H. Gao
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Woan-Yu Lin
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Megan Allen
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York City, NY, USA
| | - Xin V. Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - William D. Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Meghan Bialt De Celie
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Gregory G. Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Rhonda K. Yantiss
- MJ Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Melanie Johncilla
- MJ Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Dilek Colak
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York City, NY, USA.,Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medical College, Cornell University, New York City, NY, USA
| | - Iliyan D. Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
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14
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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15
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Burnham P, Chen F, Cheng AP, Srivatana V, Zhang LT, Edusei E, Albakry S, Botticelli B, Guo X, Renaghan A, Silberzweig J, Dadhania DM, Lenz JS, Heyang M, Iliev ID, Hayden JA, Westblade LF, De Vlaminck I, Lee JR. Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis. Kidney Med 2022; 4:100383. [PMID: 35072047 PMCID: PMC8767090 DOI: 10.1016/j.xkme.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rationale & Objective Conventional culture can be insensitive for the detection of rare infections and for the detection of common infections in the setting of recent antibiotic usage. Patients receiving peritoneal dialysis (PD) with suspected peritonitis have a significant proportion of negative conventional cultures. This study examines the utility of metagenomic sequencing of peritoneal effluent cell-free DNA (cfDNA) for evaluating the peritoneal effluent in PD patients with and without peritonitis. Study Design Prospective cohort study. Setting & Participants We prospectively characterized cfDNA in 68 peritoneal effluent samples obtained from 33 patients receiving PD at a single center from September 2016 to July 2018. Outcomes Peritoneal effluent, microbial, and human cfDNA characteristics were evaluated in culture-confirmed peritonitis and culture-negative peritonitis. Analytical Approach Descriptive statistics were analyzed and microbial cfDNA was detected in culture-confirmed peritonitis and culture-negative peritonitis. Results Metagenomic sequencing of cfDNA was able to detect and identify bacterial, viral, and eukaryotic pathogens in the peritoneal effluent from PD patients with culture-confirmed peritonitis, as well as patients with recent antibiotic usage and in cases of culture-negative peritonitis. Limitations Parallel cultures were not obtained in all the peritoneal effluent specimens. Conclusions Metagenomic cfDNA sequencing of the peritoneal effluent can identify pathogens in PD patients with peritonitis, including culture-negative peritonitis.
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16
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Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett KS, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik MF, Henaff E, Huch M, Iliev ID, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez MA, Miura K, Molloy J, Cruz AO, Platt RJ, Posey AD, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe LH, Varshney RK, Wang J. Voices of biotech research. Nat Biotechnol 2021; 39:281-286. [PMID: 33692517 DOI: 10.1038/s41587-021-00847-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nasim Annabi
- Chemical and Biomolecular Engineering, UCLA Samueli School of Engineering, Los Angeles, CA, USA
| | - Matthew Baker
- School of Biotechnology and Biomolecular Sciences at the University of New South Wales, Sydney, New South Wales, Australia
| | - Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | | | - Yvonne Chen
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Kizzmekia S Corbett
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Bruno Correia
- The Laboratory of Protein Design and Immunoengineering, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - James Dahlman
- Georgia Institute of Technology, Atlanta, GA, USA
- Emory University School of Medicine, Atlanta, GA, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ali Ertuerk
- Institute of Tissue Engineering and Regenerative Medicine, Munich Center for Neuroscience, Neuherberg, Germany
| | - Mehmet Fatih Yanik
- Department of Information Technology and Electrical Engineering, ETH, Zürich, Switzerland
| | - Elizabeth Henaff
- Integrated Design and Media, Center for Urban Science and Progress, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Iliyan D Iliev
- Weill Medical College of Cornell University, New York, NY, USA
| | - Thomas Jacobs
- VIB University of Ghent Center for Plant Systems Biology, Ghent, Belgium
| | - Howard Junca
- Microbiomas Foundation, Chia, Colombia
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Albert Keung
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Smita Krishnaswamy
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
- Department of Computer Science, School of Engineering & Applied Science, Yale University, New Haven, CT, USA
| | - Madeline Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Evan Macosko
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Kyoko Miura
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | | | - Randall J Platt
- Laboratory of Biological Engineering, ETH Zurich, Basel, Switzerland
- The Department of Chemistry, University of Basel, Basel, Switzerland
| | - Avery D Posey
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Huilin Shao
- Department of Biomedical Engineering, Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
- Department of Surgery, Institute for Health Innovation & Technology, National University of Singapore, Singapore, Singapore
| | - Mijo Simunovic
- Department of Chemical Engineering, Columbia Stem Cell Initiative, Columbia University, New York, NY, USA
- Department of Genetics and Development, Columbia Stem Cell Initiative, Columbia University, New York, NY, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Barnett Institute, Northeastern University, Boston, MA, USA
- Single Cell Proteomics Center, Northeastern University, Boston, MA, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Luk H Vandenberghe
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Grousbeck Gene Therapy Center, Mass Eye and Ear, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- State Agricultural Biotechnology Centre, and Centre for Crop Research Innovation, Murdoch University, Murdoch, Australia
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, China
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17
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Iliev ID, Cadwell K. Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases. Gastroenterology 2021; 160:1050-1066. [PMID: 33347881 PMCID: PMC7956156 DOI: 10.1053/j.gastro.2020.06.100] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, New York; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, New York.
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine, Skirball Institute, New York University Grossman School of Medicine, New York, New York; Department of Microbiology, New York University Grossman School of Medicine, New York, New York; Division of Gastroenterology and Hepatology, Department of Medicine, New York University Langone Health, New York, New York.
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18
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Doron I, Leonardi I, Li XV, Fiers WD, Semon A, Bialt-DeCelie M, Migaud M, Gao IH, Lin WY, Kusakabe T, Puel A, Iliev ID. Human gut mycobiota tune immunity via CARD9-dependent induction of anti-fungal IgG antibodies. Cell 2021; 184:1017-1031.e14. [PMID: 33548172 PMCID: PMC7936855 DOI: 10.1016/j.cell.2021.01.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/04/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022]
Abstract
Antibodies mediate natural and vaccine-induced immunity against viral and bacterial pathogens, whereas fungi represent a widespread kingdom of pathogenic species for which neither vaccine nor neutralizing antibody therapies are clinically available. Here, using a multi-kingdom antibody profiling (multiKAP) approach, we explore the human antibody repertoires against gut commensal fungi (mycobiota). We identify species preferentially targeted by systemic antibodies in humans, with Candida albicans being the major inducer of antifungal immunoglobulin G (IgG). Fungal colonization of the gut induces germinal center (GC)-dependent B cell expansion in extraintestinal lymphoid tissues and generates systemic antibodies that confer protection against disseminated C. albicans or C. auris infection. Antifungal IgG production depends on the innate immunity regulator CARD9 and CARD9+CX3CR1+ macrophages. In individuals with invasive candidiasis, loss-of-function mutations in CARD9 are associated with impaired antifungal IgG responses. These results reveal an important role of gut commensal fungi in shaping the human antibody repertoire through CARD9-dependent induction of host-protective antifungal IgG.
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Affiliation(s)
- Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - William D Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Meghan Bialt-DeCelie
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Iris H Gao
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Woan-Yu Lin
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Takato Kusakabe
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 USA; University of Paris, Imagine Institute, 75015 Paris, France
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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19
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Dohlman AB, Arguijo Mendoza D, Ding S, Gao M, Dressman H, Iliev ID, Lipkin SM, Shen X. The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host Microbe 2021; 29:281-298.e5. [PMID: 33382980 PMCID: PMC7878430 DOI: 10.1016/j.chom.2020.12.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/29/2020] [Accepted: 12/01/2020] [Indexed: 12/30/2022]
Abstract
Studying the microbial composition of internal organs and their associations with disease remains challenging due to the difficulty of acquiring clinical biopsies. We designed a statistical model to analyze the prevalence of species across sample types from The Cancer Genome Atlas (TCGA), revealing that species equiprevalent across sample types are predominantly contaminants, bearing unique signatures from each TCGA-designated sequencing center. Removing such species mitigated batch effects and isolated the tissue-resident microbiome, which was validated by original matched TCGA samples. Gene copies and nucleotide variants can further distinguish mixed-evidence species. We, thus, present The Cancer Microbiome Atlas (TCMA), a collection of curated, decontaminated microbial compositions of oropharyngeal, esophageal, gastrointestinal, and colorectal tissues. This led to the discovery of prognostic species and blood signatures of mucosal barrier injuries and enabled systematic matched microbe-host multi-omic analyses, which will help guide future studies of the microbiome's role in human health and disease.
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Affiliation(s)
- Anders B Dohlman
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA.
| | - Diana Arguijo Mendoza
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA
| | - Michael Gao
- Duke Institute for Health Innovation, Duke University, Durham, NC 27701, USA
| | - Holly Dressman
- Department of Molecular Genetics and Microbiology, Director of Duke Microbiome Center, Duke University, Durham, NC 27708, USA
| | - Iliyan D Iliev
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York City, NY 10065, USA
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York City, NY 10065, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Center for Genomics and Computational Biology, Duke Microbiome Center, Duke University, Durham, NC 27708, USA.
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20
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Clemente JC, Iliev ID. Editorial overview: Microbiota united-bacteria, fungi and host responses come into focus. Curr Opin Microbiol 2020; 56:vi-viii. [PMID: 33323167 DOI: 10.1016/j.mib.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Jose C Clemente
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Precision Immunology Institute, Icahn School of Medicine at New York, New York, NY 10029, USA.
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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21
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Abstract
The human gastrointestinal tract is home to a vibrant, diverse ecosystem of prokaryotic and eukaryotic microorganisms. The gut fungi (mycobiota) have recently risen to prominence due to their ability to modulate host immunity. Colonization of the gut occurs through a combination of vertical transmission from the maternal mycobiota and environmental and dietary exposure. Data from human and animal studies demonstrate that nutrition strongly affects the mycobiota composition and that changes in the fungal communities can aggravate metabolic diseases. The mechanisms pertaining to the mycobiota's influence on host health, pathology, and resident gastrointestinal communities through intrakingdom, transkingdom, and immune cross talk are beginning to come into focus, setting the stage for a new chapter in microbiota-host interactions. Herein, we examine the inception, maturation, and dietary modulation of gastrointestinal and nutritional fungal communities and inspect their impact on metabolic diseases in humans.
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Affiliation(s)
- William D Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA;
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA;
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA;
- Department of Microbiology and Immunology and Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
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22
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Chikina AS, Nadalin F, Maurin M, San-Roman M, Thomas-Bonafos T, Li XV, Lameiras S, Baulande S, Henri S, Malissen B, Lacerda Mariano L, Barbazan J, Blander JM, Iliev ID, Matic Vignjevic D, Lennon-Duménil AM. Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption. Cell 2020; 183:411-428.e16. [PMID: 32970988 PMCID: PMC7646275 DOI: 10.1016/j.cell.2020.08.048] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/27/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
The colon is primarily responsible for absorbing fluids. It contains a large number of microorganisms including fungi, which are enriched in its distal segment. The colonic mucosa must therefore tightly regulate fluid influx to control absorption of fungal metabolites, which can be toxic to epithelial cells and lead to barrier dysfunction. How this is achieved remains unknown. Here, we describe a mechanism by which the innate immune system allows rapid quality check of absorbed fluids to avoid intoxication of colonocytes. This mechanism relies on a population of distal colon macrophages that are equipped with "balloon-like" protrusions (BLPs) inserted in the epithelium, which sample absorbed fluids. In the absence of macrophages or BLPs, epithelial cells keep absorbing fluids containing fungal products, leading to their death and subsequent loss of epithelial barrier integrity. These results reveal an unexpected and essential role of macrophages in the maintenance of colon-microbiota interactions in homeostasis. VIDEO ABSTRACT.
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Affiliation(s)
- Aleksandra S Chikina
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France; Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Francesca Nadalin
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Mathieu Maurin
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | - Mabel San-Roman
- Institut Curie, PSL Research University, INSERM U932, F-75005 Paris, France
| | | | - Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sonia Lameiras
- Institut Curie, PSL Research University, Next Generation Sequencing Facility, F-75005 Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL Research University, Next Generation Sequencing Facility, F-75005 Paris, France
| | - Sandrine Henri
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France; Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | | | - Jorge Barbazan
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France
| | - J Magarian Blander
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
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23
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Leonardi I, Paramsothy S, Doron I, Semon A, Kaakoush NO, Clemente JC, Faith JJ, Borody TJ, Mitchell HM, Colombel JF, Kamm MA, Iliev ID. Fungal Trans-kingdom Dynamics Linked to Responsiveness to Fecal Microbiota Transplantation (FMT) Therapy in Ulcerative Colitis. Cell Host Microbe 2020; 27:823-829.e3. [PMID: 32298656 DOI: 10.1016/j.chom.2020.03.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/10/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Fecal microbiota transplantation (FMT) targeting gut microbiota has recently been successfully applied to ulcerative colitis. However, only a subset of patients responds to FMT, and there is a pressing need for biomarkers of responsiveness. Fungi (the mycobiota) represent a highly immunologically reactive component of the gut microbiota. We analyzed samples from a large randomized controlled trial of FMT for ulcerative colitis (UC). High Candida abundance pre-FMT was associated with a clinical response, whereas decreased Candida abundance post-FMT was indicative of ameliorated disease severity. High pre-FMT Candida was associated with increased bacterial diversity post-FMT, and the presence of genera was linked to FMT responsiveness. Although we detected elevated anti-Candida antibodies in placebo recipients, this increase was abrogated in FMT recipients. Our data suggest that FMT might reduce Candida to contain pro-inflammatory immunity during intestinal disease and highlight the utility of mycobiota-focused approaches to identify FMT responders prior to therapy initiation.
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Affiliation(s)
- Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Sudarshan Paramsothy
- University of New South Wales, Sydney NSW 2052, Australia; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | | | - Jose C Clemente
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeremiah J Faith
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | - Michael A Kamm
- St. Vincent's Hospital and University of Melbourne, Melbourne, VIC 3065, Australia
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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24
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Fiers WD, Gao IH, Iliev ID. Gut mycobiota under scrutiny: fungal symbionts or environmental transients? Curr Opin Microbiol 2019; 50:79-86. [PMID: 31726316 DOI: 10.1016/j.mib.2019.09.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023]
Abstract
The human gastrointestinal tract is home to a thriving community of microbes including the fungal 'mycobiota'. Although sequencing methodology has enumerated diverse fungal genera within this niche, discerning persistent symbiotic residents from contaminants and purely environmental transients remains a challenge. Recent advances in culturomics and sequencing employing metagenomics, metatranscriptomics and longitudinal studies have begun to reveal a human symbiont 'core mycobiome' that may contribute to human health and disease. Trans-kingdom interactions between the bacterial microbiota and evolution within the niche have defined C. albicans as a true symbiont, setting a bar for defining other fungi. Additionally, elegant investigations of mammalian antifungal immunity have examined mononuclear phagocytes, neutrophils, antigen-specific recognition by T cells and other mechanisms important for local and systemic effects on the host, providing further evidence supporting gut persistence. In this review we discuss current research aimed at investigating the symbiotic mycobiota and propose four criteria aiding in the differentiation of fungal symbionts from environmental transients.
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Affiliation(s)
- William D Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Iris H Gao
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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25
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Li XV, Leonardi I, Iliev ID. Gut Mycobiota in Immunity and Inflammatory Disease. Immunity 2019; 50:1365-1379. [PMID: 31216461 DOI: 10.1016/j.immuni.2019.05.023] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/01/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023]
Abstract
The mammalian intestine is colonized by a wealth of microorganisms-including bacteria, viruses, protozoa, and fungi-that are all integrated into a functional trans-kingdom community. Characterization of the composition of the fungal community-the mycobiota-has advanced further than the much-needed mechanistic studies. Recent findings have revealed roles for the gut mycobiota in the regulation of host immunity and in the development and progression of human diseases of inflammatory origin. We review these findings here while placing them in the context of the current understanding of the pathways and cellular networks that induce local and systemic immune responses to fungi in the gastrointestinal tract. We discuss gaps in knowledge and argue for the importance of considering bacteria-fungal interactions as we aim to define the roles of mycobiota in immune homeostasis and immune-associated pathologies.
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Affiliation(s)
- Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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26
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Uzzan M, Tokuyama M, Rosenstein AK, Tomescu C, SahBandar IN, Ko HM, Leyre L, Chokola A, Kaplan-Lewis E, Rodriguez G, Seki A, Corley MJ, Aberg J, La Porte A, Park EY, Ueno H, Oikonomou I, Doron I, Iliev ID, Chen BK, Lui J, Schacker TW, Furtado GC, Lira SA, Colombel JF, Horowitz A, Lim JK, Chomont N, Rahman AH, Montaner LJ, Ndhlovu LC, Mehandru S. Anti-α4β7 therapy targets lymphoid aggregates in the gastrointestinal tract of HIV-1-infected individuals. Sci Transl Med 2019; 10:10/461/eaau4711. [PMID: 30282696 DOI: 10.1126/scitranslmed.aau4711] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/11/2018] [Indexed: 12/12/2022]
Abstract
Gut homing CD4+ T cells expressing the integrin α4β7 are early viral targets and contribute to HIV-1 pathogenesis, likely by seeding the gastrointestinal (GI) tract with HIV. Although simianized anti-α4β7 monoclonal antibodies have shown promise in preventing or attenuating the disease course of simian immunodeficiency virus in nonhuman primate studies, the mechanisms of drug action remain elusive. We present a cohort of individuals with mild inflammatory bowel disease and concomitant HIV-1 infection receiving anti-α4β7 treatment. By sampling the immune inductive and effector sites of the GI tract, we have discovered that anti-α4β7 therapy led to a significant and unexpected attenuation of lymphoid aggregates, most notably in the terminal ileum. Given that lymphoid aggregates serve as important sanctuary sites for maintaining viral reservoirs, their attrition by anti-α4β7 therapy has important implications for HIV-1 therapeutics and eradication efforts and defines a rational basis for the use of anti-α4β7 therapy in HIV-1 infection.
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Affiliation(s)
- Mathieu Uzzan
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minami Tokuyama
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam K Rosenstein
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Ivo N SahBandar
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Huaibin M Ko
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Louise Leyre
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Québec H2X 0A9, Canada
| | - Anupa Chokola
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emma Kaplan-Lewis
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriela Rodriguez
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Akihiro Seki
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael J Corley
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Judith Aberg
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Annalena La Porte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eun-Young Park
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Hideki Ueno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ioannis Oikonomou
- Division of Gastroenterology, Rush University, Chicago, IL 60612, USA
| | - Itai Doron
- Gastroenterology and Hepatology Divison, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Divison, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Benjamin K Chen
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jennifer Lui
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Timothy W Schacker
- Department of Medicine, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Glaucia C Furtado
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio A Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amir Horowitz
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jean K Lim
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas Chomont
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Québec H2X 0A9, Canada
| | - Adeeb H Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Saurabh Mehandru
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. .,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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27
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Moeller JB, Leonardi I, Schlosser A, Flamar AL, Bessman NJ, Putzel GG, Thomsen T, Hammond M, Jepsen CS, Skjødt K, Füchtbauer EM, Farber DL, Sorensen GL, Iliev ID, Holmskov U, Artis D. Modulation of the fungal mycobiome is regulated by the chitin-binding receptor FIBCD1. J Exp Med 2019; 216:2689-2700. [PMID: 31601676 PMCID: PMC6888979 DOI: 10.1084/jem.20182244] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/29/2019] [Accepted: 09/10/2019] [Indexed: 12/26/2022] Open
Abstract
In the present study, Moeller et al. identify a previously unrecognized pathway through which intestinal epithelial cells expressing the novel chitin-binding receptor FIBCD1 can recognize and control intestinal fungal colonization, limit fungal dysbiosis, and dampen intestinal inflammation. Host–microbiota interactions are critical in regulating mammalian health and disease. In addition to bacteria, parasites, and viruses, beneficial communities of fungi (the mycobiome) are important modulators of immune- and tissue-homeostasis. Chitin is a major component of the fungal cell wall, and fibrinogen C containing domain 1 (FIBCD1) is a chitin-binding protein; however, the role of this molecule in influencing host–mycobiome interactions in vivo has never been examined. Here, we identify direct binding of FIBCD1 to intestinal-derived fungi and demonstrate that epithelial-specific expression of FIBCD1 results in significantly reduced fungal colonization and amelioration of fungal-driven intestinal inflammation. Collectively, these results identify FIBCD1 as a previously unrecognized microbial pattern recognition receptor through which intestinal epithelial cells can recognize and control fungal colonization, limit fungal dysbiosis, and dampen intestinal inflammation.
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Affiliation(s)
- Jesper B Moeller
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY .,Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Irina Leonardi
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY
| | - Anders Schlosser
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Anne-Laure Flamar
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY
| | - Nicholas J Bessman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY
| | - Gregory Garbès Putzel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY
| | - Theresa Thomsen
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mark Hammond
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Christine S Jepsen
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Karsten Skjødt
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Donna L Farber
- Columbia Center for Translational Immunology, Department of Surgery and Department of Microbiology and Immunology, Columbia University, New York, NY
| | - Grith L Sorensen
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Iliyan D Iliev
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY
| | - Uffe Holmskov
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY
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28
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Rosshart SP, Herz J, Vassallo BG, Hunter A, Wall MK, Badger JH, McCulloch JA, Anastasakis DG, Sarshad AA, Leonardi I, Collins N, Blatter JA, Han SJ, Tamoutounour S, Potapova S, Foster St Claire MB, Yuan W, Sen SK, Dreier MS, Hild B, Hafner M, Wang D, Iliev ID, Belkaid Y, Trinchieri G, Rehermann B. Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science 2019; 365:365/6452/eaaw4361. [PMID: 31371577 DOI: 10.1126/science.aaw4361] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/06/2019] [Accepted: 06/27/2019] [Indexed: 12/11/2022]
Abstract
Laboratory mouse studies are paramount for understanding basic biological phenomena but also have limitations. These include conflicting results caused by divergent microbiota and limited translational research value. To address both shortcomings, we transferred C57BL/6 embryos into wild mice, creating "wildlings." These mice have a natural microbiota and pathogens at all body sites and the tractable genetics of C57BL/6 mice. The bacterial microbiome, mycobiome, and virome of wildlings affect the immune landscape of multiple organs. Their gut microbiota outcompete laboratory microbiota and demonstrate resilience to environmental challenges. Wildlings, but not conventional laboratory mice, phenocopied human immune responses in two preclinical studies. A combined natural microbiota- and pathogen-based model may enhance the reproducibility of biomedical studies and increase the bench-to-bedside safety and success of immunological studies.
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Affiliation(s)
- Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
| | - Jasmin Herz
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Brian G Vassallo
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Ashli Hunter
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Morgan K Wall
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - John A McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Dimitrios G Anastasakis
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Aishe A Sarshad
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - Irina Leonardi
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Nicholas Collins
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joshua A Blatter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seong-Ji Han
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samira Tamoutounour
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Svetlana Potapova
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Mark B Foster St Claire
- Laboratory of Animal Sciences Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Wuxing Yuan
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shurjo K Sen
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.,Leidos Biomedical Research, Inc., Microbiome and Genetics Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew S Dreier
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Benedikt Hild
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD 20892, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Iliyan D Iliev
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
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29
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Ladinsky MS, Araujo LP, Zhang X, Veltri J, Galan-Diez M, Soualhi S, Lee C, Irie K, Pinker EY, Narushima S, Bandyopadhyay S, Nagayama M, Elhenawy W, Coombes BK, Ferraris RP, Honda K, Iliev ID, Gao N, Bjorkman PJ, Ivanov II. Endocytosis of commensal antigens by intestinal epithelial cells regulates mucosal T cell homeostasis. Science 2019; 363:eaat4042. [PMID: 30846568 PMCID: PMC6708280 DOI: 10.1126/science.aat4042] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 10/11/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022]
Abstract
Commensal bacteria influence host physiology, without invading host tissues. We show that proteins from segmented filamentous bacteria (SFB) are transferred into intestinal epithelial cells (IECs) through adhesion-directed endocytosis that is distinct from the clathrin-dependent endocytosis of invasive pathogens. This process transfers microbial cell wall-associated proteins, including an antigen that stimulates mucosal T helper 17 (TH17) cell differentiation, into the cytosol of IECs in a cell division control protein 42 homolog (CDC42)-dependent manner. Removal of CDC42 activity in vivo led to disruption of endocytosis induced by SFB and decreased epithelial antigen acquisition, with consequent loss of mucosal TH17 cells. Our findings demonstrate direct communication between a resident gut microbe and the host and show that under physiological conditions, IECs acquire antigens from commensal bacteria for generation of T cell responses to the resident microbiota.
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Affiliation(s)
- Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leandro P Araujo
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xiao Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - John Veltri
- Department of Pharmacology, Physiology and Neurosciences, Rutgers University, Newark, NJ 07103, USA
| | - Marta Galan-Diez
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Salima Soualhi
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Carolyn Lee
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Koichiro Irie
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Preventive Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Elisha Y Pinker
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Seiko Narushima
- RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | | | - Manabu Nagayama
- RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
- Department of Medicine, Division of Gastroenterology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Wael Elhenawy
- Department of Biochemistry & Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Brian K Coombes
- Department of Biochemistry & Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Ronaldo P Ferraris
- Department of Pharmacology, Physiology and Neurosciences, Rutgers University, Newark, NJ 07103, USA
| | - Kenya Honda
- RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Iliyan D Iliev
- Department of Microbiology and Immunology and The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ivaylo I Ivanov
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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30
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Limon JJ, Tang J, Li D, Wolf AJ, Michelsen KS, Funari V, Gargus M, Nguyen C, Sharma P, Maymi VI, Iliev ID, Skalski JH, Brown J, Landers C, Borneman J, Braun J, Targan SR, McGovern DPB, Underhill DM. Malassezia Is Associated with Crohn's Disease and Exacerbates Colitis in Mouse Models. Cell Host Microbe 2019; 25:377-388.e6. [PMID: 30850233 DOI: 10.1016/j.chom.2019.01.007] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/19/2018] [Accepted: 01/15/2019] [Indexed: 01/09/2023]
Abstract
Inflammatory bowel disease (IBD) is characterized by alterations in the intestinal microbiota and altered immune responses to gut microbiota. Evidence is accumulating that IBD is influenced by not only commensal bacteria but also commensal fungi. We characterized fungi directly associated with the intestinal mucosa in healthy people and Crohn's disease patients and identified fungi specifically abundant in patients. One of these, the common skin resident fungus Malassezia restricta, is also linked to the presence of an IBD-associated polymorphism in the gene for CARD9, a signaling adaptor important for anti-fungal defense. M. restricta elicits innate inflammatory responses largely through CARD9 and is recognized by Crohn's disease patient anti-fungal antibodies. This yeast elicits strong inflammatory cytokine production from innate cells harboring the IBD-linked polymorphism in CARD9 and exacerbates colitis via CARD9 in mouse models of disease. Collectively, these results suggest that targeting specific commensal fungi may be a therapeutic strategy for IBD.
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Affiliation(s)
- Jose J Limon
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Andrea J Wolf
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kathrin S Michelsen
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Vince Funari
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew Gargus
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christopher Nguyen
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Purnima Sharma
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Viviana I Maymi
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Iliyan D Iliev
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Joseph H Skalski
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jordan Brown
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Carol Landers
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - James Borneman
- Department of Plant Pathology and Microbiology, University of California, Riverside, Riverside, CA 92521, USA
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephan R Targan
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M Underhill
- F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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31
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Abstract
Candidalysin-induced epithelial cell damage promotes expansion of innate TCRαβ+ cells during oropharyngeal candidiasis.
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Affiliation(s)
- Xin Li
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Irina Leonardi
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iliyan D Iliev
- Division of Gastroenterology and Hepatology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA. .,Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
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Leonardi I, Li X, Semon A, Li D, Doron I, Putzel G, Bar A, Prieto D, Rescigno M, McGovern DPB, Pla J, Iliev ID. CX3CR1 + mononuclear phagocytes control immunity to intestinal fungi. Science 2018; 359:232-236. [PMID: 29326275 DOI: 10.1126/science.aao1503] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 11/15/2017] [Accepted: 12/09/2017] [Indexed: 12/23/2022]
Abstract
Intestinal fungi are an important component of the microbiota, and recent studies have unveiled their potential in modulating host immune homeostasis and inflammatory disease. Nonetheless, the mechanisms governing immunity to gut fungal communities (mycobiota) remain unknown. We identified CX3CR1+ mononuclear phagocytes (MNPs) as being essential for the initiation of innate and adaptive immune responses to intestinal fungi. CX3CR1+ MNPs express antifungal receptors and activate antifungal responses in a Syk-dependent manner. Genetic ablation of CX3CR1+ MNPs in mice led to changes in gut fungal communities and to severe colitis that was rescued by antifungal treatment. In Crohn's disease patients, a missense mutation in the gene encoding CX3CR1 was identified and found to be associated with impaired antifungal responses. These results unravel a role of CX3CR1+ MNPs in mediating interactions between intestinal mycobiota and host immunity at steady state and during inflammatory disease.
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Affiliation(s)
- Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xin Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dalin Li
- The F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gregory Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Agnieszka Bar
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Daniel Prieto
- Faculty of Pharmacy, Department of Microbiology II, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Maria Rescigno
- Department of Experimental Oncology, European Institute of Oncology, I-20141 Milan, Italy
| | - Dermot P B McGovern
- The F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jesus Pla
- Faculty of Pharmacy, Department of Microbiology II, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
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Abstract
Fungi and mammals share a co-evolutionary history and are involved in a complex web of interactions. Studies focused on commensal bacteria suggest that pathological changes in the microbiota, historically known as dysbiosis, are at the root of many inflammatory diseases of non-infectious origin. However, the importance of dysbiosis in the fungal community - the mycobiota - was only recently acknowledged to have a pathological role, as novel findings have suggested that mycobiota disruption can have detrimental effects on host immunity. Fungal dysbiosis and homeostasis are dynamic processes that are probably more common than actual fungal infections, and therefore constantly shape the immune response. In this Review, we summarize specific mycobiota patterns that are associated with fungal dysbiosis, and discuss how mucosal immunity has evolved to distinguish fungal infections from dysbiosis and how it responds to these different conditions. We propose that gut microbiota dysbiosis is a collective feature of complex interactions between prokaryotic and eukaryotic microbial communities that can affect immunity and that can influence health and disease.
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Affiliation(s)
- Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
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Abstract
Pathogenic fungi cause a wide range of syndromes in immune-competent and immune-compromised individuals, with life-threatening disease primarily seen in humans with HIV/AIDS and in patients receiving immunosuppressive therapies for cancer, autoimmunity, and end-organ failure. The discovery that specific primary immune deficiencies manifest with fungal infections and the development of animal models of mucosal and invasive mycoses have facilitated insight into fungus-specific recognition, signaling, effector pathways, and adaptive immune responses. Progress in deciphering the molecular and cellular basis of immunity against fungi is guiding preclinical studies into vaccine and immune reconstitution strategies for vulnerable patient groups. Furthermore, recent work has begun to address the role of endogenous fungal communities in human health and disease. In this review, we summarize a contemporary understanding of protective immunity against fungi.
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Affiliation(s)
- Michail S Lionakis
- Fungal Pathogenesis Unit, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Iliyan D Iliev
- Jill Roberts Institute for Research in IBD, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Müller S, Wolf AJ, Iliev ID, Berg BL, Underhill DM, Liu GY. Poorly Cross-Linked Peptidoglycan in MRSA Due to mecA Induction Activates the Inflammasome and Exacerbates Immunopathology. Cell Host Microbe 2016; 18:604-12. [PMID: 26567511 DOI: 10.1016/j.chom.2015.10.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/23/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
Methicillin-resistant S. aureus (MRSA) is a leading health problem. Compared to methicillin-sensitive S. aureus, MRSA infections are associated with greater morbidity and mortality, but the mechanisms underlying MRSA pathogenicity are unclear. Here we show that the protein conferring β-lactam antibiotic resistance, penicillin-binding protein 2A (encoded by the mecA gene), directly contributes to pathogenicity during MRSA infection. MecA induction leads to a reduction in peptidoglycan cross-linking that allows for enhanced degradation and detection by phagocytes, resulting in robust IL-1β production. Peptidoglycan isolated from β-lactam-challenged MRSA strongly induces the NLRP3 inflammasome in macrophages, but these effects are lost upon peptidoglycan solubilization. Mutant MRSA bacteria with naturally occurring reduced peptidoglycan cross-links induce high IL-1β levels in vitro and cause increased pathology in vivo. β-lactam treatment of MRSA skin infection exacerbates immunopathology, which is IL-1 dependent. Thus, antibiotic-induced expression of mecA during MRSA skin infection contributes to immunopathology by altering peptidoglycan structure.
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Affiliation(s)
- Sabrina Müller
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Andrea J Wolf
- Division of Biomedical Sciences and the F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Iliyan D Iliev
- Division of Biomedical Sciences and the F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Bethany L Berg
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M Underhill
- Division of Biomedical Sciences and the F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - George Y Liu
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, Brown J, Funari VA, Wang HL, Crother TR, Arditi M, Underhill DM, Iliev ID. Immunological Consequences of Intestinal Fungal Dysbiosis. Cell Host Microbe 2016; 19:865-73. [PMID: 27237365 DOI: 10.1016/j.chom.2016.05.003] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/11/2016] [Accepted: 05/04/2016] [Indexed: 12/17/2022]
Abstract
Compared to bacteria, the role of fungi within the intestinal microbiota is poorly understood. In this study we investigated whether the presence of a "healthy" fungal community in the gut is important for modulating immune function. Prolonged oral treatment of mice with antifungal drugs resulted in increased disease severity in acute and chronic models of colitis, and also exacerbated the development of allergic airway disease. Microbiota profiling revealed restructuring of fungal and bacterial communities. Specifically, representation of Candida spp. was reduced, while Aspergillus, Wallemia, and Epicoccum spp. were increased. Oral supplementation with a mixture of three fungi found to expand during antifungal treatment (Aspergillus amstelodami, Epicoccum nigrum, and Wallemia sebi) was sufficient to recapitulate the exacerbating effects of antifungal drugs on allergic airway disease. Taken together, these results indicate that disruption of commensal fungal populations can influence local and peripheral immune responses and enhance relevant disease states.
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Affiliation(s)
- Matthew L Wheeler
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jose J Limon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Agnieszka S Bar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christian A Leal
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew Gargus
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jordan Brown
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Vincent A Funari
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hanlin L Wang
- Department of Pathology and Laboratory Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy R Crother
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moshe Arditi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M Underhill
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Pathology and Laboratory Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
| | - Iliyan D Iliev
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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Tang J, Iliev ID, Brown J, Underhill DM, Funari VA. Mycobiome: Approaches to analysis of intestinal fungi. J Immunol Methods 2015; 421:112-121. [PMID: 25891793 PMCID: PMC4451377 DOI: 10.1016/j.jim.2015.04.004] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/06/2015] [Accepted: 04/06/2015] [Indexed: 01/21/2023]
Abstract
Massively parallel sequencing (MPSS) of bacterial 16S rDNA has been widely used to characterize the microbial makeup of the human and mouse gastrointestinal tract. However, techniques for fungal microbiota (mycobiota) profiling remain relatively under-developed. Compared to 16S profiling, the size and sequence context of the fungal Internal Transcribed Spacer 1 (ITS1), the most common target for mycobiota profiling, are highly variable. Using representative gastrointestinal tract fungi to build a known "mock" library, we examine how this sequence variability affects data quality derived from Illumina Miseq and Ion Torrent PGM sequencing pipelines. Also, while analysis of bacterial 16S profiles is facilitated by the presence of high-quality well-accepted databases of bacterial 16S sequences, such an accepted database has not yet emerged to facilitate fungal ITS sequence characterization, and we observe that redundant and inconsistent ITS1 sequence representation in publically available fungal reference databases affect quantitation and annotation of species in the gut. To address this problem, we have constructed a manually curated reference database optimized for annotation of gastrointestinal fungi. This targeted host-associated fungi (THF) database contains 1817 ITS1 sequences representing sequence diversity in genera previously identified in human and mouse gut. We observe that this database consistently outperforms three common ITS database alternatives on comprehensiveness, taxonomy assignment accuracy and computational efficiency in analyzing sequencing data from the mouse gastrointestinal tract.
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Affiliation(s)
- Jie Tang
- Genomics Core, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Iliyan D. Iliev
- Department of Biomedical Sciences, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jordan Brown
- Genomics Core, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M. Underhill
- Department of Biomedical Sciences, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- F. Widjaja Foundation, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Vincent A. Funari
- Genomics Core, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Iliev ID, Underhill DM. Striking a balance: fungal commensalism versus pathogenesis. Curr Opin Microbiol 2013; 16:366-73. [PMID: 23756050 DOI: 10.1016/j.mib.2013.05.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 02/06/2023]
Abstract
The environment is suffused with nearly countless types of fungi, and our immune systems must be tuned to cope with constant exposure to them. In addition, it is becoming increasingly clear that many surfaces of our bodies are colonized with complex populations of fungi (the mycobiome) in the same way that they are colonized with complex populations of bacteria. The immune system must tolerate colonization with commensal fungi but defend against fungal invasion. Truly life-threatening fungal infections are common only when this balance is disrupted through, for example, profound immunosuppression or genetic mutation. Recent studies have begun to shed light on how this balance is established and maintained, and suggest future studies on the role of fungi in homeostatic conditions.
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Affiliation(s)
- Iliyan D Iliev
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M, Rotter JI, Wang HL, McGovern DPB, Brown GD, Underhill DM. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 2012; 336:1314-7. [PMID: 22674328 DOI: 10.1126/science.1221789] [Citation(s) in RCA: 746] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The intestinal microflora, typically equated with bacteria, influences diseases such as obesity and inflammatory bowel disease. Here, we show that the mammalian gut contains a rich fungal community that interacts with the immune system through the innate immune receptor Dectin-1. Mice lacking Dectin-1 exhibited increased susceptibility to chemically induced colitis, which was the result of altered responses to indigenous fungi. In humans, we identified a polymorphism in the gene for Dectin-1 (CLEC7A) that is strongly linked to a severe form of ulcerative colitis. Together, our findings reveal a eukaryotic fungal community in the gut (the "mycobiome") that coexists with bacteria and substantially expands the repertoire of organisms interacting with the intestinal immune system to influence health and disease.
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Affiliation(s)
- Iliyan D Iliev
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Matteoli G, Mazzini E, Iliev ID, Mileti E, Fallarino F, Puccetti P, Chieppa M, Rescigno M. Gut CD103+ dendritic cells express indoleamine 2,3-dioxygenase which influences T regulatory/T effector cell balance and oral tolerance induction. Gut 2010; 59:595-604. [PMID: 20427394 DOI: 10.1136/gut.2009.185108] [Citation(s) in RCA: 267] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE CD103(+) gut dendritic cells (DCs) have been shown to be required for de novo conversion of adaptive T regulatory (Treg) cells. Indoleamine 2,3-dioxygenase (IDO) is an enzyme involved in tryptophan catabolism that is expressed by DCs isolated from tumour-draining lymph nodes. IDO-expressing DCs sustain and differentiate Tregs. The aim of this study was to investigate the expression and the possible physiological role of IDO in the tolerogenic properties of intestinal DCs. DESIGN The expression level of IDO in CD103(+) and CD103(-) DCs was analysed by qRT-PCR, western blot and immunofluorescence. CD103(+) and CD103(-) DCs were sorted from mesenteric lymph nodes (MLNs) and the small intestinal lamina propria, and the role of IDO in the conversion of Tregs and Th effector cell development was evaluated via specific inhibition or gene deletion. Oral tolerance, experimental colitis and T cell differentiation in vivo were assessed upon IDO inactivation. RESULTS We show that, primarily, CD103(+) but not CD103(-) gut DCs express IDO whose inhibition results in reduced CD4(+)Foxp3(+) T regulatory cell conversion and enhanced T cell proliferation. When IDO was inhibited or genetically deleted there was an increase in Th1 and Th17 differentiation both in vitro and in vivo. Finally, in vivo IDO blockade affected the development of Tregs specific for orally administered antigens, impaired oral tolerance induction and exacerbated colitis. CONCLUSIONS We identified a new IDO-dependent pathway leading to acquisition of tolerogenic functions in mucosal CD103-expressing DCs, indicating IDO as a possible therapeutic target for gut disorders.
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Affiliation(s)
- Gianluca Matteoli
- Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, Milan, Italy
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Iliev ID, Spadoni I, Mileti E, Matteoli G, Sonzogni A, Sampietro GM, Foschi D, Caprioli F, Viale G, Rescigno M. Human intestinal epithelial cells promote the differentiation of tolerogenic dendritic cells. Gut 2009; 58:1481-9. [PMID: 19570762 DOI: 10.1136/gut.2008.175166] [Citation(s) in RCA: 307] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE In mice, a subpopulation of gut dendritic cells (DCs) expressing CD103 drives the development of regulatory T (T(reg)) cells. Further, it was recently described that the cross-talk between human intestinal epithelial cells (IECs) and DCs helps in maintaining gut immune homeostasis via the induction of non-inflammatory DCs. In this study, an analysis was carried out to determine whether IECs could promote the differentiation of CD103+ tolerogenic DCs, and the function of primary CD103+ DCs isolated from human mesenteric lymph nodes (MLNs) was evaluated. METHODS Monocyte-derived DCs (MoDCs) and circulating CD1c+ DCs were conditioned or not with supernatants from Caco-2 cells or IECs isolated from healthy donors or donors with Crohn's disease and analysed for their ability to induce T(reg) cell differentiation. In some cases, transforming growth factor beta (TGFbeta), retinoic acid (RA) or thymic stromal lymphopoietin (TSLP) were neutralised before conditioning. CD103+ and CD103- DCs were sorted by fluorescence-activated cell sorting (FACS) from MLNs and used in T(reg) cell differentiation experiments. RESULTS It was found that human IECs promoted the differentiation of tolerogenic DCs able to drive the development of adaptive Foxp3+ T(reg) cells. This control was lost in patients with Crohn's disease and paralleled a reduced expression of tolerogenic factors by primary IECs. MoDCs differentiated with RA or IEC supernatant upregulated the expression of CD103. Consistently, human primary CD103+ DCs isolated from MLNs were endowed with the ability to drive T(reg) cell differentiation. This subset of DCs expressed CCR7 and probably represents a lamina propria-derived migratory population. CONCLUSIONS A population of tolerogenic CD103+ DCs was identified in the human gut that probably differentiate in response to IEC-derived factors and drive T(reg) cell development.
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Affiliation(s)
- I D Iliev
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy
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Mileti E, Matteoli G, Iliev ID, Rescigno M. Comparison of the immunomodulatory properties of three probiotic strains of Lactobacilli using complex culture systems: prediction for in vivo efficacy. PLoS One 2009; 4:e7056. [PMID: 19756155 PMCID: PMC2738944 DOI: 10.1371/journal.pone.0007056] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 08/11/2009] [Indexed: 12/13/2022] Open
Abstract
Background While the use of probiotics to treat or prevent inflammatory bowel disease (IBD) has been proposed, to this point the clinical benefits have been limited. In this report we analyzed the immunological activity of three strains of Lactobacillus to predict their in vivo efficacy in protecting against experimental colitis. Methodology/Principal Findings We compared the immunological properties of Lactobacillus plantarum NCIMB8826, L. rhamnosus GG (LGG), L. paracasei B21060 and pathogenic Salmonella typhimurium (SL1344). We studied the stimulatory effects of these different strains upon dendritic cells (DCs) either directly by co-culture or indirectly via conditioning of an epithelial intermediary. Furthermore, we characterized the effects of these strains in vivo using a Dextran sulphate sodium (DSS) model of colitis. We found that the three strains exhibited different abilities to induce inflammatory cytokine production by DCs with L. plantarum being the most effective followed by LGG and L. paracasei. L. paracasei minimally induced the release of cytokines, while it also inhibited the potential of DCs to both produce inflammatory cytokines (IL-12 and TNF-α) and to drive Th1 T cells in response to Salmonella. This effect on DCs was found under both direct and indirect stimulatory conditions – i.e. mediated by epithelial cells - and was dependent upon an as yet unidentified soluble mediator. When tested in vivo, L. plantarum and LGG exacerbated the development of DSS-induced colitis and caused the death of treated mice, while, conversely L. paracasei was protective. Conclusions We describe a new property of probiotics to either directly or indirectly inhibit DC activation by inflammatory bacteria. Moreover, some immunostimulatory probiotics not only failed to protect against colitis, they actually amplified the disease progression. In conclusion, caution must be exercised when choosing a probiotic strain to treat IBD.
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Affiliation(s)
- Erika Mileti
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Gianluca Matteoli
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Iliyan D. Iliev
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Maria Rescigno
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- * E-mail:
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Iliev ID, Tohno M, Kurosaki D, Shimosato T, He F, Hosoda M, Saito T, Kitazawa H. Immunostimulatory oligodeoxynucleotide containing TTTCGTTT motif from Lactobacillus rhamnosus GG DNA potentially suppresses OVA-specific IgE production in mice. Scand J Immunol 2008; 67:370-6. [PMID: 18248528 DOI: 10.1111/j.1365-3083.2008.02080.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In a previous study of the immunoregulatory properties of commensal bacterial DNA, we identified the strong immunostimulatory oligodeoxynucleotide (ISS-ODN) ID35 in the genomic DNA of Lactobacillus rhamnosus GG (LGG). The observed effects of ID35 are because of the unique TTTCGTTT motif located at the 5' end of the ODN, which is different from the previously identified ISS motifs in humans and mice. In the present study, we used an ovalbumin (OVA)-sensitized mouse model to show that ID35 is a potent suppressor of antigen-specific immunoglobulin E (IgE) production in vivo. This effect was toll-like receptor 9-dependent, as GpC negID35 failed to suppress antigen-specific IgE production. ID35 activated the specific subset of CD11c+CD8a+ dendritic cells, which are associated with T-helper 1 (Th1)-type systemic responses, and effectively induced interferon-gamma (IFN-gamma) production by CD4+ T cells in OVA-challenged mice. These immunoregulatory effects of ID35 were comparable with those induced by the murine prototype ODN 1826. Thus, ID35 is the first ISS-ODN with such a strong immunostimulatory and IgE suppressor activity to be found in immunobiotic bacterial DNA.
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Affiliation(s)
- I D Iliev
- Food Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Abstract
Recent work suggests that dendritic cells (DCs) in mucosal tissues are "educated" by intestinal epithelial cells (IECs) to suppress inflammation and promote immunological tolerance. After attack by pathogenic microorganisms, however, "non-educated" DCs are recruited from nearby areas, such as the dome of Peyer's patches (PPs) and the blood, to initiate inflammation and the ensuing immune response to the invader. Differential epithelial cell (EC) responses to commensals and pathogens may control these two tolorogenic and immunogenic functions of DCs.
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Affiliation(s)
- Iliyan D Iliev
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy
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Iliev ID, Kitazawa H, Shimosato T, Katoh S, Morita H, He F, Hosoda M, Saito T. Strong immunostimulation in murine immune cells by Lactobacillus rhamnosus GG DNA containing novel oligodeoxynucleotide pattern. Cell Microbiol 2005; 7:403-14. [PMID: 15679843 DOI: 10.1111/j.1462-5822.2004.00470.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Whole cells, cell wall components and some soluble factors from Lactobacillus rhamnosus GG (LGG) are known to invoke immune responses as they interact with animal and human immune cells. In the present study, we found that chromosomal DNA from LGG is a potent inducer of splenic B cell proliferation, CD86/CD69 expression and cytokine production in mice. In the genomic DNA of LGG we discovered TTTCGTTT oligodeoxynucleotide (ODN) ID35, which has a potent activity in a number of immunostimulatory assays. Phosphorothioate backbone is not required for the activity of ID35. The ODN ID35 showed levels of activity comparable with those induced by the murine prototype ODN 1826 in B cell proliferation, CD86/CD69 expression, interleukin (IL)-6, IL-12, IL-18, interferon gamma (IFN-gamma) and tumour necrosis factor alpha (TNF-alpha) mRNA expression and IFN-gamma/IL-12p70 protein production assays. Additionally, ID35 appeared to be equally active in both murine and human immune cells. These stimulatory effects are due to TTTCGTTT motif located in the 5' end of ID35. In this study we demonstrate for a first time that, DNA from LGG is a factor of immunobiotic activity. Furthermore, ODN ID35 is the first ODN, with such a strong immunostimulatory activity to be found in immunobiotic bacterial DNA.
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MESH Headings
- Adjuvants, Immunologic/chemistry
- Adjuvants, Immunologic/pharmacology
- Animals
- Antigens, CD/immunology
- Antigens, Differentiation, T-Lymphocyte/immunology
- B-Lymphocytes/cytology
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B7-2 Antigen
- Cell Proliferation/drug effects
- Cells, Cultured
- Chromosomes, Bacterial/genetics
- Cloning, Molecular
- Cytokines/biosynthesis
- Cytokines/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/pharmacology
- Humans
- Lactobacillus/genetics
- Lectins, C-Type
- Leukocytes, Mononuclear/cytology
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/immunology
- Membrane Glycoproteins/immunology
- Mice
- Oligonucleotides/chemical synthesis
- Oligonucleotides/chemistry
- Oligonucleotides/pharmacology
- Spleen/cytology
- Transcription, Genetic
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Affiliation(s)
- Iliyan D Iliev
- Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
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Iliev ID, Kitazawa H, Shimosato T, Katoh S, Morita H, He F, Hosoda M, Saito T. Strong immunostimulation in murine immune cells by Lactobacillus rhamnosus GG DNA containing novel oligodeoxynucleotide pattern. Cell Microbiol 2005. [DOI: 10.1111/j.1462-5822.2004.00492.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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