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Canales-Herrerias P, Uzzan M, Seki A, Czepielewski RS, Verstockt B, Livanos AE, Raso F, Dunn A, Dai D, Wang A, Al-Taie Z, Martin J, Laurent T, Ko HM, Tokuyama M, Tankelevich M, Meringer H, Cossarini F, Jha D, Krek A, Paulsen JD, Taylor MD, Nakadar MZ, Wong J, Erlich EC, Mintz RL, Onufer EJ, Helmink BA, Sharma K, Rosenstein A, Ganjian D, Chung G, Dawson T, Juarez J, Yajnik V, Cerutti A, Faith JJ, Suarez-Farinas M, Argmann C, Petralia F, Randolph GJ, Polydorides AD, Reboldi A, Colombel JF, Mehandru S. Gut-associated lymphoid tissue attrition associates with response to anti-α4β7 therapy in ulcerative colitis. Sci Immunol 2024; 9:eadg7549. [PMID: 38640252 DOI: 10.1126/sciimmunol.adg7549] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/20/2024] [Indexed: 04/21/2024]
Abstract
Vedolizumab (VDZ) is a first-line treatment in ulcerative colitis (UC) that targets the α4β7- mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1) axis. To determine the mechanisms of action of VDZ, we examined five distinct cohorts of patients with UC. A decrease in naïve B and T cells in the intestines and gut-homing (β7+) plasmablasts in circulation of VDZ-treated patients suggested that VDZ targets gut-associated lymphoid tissue (GALT). Anti-α4β7 blockade in wild-type and photoconvertible (KikGR) mice confirmed a loss of GALT size and cellularity because of impaired cellular entry. In VDZ-treated patients with UC, treatment responders demonstrated reduced intestinal lymphoid aggregate size and follicle organization and a reduction of β7+IgG+ plasmablasts in circulation, as well as IgG+ plasma cells and FcγR-dependent signaling in the intestine. GALT targeting represents a previously unappreciated mechanism of action of α4β7-targeted therapies, with major implications for this therapeutic paradigm in UC.
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Affiliation(s)
- Pablo Canales-Herrerias
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mathieu Uzzan
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Paris Est Créteil University UPEC, Assistance Publique-Hôpitaux de Paris (AP-HP), Henri Mondor Hospital, Gastroenterology Department, Fédération Hospitalo-Universitaire TRUE (InnovaTive theRapy for immUne disordErs), Créteil F-94010, France
| | - Akihiro Seki
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rafael S Czepielewski
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
- Translational Research in Gastrointestinal Disorders, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fiona Raso
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alexandra Dunn
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Dai
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Wang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome Martin
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d'Immunologie, CIMNA, Nantes, France
| | - Thomas Laurent
- Nantes Université, CHU Nantes, Inserm, Centre de Recherche Translationelle en Transplantation et Immunologie, UMR 1064, Nantes, France
- CHU Nantes, Nantes Université, Laboratoire d'Immunologie, CIMNA, Nantes, France
| | - Huaibin M Ko
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadar Meringer
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John D Paulsen
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew D Taylor
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mohammad Zuber Nakadar
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua Wong
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emma C Erlich
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel L Mintz
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily J Onufer
- Division of Pediatric Surgery, Department of Surgery, St. Louis Children's Hospital, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Beth A Helmink
- Department of Surgery, Section of Surgical Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Keshav Sharma
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Rosenstein
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle Ganjian
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Grace Chung
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Travis Dawson
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Translational Clinical Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gwendalyn J Randolph
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alexandros D Polydorides
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Reboldi
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Law CCY, Peraza J, Viera Feliciano N, Ungaro RC, Cheesman K, Colombel JF, Livanos AE. Do We Need AI to Diagnose AI? Diagnosis and Management of Adrenal Insufficiency Following Steroid Therapy in a Patient with Inflammatory Bowel Disease. Dig Dis Sci 2023; 68:4327-4330. [PMID: 37831398 DOI: 10.1007/s10620-023-08123-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023]
Affiliation(s)
- Cindy C Y Law
- Division of Gastroenterology, Department of MedicineSusan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jellyana Peraza
- Division of Gastroenterology, Department of MedicineSusan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Viera Feliciano
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan C Ungaro
- Division of Gastroenterology, Department of MedicineSusan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Khadeen Cheesman
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frédéric Colombel
- Division of Gastroenterology, Department of MedicineSusan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra E Livanos
- Division of Gastroenterology, Department of MedicineSusan and Leonard Feinstein IBD Clinical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Jha D, Al-Taie Z, Krek A, Eshghi ST, Fantou A, Laurent T, Tankelevich M, Cao X, Meringer H, Livanos AE, Tokuyama M, Cossarini F, Bourreille A, Josien R, Hou R, Canales-Herrerias P, Ungaro RC, Kayal M, Marion J, Polydorides AD, Ko HM, D’souza D, Merand R, Kim-Schulze S, Hackney JA, Nguyen A, McBride JM, Yuan GC, Colombel JF, Martin JC, Argmann C, Suárez-Fariñas M, Petralia F, Mehandru S. Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis. bioRxiv 2023:2023.06.02.542863. [PMID: 37333091 PMCID: PMC10274630 DOI: 10.1101/2023.06.02.542863] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ γδ+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.
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Affiliation(s)
- Divya Jha
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Shadi Toghi Eshghi
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Aurelie Fantou
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Thomas Laurent
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Michael Tankelevich
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuan Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Hadar Meringer
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra E Livanos
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arnaud Bourreille
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Regis Josien
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Pablo Canales-Herrerias
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan C. Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maia Kayal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Marion
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Huaibin M. Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center-New York Presbyterian Hospital, New York, New York
| | - Darwin D’souza
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphael Merand
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason A. Hackney
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Allen Nguyen
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Jacqueline M. McBride
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Jean Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome C. Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Carmen Argmann
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Saurabh Mehandru
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Livanos AE, Dunn A, Fischer J, Ungaro RC, Turpin W, Lee SH, Rui S, Del Valle DM, Jougon JJ, Martinez-Delgado G, Riddle MS, Murray JA, Laird RM, Torres J, Agrawal M, Magee JS, Dervieux T, Gnjatic S, Sheppard D, Sands BE, Porter CK, Croitoru K, Petralia F, Colombel JF, Mehandru S. Anti-Integrin αvβ6 Autoantibodies Are a Novel Biomarker That Antedate Ulcerative Colitis. Gastroenterology 2023; 164:619-629. [PMID: 36634824 DOI: 10.1053/j.gastro.2022.12.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS Better biomarkers for prediction of ulcerative colitis (UC) development and prognostication are needed. Anti-integrin αvβ6 (anti-αvβ6) autoantibodies have been described in patients with UC. We tested for the presence of anti-αvβ6 antibodies in the preclinical phase of UC and studied their association with disease-related outcomes after diagnosis. METHODS Anti-αvβ6 autoantibodies were measured in 4 longitudinal serum samples collected from 82 subjects who later developed UC and 82 matched controls from a Department of Defense preclinical cohort (PREDICTS [Proteomic Evaluation and Discovery in an IBD Cohort of Tri-service Subjects]). In a distinct, external validation cohort (Crohn's and Colitis Canada Genetic Environmental Microbial project cohort), we tested 12 pre-UC subjects and 49 matched controls. Furthermore, anti-αvβ6 autoantibodies were measured in 2 incident UC cohorts (COMPASS [Comprehensive Care for the Recently Diagnosed IBD Patients], n = 55 and OSCCAR [Ocean State Crohn's and Colitis Area Registry], n = 104) and associations between anti-αvβ6 autoantibodies and UC-related outcomes were defined using Cox proportional hazards model. RESULTS Anti-αvβ6 autoantibodies were significantly higher among individuals who developed UC compared with controls up to 10 years before diagnosis in PREDICTS. The anti-αvβ6 autoantibody seropositivity was 12.2% 10 years before diagnosis and increased to 52.4% at the time of diagnosis in subjects who developed UC compared with 2.7% in controls across the 4 time points. Anti-αvβ6 autoantibodies predicted UC development with an area under the curve of at least 0.8 up to 10 years before diagnosis. The presence of anti-αvβ6 autoantibodies in preclinical UC samples was validated in the GEM cohort. Finally, high anti-αvβ6 autoantibodies was associated with a composite of adverse UC outcomes, including hospitalization, disease extension, colectomy, systemic steroid use, and/or escalation to biologic therapy in recently diagnosed UC. CONCLUSIONS Anti-integrin αvβ6 autoantibodies precede the clinical diagnosis of UC by up to 10 years and are associated with adverse UC-related outcomes.
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Affiliation(s)
- Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexandra Dunn
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jeremy Fischer
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ryan C Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology and Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sun-Ho Lee
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology and Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shumin Rui
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Diane Marie Del Valle
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Julia J Jougon
- Hepato-Gastroenterology Department, Claude Huriez Hospital, University of Lille, Lille, France
| | | | - Mark S Riddle
- University of Nevada, Reno School of Medicine, Reno, Nevada; Veterans Affairs Sierra Nevada Health Care System, Reno, Nevada
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Renee M Laird
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, Maryland; Henry M. Jackson Foundation for Military Medicine, Bethesda, Maryland
| | - Joana Torres
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal; Gastroenterology Division, Hospital da Luz, Lisbon, Portugal; Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Manasi Agrawal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jared S Magee
- Gastroenterology, Walter Reed National Military Medical Center, Bethesda, Maryland
| | | | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Bruce E Sands
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chad K Porter
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, Maryland
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada; Division of Gastroenterology and Hepatology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Jean-Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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Britton GJ, Chen-Liaw A, Cossarini F, Livanos AE, Spindler MP, Plitt T, Eggers J, Mogno I, Gonzalez-Reiche AS, Siu S, Tankelevich M, Grinspan LT, Dixon RE, Jha D, van de Guchte A, Khan Z, Martinez-Delgado G, Amanat F, Hoagland DA, tenOever BR, Dubinsky MC, Merad M, van Bakel H, Krammer F, Bongers G, Mehandru S, Faith JJ. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19. Sci Rep 2021; 11:13308. [PMID: 34172783 PMCID: PMC8233421 DOI: 10.1038/s41598-021-92740-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/10/2021] [Indexed: 12/20/2022] Open
Abstract
Gastrointestinal symptoms are common in COVID-19 patients but the nature of the gut immune response to SARS-CoV-2 remains poorly characterized, partly due to the difficulty of obtaining biopsy specimens from infected individuals. In lieu of tissue samples, we measured cytokines, inflammatory markers, viral RNA, microbiome composition, and antibody responses in stool samples from a cohort of 44 hospitalized COVID-19 patients. SARS-CoV-2 RNA was detected in stool of 41% of patients and more frequently in patients with diarrhea. Patients who survived had lower fecal viral RNA than those who died. Strains isolated from stool and nasopharynx of an individual were the same. Compared to uninfected controls, COVID-19 patients had higher fecal levels of IL-8 and lower levels of fecal IL-10. Stool IL-23 was higher in patients with more severe COVID-19 disease, and we found evidence of intestinal virus-specific IgA responses associated with more severe disease. We provide evidence for an ongoing humeral immune response to SARS-CoV-2 in the gastrointestinal tract, but little evidence of overt inflammation.
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Affiliation(s)
- Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Francesca Cossarini
- Precision Immunology Institute, 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
| | - Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew P Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joseph Eggers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ana S Gonzalez-Reiche
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sophia Siu
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren Tal Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rebekah E Dixon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adriana van de Guchte
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zenab Khan
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harm van Bakel
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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6
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Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, Aydillo T, Parigi TL, Ladinsky MS, Ramos I, Dunleavy K, Lee B, Dixon RE, Chen ST, Martinez-Delgado G, Nagula S, Bruce EA, Ko HM, Glicksberg BS, Nadkarni G, Pujadas E, Reidy J, Naymagon S, Grinspan A, Ahmad J, Tankelevich M, Bram Y, Gordon R, Sharma K, Houldsworth J, Britton GJ, Chen-Liaw A, Spindler MP, Plitt T, Wang P, Cerutti A, Faith JJ, Colombel JF, Kenigsberg E, Argmann C, Merad M, Gnjatic S, Harpaz N, Danese S, Cordon-Cardo C, Rahman A, Schwartz RE, Kumta NA, Aghemo A, Bjorkman PJ, Petralia F, van Bakel H, Garcia-Sastre A, Mehandru S. Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms. Gastroenterology 2021; 160:2435-2450.e34. [PMID: 33676971 PMCID: PMC7931673 DOI: 10.1053/j.gastro.2021.02.056] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of COVID-19, we investigated intestinal infection with SARS-CoV-2, its effect on pathogenesis, and clinical significance. METHODS Human intestinal biopsy tissues were obtained from patients with COVID-19 (n = 19) and uninfected control individuals (n = 10) for microscopic examination, cytometry by time of flight analyses, and RNA sequencing. Additionally, disease severity and mortality were examined in patients with and without GI symptoms in 2 large, independent cohorts of hospitalized patients in the United States (N = 634) and Europe (N = 287) using multivariate logistic regressions. RESULTS COVID-19 case patients and control individuals in the biopsy cohort were comparable for age, sex, rates of hospitalization, and relevant comorbid conditions. SARS-CoV-2 was detected in small intestinal epithelial cells by immunofluorescence staining or electron microscopy in 15 of 17 patients studied. High-dimensional analyses of GI tissues showed low levels of inflammation, including down-regulation of key inflammatory genes including IFNG, CXCL8, CXCL2, and IL1B and reduced frequencies of proinflammatory dendritic cells compared with control individuals. Consistent with these findings, we found a significant reduction in disease severity and mortality in patients presenting with GI symptoms that was independent of sex, age, and comorbid illnesses and despite similar nasopharyngeal SARS-CoV-2 viral loads. Furthermore, there was reduced levels of key inflammatory proteins in circulation in patients with GI symptoms. CONCLUSIONS These data highlight the absence of a proinflammatory response in the GI tract despite detection of SARS-CoV-2. In parallel, reduced mortality in patients with COVID-19 presenting with GI symptoms was observed. A potential role of the GI tract in attenuating SARS-CoV-2-associated inflammation needs to be further examined.
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Affiliation(s)
- Alexandra E Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Minami Tokuyama
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tommaso L Parigi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Irene Ramos
- Department of Neurology and Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Katie Dunleavy
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brian Lee
- Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York
| | - Rebekah E Dixon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven T Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Satish Nagula
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emily A Bruce
- Division of Immunobiology, Department of Medicine, University of Vermont, Larner College of Medicine, Burlington, Vermont
| | - Huaibin M Ko
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish Nadkarni
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York; The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elisabet Pujadas
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jason Reidy
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Steven Naymagon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ari Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jawad Ahmad
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Ronald Gordon
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Keshav Sharma
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jane Houldsworth
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Graham J Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Matthew P Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Catalan Institute for Research and Advanced Studies, Barcelona, Spain; Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Jeremiah J Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ephraim Kenigsberg
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sacha Gnjatic
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Noam Harpaz
- Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Carlos Cordon-Cardo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Pathology, Molecular and Cell Based Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adeeb Rahman
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Human Immune Monitoring Center (HIMC) Icahn School of Medicine at Mount Sinai New York, New York, New York; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Nikhil A Kumta
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alessio Aghemo
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Adolfo Garcia-Sastre
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York; The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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7
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Britton GJ, Chen-Liaw A, Cossarini F, Livanos AE, Spindler MP, Plitt T, Eggers J, Mogno I, Gonzalez-Reiche AS, Siu S, Tankelevich M, Grinspan LT, Dixon RE, Jha D, van de Guchte A, Khan Z, Martinez-Delgado G, Amanat F, Hoagland DA, tenOever BR, Dubinsky MC, Merad M, van Bakel H, Krammer F, Bongers G, Mehandru S, Faith JJ. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19. medRxiv 2020:2020.09.03.20183947. [PMID: 32909002 PMCID: PMC7480054 DOI: 10.1101/2020.09.03.20183947] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We sought to characterize the role of the gastrointestinal immune system in the pathogenesis of the inflammatory response associated with COVID-19. We measured cytokines, inflammatory markers, viral RNA, microbiome composition and antibody responses in stool from a cohort of 44 hospitalized COVID-19 patients. SARS-CoV-2 RNA was detected in stool of 41% of patients and more frequently in patients with diarrhea. Patients who survived had lower fecal viral RNA than those who died. Strains isolated from stool and nasopharynx of an individual were the same. Compared to uninfected controls, COVID-19 patients had higher fecal levels of IL-8 and lower levels of fecal IL-10. Stool IL-23 was higher in patients with more severe COVID-19 disease, and we found evidence of intestinal virus-specific IgA responses associated with more severe disease. We provide evidence for an ongoing humeral immune response to SARS-CoV-2 in the gastrointestinal tract, but little evidence of overt inflammation.
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Affiliation(s)
- Graham J. Britton
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Francesca Cossarini
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Alexandra E. Livanos
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Matthew P. Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Tamar Plitt
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Joseph Eggers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ilaria Mogno
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Ana S. Gonzalez-Reiche
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Sophia Siu
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Michael Tankelevich
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lauren Tal Grinspan
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rebekah E. Dixon
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Divya Jha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adriana van de Guchte
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Zenab Khan
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Gustavo Martinez-Delgado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
| | - Daisy A. Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Benjamin R. tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C. Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Harm van Bakel
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gerold Bongers
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Saurabh Mehandru
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029
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8
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Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, Aydillo T, Parigi TL, Ramos I, Dunleavy K, Lee B, Dixon R, Chen ST, Martinez-Delgado G, Nagula S, Ko HM, Glicksberg BS, Nadkarni G, Pujadas E, Reidy J, Naymagon S, Grinspan A, Ahmad J, Tankelevich M, Gordon R, Sharma K, Houldsworth J, Britton GJ, Chen-Liaw A, Spindler MP, Plitt T, Wang P, Cerutti A, Faith JJ, Colombel JF, Kenigsberg E, Argmann C, Merad M, Gnjatic S, Harpaz N, Danese S, Cordon-Cardo C, Rahman A, Kumta NA, Aghemo A, Petralia F, van Bakel H, Garcia-Sastre A, Mehandru S. Gastrointestinal involvement attenuates COVID-19 severity and mortality. medRxiv 2020. [PMID: 32935117 DOI: 10.1101/2020.09.07.20187666] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of coronavirus disease 2019 (COVID-19), we investigated intestinal infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its effect on disease pathogenesis. SARS-CoV-2 was detected in small intestinal enterocytes by immunofluorescence staining or electron microscopy, in 13 of 15 patients studied. High dimensional analyses of GI tissues revealed low levels of inflammation in general, including active downregulation of key inflammatory genes such as IFNG, CXCL8, CXCL2 and IL1B and reduced frequencies of proinflammatory dendritic cell subsets. To evaluate the clinical significance of these findings, examination of two large, independent cohorts of hospitalized patients in the United States and Europe revealed a significant reduction in disease severity and mortality that was independent of gender, age, and examined co-morbid illnesses. The observed mortality reduction in COVID-19 patients with GI symptoms was associated with reduced levels of key inflammatory proteins including IL-6, CXCL8, IL-17A and CCL28 in circulation but was not associated with significant differences in nasopharyngeal viral loads. These data draw attention to organ-level heterogeneity in disease pathogenesis and highlight the role of the GI tract in attenuating SARS-CoV-2-associated inflammation with related mortality benefit. One Sentence Summary Intestinal infection with SARS-CoV-2 is associated with a mild inflammatory response and improved clinical outcomes.
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9
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Livanos AE, Snider EJ, Whittier S, Chong DH, Wang TC, Abrams JA, Freedberg DE. Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens. PLoS One 2018; 13:e0200322. [PMID: 30067768 PMCID: PMC6070193 DOI: 10.1371/journal.pone.0200322] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/23/2018] [Indexed: 12/15/2022] Open
Abstract
Commensal gastrointestinal bacteria resist the expansion of pathogens and are lost during critical illness, facilitating pathogen colonization and infection. We performed a prospective, ICU-based study to determine risk factors for loss of gut colonization resistance during the initial period of critical illness. Rectal swabs were taken from adult ICU patients within 4 hours of admission and 72 hours later, and analyzed using 16S rRNA gene sequencing and selective culture for vancomycin-resistant Enterococcus (VRE). Microbiome data was visualized using principal coordinate analyses (PCoA) and assessed using a linear discriminant analysis algorithm and logistic regression modeling. 93 ICU patients were analyzed. At 72 hours following ICU admission, there was a significant decrease in the proportion of Clostridial Clusters IV/XIVa, taxa that produce short chain fatty acids (SCFAs). At the same time, there was a significant expansion in Enterococcus. Decreases in Cluster IV/XIVa Clostridia were associated with loss of gut microbiome colonization resistance (reduced diversity and community stability over time). In multivariable analysis, both decreased Cluster IV/XIVa Clostridia and increased Enterococcus after 72 hours were associated with receipt of antibiotics. Cluster IV/XIVa Clostridia, although a small fraction of the overall gastrointestinal microbiome, drove distinct clustering on PCoA. During initial treatment for critical illness, there was a loss of Cluster IV/XIVa Clostridia within the distal gut microbiome which associated with an expansion of VRE and with a loss of gut microbiome colonization resistance. Receipt of broad-spectrum antibiotics was associated with these changes.
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Affiliation(s)
- Alexandra E. Livanos
- Division of General Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Erik J. Snider
- Division of General Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Susan Whittier
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States of America
| | - David H. Chong
- Division of Allergy, Pulmonary, and Critical Care Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Timothy C. Wang
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, United States of America
| | - Julian A. Abrams
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, United States of America
| | - Daniel E. Freedberg
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, United States of America
- * E-mail:
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10
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Abstract
BACKGROUND There has been increasing interest in discovering microbial taxa that are associated with human health or disease, gathering momentum through the advances in next-generation sequencing technologies. Investigators have also increasingly employed prospective study designs to survey survival (i.e., time-to-event) outcomes, but current item-by-item statistical methods have limitations due to the unknown true association pattern. Here, we propose a new adaptive microbiome-based association test for survival outcomes, namely, optimal microbiome-based survival analysis (OMiSA). OMiSA approximates to the most powerful association test in two domains: 1) microbiome-based survival analysis using linear and non-linear bases of OTUs (MiSALN) which weighs rare, mid-abundant, and abundant OTUs, respectively, and 2) microbiome regression-based kernel association test for survival traits (MiRKAT-S) which incorporates different distance metrics (e.g., unique fraction (UniFrac) distance and Bray-Curtis dissimilarity), respectively. RESULTS We illustrate that OMiSA powerfully discovers microbial taxa whether their underlying associated lineages are rare or abundant and phylogenetically related or not. OMiSA is a semi-parametric method based on a variance-component score test and a re-sampling method; hence, it is free from any distributional assumption on the effect of microbial composition and advantageous to robustly control type I error rates. Our extensive simulations demonstrate the highly robust performance of OMiSA. We also present the use of OMiSA with real data applications. CONCLUSIONS OMiSA is attractive in practice as the true association pattern is unpredictable in advance and, for survival outcomes, no adaptive microbiome-based association test is currently available.
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Affiliation(s)
- Hyunwook Koh
- Department of Population Health, New York University School of Medicine, 650 First Avenue, Room 547, New York, NY, 10016, USA
| | - Alexandra E Livanos
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Martin J Blaser
- Departments of Medicine and Microbiology, New York University School of Medicine, New York, NY, 10016, USA.,Medical Service, New York Harbor Department of Veterans Affairs Medical Center, New York, NY, 10010, USA
| | - Huilin Li
- Department of Population Health, New York University School of Medicine, 650 First Avenue, Room 547, New York, NY, 10016, USA.
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11
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Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z, Barber C, Kim J, Ng S, Rogers AB, Sumner S, Zhang XS, Cadwell K, Knights D, Alekseyenko A, Bäckhed F, Blaser MJ. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol 2016; 1:16140. [PMID: 27782139 PMCID: PMC5808443 DOI: 10.1038/nmicrobiol.2016.140] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [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: 01/05/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022]
Abstract
The early life microbiome plays important roles in host immunological and metabolic development. Because the incidence of type 1 diabetes (T1D) has been increasing substantially in recent decades, we hypothesized that early-life antibiotic use alters gut microbiota, which predisposes to disease. Using non-obese diabetic mice that are genetically susceptible to T1D, we examined the effects of exposure to either continuous low-dose antibiotics or pulsed therapeutic antibiotics (PAT) early in life, mimicking childhood exposures. We found that in mice receiving PAT, T1D incidence was significantly higher, and microbial community composition and structure differed compared with controls. In pre-diabetic male PAT mice, the intestinal lamina propria had lower Th17 and Treg proportions and intestinal SAA expression than in controls, suggesting key roles in transducing the altered microbiota signals. PAT affected microbial lipid metabolism and host cholesterol biosynthetic gene expression. These findings show that early-life antibiotic treatments alter the gut microbiota and its metabolic capacities, intestinal gene expression and T-cell populations, accelerating T1D onset in non-obese diabetic mice.
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Affiliation(s)
- Alexandra E. Livanos
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Thomas U. Greiner
- Department of Molecular and Clinical Medicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Pajau Vangay
- Biomedical Informatics and Computational Biology Program, University of Minnesota, Minneapolis, Minneapolis 55455, USA
| | - Wimal Pathmasiri
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Delisha Stewart
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Susan McRitchie
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Huilin Li
- Departments of Population Health, New York University Langone Medical Center, New York, New York 10016, USA
| | - Jennifer Chung
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Jiho Sohn
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Sara Kim
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Zhan Gao
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Cecily Barber
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Joanne Kim
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Sandy Ng
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Arlin B. Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, USA
| | - Susan Sumner
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Xue-Song Zhang
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Ken Cadwell
- Department of Microbiology, New York University Langone Medical Center, New York, New York 10016, USA
- Skirball Institute, New York University Langone Medical Center, New York, New York 10016, USA
| | - Dan Knights
- Computer Science and Engineering, University of Minnesota, Minneapolis, Minneapolis 55455, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, Minneapolis 55108, USA
| | - Alexander Alekseyenko
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
- CHIBI, New York University Langone Medical Center, New York, New York 10016, USA
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg, 40530 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Martin J. Blaser
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
- New York Harbor Veterans Affairs Medical Center, New York, New York 10010, USA
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