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Friedrich M, Pohin M, Jackson MA, Korsunsky I, Bullers SJ, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Thomas T, Ravindran R, Tandon R, Peres RS, Sharpe H, Wei K, Watts GFM, Mann EH, Geremia A, Attar M, McCuaig S, Thomas L, Collantes E, Uhlig HH, Sansom SN, Easton A, Raychaudhuri S, Travis SP, Powrie FM. IL-1-driven stromal-neutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies. Nat Med 2021; 27:1970-1981. [PMID: 34675383 PMCID: PMC8604730 DOI: 10.1038/s41591-021-01520-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [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: 02/06/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023]
Abstract
Current inflammatory bowel disease (IBD) therapies are ineffective in a high proportion of patients. Combining bulk and single-cell transcriptomics, quantitative histopathology and in situ localization across three cohorts of patients with IBD (total n = 376), we identify coexpressed gene modules within the heterogeneous tissular inflammatory response in IBD that map to distinct histopathological and cellular features (pathotypes). One of these pathotypes is defined by high neutrophil infiltration, activation of fibroblasts and vascular remodeling at sites of deep ulceration. Activated fibroblasts in the ulcer bed display neutrophil-chemoattractant properties that are IL-1R, but not TNF, dependent. Pathotype-associated neutrophil and fibroblast signatures are increased in nonresponders to several therapies across four independent cohorts (total n = 343). The identification of distinct, localized, tissular pathotypes will aid precision targeting of current therapeutics and provides a biological rationale for IL-1 signaling blockade in ulcerating disease.
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Affiliation(s)
- Matthias Friedrich
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Mathilde Pohin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Matthew A Jackson
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Ilya Korsunsky
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel J Bullers
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Kevin Rue-Albrecht
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Zoe Christoforidou
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Dharshan Sathananthan
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Tom Thomas
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Rahul Ravindran
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Ruchi Tandon
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Raphael Sanches Peres
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Hannah Sharpe
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Wei
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth H Mann
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alessandra Geremia
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Moustafa Attar
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah McCuaig
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Lloyd Thomas
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Elena Collantes
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
- Department of Paediatrics, John Radcliffe Hospital, Oxford, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alistair Easton
- Old Road Campus Research Building, Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Simon P Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Fiona M Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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Christoforidou Z, Mora Ortiz M, Poveda C, Abbas M, Walton G, Bailey M, Lewis MC. Sexual Dimorphism in Immune Development and in Response to Nutritional Intervention in Neonatal Piglets. Front Immunol 2019; 10:2705. [PMID: 31921096 PMCID: PMC6911813 DOI: 10.3389/fimmu.2019.02705] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/04/2019] [Indexed: 12/13/2022] Open
Abstract
Although sex disparity in immunological function and susceptibility to various inflammatory and infectious disease is recognized in adults, far less is known about the situation in young infants during immune development. We have used an outbred piglet model to explore potential early sex disparity underlying both mucosal immune development and systemic responses to novel antigen. Despite similarities in intestinal barrier function and therefore, presumably, antigen exposure, females had less CD172+ (Sirp-α) antigen presenting cells and expression of MHCIIDR at 28 days old compared to males, along with greater regulatory T-cell numbers. This suggests that, during infancy, females may have greater potential for local immune regulation than their male counterparts. However, females also presented with significantly greater systemic antibody responses to injected ovalbumin and dietary soya. Females also synthesized significantly more IgA in mesenteric lymph nodes, whereas males synthesized more in caecal mucosa, suggesting that plasma cells were retained within the MLN in females, but increased numbers of plasma cells circulated through to the mucosal tissue in males. Significant effects of inulin and Bifidobacterium lactis NCC2818 on the developing immune system were also sex-dependent. Our results may start to explain inconsistencies in outcomes of trials of functional foods in infants, as distinction between males and females is seldom made. Since later functionality of the immune system is highly dependent on appropriate development during infancy, stratifying nutritional interventions by sex may present a novel means of optimizing treatments and preventative strategies to reduce the risk of the development of immunological disorders in later life.
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Affiliation(s)
- Zoe Christoforidou
- Infection and Immunity, School of Veterinary Science, University of Bristol, Bristol, United Kingdom
| | - Marina Mora Ortiz
- Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, United Kingdom
| | - Carlos Poveda
- Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, United Kingdom
| | - Munawar Abbas
- Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, United Kingdom
| | - Gemma Walton
- Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, United Kingdom
| | - Michael Bailey
- Infection and Immunity, School of Veterinary Science, University of Bristol, Bristol, United Kingdom
| | - Marie C Lewis
- Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, United Kingdom
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Leng T, Akther HD, Hackstein CP, Powell K, King T, Friedrich M, Christoforidou Z, McCuaig S, Neyazi M, Arancibia-Cárcamo CV, Hagel J, Powrie F, Peres RS, Millar V, Ebner D, Lamichhane R, Ussher J, Hinks TSC, Marchi E, Willberg C, Klenerman P. TCR and Inflammatory Signals Tune Human MAIT Cells to Exert Specific Tissue Repair and Effector Functions. Cell Rep 2019; 28:3077-3091.e5. [PMID: 31533032 PMCID: PMC6899450 DOI: 10.1016/j.celrep.2019.08.050] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 04/17/2019] [Accepted: 08/15/2019] [Indexed: 01/10/2023] Open
Abstract
MAIT cells are an unconventional T cell population that can be activated through both TCR-dependent and TCR-independent mechanisms. Here, we examined the impact of combinations of TCR-dependent and TCR-independent signals in human CD8+ MAIT cells. TCR-independent activation of these MAIT cells from blood and gut was maximized by extending the panel of cytokines to include TNF-superfamily member TL1A. RNA-seq experiments revealed that TCR-dependent and TCR-independent signals drive MAIT cells to exert overlapping and specific effector functions, affecting both host defense and tissue homeostasis. Although TCR triggering alone is insufficient to drive sustained activation, TCR-triggered MAIT cells showed specific enrichment of tissue-repair functions at the gene and protein levels and in in vitro assays. Altogether, these data indicate the blend of TCR-dependent and TCR-independent signaling to CD8+ MAIT cells may play a role in controlling the balance between healthy and pathological processes of tissue inflammation and repair.
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Affiliation(s)
- Tianqi Leng
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Hossain Delowar Akther
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Carl-Philipp Hackstein
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Kate Powell
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK; Department of Microbiology and Immunology, University of Otago, Otago, New Zealand
| | - Thomas King
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Matthias Friedrich
- The Kennedy Institute of Rheumatology, Roosevelt Dr., Oxford OX3 7FY, UK
| | - Zoe Christoforidou
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Sarah McCuaig
- The Kennedy Institute of Rheumatology, Roosevelt Dr., Oxford OX3 7FY, UK
| | - Mastura Neyazi
- The Kennedy Institute of Rheumatology, Roosevelt Dr., Oxford OX3 7FY, UK
| | | | - Joachim Hagel
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, Roosevelt Dr., Oxford OX3 7FY, UK
| | | | - Val Millar
- Target Discovery Institute, Roosevelt Dr., Oxford OX3 7FZ, UK
| | - Daniel Ebner
- Target Discovery Institute, Roosevelt Dr., Oxford OX3 7FZ, UK
| | - Rajesh Lamichhane
- Department of Microbiology and Immunology, University of Otago, Otago, New Zealand
| | - James Ussher
- Department of Microbiology and Immunology, University of Otago, Otago, New Zealand
| | - Timothy S C Hinks
- NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK; Respiratory Medicine Unit, Nuffield Department of Medicine Experimental Medicine, University of Oxford, Oxford OX3 9DU, UK; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Emanuele Marchi
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Chris Willberg
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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Christoforidou Z, Burt R, Mulder I, Gill BP, Pluske J, Kelly D, Stokes CR, Bailey M, Lewis MC. Development of Immune Cells in the Intestinal Mucosa Can Be Affected by Intensive and Extensive Farm Environments, and Antibiotic Use. Front Immunol 2018; 9:1061. [PMID: 29868021 PMCID: PMC5964130 DOI: 10.3389/fimmu.2018.01061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/27/2018] [Indexed: 12/30/2022] Open
Abstract
Epidemiological studies have demonstrated that exposure to farm environments during childhood can be linked to reductions in the incidence of immune disorders, but generating an appropriate model is difficult. 108 half-sibling piglets were born on either extensive (outdoor) or intensive (indoor) farms: at 1 day old, a subset of piglets from each litter were transferred to a high-hygiene isolator facility to create differences in rearing environment either during birth/first day or during the subsequent 56 days of life. Interactions between CD14, CD16, MHCIIDR, and capillary endothelium were assessed using four-color quantitative fluorescence immunohistology. Effects of birth and rearing environment on the antigen-presenting microenvironment of the proximal and distal jejunum (professional and stromal) were apparent at 5, 28, and 56 days after birth However, effects on CD4+CD25+Foxp3+ regulatory T-cells (Tregs) in the intestinal mucosa were apparent around weaning at 28 days but had disappeared by 56 days. These Tregs were reduced in the isolator piglets compared to their farm-reared siblings, but this effect was less marked in piglets born on the extensive farm and required administration of antibiotics. Our results suggest that there may be at least two windows of opportunity in which different farm environments were influencing immune development: one during the perinatal period (up to the first day of life), and one during later infancy. Furthermore, the differences on Tregs suggest that the effects of early life influences may be particularly critical around weaning.
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Affiliation(s)
- Zoe Christoforidou
- Infection and Immunity, School of Veterinary Science, University of Bristol, Langford, United Kingdom
| | - Rachel Burt
- Infection and Immunity, School of Veterinary Science, University of Bristol, Langford, United Kingdom
| | - Imke Mulder
- Gut Immunology Group, Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Bhupinder P Gill
- Agricultural and Horticultural Development Board, Milton Keynes, United Kingdom
| | - John Pluske
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Denise Kelly
- Gut Immunology Group, Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Christopher R Stokes
- Infection and Immunity, School of Veterinary Science, University of Bristol, Langford, United Kingdom
| | - Michael Bailey
- Infection and Immunity, School of Veterinary Science, University of Bristol, Langford, United Kingdom
| | - Marie C Lewis
- Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading, United Kingdom
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