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Ng MTH, Borst R, Gacaferi H, Davidson S, Ackerman JE, Johnson PA, Machado CC, Reekie I, Attar M, Windell D, Kurowska-Stolarska M, MacDonald L, Alivernini S, Garvilles M, Jansen K, Bhalla A, Lee A, Charlesworth J, Chowdhury R, Klenerman P, Powell K, Hackstein CP, Furniss D, Rees J, Gilroy D, Coles M, Carr AJ, Sansom SN, Buckley CD, Dakin SG. A single cell atlas of frozen shoulder capsule identifies features associated with inflammatory fibrosis resolution. Nat Commun 2024; 15:1394. [PMID: 38374174 PMCID: PMC10876649 DOI: 10.1038/s41467-024-45341-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
Frozen shoulder is a spontaneously self-resolving chronic inflammatory fibrotic human disease, which distinguishes the condition from most fibrotic diseases that are progressive and irreversible. Using single-cell analysis, we identify pro-inflammatory MERTKlowCD48+ macrophages and MERTK + LYVE1 + MRC1+ macrophages enriched for negative regulators of inflammation which co-exist in frozen shoulder capsule tissues. Micro-cultures of patient-derived cells identify integrin-mediated cell-matrix interactions between MERTK+ macrophages and pro-resolving DKK3+ and POSTN+ fibroblasts, suggesting that matrix remodelling plays a role in frozen shoulder resolution. Cross-tissue analysis reveals a shared gene expression cassette between shoulder capsule MERTK+ macrophages and a respective population enriched in synovial tissues of rheumatoid arthritis patients in disease remission, supporting the concept that MERTK+ macrophages mediate resolution of inflammation and fibrosis. Single-cell transcriptomic profiling and spatial analysis of human foetal shoulder tissues identify MERTK + LYVE1 + MRC1+ macrophages and DKK3+ and POSTN+ fibroblast populations analogous to those in frozen shoulder, suggesting that the template to resolve fibrosis is established during shoulder development. Crosstalk between MerTK+ macrophages and pro-resolving DKK3+ and POSTN+ fibroblasts could facilitate resolution of frozen shoulder, providing a basis for potential therapeutic resolution of persistent fibrotic diseases.
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Affiliation(s)
| | | | | | | | | | | | - Caio C Machado
- University of Oxford, Oxford, UK
- University of Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | - Lucy MacDonald
- Research into Inflammatory Arthritis Centre Versus Arthritis (RACE), University of Glasgow, Glasgow, UK
| | - Stefano Alivernini
- Fondazione Policlinico Universitario Agostino Gemelli - IRCCS, Rome, Italy
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Garvilles M, Coles M. Adipose tissue maintains healthy joint fibroblasts via cortisol signalling. Nat Rev Immunol 2024; 24:4. [PMID: 38057450 DOI: 10.1038/s41577-023-00977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Affiliation(s)
| | - Mark Coles
- Preprint Club, University of Oxford, Oxford, UK
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Johnson PA, Ackerman JE, Kurowska-Stolarska M, Coles M, Buckley CD, Dakin SG. Three-dimensional, in-vitro approaches for modelling soft-tissue joint diseases. Lancet Rheumatol 2023; 5:e553-e563. [PMID: 38251499 DOI: 10.1016/s2665-9913(23)00190-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 01/23/2024]
Abstract
Diseases affecting the soft tissues of the joint represent a considerable global health burden, causing pain and disability and increasing the likelihood of developing metabolic comorbidities. Current approaches to investigating the cellular basis of joint diseases, including osteoarthritis, rheumatoid arthritis, tendinopathy, and arthrofibrosis, involve well phenotyped human tissues, animal disease models, and in-vitro tissue culture models. Inherent challenges in preclinical drug discovery have driven the development of state-of-the-art, in-vitro human tissue models to rapidly advance therapeutic target discovery. The clinical potential of such models has been substantiated through successful recapitulation of the pathobiology of cancers, generating accurate predictions of patient responses to therapeutics and providing a basis for equivalent musculoskeletal models. In this Review, we discuss the requirement to develop physiologically relevant three-dimensional (3D) culture systems that could advance understanding of the cellular and molecular basis of diseases that affect the soft tissues of the joint. We discuss the practicalities and challenges associated with modelling the complex extracellular matrix of joint tissues-including cartilage, synovium, tendon, and ligament-highlighting the importance of considering the joint as a whole organ to encompass crosstalk across tissues and between diverse cell types. The design of bespoke in-vitro models for soft-tissue joint diseases has the potential to inform functional studies of the cellular and molecular mechanisms underlying disease onset, progression, and resolution. Use of these models could inform precision therapeutic targeting and advance the field towards personalised medicine for patients with common musculoskeletal diseases.
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Affiliation(s)
- Peter A Johnson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Jessica E Ackerman
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Mark Coles
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Christopher D Buckley
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Stephanie G Dakin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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Drennan PG, Karponis D, Richards D, Coles M, Fullerton JN. In vivo human keyhole limpet hemocyanin challenge in early phase drug development: A systematic review. Clin Transl Sci 2023; 16:357-382. [PMID: 36420645 PMCID: PMC10014697 DOI: 10.1111/cts.13457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022] Open
Abstract
Experimental exposure of healthy volunteers to the T-cell dependent neoantigen keyhole limpet hemocyanin (KLH) permits the evaluation of immunomodulatory investigational medicinal product (IMP) pharmacology prior to the recruitment of patient populations. Despite widespread use, no standardized approach to the design and conduct of such studies has been agreed. The objective of this systematic review was to survey the published literature where KLH was used as a challenge agent, describing methodology, therapeutic targets addressed, and pharmacodynamic outcome measures. We searched MEDLINE, EMBASE, clinicaltrials.gov, and Cochrane CENTRAL for studies using KLH challenge in humans between January 1, 1994, and April 1, 2022. We described key study features, including KLH formulation, dose, use of adjuvants, route of administration, co-administered IMPs, and end points. Of 2421 titles and abstracts screened, 46 met the inclusion criteria, including 14 (31%) early phase trials of IMP, of which 10 (71%) targeted T-cell co-stimulation. IMPs with diverse mechanisms demonstrated modulation of the humoral response to KLH, suggesting limited specificity of this end point. Two early phase IMP studies (14%) described the response to intradermal re-challenge (delayed type hypersensitivity). Challenge regimens for IMP assessment were often incompletely described, and exhibited marked heterogeneity, including primary KLH dose (25-fold variation: 100-2500 mcg), KLH formulation, and co-administration with adjuvants. Methodological heterogeneity and failure to exploit the access to tissue-level mechanism-relevant end points afforded by KLH challenge has impaired the translational utility of this paradigm to date. Future standardization, characterization, and methodological development is required to permit tailored, appropriately powered, mechanism-dependent study design to optimize drug development decisions.
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Affiliation(s)
- Philip G Drennan
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Duncan Richards
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Medicine, University of Oxford, Oxford, UK
| | - Mark Coles
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Medicine, University of Oxford, Oxford, UK
| | - James N Fullerton
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Medicine, University of Oxford, Oxford, UK
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Abstract
Fibroblasts are known for their ability to make and modify the extracellular matrix. However, there is more to them than meets the eye. It is now clear that they help define tissue microenvironments and support immune responses in organs. As technology advances, we have started to uncover the secrets of fibroblasts. In this Essay, we present fibroblasts as not only the builders and renovators of tissue environments but also the rheostat cells for immune circuits. Although they perform location-specific functions, they do not have badges of fixed identity. Instead, they display a spectrum of functional states and can swing between these states depending on the needs of the organ. As fibroblasts participate in a range of activities both in health and disease, finding the key factors that alter their development and functional states will be an important goal to restore homeostasis in maladapted tissues.
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Affiliation(s)
- Zhi Yi Wong
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Eloise Nee
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Mark Coles
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Christopher D. Buckley
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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6
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Korsunsky I, Wei K, Pohin M, Kim EY, Barone F, Major T, Taylor E, Ravindran R, Kemble S, Watts GFM, Jonsson AH, Jeong Y, Athar H, Windell D, Kang JB, Friedrich M, Turner J, Nayar S, Fisher BA, Raza K, Marshall JL, Croft AP, Tamura T, Sholl LM, Vivero M, Rosas IO, Bowman SJ, Coles M, Frei AP, Lassen K, Filer A, Powrie F, Buckley CD, Brenner MB, Raychaudhuri S. Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases. Med 2022; 3:481-518.e14. [PMID: 35649411 PMCID: PMC9271637 DOI: 10.1016/j.medj.2022.05.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Pro-inflammatory fibroblasts are critical for pathogenesis in rheumatoid arthritis, inflammatory bowel disease, interstitial lung disease, and Sjögren's syndrome and represent a novel therapeutic target for chronic inflammatory disease. However, the heterogeneity of fibroblast phenotypes, exacerbated by the lack of a common cross-tissue taxonomy, has limited our understanding of which pathways are shared by multiple diseases. METHODS We profiled fibroblasts derived from inflamed and non-inflamed synovium, intestine, lungs, and salivary glands from affected individuals with single-cell RNA sequencing. We integrated all fibroblasts into a multi-tissue atlas to characterize shared and tissue-specific phenotypes. FINDINGS Two shared clusters, CXCL10+CCL19+ immune-interacting and SPARC+COL3A1+ vascular-interacting fibroblasts, were expanded in all inflamed tissues and mapped to dermal analogs in a public atopic dermatitis atlas. We confirmed these human pro-inflammatory fibroblasts in animal models of lung, joint, and intestinal inflammation. CONCLUSIONS This work represents a thorough investigation into fibroblasts across organ systems, individual donors, and disease states that reveals shared pathogenic activation states across four chronic inflammatory diseases. FUNDING Grant from F. Hoffmann-La Roche (Roche) AG.
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Affiliation(s)
- Ilya Korsunsky
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mathilde Pohin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Edy Y Kim
- Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Francesca Barone
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Triin Major
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
| | - Emily Taylor
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
| | - Rahul Ravindran
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Samuel Kemble
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - A Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yunju Jeong
- Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Humra Athar
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dylan Windell
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Joyce B Kang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Matthias Friedrich
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Jason Turner
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
| | - Saba Nayar
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Benjamin A Fisher
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Karim Raza
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Jennifer L Marshall
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Adam P Croft
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK
| | - Tomoyoshi Tamura
- Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Marina Vivero
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Dallas, TX 75246, USA
| | - Simon J Bowman
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Mark Coles
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK
| | - Andreas P Frei
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Kara Lassen
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, Basel 4070, Switzerland
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; Birmingham Tissue Analytics, Institute for Inflammation and Ageing, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK.
| | - Christopher D Buckley
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, University of Oxford, Oxford OX3 7FY, UK; Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2WD, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TT, UK.
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester M14 9PR UK.
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7
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Isaacs JD, Brockbank S, Pedersen AW, Hilkens C, Anderson A, Stocks P, Lendrem D, Tarn J, Smith GR, Allen B, Casement J, Diboll J, Harry R, Cooles FAH, Cope AP, Simpson G, Toward R, Noble H, Parke A, Wu W, Clarke F, Scott D, Scott IC, Galloway J, Lempp H, Ibrahim F, Schwank S, Molyneux G, Lazarov T, Geissmann F, Goodyear CS, McInnes IB, Donnelly I, Gilmour A, Virlan AT, Porter D, Ponchel F, Emery P, El-Jawhari J, Parmar R, McDermott MF, Fisher BA, Young SP, Jones P, Raza K, Filer A, Pitzalis C, Barnes MR, Watson DS, Henkin R, Thorborn G, Fossati-Jimack L, Kelly S, Humby F, Bombardieri M, Rana S, Jia Z, Goldmann K, Lewis M, Ng S, Barbosa-Silva A, Tzanis E, Gallagher-Syed A, John CR, Ehrenstein MR, Altobelli G, Martins S, Nguyen D, Ali H, Ciurtin C, Buch M, Symmons D, Worthington J, Bruce IN, Sergeant JC, Verstappen SMM, Stirling F, Hughes-Morley A, Tom B, Farewell V, Zhong Y, Taylor PC, Buckley CD, Keidel S, Cuff C, Levesque M, Long A, Liu Z, Lipsky S, Harvey B, Macoritto M, Hong F, Kaymakcalan S, Tsuji W, Sabin T, Ward N, Talbot S, Padhji D, Sleeman M, Finch D, Herath A, Lindholm C, Jenkins M, Ho M, Hollis S, Marshall C, Parker G, Page M, Edwards H, Cuza A, Gozzard N, Pandis I, Rowe A, Capdevila FB, Loza MJ, Curran M, Verbeeck D, Dan Baker, Mela CM, Vranic I, Mela CT, Wright S, Rowell L, Vernon E, Joseph N, Payne N, Rao R, Binks M, Belson A, Ludbrook V, Hicks K, Tipney H, Ellis J, Hasan S, Didierlaurent A, Burny W, Haynes A, Larminie C, Harris R, Dastros-Pitei D, Carini C, Kola B, Jelinsky S, Hodge M, Maciejewski M, Ziemek D, Schulz-Knappe P, Zucht HD, Budde P, Coles M, Butler JA, Read S. RA-MAP, molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients. Sci Data 2022; 9:196. [PMID: 35534493 PMCID: PMC9085807 DOI: 10.1038/s41597-022-01264-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/04/2022] [Indexed: 11/21/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of early, drug naive RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 healthy vaccine recipients for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into immune-mediated disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.
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Ahern DJ, Ai Z, Ainsworth M, Allan C, Allcock A, Angus B, Ansari MA, Arancibia-Cárcamo CV, Aschenbrenner D, Attar M, Baillie JK, Barnes E, Bashford-Rogers R, Bashyal A, Beer S, Berridge G, Beveridge A, Bibi S, Bicanic T, Blackwell L, Bowness P, Brent A, Brown A, Broxholme J, Buck D, Burnham KL, Byrne H, Camara S, Candido Ferreira I, Charles P, Chen W, Chen YL, Chong A, Clutterbuck EA, Coles M, Conlon CP, Cornall R, Cribbs AP, Curion F, Davenport EE, Davidson N, Davis S, Dendrou CA, Dequaire J, Dib L, Docker J, Dold C, Dong T, Downes D, Drakesmith H, Dunachie SJ, Duncan DA, Eijsbouts C, Esnouf R, Espinosa A, Etherington R, Fairfax B, Fairhead R, Fang H, Fassih S, Felle S, Fernandez Mendoza M, Ferreira R, Fischer R, Foord T, Forrow A, Frater J, Fries A, Gallardo Sanchez V, Garner LC, Geeves C, Georgiou D, Godfrey L, Golubchik T, Gomez Vazquez M, Green A, Harper H, Harrington HA, Heilig R, Hester S, Hill J, Hinds C, Hird C, Ho LP, Hoekzema R, Hollis B, Hughes J, Hutton P, Jackson-Wood MA, Jainarayanan A, James-Bott A, Jansen K, Jeffery K, Jones E, Jostins L, Kerr G, Kim D, Klenerman P, Knight JC, Kumar V, Kumar Sharma P, Kurupati P, Kwok A, Lee A, Linder A, Lockett T, Lonie L, Lopopolo M, Lukoseviciute M, Luo J, Marinou S, Marsden B, Martinez J, Matthews PC, Mazurczyk M, McGowan S, McKechnie S, Mead A, Mentzer AJ, Mi Y, Monaco C, Montadon R, Napolitani G, Nassiri I, Novak A, O'Brien DP, O'Connor D, O'Donnell D, Ogg G, Overend L, Park I, Pavord I, Peng Y, Penkava F, Pereira Pinho M, Perez E, Pollard AJ, Powrie F, Psaila B, Quan TP, Repapi E, Revale S, Silva-Reyes L, Richard JB, Rich-Griffin C, Ritter T, Rollier CS, Rowland M, Ruehle F, Salio M, Sansom SN, Sanches Peres R, Santos Delgado A, Sauka-Spengler T, Schwessinger R, Scozzafava G, Screaton G, Seigal A, Semple MG, Sergeant M, Simoglou Karali C, Sims D, Skelly D, Slawinski H, Sobrinodiaz A, Sousos N, Stafford L, Stockdale L, Strickland M, Sumray O, Sun B, Taylor C, Taylor S, Taylor A, Thongjuea S, Thraves H, Todd JA, Tomic A, Tong O, Trebes A, Trzupek D, Tucci FA, Turtle L, Udalova I, Uhlig H, van Grinsven E, Vendrell I, Verheul M, Voda A, Wang G, Wang L, Wang D, Watkinson P, Watson R, Weinberger M, Whalley J, Witty L, Wray K, Xue L, Yeung HY, Yin Z, Young RK, Youngs J, Zhang P, Zurke YX. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity. Cell 2022; 185:916-938.e58. [PMID: 35216673 PMCID: PMC8776501 DOI: 10.1016/j.cell.2022.01.012] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/16/2021] [Accepted: 01/17/2022] [Indexed: 02/06/2023]
Abstract
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19.
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Fisher BA, Veenith T, Slade D, Gaskell C, Rowland M, Whitehouse T, Scriven J, Parekh D, Balasubramaniam MS, Cooke G, Morley N, Gabriel Z, Wise MP, Porter J, McShane H, Ho LP, Newsome PN, Rowe A, Sharpe R, Thickett DR, Bion J, Gates S, Richards D, Kearns P, Turner R, Libri V, Mussai F, Middleton G, Bowden S, Bangash M, Gao-Smith F, Patel J, Sapey E, Thomas M, Coles M, Watkinson P, Rahman N, Angus B, Mentzer AJ, Novak A, Feldman M, Richter A, Faustini S, Bathurst C, Van de Wiel J, Mee S, James K, Rahman B, Turner K, Hill A, Gordon A, Yap C, Matthay M, McAuley D, Hall A, Dark P, McMichael A. Namilumab or infliximab compared with standard of care in hospitalised patients with COVID-19 (CATALYST): a randomised, multicentre, multi-arm, multistage, open-label, adaptive, phase 2, proof-of-concept trial. Lancet Respir Med 2022; 10:255-266. [PMID: 34922649 PMCID: PMC8676420 DOI: 10.1016/s2213-2600(21)00460-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Dysregulated inflammation is associated with poor outcomes in COVID-19. We aimed to assess the efficacy of namilumab (a granulocyte-macrophage colony stimulating factor inhibitor) and infliximab (a tumour necrosis factor inhibitor) in hospitalised patients with COVID-19, to prioritise agents for phase 3 trials. METHODS In this randomised, multicentre, multi-arm, multistage, parallel-group, open-label, adaptive, phase 2, proof-of-concept trial (CATALYST), we recruited patients (aged ≥16 years) admitted to hospital with COVID-19 pneumonia and C-reactive protein (CRP) concentrations of 40 mg/L or greater, at nine hospitals in the UK. Participants were randomly assigned with equal probability to usual care or usual care plus a single intravenous dose of namilumab (150 mg) or infliximab (5 mg/kg). Randomisation was stratified by care location within the hospital (ward vs intensive care unit [ICU]). Patients and investigators were not masked to treatment allocation. The primary endpoint was improvement in inflammation, measured by CRP concentration over time, analysed using Bayesian multilevel models. This trial is now complete and is registered with ISRCTN, 40580903. FINDINGS Between June 15, 2020, and Feb 18, 2021, we screened 299 patients and 146 were enrolled and randomly assigned to usual care (n=54), namilumab (n=57), or infliximab (n=35). For the primary outcome, 45 patients in the usual care group were compared with 52 in the namilumab group, and 29 in the usual care group were compared with 28 in the infliximab group. The probabilities that the interventions were superior to usual care alone in reducing CRP concentration over time were 97% for namilumab and 15% for infliximab; the point estimates for treatment-time interactions were -0·09 (95% CI -0·19 to 0·00) for namilumab and 0·06 (-0·05 to 0·17) for infliximab. 134 adverse events occurred in 30 (55%) of 55 patients in the namilumab group compared with 145 in 29 (54%) of 54 in the usual care group. 102 adverse events occurred in 20 (69%) of 29 patients in the infliximab group compared with 112 in 17 (50%) of 34 in the usual care group. Death occurred in six (11%) patients in the namilumab group compared with ten (19%) in the usual care group, and in four (14%) in the infliximab group compared with five (15%) in the usual care group. INTERPRETATION Namilumab, but not infliximab, showed proof-of-concept evidence for reduction in inflammation-as measured by CRP concentration-in hospitalised patients with COVID-19 pneumonia. Namilumab should be prioritised for further investigation in COVID-19. FUNDING Medical Research Council.
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Affiliation(s)
- Benjamin A Fisher
- Rheumatology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK,Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK,National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK,Correspondence to: Dr Benjamin A Fisher, Rheumatology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tonny Veenith
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK,Department of Critical Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Daniel Slade
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Charlotte Gaskell
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Matthew Rowland
- Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Tony Whitehouse
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK,Department of Critical Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - James Scriven
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK,Department of Infectious Diseases, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Dhruv Parekh
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK,Department of Critical Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK,Department of Respiratory Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | | | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, UK
| | - Nick Morley
- Department of Haematology, Royal Hallamshire Hospital, Sheffield, UK
| | - Zoe Gabriel
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Matthew P Wise
- Department of Critical Care Medicine, University Hospital of Wales, Cardiff, UK
| | - Joanna Porter
- Department of Respiratory Medicine, University College Hospital, London, UK
| | | | - Ling-Pei Ho
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK,Oxford Interstitial Lung Disease Service, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Philip N Newsome
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK,National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Anna Rowe
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK,National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Rowena Sharpe
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - David R Thickett
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK,Department of Respiratory Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Julian Bion
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK,Department of Critical Care Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Simon Gates
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Duncan Richards
- Oxford Clinical Trials Research Unit, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Pamela Kearns
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK,National Institute for Health Research (NIHR) Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
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Shrivastava M, Feng J, Coles M, Clark B, Islam A, Dumeaux V, Whiteway M. Modulation of the complex regulatory network for methionine biosynthesis in fungi. Genetics 2021; 217:6078591. [PMID: 33724418 DOI: 10.1093/genetics/iyaa049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/07/2020] [Indexed: 01/19/2023] Open
Abstract
The assimilation of inorganic sulfate and the synthesis of the sulfur-containing amino acids methionine and cysteine is mediated by a multibranched biosynthetic pathway. We have investigated this circuitry in the fungal pathogen Candida albicans, which is phylogenetically intermediate between the filamentous fungi and Saccharomyces cerevisiae. In S. cerevisiae, this pathway is regulated by a collection of five transcription factors (Met4, Cbf1, Met28, and Met31/Met32), while in the filamentous fungi the pathway is controlled by a single Met4-like factor. We found that in C. albicans, the Met4 ortholog is also a core regulator of methionine biosynthesis, where it functions together with Cbf1. While C. albicans encodes this Met4 protein, a Met4 paralog designated Met28 (Orf19.7046), and a Met31 protein, deletion, and activation constructs suggest that of these proteins only Met4 is actually involved in the regulation of methionine biosynthesis. Both Met28 and Met31 are linked to other functions; Met28 appears essential, and Met32 appears implicated in the regulation of genes of central metabolism. Therefore, while S. cerevisiae and C. albicans share Cbf1 and Met4 as central elements of the methionine biosynthesis control, the other proteins that make up the circuit in S. cerevisiae are not members of the C. albicans control network, and so the S. cerevisiae circuit likely represents a recently evolved arrangement.
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Affiliation(s)
| | - Jinrong Feng
- Medical School, Nantong University, Nangtong, Jiangsu, China
| | - Mark Coles
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Benjamin Clark
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Amjad Islam
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Vanessa Dumeaux
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Malcolm Whiteway
- Depatment of Biology, Concordia University, Montreal, QC, Canada
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11
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Aschenbrenner D, Quaranta M, Banerjee S, Ilott N, Jansen J, Steere B, Chen YH, Ho S, Cox K, Arancibia-Cárcamo CV, Coles M, Gaffney E, Travis SP, Denson L, Kugathasan S, Schmitz J, Powrie F, Sansom SN, Uhlig HH. Deconvolution of monocyte responses in inflammatory bowel disease reveals an IL-1 cytokine network that regulates IL-23 in genetic and acquired IL-10 resistance. Gut 2021; 70:1023-1036. [PMID: 33037057 PMCID: PMC8108288 DOI: 10.1136/gutjnl-2020-321731] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/16/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Dysregulated immune responses are the cause of IBDs. Studies in mice and humans suggest a central role of interleukin (IL)-23-producing mononuclear phagocytes in disease pathogenesis. Mechanistic insights into the regulation of IL-23 are prerequisite for selective IL-23 targeting therapies as part of personalised medicine. DESIGN We performed transcriptomic analysis to investigate IL-23 expression in human mononuclear phagocytes and peripheral blood mononuclear cells. We investigated the regulation of IL-23 expression and used single-cell RNA sequencing to derive a transcriptomic signature of hyperinflammatory monocytes. Using gene network correlation analysis, we deconvolved this signature into components associated with homeostasis and inflammation in patient biopsy samples. RESULTS We characterised monocyte subsets of healthy individuals and patients with IBD that express IL-23. We identified autosensing and paracrine sensing of IL-1α/IL-1β and IL-10 as key cytokines that control IL-23-producing monocytes. Whereas Mendelian genetic defects in IL-10 receptor signalling induced IL-23 secretion after lipopolysaccharide stimulation, whole bacteria exposure induced IL-23 production in controls via acquired IL-10 signalling resistance. We found a transcriptional signature of IL-23-producing inflammatory monocytes that predicted both disease and resistance to antitumour necrosis factor (TNF) therapy and differentiated that from an IL-23-associated lymphocyte differentiation signature that was present in homeostasis and in disease. CONCLUSION Our work identifies IL-10 and IL-1 as critical regulators of monocyte IL-23 production. We differentiate homeostatic IL-23 production from hyperinflammation-associated IL-23 production in patients with severe ulcerating active Crohn's disease and anti-TNF treatment non-responsiveness. Altogether, we identify subgroups of patients with IBD that might benefit from IL-23p19 and/or IL-1α/IL-1β-targeting therapies upstream of IL-23.
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Affiliation(s)
- Dominik Aschenbrenner
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Maria Quaranta
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy
| | - Soumya Banerjee
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- Department of Psychology, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Nicholas Ilott
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Joanneke Jansen
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- Wolfson Centre for Mathematical Biology, University of Oxford, Oxford, Oxfordshire, UK
| | - Boyd Steere
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Yin-Huai Chen
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Stephen Ho
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Karen Cox
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Carolina V Arancibia-Cárcamo
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Mark Coles
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Eamonn Gaffney
- Wolfson Centre for Mathematical Biology, University of Oxford, Oxford, Oxfordshire, UK
| | - Simon Pl Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
| | - Lee Denson
- Pediatric Gastroenterology, Cincinnati Childrens Hospital Medical Center, Cincinnati, Ohio, USA
| | - Subra Kugathasan
- Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jochen Schmitz
- Immunology Translational Sciences, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Stephen N Sansom
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, Oxfordshire, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, University of Oxford, Oxford, Oxfordshire, UK
- Department of Paediatrics, University of Oxford, Oxford, Oxfordshire, UK
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12
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Ye W, Olsson-Brown A, Watson RA, Cheung VTF, Morgan RD, Nassiri I, Cooper R, Taylor CA, Akbani U, Brain O, Matin RN, Coupe N, Middleton MR, Coles M, Sacco JJ, Payne MJ, Fairfax BP. Checkpoint-blocker-induced autoimmunity is associated with favourable outcome in metastatic melanoma and distinct T-cell expression profiles. Br J Cancer 2021; 124:1661-1669. [PMID: 33723392 PMCID: PMC8110747 DOI: 10.1038/s41416-021-01310-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 12/14/2020] [Revised: 01/13/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Immune checkpoint blockers (ICBs) activate CD8+ T cells, eliciting both anti-cancer activity and immune-related adverse events (irAEs). The relationship of irAEs with baseline parameters and clinical outcome is unclear. METHODS Retrospective evaluation of irAEs on survival was performed across primary (N = 144) and secondary (N = 211) independent cohorts of patients with metastatic melanoma receiving single agent (pembrolizumab/nivolumab-sICB) or combination (nivolumab and ipilimumab-cICB) checkpoint blockade. RNA from pre-treatment and post-treatment CD8+ T cells was sequenced and differential gene expression according to irAE development assessed. RESULTS 58.3% of patients developed early irAEs and this was associated with longer progression-free (PFS) and overall survival (OS) across both cohorts (log-rank test, OS: P < 0.0001). Median survival for patients without irAEs was 16.6 months (95% CI: 10.9-33.4) versus not-reached (P = 2.8 × 10-6). Pre-treatment monocyte and neutrophil counts, but not BMI, were additional predictors of clinical outcome. Differential expression of numerous gene pathway members was observed in CD8+ T cells according to irAE development, and patients not developing irAEs demonstrating upregulated CXCR1 pre- and post-treatment. CONCLUSIONS Early irAE development post-ICB is associated with favourable survival in MM. Development of irAEs is coupled to expression of numerous gene pathways, suggesting irAE development in-part reflects baseline immune activation.
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Affiliation(s)
- Weiyu Ye
- grid.4991.50000 0004 1936 8948Oxford University Clinical Academic Graduate School, University of Oxford, Oxford, UK
| | - Anna Olsson-Brown
- grid.418624.d0000 0004 0614 6369The Clatterbridge Cancer Centre, Wirral, UK ,grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Robert A. Watson
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Vincent T. F. Cheung
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Robert D. Morgan
- grid.412917.80000 0004 0430 9259Department of Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Isar Nassiri
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rosalin Cooper
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chelsea A. Taylor
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Umair Akbani
- grid.418624.d0000 0004 0614 6369The Clatterbridge Cancer Centre, Wirral, UK ,grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Oliver Brain
- grid.4991.50000 0004 1936 8948Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Rubeta N. Matin
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.415719.f0000 0004 0488 9484Department of Dermatology, Churchill Hospital, Oxford, UK
| | - Nicholas Coupe
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK
| | - Mark R. Middleton
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.8348.70000 0001 2306 7492NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Mark Coles
- grid.8348.70000 0001 2306 7492NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Joseph J. Sacco
- grid.418624.d0000 0004 0614 6369The Clatterbridge Cancer Centre, Wirral, UK ,grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK
| | - Miranda J. Payne
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK
| | - Benjamin P. Fairfax
- grid.415719.f0000 0004 0488 9484Department of Oncology, Churchill Hospital, Oxford, UK ,grid.4991.50000 0004 1936 8948The MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK ,grid.8348.70000 0001 2306 7492NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
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Olsson-Brown A, Scheppers J, Bossenbroek H, van Mierloo M, Coles M, Wagg J. 1974P MediGrid: A novel interface for real time collection and analysis of real world clinical data. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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14
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Acenowr C, Coles M, Stewart E. 0248 Does Attentional Control Relate to Sleep Disruption and Repetitive Negative Thinking? Sleep 2020. [DOI: 10.1093/sleep/zsaa056.246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Insomnia is associated with increased repetitive negative thinking (RNT) and poor attentional control. There is increasing interest in the relevance of these processes for psychopathology. For example, Cox, Cole, Kramer and Olatunji (2018) proposed that focusing and shifting in attentional control may help explain the link between sleep disturbance and RNT. In support, attentional focus was found to be significant in the relationship between insomnia and RNT. As this study looked at disorder-specific measures of RNT and only insomnia, the current study aimed to replicate and extend the findings by also examining circadian sleep disruption and transdiagnostic RNT.
Methods
The current study included 127 participants. Sleep disruption was assessed by the SLEEP-50 (Spoormaker, Verbeek, van den Bout & Klip, 2005). This measure provides several subscale scores, including disruption in circadian rhythms and insomnia. The Attentional Control Scale (Derryberry & Reed, 2002) is a measure of attentional focus and shifting which was also utilized. Lastly, the Perseverative Thinking Questionnaire (Ehring et al., 2011) is a widely used transdiagnostic measure of RNT.
Results
Pearson’s Correlations indicated that both insomnia and circadian disruptions were significantly associated with RNT (insomnia, r=.27; circadian, r=.24). Mirroring the results of Cox, Cole, Kramer and Olatunji, attentional focus was significant (insomnia, r=-.29; circadian, r=-.28), whereas attentional shift was not (insomnia, r=.02; circadian, r=.06).
Conclusion
The connection between sleep disruption and factors that contribute to psychopathology needs to be better understood. This study differentiates types of attention and their relation to insomnia and circadian sleep disruption, and RNT. If attentional focus can link sleep disruption and RNT, clinicians can move one step closer to understanding the development of risk factors that may jeopardize an individual.
Support
n/a
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Affiliation(s)
- C Acenowr
- Binghamton University, Binghamton, NY
| | - M Coles
- Binghamton University, Binghamton, NY
| | - E Stewart
- Binghamton University, Binghamton, NY
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Stewart E, Acenowr C, Coles M. 0234 Sleep Timing and Duration Predict Levels of Repetitive Negative Thinking the Following Day. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Several forms of psychopathology characterized by repetitive negative thinking (RNT) are also associated with problems in sleep timing and sleep duration (Morin & Ware, 1996). These relations have been documented in cross-sectional studies but only a few studies have investigated this relation using a prospective design. This study aimed to: (1) replicate cross-sectional findings linking sleep duration and sleep timing to RNT and (2) use prospective longitudinal methods to extend previous research regarding this relation.
Methods
Participants (N = 127) were undergraduates who completed daily measures of sleep, mood, and RNT for 18 days. Participants mean age was 19.31(SD = 1.41) and 49% were male, and 60% were Caucasian. Measures included the Perseverative Thoughts Questionnaire, the Sleep-50, and a Daily Monitoring Questionnaire (DMQ) comprised of items from the Pittsburgh Sleep Quality Index.
Results
Insomnia severity and circadian disruption severity was correlated with RNT, and these relations remained significant after statistically controlling for the influence of negative affect (Insomnia: r(123)=.22, p=.01; Circadian: r(123)=.21, p=.02). When looking longitudinally within person Hierarchical Linear Modeling (HLM) revealed later bedtimes (t(125) = 2.01, p = .05) and shorter sleep durations (t(125) = -3.17, p = .002) were predictors of heightened RNT the next day, even after statistically controlling for negative affect (RNTij=π oj+π 1j(RNT_lag) + π 2j(bedtime_lag/hours slept_lag) + π 3j(mood_lag) + eij). RNT did not predict sleep variables when running the reverse of these models, yet negative affect emerged as a significant predictor of sleep timing (t(125) = 2.41, p = .02) and sleep duration (t(125)= -2.44, p=.02), indicating that mood, not RNT, may influence bedtimes and hours slept.
Conclusion
Results indicate that bedtime and sleep duration may be contributors to RNT, and that sleep disruptions may precede the onset of RNT. If future studies replicate the current study’s findings, then sleep variables may serve as an important area of intervention and prevention of excessive RNT.
Support
N/A
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Affiliation(s)
- E Stewart
- Binghamton University, Binghamton, NY
| | - C Acenowr
- Binghamton University, Binghamton, NY
| | - M Coles
- Binghamton University, Binghamton, NY
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Olsson-Brown A, Lord R, Sacco J, Wagg J, Coles M, Pirmohamed M. Two distinct clinical patterns of checkpoint inhibitor-induced thyroid dysfunction. Endocr Connect 2020; 9:318-325. [PMID: 32163916 PMCID: PMC7159260 DOI: 10.1530/ec-19-0473] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/11/2020] [Indexed: 11/08/2022]
Abstract
INTRODUCTION Immune checkpoint inhibitors can lead to thyroid dysfunction. However, the understanding of the clinical phenotype of ICI-induced thyroid dysfunction in the real-world population is limited. The purpose of this study was to characterise the clinical patterns of dysfunction and evaluate the demographic, biochemical and immunological features associated with this patient cohort. MATERIALS AND METHODS To characterise the longitudinal clinical course of thyroid dysfunction in patients from a single, UK regional cancer centre, a retrospective review of patients was conducted. Inclusion criteria included all patients treated with antiPD-1 checkpoint inhibitors (ICI), either as monotherapy (pembrolizumab/nivolumab) or in combination with a CTLA-4 inhibitor (ipilimumab). Patterns of toxicity were evaluated together with assessment of antibody titres. RESULTS Over 16 months, thyroid dysfunction was seen in 13/90 and 3/13 patients treated with anti-PD1 monotherapy and in combination with ipilimumab, respectively. Patients either developed hyperthyroidism followed by hypothyroidism (12/16) or de novo hypothyroidism (4/16). Most patients were female (n = 11). All patients required thyroid replacement therapy. There was no relationship between clinical pattern of dysfunction and the presence of thyroid autoantibodies. CONCLUSIONS There are two distinct patterns of thyroid dysfunction in ICI-treated patients. Patients with thyroiditis develop subsequent hypothyroidism in the vast majority of cases. The potential benefit from steroids or other therapy to manage the hyperthyroid phase remains unclear. Early detection of these patients through appropriate monitoring will improve clinical management and early hormone replacement, reducing the symptomatic burden of hypothyroidism.
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Affiliation(s)
- Anna Olsson-Brown
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
- The Clatterbridge Cancer Centre, Wirral, UK
- Correspondence should be addressed to A Olsson-Brown:
| | | | - Joseph Sacco
- The Clatterbridge Cancer Centre, Wirral, UK
- Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | | | - Mark Coles
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
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17
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Alden K, Cosgrove J, Coles M, Timmis J. Using Emulation to Engineer and Understand Simulations of Biological Systems. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:302-315. [PMID: 29994223 DOI: 10.1109/tcbb.2018.2843339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Modeling and simulation techniques have demonstrated success in studying biological systems. As the drive to better capture biological complexity leads to more sophisticated simulators, it becomes challenging to perform statistical analyses that help translate predictions into increased understanding. These analyses may require repeated executions and extensive sampling of high-dimensional parameter spaces: analyses that may become intractable due to time and resource limitations. Significant reduction in these requirements can be obtained using surrogate models, or emulators, that can rapidly and accurately predict the output of an existing simulator. We apply emulation to evaluate and enrich understanding of a previously published agent-based simulator of lymphoid tissue organogenesis, showing an ensemble of machine learning techniques can reproduce results obtained using a suite of statistical analyses within seconds. This performance improvement permits incorporation of previously intractable analyses, including multi-objective optimization to obtain parameter sets that yield a desired response, and Approximate Bayesian Computation to assess parametric uncertainty. To facilitate exploitation of emulation in simulation-focused studies, we extend our open source statistical package, spartan, to provide a suite of tools for emulator development, validation, and application. Overcoming resource limitations permits enriched evaluation and refinement, easing translation of simulator insights into increased biological understanding.
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18
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Croft AP, Campos J, Jansen K, Turner JD, Marshall J, Attar M, Savary L, Wehmeyer C, Naylor AJ, Kemble S, Begum J, Dürholz K, Perlman H, Barone F, McGettrick HM, Fearon DT, Wei K, Raychaudhuri S, Korsunsky I, Brenner MB, Coles M, Sansom SN, Filer A, Buckley CD. Distinct fibroblast subsets drive inflammation and damage in arthritis. Nature 2019; 570:246-251. [PMID: 31142839 PMCID: PMC6690841 DOI: 10.1038/s41586-019-1263-7] [Citation(s) in RCA: 477] [Impact Index Per Article: 95.4] [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: 07/22/2018] [Accepted: 05/02/2019] [Indexed: 01/18/2023]
Abstract
The identification of lymphocyte subsets with non-overlapping effector functions has been pivotal to the development of targeted therapies in immune-mediated inflammatory diseases (IMIDs)1,2. However, it remains unclear whether fibroblast subclasses with non-overlapping functions also exist and are responsible for the wide variety of tissue-driven processes observed in IMIDs, such as inflammation and damage3-5. Here we identify and describe the biology of distinct subsets of fibroblasts responsible for mediating either inflammation or tissue damage in arthritis. We show that deletion of fibroblast activation protein-α (FAPα)+ fibroblasts suppressed both inflammation and bone erosions in mouse models of resolving and persistent arthritis. Single-cell transcriptional analysis identified two distinct fibroblast subsets within the FAPα+ population: FAPα+THY1+ immune effector fibroblasts located in the synovial sub-lining, and FAPα+THY1- destructive fibroblasts restricted to the synovial lining layer. When adoptively transferred into the joint, FAPα+THY1- fibroblasts selectively mediate bone and cartilage damage with little effect on inflammation, whereas transfer of FAPα+ THY1+ fibroblasts resulted in a more severe and persistent inflammatory arthritis, with minimal effect on bone and cartilage. Our findings describing anatomically discrete, functionally distinct fibroblast subsets with non-overlapping functions have important implications for cell-based therapies aimed at modulating inflammation and tissue damage.
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Affiliation(s)
- Adam P Croft
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Versus Arthritis Centre of Excellence in the Pathogenesis of Rheumatoid Arthritis, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Joana Campos
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Kathrin Jansen
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Jason D Turner
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Jennifer Marshall
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Moustafa Attar
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Loriane Savary
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Corinna Wehmeyer
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Musculoskeletal Medicine, University of Muenster, Muenster, Germany
| | - Amy J Naylor
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Samuel Kemble
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Jenefa Begum
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Kerstin Dürholz
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Department of Internal Medicine 3, Rheumatology and Immunology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Harris Perlman
- Department of Medicine, Division of Rheumatology, Northwestern University, Feinberg School of Medicine Chicago, Evanston, IL, USA
| | - Francesca Barone
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Helen M McGettrick
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | | | - Kevin Wei
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ilya Korsunsky
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark Coles
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Stephen N Sansom
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Versus Arthritis Centre of Excellence in the Pathogenesis of Rheumatoid Arthritis, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- MRC and Versus Arthritis Centre for Musculoskeletal Ageing Research (CMAR), College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Christopher D Buckley
- Rheumatology Research Group, Institute for Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK.
- Versus Arthritis Centre of Excellence in the Pathogenesis of Rheumatoid Arthritis, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK.
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
- MRC and Versus Arthritis Centre for Musculoskeletal Ageing Research (CMAR), College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK.
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19
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Balzano M, De Grandis M, Vu Manh TP, Chasson L, Bardin F, Farina A, Sergé A, Bidaut G, Charbord P, Hérault L, Bailly AL, Cartier-Michaud A, Boned A, Dalod M, Duprez E, Genever P, Coles M, Bajenoff M, Xerri L, Aurrand-Lions M, Schiff C, Mancini SJ. Nidogen-1 Contributes to the Interaction Network Involved in Pro-B Cell Retention in the Peri-sinusoidal Hematopoietic Stem Cell Niche. Cell Rep 2019; 26:3257-3271.e8. [DOI: 10.1016/j.celrep.2019.02.065] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/24/2018] [Accepted: 02/15/2019] [Indexed: 12/11/2022] Open
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20
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Fu H, Jangani M, Parmar A, Wang G, Coe D, Spear S, Sandrock I, Capasso M, Coles M, Cornish G, Helmby H, Marelli-Berg FM. A Subset of CCL25-Induced Gut-Homing T Cells Affects Intestinal Immunity to Infection and Cancer. Front Immunol 2019; 10:271. [PMID: 30863398 PMCID: PMC6400137 DOI: 10.3389/fimmu.2019.00271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 10/11/2018] [Accepted: 01/31/2019] [Indexed: 12/31/2022] Open
Abstract
Protective immunity relies upon differentiation of T cells into the appropriate subtype required to clear infections and efficient effector T cell localization to antigen-rich tissue. Recent studies have highlighted the role played by subpopulations of tissue-resident memory (TRM) T lymphocytes in the protection from invading pathogens. The intestinal mucosa and associated lymphoid tissue are densely populated by a variety of resident lymphocyte populations, including αβ and γδ CD8+ intraepithelial T lymphocytes (IELs) and CD4+ T cells. While the development of intestinal γδ CD8+ IELs has been extensively investigated, the origin and function of intestinal CD4+ T cells have not been clarified. We report that CCR9 signals delivered during naïve T cell priming promote the differentiation of a population of α4β7+ IFN-γ-producing memory CD4+ T cells, which displays a TRM molecular signature, preferentially localizes to the gastrointestinal (GI) tract and associated lymphoid tissue and cannot be mobilized by remote antigenic challenge. We further show that this population shapes the immune microenvironment of GI tissue, thus affecting effector immunity in infection and cancer.
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Affiliation(s)
- Hongmei Fu
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Maryam Jangani
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Aleesha Parmar
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Guosu Wang
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - David Coe
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Sarah Spear
- Bart's Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Melania Capasso
- Bart's Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mark Coles
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Georgina Cornish
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Helena Helmby
- Department for Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Federica M Marelli-Berg
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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21
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Dakin SG, Coles M, Sherlock JP, Powrie F, Carr AJ, Buckley CD. Author Correction: Pathogenic stromal cells as therapeutic targets in joint inflammation. Nat Rev Rheumatol 2018; 15:61. [PMID: 30498256 DOI: 10.1038/s41584-018-0134-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the originally published version of this article, the acknowledgements and affiliations contained errors. In the acknowledgements, "NIHR Oxford and Birmingham Biomedical Research Centres" and "the Department of Health and Social Care" were incorrectly presented as "NIHR Oxford Biomedical Research Centres" and "the Department of Health". For affiliation 4, "NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Institute of Inflammation and Ageing, Birmingham, UK" was incorrectly presented as "Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK". For affiliation 3, "Institute" was incorrectly spelt. These errors have now been corrected in the HTML and PDF versions of the manuscript.
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Affiliation(s)
- Stephanie G Dakin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Mark Coles
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Jonathan P Sherlock
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Fiona Powrie
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Andrew J Carr
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Christopher D Buckley
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK. .,Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK. .,NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Institute of Inflammation and Ageing, Birmingham, UK.
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22
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Yang J, Cornelissen F, Papazian N, Reijmers RM, Llorian M, Cupedo T, Coles M, Seddon B. IL-7-dependent maintenance of ILC3s is required for normal entry of lymphocytes into lymph nodes. J Exp Med 2018; 215:1069-1077. [PMID: 29472496 PMCID: PMC5881462 DOI: 10.1084/jem.20170518] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 12/21/2017] [Accepted: 01/29/2018] [Indexed: 01/07/2023] Open
Abstract
Yang et al. identify a new function for IL-7 in permitting efficient entry of T and B lymphocytes into lymph nodes. Maintenance of ILC3s by IL-7 is implicated because ILC3-deficient chimeras exhibit similar trafficking defects. IL-7 is essential for the development and homeostasis of T and B lymphocytes and is critical for neonatal lymph node organogenesis because Il7−/− mice lack normal lymph nodes. Whether IL-7 is a continued requirement for normal lymph node structure and function is unknown. To address this, we ablated IL-7 function in normal adult hosts. Either inducible Il7 gene deletion or IL-7R blockade in adults resulted in a rapid loss of lymph node cellularity and a corresponding defect in lymphocyte entry into lymph nodes. Although stromal and dendritic cell components of lymph nodes were present in normal numbers and representation, innate lymphoid cell (ILC) subpopulations were substantially decreased after IL-7 ablation. Testing lymphocyte homing in bone marrow chimeras reconstituted with Rorc−/− bone marrow confirmed that ILC3s in lymph nodes are required for normal lymphocyte homing. Collectively, our data suggest that maintenance of intact lymph nodes relies on IL-7–dependent maintenance of ILC3 cells.
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Affiliation(s)
- Jie Yang
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, Royal Free Hospital, London, England, UK
| | - Ferry Cornelissen
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Natalie Papazian
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Rogier M Reijmers
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Miriam Llorian
- The Francis Crick Institute, Kings Cross, London, England, UK
| | - Tom Cupedo
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mark Coles
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, England, UK
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, Royal Free Hospital, London, England, UK
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23
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Cuthbert RJ, Fragkakis EM, Dunsmuir R, Li Z, Coles M, Marzo-Ortega H, Giannoudis PV, Jones E, El-Sherbiny YM, McGonagle D. Brief Report: Group 3 Innate Lymphoid Cells in Human Enthesis. Arthritis Rheumatol 2017; 69:1816-1822. [PMID: 28511289 DOI: 10.1002/art.40150] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [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: 11/25/2016] [Accepted: 05/09/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Group 3 innate lymphoid cells (ILC3s) play a pivotal role in barrier tissues such as the gut and the skin, two important sites of disease in spondyloarthritis (SpA). This study was undertaken to investigate whether normal or injured human enthesis, a key target tissue in early SpA, harbors ILC3s in entheseal soft tissue and adjacent perientheseal bone. METHODS Interspinous ligament and spinous process bone from donors with no systemic inflammatory disease were collected, enzymatically digested, and immunophenotyped. The immunologic profile of entheseal cells was examined, and the transcriptional profile of sorted ILC3s was compared to that of ILC3s isolated from SpA synovial fluid (SF). To assess the ability of entheseal tissue to produce interleukin-17 (IL-17) and IL-22, entheseal digests were stimulated with IL-23 and IL-1β. Osteoarthritic and ruptured Achilles tendon tissue was examined histologically. RESULTS The proportion of ILCs in human entheseal soft tissue was higher than that in peripheral blood (P = 0.008); entheseal soft tissue and perientheseal bone both had a higher proportion of NKp44+ ILC3s (P = 0.001 and P = 0.043, respectively). Studies of retinoic acid receptor-related orphan nuclear receptor γt (RORγt), STAT3, and IL-23 receptor transcript expression validated the entheseal ILC3 phenotype. Cytokine transcript expression was similar in ILC3s isolated from enthesis and from SpA SF. Stimulation of normal entheseal digests with IL-23/IL-1β led to up-regulation of IL-17A transcript, and histologic examination of injured/damaged entheses revealed the presence of RORγt-expressing cells. CONCLUSION This work shows that human enthesis harbors a resident population of ILC3s, with the potential to participate in the pathogenesis of SpA.
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Affiliation(s)
| | | | | | - Zhi Li
- University of York, York, UK
| | | | - Helena Marzo-Ortega
- University of Leeds and NIHR-Leeds Musculoskeletal and Biomedical Research Unit, Leeds Teaching Hospital Trust, Leeds, UK
| | | | | | - Yasser M El-Sherbiny
- University of Leeds and NIHR-Leeds Musculoskeletal and Biomedical Research Unit, Leeds Teaching Hospital Trust, Leeds, UK, and Mansoura University Hospitals, Mansoura University, Mansoura, Egypt
| | - Dennis McGonagle
- University of Leeds and NIHR-Leeds Musculoskeletal and Biomedical Research Unit, Leeds Teaching Hospital Trust, Leeds, UK
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24
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Nayar S, Campos J, Caamaňo J, Fisher B, Bowman S, Luther S, Coles M, Buckley C, Barone F. O16. STROMAL CELLS IN TERTIARY LYMPHOID STRUCTURES: A NOVEL PATHOGENIC PARADIGM AND THERAPEUTIC TARGET IN SJÖGREN’S SYNDROME. Rheumatology (Oxford) 2017. [DOI: 10.1093/rheumatology/kex061.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Coles M. I58. INVITED SPEAKER. Rheumatology (Oxford) 2017. [DOI: 10.1093/rheumatology/kex060.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Alden K, Timmis J, Andrews PS, Veiga-Fernandes H, Coles M. Extending and Applying Spartan to Perform Temporal Sensitivity Analyses for Predicting Changes in Influential Biological Pathways in Computational Models. IEEE/ACM Trans Comput Biol Bioinform 2017; 14:431-442. [PMID: 26887007 DOI: 10.1109/tcbb.2016.2527654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Through integrating real time imaging, computational modelling, and statistical analysis approaches, previous work has suggested that the induction of and response to cell adhesion factors is the key initiating pathway in early lymphoid tissue development, in contrast to the previously accepted view that the process is triggered by chemokine mediated cell recruitment. These model derived hypotheses were developed using spartan, an open-source sensitivity analysis toolkit designed to establish and understand the relationship between a computational model and the biological system that model captures. Here, we extend the functionality available in spartan to permit the production of statistical analyses that contrast the behavior exhibited by a computational model at various simulated time-points, enabling a temporal analysis that could suggest whether the influence of biological mechanisms changes over time. We exemplify this extended functionality by using the computational model of lymphoid tissue development as a time-lapse tool. By generating results at twelve- hour intervals, we show how the extensions to spartan have been used to suggest that lymphoid tissue development could be biphasic, and predict the time-point when a switch in the influence of biological mechanisms might occur.
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27
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Timmis J, Alden K, Andrews P, Clark E, Nellis A, Naylor B, Coles M, Kaye P. Building confidence in quantitative systems pharmacology models: An engineer's guide to exploring the rationale in model design and development. CPT Pharmacometrics Syst Pharmacol 2017; 6:156-167. [PMID: 27863172 PMCID: PMC5351409 DOI: 10.1002/psp4.12157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/30/2016] [Accepted: 11/06/2016] [Indexed: 11/11/2022]
Abstract
This tutorial promotes good practice for exploring the rationale of systems pharmacology models. A safety systems engineering inspired notation approach provides much needed rigor and transparency in development and application of models for therapeutic discovery and design of intervention strategies. Structured arguments over a model's development, underpinning biological knowledge, and analyses of model behaviors are constructed to determine the confidence that a model is fit for the purpose for which it will be applied.
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Affiliation(s)
- J Timmis
- Department of Electronics, The University of York, York, UK.,SimOmics Limited, York, UK
| | - K Alden
- Department of Electronics, The University of York, York, UK
| | | | | | | | - B Naylor
- Department of Electronics, The University of York, York, UK.,SimOmics Limited, York, UK
| | - M Coles
- Centre for Immunology and Infection, Hull York Medical School/University of York, York, UK
| | - P Kaye
- Centre for Immunology and Infection, Hull York Medical School/University of York, York, UK
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28
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Peters DT, Fung HKH, Levdikov VM, Irmscher T, Warrander FC, Greive SJ, Kovalevskiy O, Isaacs HV, Coles M, Antson AA. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363. Biochemistry 2016; 55:5021-7. [PMID: 27559824 PMCID: PMC5193468 DOI: 10.1021/acs.biochem.6b00682] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein-RNA complex are unknown. Characterization of human Lin28's interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions.
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Affiliation(s)
- Daniel T Peters
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom.,Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Vladimir M Levdikov
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Tobias Irmscher
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Fiona C Warrander
- Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Oleg Kovalevskiy
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
| | - Harry V Isaacs
- Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Mark Coles
- Department of Biology, University of York , York YO10 5DD, United Kingdom
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York , York YO10 5DD, United Kingdom
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29
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Agrawal T, Chan WY, Sage E, Kolluri K, Sladen P, Sturges G, Vallath S, Janes S, Coles M, Ambler C, Brown J, Giangreco A. Epithelial ErbB2 activity determines thymus homeostasis and T cell maturation. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.194.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Thymus involution, the age-dependent loss in organ structure and functionality, promotes increased immune dysfunction in humans, causing increased susceptibility to opportunistic infections, peripheral autoimmunity and reduced vaccine efficacy. Despite this, the mechanisms that regulate thymus involution remain incompletely understood. This has resulted in a lack of clinically approved therapies capable of reversing age-associated thymus involution. Here, we identify that thymic epithelial cell (TEC) specific ErbB2 activity determines thymus homeostasis and T cell maturation.
In these studies, we use a conditionally regulated bitransgenic mouse model in which a dominant-active ErbB2 transgene is expressed in keratin14 positive TECs following doxycycline administration. We show that increased ErbB2 expression causes rapid onset of thymus atrophy that resembles age-associated involution. Specific changes include destruction of thymic cortico-medullary boundaries, abnormal TEC differentiation, reduced thymus size and cellularity, and abnormal T cell differentiation. Using foetal thymus organ cultures derived from wild type and bitransgenic animals, we confirm that these phenotypes are due to TEC autonomous ErbB2 expression. Finally, we establish that treating aged mice with the clinically approved Erbb2 inhibitor Lapatinib restores thymus function, improves Streptococcus pneumoniae vaccine efficacy, and promotes infection resistance.
Overall, these results demonstrate a previously unknown role for ErbB2 in adult thymus homeostasis and suggest the potential translational relevance of ErbB2 inhibition as a means to reduce or reverse age-associated thymus involution.
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James S, Fox J, Afsari F, Lee J, Clough S, Knight C, Ashmore J, Ashton P, Preham O, Hoogduijn M, Ponzoni RDAR, Hancock Y, Coles M, Genever P. Multiparameter Analysis of Human Bone Marrow Stromal Cells Identifies Distinct Immunomodulatory and Differentiation-Competent Subtypes. Stem Cell Reports 2016; 4:1004-15. [PMID: 26070611 PMCID: PMC4471830 DOI: 10.1016/j.stemcr.2015.05.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 05/05/2015] [Accepted: 05/05/2015] [Indexed: 12/20/2022] Open
Abstract
Bone marrow stromal cells (BMSCs, also called bone-marrow-derived mesenchymal stromal cells) provide hematopoietic support and immunoregulation and contain a stem cell fraction capable of skeletogenic differentiation. We used immortalized human BMSC clonal lines for multi-level analysis of functional markers for BMSC subsets. All clones expressed typical BMSC cell-surface antigens; however, clones with trilineage differentiation capacity exhibited enhanced vascular interaction gene sets, whereas non-differentiating clones were uniquely CD317 positive with significantly enriched immunomodulatory transcriptional networks and high IL-7 production. IL-7 lineage tracing and CD317 immunolocalization confirmed the existence of a rare non-differentiating BMSC subtype, distinct from Cxcl12-DsRed(+) perivascular stromal cells in vivo. Colony-forming CD317(+) IL-7(hi) cells, identified at ∼ 1%-3% frequency in heterogeneous human BMSC fractions, were found to have the same biomolecular profile as non-differentiating BMSC clones using Raman spectroscopy. Distinct functional identities can be assigned to BMSC subpopulations, which are likely to have specific roles in immune control, lymphopoiesis, and bone homeostasis.
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Affiliation(s)
- Sally James
- Department of Biology, University of York, York YO10 5DD, UK
| | - James Fox
- Department of Biology, University of York, York YO10 5DD, UK
| | - Farinaz Afsari
- Department of Biology, University of York, York YO10 5DD, UK
| | - Jennifer Lee
- Department of Biology, University of York, York YO10 5DD, UK
| | - Sally Clough
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - James Ashmore
- Department of Biology, University of York, York YO10 5DD, UK
| | - Peter Ashton
- Department of Biology, University of York, York YO10 5DD, UK
| | - Olivier Preham
- Department of Biology, University of York, York YO10 5DD, UK
| | - Martin Hoogduijn
- Erasmus Medical Centre, Dr. Molewaterplein 50, Rotterdam 3015 GE, the Netherlands
| | | | - Y Hancock
- Department of Physics, University of York, York YO10 5DD, UK; York Centre for Complex Systems Analysis, University of York, York YO10 5GE, UK
| | - Mark Coles
- Department of Biology, University of York, York YO10 5DD, UK
| | - Paul Genever
- Department of Biology, University of York, York YO10 5DD, UK.
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Suman R, Smith G, Hazel KEA, Kasprowicz R, Coles M, O'Toole P, Chawla S. Label-free imaging to study phenotypic behavioural traits of cells in complex co-cultures. Sci Rep 2016; 6:22032. [PMID: 26915695 PMCID: PMC4768090 DOI: 10.1038/srep22032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/04/2016] [Indexed: 01/16/2023] Open
Abstract
Time-lapse imaging is a fundamental tool for studying cellular behaviours, however studies of primary cells in complex co-culture environments often requires fluorescent labelling and significant light exposure that can perturb their natural function over time. Here, we describe ptychographic phase imaging that permits prolonged label-free time-lapse imaging of microglia in the presence of neurons and astrocytes, which better resembles in vivo microenvironments. We demonstrate the use of ptychography as an assay to study the phenotypic behaviour of microglial cells in primary neuronal co-cultures through the addition of cyclosporine A, a potent immune-modulator.
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Affiliation(s)
- Rakesh Suman
- Phasefocus Ltd, Sheffield, UK.,Technology Facility, University of York, UK
| | | | | | | | - Mark Coles
- Centre for Immunology and Infection, York, UK.,Department of Biology, University of York, UK
| | - Peter O'Toole
- Technology Facility, University of York, UK.,Department of Biology, University of York, UK
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Warrander F, Faas L, Kovalevskiy O, Peters D, Coles M, Antson AA, Genever P, Isaacs HV. lin28 proteins promote expression of 17∼92 family miRNAs during amphibian development. Dev Dyn 2015; 245:34-46. [PMID: 26447465 PMCID: PMC4982076 DOI: 10.1002/dvdy.24358] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 07/14/2015] [Revised: 09/22/2015] [Accepted: 09/24/2015] [Indexed: 12/13/2022] Open
Abstract
Background: Lin28 proteins are post‐transcriptional regulators of gene expression with multiple roles in development and the regulation of pluripotency in stem cells. Much attention has focussed on Lin28 proteins as negative regulators of let‐7 miRNA biogenesis; a function that is conserved in several animal groups and in multiple processes. However, there is increasing evidence that Lin28 proteins have additional roles, distinct from regulation of let‐7 abundance. We have previously demonstrated that lin28 proteins have functions associated with the regulation of early cell lineage specification in Xenopus embryos, independent of a lin28/let‐7 regulatory axis. However, the nature of lin28 targets in Xenopus development remains obscure. Results: Here, we show that mir‐17∼92 and mir‐106∼363 cluster miRNAs are down‐regulated in response to lin28 knockdown, and RNAs from these clusters are co‐expressed with lin28 genes during germ layer specification. Mature miRNAs derived from pre‐mir‐363 are most sensitive to lin28 inhibition. We demonstrate that lin28a binds to the terminal loop of pre‐mir‐363 with an affinity similar to that of let‐7, and that this high affinity interaction requires to conserved a GGAG motif. Conclusions: Our data suggest a novel function for amphibian lin28 proteins as positive regulators of mir‐17∼92 family miRNAs. Developmental Dynamics 245:34–46, 2016. © 2015 Wiley Periodicals, Inc. We show that mir‐17∼92 and mir‐106∼363 cluster miRNAs are down regulated in response to lin28 knockdown in Xenopus embryos. We demonstrate that lin28a binds to the terminal loop of pre‐mir‐363 and this interaction requires a conserved a GGAG motif.
Our data suggest a novel function for amphibian lin28 proteins as positive regulators of mir‐17∼92 family miRNAs.
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Affiliation(s)
- Fiona Warrander
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Laura Faas
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Oleg Kovalevskiy
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Daniel Peters
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Mark Coles
- Centre for Immunology and Infection, University of York, Heslington York, YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington York, YO10 5DD, UK
| | - Paul Genever
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Harry V Isaacs
- Department of Biology, University of York, York, YO10 5DD, UK
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Cosgrove J, Butler J, Alden K, Read M, Kumar V, Cucurull-Sanchez L, Timmis J, Coles M. Agent-Based Modeling in Systems Pharmacology. CPT Pharmacometrics Syst Pharmacol 2015; 4:615-29. [PMID: 26783498 PMCID: PMC4716580 DOI: 10.1002/psp4.12018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 06/29/2015] [Accepted: 07/31/2015] [Indexed: 02/06/2023]
Abstract
Modeling and simulation (M&S) techniques provide a platform for knowledge integration and hypothesis testing to gain insights into biological systems that would not be possible a priori. Agent‐based modeling (ABM) is an M&S technique that focuses on describing individual components rather than homogenous populations. This tutorial introduces ABM to systems pharmacologists, using relevant case studies to highlight how ABM‐specific strengths have yielded success in the area of preclinical mechanistic modeling.
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Affiliation(s)
- J Cosgrove
- York Computational Immunology LabUniversity of YorkYorkUK; Centre for Immunology and InfectionUniversity of YorkYorkUK; Department of ElectronicsUniversity of YorkYorkUK
| | - J Butler
- York Computational Immunology LabUniversity of YorkYorkUK; Centre for Immunology and InfectionUniversity of YorkYorkUK; Department of ElectronicsUniversity of YorkYorkUK
| | - K Alden
- York Computational Immunology LabUniversity of YorkYorkUK; Centre for Immunology and InfectionUniversity of YorkYorkUK
| | - M Read
- Charles Perkins Centre University of Sydney Sydney Australia
| | - V Kumar
- University of California School of Medicine LA Jolla California USA
| | | | - J Timmis
- York Computational Immunology LabUniversity of YorkYorkUK; Department of ElectronicsUniversity of YorkYorkUK; SimOmicsYorkUK
| | - M Coles
- York Computational Immunology LabUniversity of YorkYorkUK; Centre for Immunology and InfectionUniversity of YorkYorkUK; SimOmicsYorkUK
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Read M, Andrews PS, Timmis J, Williams RA, Greaves RB, Sheng H, Coles M, Kumar V. Correction: Determining disease intervention strategies using spatially resolved simulations. PLoS One 2015; 10:e0128170. [PMID: 25955716 PMCID: PMC4425704 DOI: 10.1371/journal.pone.0128170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Alden K, Andrews PS, Veiga-Fernandes H, Timmis J, Coles M. Utilising a simulation platform to understand the effect of domain model assumptions. Nat Comput 2015; 14:99-107. [PMID: 25722664 PMCID: PMC4333240 DOI: 10.1007/s11047-014-9428-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Computational and mathematical modelling approaches are increasingly being adopted in attempts to further our understanding of complex biological systems. This approach can be subjected to strong criticism as substantial aspects of the biological system being captured are not currently known, meaning assumptions need to be made that could have a critical impact on simulation response. We have utilised the CoSMoS process in the development of an agent-based simulation of the formation of Peyer's patches (PP), gut-associated lymphoid organs that have a key role in the initiation of adaptive immune responses to infection. Although the use of genetic tools, imaging technologies and ex vivo culture systems has provided significant insight into the cellular components and associated pathways involved in PP development, interesting questions remain that cannot be addressed using these approaches, and as such well justified assumptions have been introduced into our model to counter this. Here we focus not on the development of the model itself, but instead demonstrate how the resultant simulation can be used to assess how these assumptions impact the simulation response. For example, we consider the impact of our assumption that the migration rate of lymphoid tissue cells into the gut remains constant throughout PP development. We demonstrate that an analysis of the assumptions made in the construction of the domain model may either increase confidence in the model as a representation of the biological system it captures, or may suggest areas where further biological experimentation is required.
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Affiliation(s)
- Kieran Alden
- York Computational Immunology Lab, University of York, York, UK
- Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK
| | - Paul S. Andrews
- York Computational Immunology Lab, University of York, York, UK
- Department of Computer Science, University of York, York, UK
| | | | - Jon Timmis
- York Computational Immunology Lab, University of York, York, UK
- Department of Electronics, University of York, York, UK
| | - Mark Coles
- York Computational Immunology Lab, University of York, York, UK
- Centre for Immunology and Infection, University of York and Hull York Medical School, York, UK
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Burger NB, Stuurman KE, Kok E, Konijn T, Schooneman D, Niederreither K, Coles M, Agace WW, Christoffels VM, Mebius RE, van de Pavert SA, Bekker MN. Involvement of neurons and retinoic acid in lymphatic development: new insights in increased nuchal translucency. Prenat Diagn 2014; 34:1312-9. [PMID: 25088217 DOI: 10.1002/pd.4473] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/28/2014] [Accepted: 07/28/2014] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Increased nuchal translucency originates from disturbed lymphatic development. Abnormal neural crest cell (NCC) migration may be involved in lymphatic development. Because both neuronal and lymphatic development share retinoic acid (RA) as a common factor, this study investigated the involvement of NCCs and RA in specific steps in lymphatic endothelial cell (LEC) differentiation and nuchal edema, which is the morphological equivalent of increased nuchal translucency. METHODS Mouse embryos in which all NCCs were fluorescently labeled (Wnt1-Cre;Rosa26(eYfp) ), reporter embryos for in vivo RA activity (DR5-luciferase) and embryos with absent (Raldh2(-/-) ) or in utero inhibition of RA signaling (BMS493) were investigated. Immunofluorescence using markers for blood vessels, lymphatic endothelium and neurons was applied. Flow cytometry was performed to measure specific LEC populations. RESULTS Cranial nerves were consistently close to the jugular lymph sac (JLS), in which NCCs were identified. In the absence of RA synthesis, enlarged JLS and nuchal edema were observed. Inhibiting RA signaling in utero resulted in a significantly higher amount of precursor-LECs at the expense of mature LECs and caused nuchal edema. CONCLUSIONS Neural crest cells are involved in lymphatic development. RA is required for differentiation into mature LECs. Blocking RA signaling in mouse embryos results in abnormal lymphatic development and nuchal edema.
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Affiliation(s)
- Nicole B Burger
- Department of Obstetrics and Gynecology, VU University Medical Center, Amsterdam, The Netherlands
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Nguyen Hoang AT, Chen P, Björnfot S, Högstrand K, Lock JG, Grandien A, Coles M, Svensson M. Technical advance: live-imaging analysis of human dendritic cell migrating behavior under the influence of immune-stimulating reagents in an organotypic model of lung. J Leukoc Biol 2014; 96:481-9. [PMID: 24899587 DOI: 10.1189/jlb.3ta0513-303r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
This manuscript describes technical advances allowing manipulation and quantitative analyses of human DC migratory behavior in lung epithelial tissue. DCs are hematopoietic cells essential for the maintenance of tissue homeostasis and the induction of tissue-specific immune responses. Important functions include cytokine production and migration in response to infection for the induction of proper immune responses. To design appropriate strategies to exploit human DC functional properties in lung tissue for the purpose of clinical evaluation, e.g., candidate vaccination and immunotherapy strategies, we have developed a live-imaging assay based on our previously described organotypic model of the human lung. This assay allows provocations and subsequent quantitative investigations of DC functional properties under conditions mimicking morphological and functional features of the in vivo parental tissue. We present protocols to set up and prepare tissue models for 4D (x, y, z, time) fluorescence-imaging analysis that allow spatial and temporal studies of human DCs in live epithelial tissue, followed by flow cytometry analysis of DCs retrieved from digested tissue models. This model system can be useful for elucidating incompletely defined pathways controlling DC functional responses to infection and inflammation in lung epithelial tissue, as well as the efficacy of locally administered candidate interventions.
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Affiliation(s)
| | - Puran Chen
- Center for Infectious Medicine, Department of Medicine, and
| | - Sofia Björnfot
- Center for Infectious Medicine, Department of Medicine, and
| | - Kari Högstrand
- Center for Infectious Medicine, Department of Medicine, and
| | - John G Lock
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; and
| | - Alf Grandien
- Center for Infectious Medicine, Department of Medicine, and
| | - Mark Coles
- Centre for Immunology and Infection, Hull York Medical School and Department of Biology, University of York, United Kingdom
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Nayar S, Glaysher B, Campos J, Coles M, Buckley CD, Barone F. A8.33 Unexpexpected role of IL-4Rα in regulating local tissue-resident stromal cells to support tertiary lymphoid structure formation at site of inflammation. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2013-205124.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Alden K, Read M, Andrews P, Timmis J, Coles M. Applying spartan to Understand Parameter Uncertainty in Simulations. The R Journal 2014. [DOI: 10.32614/rj-2014-025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Reynolds J, Coles M, Lythe G, Molina-París C. Mathematical Model of Naive T Cell Division and Survival IL-7 Thresholds. Front Immunol 2013; 4:434. [PMID: 24391638 PMCID: PMC3870322 DOI: 10.3389/fimmu.2013.00434] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [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: 07/31/2013] [Accepted: 11/22/2013] [Indexed: 11/18/2022] Open
Abstract
We develop a mathematical model of the peripheral naive T cell population to study the change in human naive T cell numbers from birth to adulthood, incorporating thymic output and the availability of interleukin-7 (IL-7). The model is formulated as three ordinary differential equations: two describe T cell numbers, in a resting state and progressing through the cell cycle. The third is introduced to describe changes in IL-7 availability. Thymic output is a decreasing function of time, representative of the thymic atrophy observed in aging humans. Each T cell is assumed to possess two interleukin-7 receptor (IL-7R) signaling thresholds: a survival threshold and a second, higher, proliferation threshold. If the IL-7R signaling strength is below its survival threshold, a cell may undergo apoptosis. When the signaling strength is above the survival threshold, but below the proliferation threshold, the cell survives but does not divide. Signaling strength above the proliferation threshold enables entry into cell cycle. Assuming that individual cell thresholds are log-normally distributed, we derive population-average rates for apoptosis and entry into cell cycle. We have analyzed the adiabatic change in homeostasis as thymic output decreases. With a parameter set representative of a healthy individual, the model predicts a unique equilibrium number of T cells. In a parameter range representative of persistent viral or bacterial infection, where naive T cell cycle progression is impaired, a decrease in thymic output may result in the collapse of the naive T cell repertoire.
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Affiliation(s)
- Joseph Reynolds
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Mark Coles
- Centre for Immunology and Infection, University of York , York , UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
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Read M, Andrews PS, Timmis J, Williams RA, Greaves RB, Sheng H, Coles M, Kumar V. Determining disease intervention strategies using spatially resolved simulations. PLoS One 2013; 8:e80506. [PMID: 24244694 PMCID: PMC3828403 DOI: 10.1371/journal.pone.0080506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 06/28/2013] [Accepted: 10/02/2013] [Indexed: 01/12/2023] Open
Abstract
Predicting efficacy and optimal drug delivery strategies for small molecule and biological therapeutics is challenging due to the complex interactions between diverse cell types in different tissues that determine disease outcome. Here we present a new methodology to simulate inflammatory disease manifestation and test potential intervention strategies in silico using agent-based computational models. Simulations created using this methodology have explicit spatial and temporal representations, and capture the heterogeneous and stochastic cellular behaviours that lead to emergence of pathology or disease resolution. To demonstrate this methodology we have simulated the prototypic murine T cell-mediated autoimmune disease experimental autoimmune encephalomyelitis, a mouse model of multiple sclerosis. In the simulation immune cell dynamics, neuronal damage and tissue specific pathology emerge, closely resembling behaviour found in the murine model. Using the calibrated simulation we have analysed how changes in the timing and efficacy of T cell receptor signalling inhibition leads to either disease exacerbation or resolution. The technology described is a powerful new method to understand cellular behaviours in complex inflammatory disease, permits rational design of drug interventional strategies and has provided new insights into the role of TCR signalling in autoimmune disease progression.
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Affiliation(s)
- Mark Read
- Department of Electronics, the University of York, York, United Kingdom
- * E-mail:
| | - Paul S. Andrews
- Department of Computer Science, the University of York, York, United Kingdom
| | - Jon Timmis
- Department of Electronics, the University of York, York, United Kingdom
- Department of Computer Science, the University of York, York, United Kingdom
| | - Richard A. Williams
- Department of Computer Science, the University of York, York, United Kingdom
| | - Richard B. Greaves
- Centre for Immunology and Infection, Department of Biology and HYMS, University of York, York, United Kingdom
| | - Huiming Sheng
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Mark Coles
- Centre for Immunology and Infection, Department of Biology and HYMS, University of York, York, United Kingdom
| | - Vipin Kumar
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
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Abstract
Secondary lymphoid organs (SLO) are crucial structures for immune-surveillance and rapid immune responses allowing resident lymphocytes to encounter antigen-presenting cells that carry antigens from peripheral tissues. These structures develop during embryonic life through a tightly regulated process that involves interactions between haematopoietic and mesenchymal cells. Importantly, this morphogenesis potential is maintained throughout life since in chronic inflammatory conditions novel "tertiary lymphoid organs" can be generated by processes that are reminiscent of embryonic SLO development. In this review we will discuss early events in SLO morphogenesis, focusing on haematopoietic and mesenchymal cell subsets implicated on the development of lymphoid organs.
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Affiliation(s)
- Mark Coles
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York YO10 5DD, UK.
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Coles M. SP0113 Innate lymphoid cells in the formation of lymphoid tissue. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2012-eular.1588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nayar S, Cloake T, Lane P, Pitzalis C, Coles M, Luther S, Buckley C, Barone F. OP0258 IL-22 Regulates Lymphoid Stromal Cell Expansion, Development of Germinal Centers and Humoral Response in Mucosal Ectopic Lymphoneogenesis. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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R.Pillai M, Van Wyhe R, Vogel P, Glaysher B, Coleman M, Ratcliffe P, Coles M, Bix M. Host resistance to a gastrointestinal parasite regulated by Mina, an immunoregulatory member of the JmjC protein family (P1014). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.65.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
T helper (Th) 1 and Th2 responses while critical for clearance of pathogens, when dysregulated results in autoimmune disease or allergy and asthma respectively. The genetic predisposition of certain inbred mouse strains towards developing Th2 as opposed to Th1 response (Th2-bias) has long been associated with differential susceptibility across a wide range of immunological diseases. However, its molecular genetic basis and thus the causal relationship to disease states are poorly understood. Prior investigations into the nature of this relationship resulted in the physical isolation of Dice1.2 on chromosome 16 and identification of Mina as a Dice1.2 resident gene exhibiting Il4 repressor activity. Thus, we hypothesized that Mina’s physiological role is to negatively regulate Th2 responses. To test this, we generated Mina KO mice and studied their response to the intestinal nematode T. muris. We found that Mina KO mice are hyper-resistant to T. muris infection. Surprisingly, the elevated T. muris resistance of Mina KO mice was not associated with an increased Th2 response but a defect in Th1 response. This correlated well with reduced inflammation in the cecum and reduced expression of antigen specific serum IgG2a. Further analysis revealed diminished expression of epithelial cell-specific Relmβ in Mina KO mice. These results highlight the importance of Mina in immune regulation and provide insight into the complex immune network perturbed by its expression and function.
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Affiliation(s)
- Meenu R.Pillai
- 1Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Renae Van Wyhe
- 1Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Peter Vogel
- 2Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Bridget Glaysher
- 3Centre for Immunology and Infection Department of Biology & HYMS, University of York, York, United Kingdom
| | - Mathew Coleman
- 4Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter Ratcliffe
- 4Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mark Coles
- 3Centre for Immunology and Infection Department of Biology & HYMS, University of York, York, United Kingdom
| | - Mark Bix
- 1Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
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Alden K, Read M, Timmis J, Andrews PS, Veiga-Fernandes H, Coles M. Spartan: a comprehensive tool for understanding uncertainty in simulations of biological systems. PLoS Comput Biol 2013; 9:e1002916. [PMID: 23468606 PMCID: PMC3585389 DOI: 10.1371/journal.pcbi.1002916] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 12/03/2012] [Indexed: 11/25/2022] Open
Abstract
Integrating computer simulation with conventional wet-lab research has proven to have much potential in furthering the understanding of biological systems. Success requires the relationship between simulation and the real-world system to be established: substantial aspects of the biological system are typically unknown, and the abstract nature of simulation can complicate interpretation of in silico results in terms of the biology. Here we present spartan (Simulation Parameter Analysis RToolkit ApplicatioN), a package of statistical techniques specifically designed to help researchers understand this relationship and provide novel biological insight. The tools comprising spartan help identify which simulation results can be attributed to the dynamics of the modelled biological system, rather than artefacts of biological uncertainty or parametrisation, or simulation stochasticity. Statistical analyses reveal the influence that pathways and components have on simulation behaviour, offering valuable biological insight into aspects of the system under study. We demonstrate the power of spartan in providing critical insight into aspects of lymphoid tissue development in the small intestine through simulation. Spartan is released under a GPLv2 license, implemented within the open source R statistical environment, and freely available from both the Comprehensive R Archive Network (CRAN) and http://www.cs.york.ac.uk/spartan. The techniques within the package can be applied to traditional ordinary or partial differential equation simulations as well as agent-based implementations. Manuals, comprehensive tutorials, and example simulation data upon which spartan can be applied are available from the website.
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Affiliation(s)
- Kieran Alden
- Centre for Systems Biology, School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
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Cupedo T, Stroock A, Coles M. Application of tissue engineering to the immune system: development of artificial lymph nodes. Front Immunol 2012; 3:343. [PMID: 23162557 PMCID: PMC3499788 DOI: 10.3389/fimmu.2012.00343] [Citation(s) in RCA: 41] [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: 07/13/2012] [Accepted: 10/28/2012] [Indexed: 01/05/2023] Open
Abstract
The goal of tissue engineering and regenerative medicine is to develop synthetic versions of human organs for transplantation, in vitro toxicology testing and to understand basic mechanisms of organ function. A variety of different approaches have been utilized to replicate the microenvironments found in lymph nodes including the use of a variety of different bio-materials, culture systems, and the application of different cell types to replicate stromal networks found in vivo. Although no system engineered so far can fully replicate lymph node function, progress has been made in the development of microenvironments that can promote the initiation of protective immune responses. In this review we will explore the different approaches utilized to recreate lymph node microenvironments and the technical challenges required to recreate a fully functional immune system in vitro.
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Affiliation(s)
- Tom Cupedo
- Department of Hematology, Erasmus University Medical Center Rotterdam, Netherlands
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Heathfield S, Parker B, Zeef L, Bruce I, Alexander Y, Collins F, Stone M, Wang E, Williams AS, Wright HL, Thomas HB, Moots RJ, Edwards SW, Bullock C, Chapman V, Walsh DA, Mobasheri A, Kendall D, Kelly S, Bayley R, Buckley CD, Young SP, Rump-Goodrich L, Middleton J, Chen L, Fisher R, Kollnberger S, Shastri N, Kessler BM, Bowness P, Nazeer Moideen A, Evans L, Osgood L, Williams AS, Jones SA, Nowell MA, Mahadik Y, Young S, Morgan M, Gordon C, Harper L, Giles JL, Paul Morgan B, Harris CL, Rysnik OJ, McHugh K, Kollnberger S, Payeli S, Marroquin O, Shaw J, Renner C, Bowness P, Nayar S, Cloake T, Bombardieri M, Pitzalis C, Buckley C, Barone F, Barone F, Nayar S, Cloake T, Lane P, Coles M, Buckley C, Williams EL, Edwards CJ, Cooper C, Oreffo RO, Dunn S, Crawford A, Wilkinson M, Le Maitre C, Bunning R, Daniels J, Phillips KLE, Chiverton N, Le Maitre CL, Kollnberger S, Shaw J, Ridley A, Wong-Baeza I, McHugh K, Keidel S, Chan A, Bowness P, Gullick NJ, Abozaid HS, Jayaraj DM, Evans HG, Scott DL, Choy EH, Taams LS, Hickling M, Golor G, Jullion A, Shaw S, Kretsos K, Bari SF, Rhys-Dillon B, Amos N, Siebert S, Phillips KLE, Chiverton N, Bunning RD, Haddock G, Cross AK, Le Maitre CL, Kate I, Phillips E, Cross A, Chiverton N, Haddock G, Bunning RAD, Le Maitre CL, Ceeraz S, Spencer J, Choy E, Corrigall V, Crilly A, Palmer H, Lockhart J, Plevin R, Ferrell WR, McInnes I, Hutchinson D, Perry L, DiCicco M, Humby F, Kelly S, Hands R, Buckley C, McInnes I, Taylor P, Bombardieri M, Pitzalis C, Mehta P, Mitchell A, Tysoe C, Caswell R, Owens M, Vincent T, Hashmi TM, Price-Forbes A, Sharp CA, Murphy H, Wood EF, Doherty T, Sheldon J, Sofat N, Goff I, Platt PN, Abdulkader R, Clunie G, Ismajli M, Nikiphorou E, Young A, Tugnet N, Dixey J, Banik S, Alcorn D, Hunter J, Win Maw W, Patil P, Hayes F, Main Wong W, Borg FA, Dasgupta B, Malaviya AP, Ostor AJ, Chana JK, Ahmed AA, Edmonds S, Hayes F, Coward L, Borg F, Heaney J, Amft N, Simpson J, Dhillon V, Ayalew Y, Khattak F, Gayed M, Amarasena RI, McKenna F, Amarasena RI, McKenna F, Mc Laughlin M, Baburaj K, Fattah Z, Ng N, Wilson J, Colaco B, Williams MR, Adizie T, Dasgupta B, Casey M, Lip S, Tan S, Anderson D, Robertson C, Devanny I, Field M, Walker D, Robinson S, Ryan S, Hassell A, Bateman J, Allen M, Davies D, Crouch C, Walker-Bone K, Gainsborough N, Gullick NJ, Lutalo PM, Davies UM, Walker-Bone K, Mckew JR, Millar AM, Wright SA, Bell AL, Thapper M, Roussou T, Cumming J, Hull RG, Thapper M, Roussou T, McKeogh J, O'Connor MB, Hassan AI, Bond U, Swan J, Phelan MJ, Coady D, Kumar N, Farrow L, Bukhari M, Oldroyd AG, Greenbank C, McBeth J, Duncan R, Brown D, Horan M, Pendleton N, Littlewood A, Cordingley L, Mulvey M, Curtis EM, Cole ZA, Crozier SR, Georgia N, Robinson SM, Godfrey KM, Sayer AA, Inskip HM, Cooper C, Harvey NC, Davies R, Mercer L, Galloway J, Low A, Watson K, Lunt M, Symmons D, Hyrich K, Chitale S, Estrach C, Moots RJ, Goodson NJ, Rankin E, Jiang CQ, Cheng KK, Lam TH, Adab P, Ling S, Chitale S, Moots RJ, Estrach C, Goodson NJ, Humphreys J, Ellis C, Bunn D, Verstappen SM, Symmons D, Fluess E, Macfarlane GJ, Bond C, Jones GT, Scott IC, Steer S, Lewis CM, Cope A, Mulvey MR, Macfarlane GJ, Symmons D, Lovell K, Keeley P, Woby S, Beasley M, McBeth J, Viatte S, Plant D, Lunt M, Fu B, Parker B, Galloway J, Solymossy C, Worthington J, Symmons D, Dixey J, Young A, Barton A, Williams FM, Osei-Bordom DC, Popham M, MacGregor A, Spector T, Little J, Herrick A, Pushpakom S, Ennis H, McBurney H, Worthington J, Newman W, Ibrahim I, Plant D, Hyrich K, Morgan A, Wilson A, Isaacs J, Barton A, Sanderson T, Hewlett S, Calnan M, Morris M, Raza K, Kumar K, Cardy CM, Pauling JD, Jenkins J, Brown SJ, McHugh N, Nikiphorou E, Mugford M, Davies C, Cooper N, Brooksby A, Bunn D, Symmons D, MacGregor A, Dures E, Ambler N, Fletcher D, Pope D, Robinson F, Rooke R, Hewlett S, Gorman CL, Reynolds P, Hakim AJ, Bosworth A, Weaver D, Kiely PD, Skeoch S, Jani M, Amarasena R, Rao C, Macphie E, McLoughlin Y, Shah P, Else S, Semenova O, Thompson H, Ogunbambi O, Kallankara S, Patel Y, Baguley E, Jani M, Halsey J, Severn A, Bukhari M, Selvan S, Price E, Husain MJ, Brophy S, Phillips CJ, Cooksey R, Irvine E, Siebert S, Lendrem D, Mitchell S, Bowman S, Price E, Pease CT, Emery P, Andrews J, Bombardieri M, Sutcliffe N, Pitzalis C, Lanyon P, Hunter J, Gupta M, McLaren J, Regan M, Cooper A, Giles I, Isenberg D, Griffiths B, Foggo H, Edgar S, Vadivelu S, Coady D, McHugh N, Ng WF, Dasgupta B, Taylor P, Iqbal I, Heron L, Pilling C, Marks J, Hull R, Ledingham J, Han C, Gathany T, Tandon N, Hsia E, Taylor P, Strand V, Sensky T, Harta N, Fleming S, Kay L, Rutherford M, Nicholl K, Kay L, Rutherford M, Nicholl K, Eyre T, Wilson G, Johnson P, Russell M, Timoshanko J, Duncan G, Spandley A, Roskell S, Coady D, West L, Adshead R, Donnelly SP, Ashton S, Tahir H, Patel D, Darroch J, Goodson NJ, Boulton J, Ellis B, Finlay R, Lendrem D, Mitchell S, Bowman S, Price E, Pease CT, Emery P, Andrews J, Bombardieri M, Sutcliffe N, Pitzalis C, Lanyon P, Hunter J, Gupta M, McLaren J, Regan M, Cooper A, Giles I, Isenberg D, Vadivelu S, Coady D, McHugh N, Griffiths B, Foggo H, Edgar S, Ng WF, Murray-Brown W, Priori R, Tappuni T, Vartoukian S, Seoudi N, Picarelli G, Fortune F, Valesini G, Pitzalis C, Bombardieri M, Ball E, Rooney M, Bell A, Merida AA, Isenberg D, Tarelli E, Axford J, Giles I, Pericleous C, Pierangeli SS, Ioannou J, Rahman A, Alavi A, Hughes M, Evans B, Bukhari M, Parker B, Zaki A, Alexander Y, Bruce I, Hui M, Garner R, Rees F, Bavakunji R, Daniel P, Varughese S, Srikanth A, Andres M, Pearce F, Leung J, Lim K, Regan M, Lanyon P, Oomatia A, Petri M, Fang H, Birnbaum J, Amissah-Arthur M, Gayed M, Stewart K, Jennens H, Braude S, Gordon C, Sutton EJ, Watson KD, Gordon C, Yee CS, Lanyon P, Jayne D, Isenberg D, Rahman A, Akil M, McHugh N, Ahmad Y, Amft N, D'Cruz D, Edwards CJ, Griffiths B, Khamashta M, Teh LS, Zoma A, Bruce I, Dey ID, Kenu E, Isenberg D, Pericleous C, Garza-Garcia A, Murfitt L, Driscoll PC, Isenberg D, Pierangeli S, Giles I, Ioannou Y, Rahman A, Reynolds JA, Ray DW, O'Neill T, Alexander Y, Bruce I, Segeda I, Shevchuk S, Kuvikova I, Brown N, Bruce I, Venning M, Mehta P, Dhanjal M, Mason J, Nelson-Piercy C, Basu N, Paudyal P, Stockton M, Lawton S, Dent C, Kindness K, Meldrum G, John E, Arthur C, West L, Macfarlane MV, Reid DM, Jones GT, Macfarlane GJ, Yates M, Loke Y, Watts R, MacGregor A, Adizie T, Christidis D, Dasgupta B, Williams M, Sivakumar R, Misra R, Danda D, Mahendranath KM, Bacon PA, Mackie SL, Pease CT. Basic science * 232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function. Rheumatology (Oxford) 2012. [DOI: 10.1093/rheumatology/kes108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Nayar S, Cloake T, Bombardieri M, Pitzalis C, Lane PJ, Coles M, Buckley CD, Barone F. Cooperation of innate and acquired immune system derived signals induces stromal cell activation in chronic inflammation and ectopic lymphoneogenesis. Ann Rheum Dis 2012. [DOI: 10.1136/annrheumdis-2011-201235.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Nguyen Hoang AT, Chen P, Juarez J, Sachamitr P, Billing B, Bosnjak L, Dahlén B, Coles M, Svensson M. Dendritic cell functional properties in a three-dimensional tissue model of human lung mucosa. Am J Physiol Lung Cell Mol Physiol 2011; 302:L226-37. [PMID: 22101763 DOI: 10.1152/ajplung.00059.2011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In lung tissue, dendritic cells (DC) are found in close association with the epithelial cell layer, and there is evidence of DC regulation by the epithelium; that epithelial dysfunction leads to overzealous immune cell activation. However, dissecting basic mechanisms of DC interactions with epithelial cells in human tissue is difficult. Here, we describe a method to generate a three-dimensional organotypic model of the human airway mucosa in which we have implanted human DC. The model recapitulates key anatomical and functional features of lung mucosal tissue, including a stratified epithelial cell layer, deposition of extracellular matrix proteins, and the production of tight junction and adherence junction proteins. Labeling of fixed tissue model sections and imaging of live tissue models also revealed that DC distribute in close association with the epithelial layer. As functional properties of DC may be affected by the local tissue microenvironment, this system provides a tool to study human DC function associated with lung mucosal tissue. As an example, we report that the lung tissue model regulates the capacity of DC to produce the chemokines CCL17, CCL18, and CCL22, leading to enhanced CCL18 expression and reduced CCL17 and CCL22 expression. This novel tissue model thus provides a tool well suited for a wide range of studies, including those on the regulation of DC functional properties within the local tissue microenvironment during homeostasis and inflammatory reactions.
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Affiliation(s)
- Anh Thu Nguyen Hoang
- Center for Infectious Medicine, F59, Dept. of Medicine, Karolinska Institutet, Karolinska Univ. Hospital, Huddinge, 141 86 Stockholm, Sweden
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