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Pavlidis P, Tsakmaki A, Pantazi E, Li K, Cozzetto D, Digby-Bell J, Yang F, Lo JW, Alberts E, Sa ACC, Niazi U, Friedman J, Long AK, Ding Y, Carey CD, Lamb C, Saqi M, Madgwick M, Gul L, Treveil A, Korcsmaros T, Macdonald TT, Lord GM, Bewick G, Powell N. Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy. Nat Commun 2022; 13:5820. [PMID: 36192482 PMCID: PMC9530232 DOI: 10.1038/s41467-022-33331-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 10/20/2020] [Accepted: 09/14/2022] [Indexed: 11/28/2022] Open
Abstract
The function of interleukin-22 (IL-22) in intestinal barrier homeostasis remains controversial. Here, we map the transcriptional landscape regulated by IL-22 in human colonic epithelial organoids and evaluate the biological, functional and clinical significance of the IL-22 mediated pathways in ulcerative colitis (UC). We show that IL-22 regulated pro-inflammatory pathways are involved in microbial recognition, cancer and immune cell chemotaxis; most prominently those involving CXCR2+ neutrophils. IL-22-mediated transcriptional regulation of CXC-family neutrophil-active chemokine expression is highly conserved across species, is dependent on STAT3 signaling, and is functionally and pathologically important in the recruitment of CXCR2+ neutrophils into colonic tissue. In UC patients, the magnitude of enrichment of the IL-22 regulated transcripts in colonic biopsies correlates with colonic neutrophil infiltration and is enriched in non-responders to ustekinumab therapy. Our data provide further insights into the biology of IL-22 in human disease and highlight its function in the regulation of pathogenic immune pathways, including neutrophil chemotaxis. The transcriptional networks regulated by IL-22 are functionally and clinically important in UC, impacting patient trajectories and responsiveness to biological intervention. Mechanisms of non-response to ustekinumab, a biologic targeting IL-23, are currently unclear. Here, the authors show that the transcriptional program regulated by IL-22, an IL-23 responsive cytokine, is enriched in patients with ulcerative colitis unresponsive to ustekinumab and associated with higher colon neutrophil recruitment and activation of upstream IL-22 regulators.
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Affiliation(s)
| | - Anastasia Tsakmaki
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Eirini Pantazi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katherine Li
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Domenico Cozzetto
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Jonathan Digby-Bell
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Feifei Yang
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Jonathan W Lo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Elena Alberts
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Umar Niazi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Joshua Friedman
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Anna K Long
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Yuchun Ding
- Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher D Carey
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher Lamb
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Mansoor Saqi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Matthew Madgwick
- Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Leila Gul
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.,Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.,Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Thomas T Macdonald
- Centre for Immunobiology, Barts and the London School of Medicine and Dentistry, QMUL, London, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, UK.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gavin Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.
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Pavlidis P, Tsakmaki A, Treveil A, Li K, Cozzetto D, Yang F, Niazi U, Hayee BH, Saqi M, Friedman J, Korcsmaros T, Bewick G, Powell N. Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease. Cell Rep 2022; 40:111439. [PMID: 36170836 PMCID: PMC10731404 DOI: 10.1016/j.celrep.2022.111439] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/03/2021] [Accepted: 09/09/2022] [Indexed: 11/28/2022] Open
Abstract
Interactions between the epithelium and the immune system are critical in the pathogenesis of inflammatory bowel disease (IBD). In this study, we mapped the transcriptional landscape of human colonic epithelial organoids in response to different cytokines responsible for mediating canonical mucosal immune responses. By profiling the transcriptome of human colonic organoids treated with the canonical cytokines interferon gamma, interleukin-13, -17A, and tumor necrosis factor alpha with next-generation sequencing, we unveil shared and distinct regulation patterns of epithelial function by different cytokines. An integrative analysis of cytokine responses in diseased tissue from patients with IBD (n = 1,009) reveals a molecular classification of mucosal inflammation defined by gradients of cytokine-responsive transcriptional signatures. Our systems biology approach detected signaling bottlenecks in cytokine-responsive networks and highlighted their translational potential as theragnostic targets in intestinal inflammation.
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Affiliation(s)
- Polychronis Pavlidis
- Centre for Inflammation Biology and Cancer Immunology, King's College London, London, UK; School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Anastasia Tsakmaki
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Katherine Li
- Janssen Research and Development, 1400 McKean Road, Spring House, PA 19477, USA
| | - Domenico Cozzetto
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Feifei Yang
- Janssen Research and Development, 1400 McKean Road, Spring House, PA 19477, USA
| | - Umar Niazi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Bu Hussain Hayee
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Mansoor Saqi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Joshua Friedman
- Janssen Research and Development, 1400 McKean Road, Spring House, PA 19477, USA
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Gavin Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.
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3
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Poletti M, Treveil A, Csabai L, Gul L, Modos D, Madgwick M, Olbei M, Bohar B, Valdeolivas A, Turei D, Verstockt B, Triana S, Alexandrov T, Saez-Rodriguez J, Stanifer ML, Boulant S, Korcsmaros T. Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways. NPJ Syst Biol Appl 2022; 8:15. [PMID: 35501398 PMCID: PMC9061772 DOI: 10.1038/s41540-022-00224-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/04/2022] [Indexed: 12/14/2022] Open
Abstract
Increasing evidence points towards the key role of the epithelium in the systemic and over-activated immune response to viral infection, including SARS-CoV-2 infection. Yet, how viral infection alters epithelial-immune cell interactions regulating inflammatory responses, is not well known. Available experimental approaches are insufficient to properly analyse this complex system, and computational predictions and targeted data integration are needed as an alternative approach. In this work, we propose an integrated computational biology framework that models how infection alters intracellular signalling of epithelial cells and how this change impacts the systemic immune response through modified interactions between epithelial cells and local immune cell populations. As a proof-of-concept, we focused on the role of intestinal and upper-airway epithelial infection. To characterise the modified epithelial-immune interactome, we integrated intra- and intercellular networks with single-cell RNA-seq data from SARS-CoV-2 infected human ileal and colonic organoids as well as from infected airway ciliated epithelial cells. This integrated methodology has proven useful to point out specific epithelial-immune interactions driving inflammation during disease response, and propose relevant molecular targets to guide focused experimental analysis.
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Grants
- BB/CSP17270/1 Biotechnology and Biological Sciences Research Council
- BB/P016774/1 Biotechnology and Biological Sciences Research Council
- BB/R012490/1 Biotechnology and Biological Sciences Research Council
- BBS/E/T/000PR9817 Biotechnology and Biological Sciences Research Council
- BBS/E/F/000PR10355 Biotechnology and Biological Sciences Research Council
- BB/S50743X/1 Biotechnology and Biological Sciences Research Council
- BB/M011216/1 Biotechnology and Biological Sciences Research Council
- BBS/E/F/000PR10353 Biotechnology and Biological Sciences Research Council
- BB/J004529/1 Biotechnology and Biological Sciences Research Council
- The work of T.K. was supported by the Earlham Institute (Norwich, UK) in partnership with the Quadram Institute (Norwich, UK) and strategically supported by the UKRI BBSRC UK grants (BB/J004529/1, BB/P016774/1, and BB/CSP17270/1). T.K. was also funded by a BBSRC ISP grant for Gut Microbes and Health BB/R012490/1 and its constituent projects, BBS/E/F/000PR10353 and BBS/E/F/000PR10355.
- M.P. is supported by the UKRI Biotechnological and Biosciences Research Council (BBSRC) funded Norwich Research Park Biosciences Doctoral Training Partnership (grant numbers BB/M011216/1 and BB/S50743X/1).
- A.T. is supported by the UKRI Biotechnological and Biosciences Research Council (BBSRC) funded Norwich Research Park Biosciences Doctoral Training Partnership (grant numbers BB/M011216/1 and BB/S50743X/1).
- L.G. is supported by the UKRI Biotechnological and Biosciences Research Council (BBSRC) funded Norwich Research Park Biosciences Doctoral Training Partnership (grant numbers BB/M011216/1 and BB/S50743X/1).
- The work of D.M. was supported by the Earlham Institute (Norwich, UK) in partnership with the Quadram Institute (Norwich, UK) and strategically supported by the UKRI BBSRC UK grants (BB/J004529/1, BB/P016774/1, and BB/CSP17270/1). D.M. was also funded by a BBSRC ISP grant for Gut Microbes and Health BB/R012490/1 and its constituent projects, BBS/E/F/000PR10353 and BBS/E/F/000PR10355.
- M.O. is supported by the UKRI Biotechnological and Biosciences Research Council (BBSRC) funded Norwich Research Park Biosciences Doctoral Training Partnership (grant numbers BB/M011216/1 and BB/S50743X/1).
- B.V. is supported by the Clinical Research Fund (KOOR) University Hospitals Leuven.
- S.T. acknowledges the funding from the Darwin Trust of Edinburgh and from the ERC Consolidator grant METACELL from European Union’s Horizon 2020 program. S.T. acknowledges support from the EMBL Genomics Core Facility and particularly help from Vladimir Benes.
- T.A. acknowledges the funding from the Darwin Trust of Edinburgh and from the ERC Consolidator grant METACELL from European Union’s Horizon 2020 program. T.A. acknowledges support from the EMBL Genomics Core Facility and particularly help from Vladimir Benes.
- M.L.S. was supported by the DFG (416072091) and the BMBF (01KI20239B). D.T. was supported by the Federal Ministry of Education and Research (BMBF, Computational Life Sciences grant no. 031L0181B) to J.S.R.
- S.B. was supported by research grants from the Deutsche Forschungsgemeinschaft (DFG): project numbers 415089553 (Heisenberg program), 240245660 (SFB1129), 278001972 (TRR186), and 272983813 (TRR179), the state of Baden Wuerttemberg (AZ: 33.7533.-6-21/5/1) and the Bundesministerium Bildung und Forschung (BMBF) (01KI20198A).
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Affiliation(s)
- Martina Poletti
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Luca Csabai
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | - Leila Gul
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Dezso Modos
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Matthew Madgwick
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Marton Olbei
- Earlham Institute, Norwich Research Park, Norwich, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Balazs Bohar
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | - Alberto Valdeolivas
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Denes Turei
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, Translational Research in GI disorders, KU Leuven, Leuven, Belgium
| | - Sergio Triana
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Theodore Alexandrov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, Heidelberg, Germany
| | - Megan L Stanifer
- Department of Infectious Diseases, Heidelberg University Hospital Heidelberg, Heidelberg, Germany
| | - Steeve Boulant
- Department of Infectious Diseases, Heidelberg University Hospital Heidelberg, Heidelberg, Germany
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
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4
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Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol 2021; 17:e10851. [PMID: 34939300 PMCID: PMC8696085 DOI: 10.15252/msb.202110851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
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5
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Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta‐Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic‐Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban‐Medina M, Peña‐Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez‐Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol 2021; 17:e10387. [PMID: 34664389 PMCID: PMC8524328 DOI: 10.15252/msb.202110387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.
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Affiliation(s)
- Marek Ostaszewski
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Anna Niarakis
- Université Paris‐SaclayLaboratoire Européen de Recherche pour la Polyarthrite rhumatoïde ‐ GenhotelUniv EvryEvryFrance
- Lifeware GroupInria Saclay‐Ile de FrancePalaiseauFrance
| | - Alexander Mazein
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Inna Kuperstein
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Robert Phair
- Integrative Bioinformatics, Inc.Mountain ViewCAUSA
| | - Aurelio Orta‐Resendiz
- Institut PasteurUniversité de Paris, Unité HIVInflammation et PersistanceParisFrance
- Bio Sorbonne Paris CitéUniversité de ParisParisFrance
| | - Vidisha Singh
- Université Paris‐SaclayLaboratoire Européen de Recherche pour la Polyarthrite rhumatoïde ‐ GenhotelUniv EvryEvryFrance
| | - Sara Sadat Aghamiri
- Inserm‐ Institut national de la santé et de la recherche médicaleParisFrance
| | - Marcio Luis Acencio
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Andreas Ruepp
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Gisela Fobo
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Corinna Montrone
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Barbara Brauner
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Goar Frishman
- Institute of Experimental Genetics (IEG)Helmholtz Zentrum München‐German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Luis Cristóbal Monraz Gómez
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Julia Somers
- Department of Molecular and Medical GeneticsOregon Health & Sciences UniversityPortlandORUSA
| | - Matti Hoch
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
| | | | - Julia Scheel
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
| | - Hanna Borlinghaus
- Department of Computer and Information ScienceUniversity of KonstanzKonstanzGermany
| | - Tobias Czauderna
- Faculty of Information TechnologyDepartment of Human‐Centred ComputingMonash UniversityClaytonVic.Australia
| | - Falk Schreiber
- Department of Computer and Information ScienceUniversity of KonstanzKonstanzGermany
- Faculty of Information TechnologyDepartment of Human‐Centred ComputingMonash UniversityClaytonVic.Australia
| | | | | | - Akira Funahashi
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Yusuke Hiki
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Noriko Hiroi
- Graduate School of Media and GovernanceResearch Institute at SFCKeio UniversityKanagawaJapan
| | - Takahiro G Yamada
- Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial‐Resistant PathogensInstitute for Bioinformatics and Medical Informatics (IBMI)University of TübingenTübingenGermany
- Department of Computer ScienceUniversity of TübingenTübingenGermany
- German Center for Infection Research (DZIF), partner siteTübingenGermany
| | - Alina Renz
- Computational Systems Biology of Infections and Antimicrobial‐Resistant PathogensInstitute for Bioinformatics and Medical Informatics (IBMI)University of TübingenTübingenGermany
- Department of Computer ScienceUniversity of TübingenTübingenGermany
| | - Muhammad Naveez
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
- Institute of Applied Computer SystemsRiga Technical UniversityRigaLatvia
| | - Zsolt Bocskei
- Sanofi R&DTranslational SciencesChilly‐MazarinFrance
| | - Francesco Messina
- Dipartimento di Epidemiologia Ricerca Pre‐Clinica e Diagnostica AvanzataNational Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.S.RomeItaly
- COVID‐19 INMI Network Medicine for IDs Study GroupNational Institute for Infectious Diseases 'Lazzaro Spallanzani' I.R.C.C.SRomeItaly
| | - Daniela Börnigen
- Bioinformatics Core FacilityUniversitätsklinikum Hamburg‐EppendorfHamburgGermany
| | - Liam Fergusson
- Royal (Dick) School of Veterinary MedicineThe University of EdinburghEdinburghUK
| | - Marta Conti
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Marius Rameil
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Vanessa Nakonecnij
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Jakob Vanhoefer
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
| | - Leonard Schmiester
- Faculty of Mathematics and Natural SciencesUniversity of BonnBonnGermany
- Center for MathematicsChair of Mathematical Modeling of Biological SystemsTechnische Universität MünchenGarchingGermany
| | - Muying Wang
- Department of Chemical and Petroleum EngineeringUniversity of PittsburghPittsburghPAUSA
| | - Emily E Ackerman
- Department of Chemical and Petroleum EngineeringUniversity of PittsburghPittsburghPAUSA
| | - Jason E Shoemaker
- Department of Chemical and Petroleum EngineeringUniversity of PittsburghPittsburghPAUSA
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPAUSA
| | | | | | | | | | | | - Kristina Hanspers
- Institute of Data Science and BiotechnologyGladstone InstitutesSan FranciscoCAUSA
| | - Martina Kutmon
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht Centre for Systems Biology (MaCSBio)Maastricht UniversityMaastrichtThe Netherlands
| | - Susan Coort
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Lars Eijssen
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht University Medical CentreMaastrichtThe Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht University Medical CentreMaastrichtThe Netherlands
| | | | - Denise Slenter
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Marvin Martens
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Nhung Pham
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Robin Haw
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | - Bijay Jassal
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | | | | | - Andrea Senff Ribeiro
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
- Universidade Federal do ParanáCuritibaBrasil
| | - Karen Rothfels
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | | | - Ralf Stephan
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
| | - Cristoffer Sevilla
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | - Thawfeek Varusai
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | - Jean‐Marie Ravel
- INSERM UMR_S 1256Nutrition, Genetics, and Environmental Risk Exposure (NGERE)Faculty of Medicine of NancyUniversity of LorraineNancyFrance
- Laboratoire de génétique médicaleCHRU NancyNancyFrance
| | - Rupsha Fraser
- Queen's Medical Research InstituteThe University of EdinburghEdinburghUK
| | - Vera Ortseifen
- Senior Research Group in Genome Research of Industrial MicroorganismsCenter for BiotechnologyBielefeld UniversityBielefeldGermany
| | - Silvia Marchesi
- Department of Surgical ScienceUppsala UniversityUppsalaSweden
| | - Piotr Gawron
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
- Institute of Computing SciencePoznan University of TechnologyPoznanPoland
| | - Ewa Smula
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Laurent Heirendt
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Venkata Satagopam
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Guanming Wu
- Department of Medical Informatics and Clinical EpidemiologyOregon Health & Science UniversityPortlandORUSA
| | - Anders Riutta
- Institute of Data Science and BiotechnologyGladstone InstitutesSan FranciscoCAUSA
| | | | - Stuart Owen
- Department of Computer ScienceThe University of ManchesterManchesterUK
| | - Carole Goble
- Department of Computer ScienceThe University of ManchesterManchesterUK
| | - Xiaoming Hu
- Heidelberg Institute for Theoretical Studies (HITS)HeidelbergGermany
| | - Rupert W Overall
- German Center for Neurodegenerative Diseases (DZNE) DresdenDresdenGermany
- Center for Regenerative Therapies Dresden (CRTD)Technische Universität DresdenDresdenGermany
- Institute for BiologyHumboldt University of BerlinBerlinGermany
| | | | | | - Benjamin M Gyori
- Harvard Medical SchoolLaboratory of Systems PharmacologyBostonMAUSA
| | - John A Bachman
- Harvard Medical SchoolLaboratory of Systems PharmacologyBostonMAUSA
| | - Carlos Vega
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Valentin Grouès
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | | | - Pablo Porras
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | - Luana Licata
- Department of BiologyUniversity of Rome Tor VergataRomeItaly
| | | | - Francesca Sacco
- Department of BiologyUniversity of Rome Tor VergataRomeItaly
| | | | | | | | - Denes Turei
- Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Augustin Luna
- cBio Center, Divisions of Biostatistics and Computational BiologyDepartment of Data SciencesDana‐Farber Cancer InstituteBostonMAUSA
- Department of Cell BiologyHarvard Medical SchoolBostonMAUSA
| | - Ozgun Babur
- Computer Science DepartmentUniversity of Massachusetts BostonBostonMAUSA
| | | | - Alberto Valdeolivas
- Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Marina Esteban‐Medina
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
| | - Maria Peña‐Chilet
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPS, Hospital Virgen del RocíoSevillaSpain
| | - Kinza Rian
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
| | - Tomáš Helikar
- Department of BiochemistryUniversity of Nebraska‐LincolnLincolnNEUSA
| | | | - Dezso Modos
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Agatha Treveil
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Marton Olbei
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Stephane Ballereau
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Aurélien Dugourd
- Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
- Institute of Experimental Medicine and Systems BiologyFaculty of Medicine, RWTHAachen UniversityAachenGermany
| | | | - Vincent Noël
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Laurence Calzone
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Chris Sander
- cBio Center, Divisions of Biostatistics and Computational BiologyDepartment of Data SciencesDana‐Farber Cancer InstituteBostonMAUSA
- Department of Cell BiologyHarvard Medical SchoolBostonMAUSA
| | - Emek Demir
- Department of Molecular and Medical GeneticsOregon Health & Sciences UniversityPortlandORUSA
| | | | - Tom C Freeman
- The Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Franck Augé
- Sanofi R&DTranslational SciencesChilly‐MazarinFrance
| | | | - Jan Hasenauer
- Helmholtz Zentrum München – German Research Center for Environmental HealthInstitute of Computational BiologyNeuherbergGermany
- Interdisciplinary Research Unit Mathematics and Life SciencesUniversity of BonnBonnGermany
| | - Olaf Wolkenhauer
- Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
| | - Egon L Wilighagen
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
| | - Alexander R Pico
- Institute of Data Science and BiotechnologyGladstone InstitutesSan FranciscoCAUSA
| | - Chris T Evelo
- Department of Bioinformatics ‐ BiGCaTNUTRIMMaastricht UniversityMaastrichtThe Netherlands
- Maastricht Centre for Systems Biology (MaCSBio)Maastricht UniversityMaastrichtThe Netherlands
| | - Marc E Gillespie
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
- St. John’s University College of Pharmacy and Health SciencesQueensNYUSA
| | - Lincoln D Stein
- MaRS CentreOntario Institute for Cancer ResearchTorontoONCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoONCanada
| | - Henning Hermjakob
- European Bioinformatics Institute (EMBL‐EBI)European Molecular Biology LaboratoryHinxton, CambridgeshireUK
| | | | | | - Joaquin Dopazo
- Clinical Bioinformatics AreaFundación Progreso y Salud (FPS)Hospital Virgen del RocioSevillaSpain
- Computational Systems Medicine GroupInstitute of Biomedicine of Seville (IBIS)Hospital Virgen del RocioSevillaSpain
- Bioinformatics in Rare Diseases (BiER)Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)FPS, Hospital Virgen del RocíoSevillaSpain
- FPS/ELIXIR‐esHospital Virgen del RocíoSevillaSpain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Hiroaki Kitano
- Systems Biology InstituteTokyoJapan
- Okinawa Institute of Science and Technology Graduate SchoolOkinawaJapan
| | - Emmanuel Barillot
- Institut CuriePSL Research UniversityParisFrance
- INSERMParisFrance
- MINES ParisTechPSL Research UniversityParisFrance
| | - Charles Auffray
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Rudi Balling
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch‐sur‐AlzetteLuxembourg
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Olbei M, Thomas JP, Hautefort I, Treveil A, Bohar B, Madgwick M, Gul L, Csabai L, Modos D, Korcsmaros T. CytokineLink: A Cytokine Communication Map to Analyse Immune Responses-Case Studies in Inflammatory Bowel Disease and COVID-19. Cells 2021; 10:2242. [PMID: 34571891 PMCID: PMC8469673 DOI: 10.3390/cells10092242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the secretion of other cytokines downstream. However, there are no readily available bioinformatic resources that can model cytokine-cytokine interactions. In this effort, we built a communication map between major tissues and blood cells that reveals how cytokine-mediated intercellular networks form during homeostatic conditions. We collated the most prevalent cytokines from the literature and assigned the proteins and their corresponding receptors to source tissue and blood cell types based on enriched consensus RNA-Seq data from the Human Protein Atlas database. To assign more confidence to the interactions, we integrated the literature information on cell-cytokine interactions from two systems of immunology databases, immuneXpresso and ImmunoGlobe. From the collated information, we defined two metanetworks: a cell-cell communication network connected by cytokines; and a cytokine-cytokine interaction network depicting the potential ways in which cytokines can affect the activity of each other. Using expression data from disease states, we then applied this resource to reveal perturbations in cytokine-mediated intercellular signalling in inflammatory and infectious diseases (ulcerative colitis and COVID-19, respectively). For ulcerative colitis, with CytokineLink, we demonstrated a significant rewiring of cytokine-mediated intercellular communication between non-inflamed and inflamed colonic tissues. For COVID-19, we were able to identify cell types and cytokine interactions following SARS-CoV-2 infection, highlighting important cytokine interactions that might contribute to severe illness in a subgroup of patients. Such findings have the potential to inform the development of novel, cytokine-targeted therapeutic strategies. CytokineLink is freely available for the scientific community through the NDEx platform and the project github repository.
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Affiliation(s)
- Marton Olbei
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Quadram Institute Bioscience, Norwich NR4 7UZ, UK
| | - John P. Thomas
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Quadram Institute Bioscience, Norwich NR4 7UZ, UK
- Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich NR4 7UZ, UK
| | - Isabelle Hautefort
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
| | - Agatha Treveil
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Quadram Institute Bioscience, Norwich NR4 7UZ, UK
| | - Balazs Bohar
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Department of Genetics, Eotvos Lorand University, 1117 Budapest, Hungary
| | - Matthew Madgwick
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Quadram Institute Bioscience, Norwich NR4 7UZ, UK
| | - Lejla Gul
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
| | - Luca Csabai
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Department of Genetics, Eotvos Lorand University, 1117 Budapest, Hungary
| | - Dezso Modos
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Quadram Institute Bioscience, Norwich NR4 7UZ, UK
| | - Tamas Korcsmaros
- Earlham Institute, Norwich NR4 7UZ, UK; (M.O.); (J.P.T.); (I.H.); (A.T.); (B.B.); (M.M.); (L.G.); (L.C.); (D.M.)
- Quadram Institute Bioscience, Norwich NR4 7UZ, UK
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Olbei M, Hautefort I, Modos D, Treveil A, Poletti M, Gul L, Shannon-Lowe CD, Korcsmaros T. SARS-CoV-2 Causes a Different Cytokine Response Compared to Other Cytokine Storm-Causing Respiratory Viruses in Severely Ill Patients. Front Immunol 2021; 12:629193. [PMID: 33732251 PMCID: PMC7956943 DOI: 10.3389/fimmu.2021.629193] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/21/2022] Open
Abstract
Hyper-induction of pro-inflammatory cytokines, also known as a cytokine storm or cytokine release syndrome (CRS), is one of the key aspects of the currently ongoing SARS-CoV-2 pandemic. This process occurs when a large number of innate and adaptive immune cells activate and start producing pro-inflammatory cytokines, establishing an exacerbated feedback loop of inflammation. It is one of the factors contributing to the mortality observed with coronavirus 2019 (COVID-19) for a subgroup of patients. CRS is not unique to the SARS-CoV-2 infection; it was prevalent in most of the major human coronavirus and influenza A subtype outbreaks of the past two decades (H5N1, SARS-CoV, MERS-CoV, and H7N9). With a comprehensive literature search, we collected changing the cytokine levels from patients upon infection with the viral pathogens mentioned above. We analyzed published patient data to highlight the conserved and unique cytokine responses caused by these viruses. Our curation indicates that the cytokine response induced by SARS-CoV-2 is different compared to other CRS-causing respiratory viruses, as SARS-CoV-2 does not always induce specific cytokines like other coronaviruses or influenza do, such as IL-2, IL-10, IL-4, or IL-5. Comparing the collated cytokine responses caused by the analyzed viruses highlights a SARS-CoV-2-specific dysregulation of the type-I interferon (IFN) response and its downstream cytokine signatures. The map of responses gathered in this study could help specialists identify interventions that alleviate CRS in different diseases and evaluate whether they could be used in the COVID-19 cases.
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Affiliation(s)
- Marton Olbei
- Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Dezso Modos
- Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Agatha Treveil
- Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Martina Poletti
- Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Lejla Gul
- Earlham Institute, Norwich, United Kingdom
| | - Claire D. Shannon-Lowe
- Institute of Immunology and Immunotherapy, The University of Birmingham, Birmingham, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
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8
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Treveil A, Bohar B, Sudhakar P, Gul L, Csabai L, Olbei M, Poletti M, Madgwick M, Andrighetti T, Hautefort I, Modos D, Korcsmaros T. ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PLoS Comput Biol 2021; 17:e1008685. [PMID: 33534793 PMCID: PMC7886129 DOI: 10.1371/journal.pcbi.1008685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 06/26/2020] [Revised: 02/16/2021] [Accepted: 01/10/2021] [Indexed: 12/21/2022] Open
Abstract
The SARS-CoV-2 pandemic of 2020 has mobilised scientists around the globe to research all aspects of the coronavirus virus and its infection. For fruitful and rapid investigation of viral pathomechanisms, a collaborative and interdisciplinary approach is required. Therefore, we have developed ViralLink: a systems biology workflow which reconstructs and analyses networks representing the effect of viruses on intracellular signalling. These networks trace the flow of signal from intracellular viral proteins through their human binding proteins and downstream signalling pathways, ending with transcription factors regulating genes differentially expressed upon viral exposure. In this way, the workflow provides a mechanistic insight from previously identified knowledge of virally infected cells. By default, the workflow is set up to analyse the intracellular effects of SARS-CoV-2, requiring only transcriptomics counts data as input from the user: thus, encouraging and enabling rapid multidisciplinary research. However, the wide-ranging applicability and modularity of the workflow facilitates customisation of viral context, a priori interactions and analysis methods. Through a case study of SARS-CoV-2 infected bronchial/tracheal epithelial cells, we evidence the functionality of the workflow and its ability to identify key pathways and proteins in the cellular response to infection. The application of ViralLink to different viral infections in a context specific manner using different available transcriptomics datasets will uncover key mechanisms in viral pathogenesis.
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Affiliation(s)
- Agatha Treveil
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Balazs Bohar
- Earlham Institute, Norwich, United Kingdom
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
- Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lejla Gul
- Earlham Institute, Norwich, United Kingdom
| | - Luca Csabai
- Earlham Institute, Norwich, United Kingdom
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | - Marton Olbei
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Martina Poletti
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Matthew Madgwick
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Tahila Andrighetti
- Earlham Institute, Norwich, United Kingdom
- Institute of Biosciences, São Paulo University, Botucatu, Brazil
| | | | - Dezso Modos
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich, United Kingdom
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9
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Treveil A, Sudhakar P, Matthews ZJ, Wrzesiński T, Jones EJ, Brooks J, Ölbei M, Hautefort I, Hall LJ, Carding SR, Mayer U, Powell PP, Wileman T, Di Palma F, Haerty W, Korcsmáros T. Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches. Mol Omics 2021; 16:39-58. [PMID: 31819932 DOI: 10.1039/c9mo00130a] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn's disease or ulcerative colitis.
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Affiliation(s)
- A Treveil
- Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK.
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10
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Kiu R, Treveil A, Harnisch LC, Caim S, Leclaire C, van Sinderen D, Korcsmaros T, Hall LJ. Bifidobacterium breve UCC2003 Induces a Distinct Global Transcriptomic Program in Neonatal Murine Intestinal Epithelial Cells. iScience 2020; 23:101336. [PMID: 32683312 PMCID: PMC7371750 DOI: 10.1016/j.isci.2020.101336] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
The underlying health-driving mechanisms of Bifidobacterium during early life are not well understood, particularly how this microbiota member may modulate the intestinal barrier via programming of intestinal epithelial cells (IECs). We investigated the impact of Bifidobacterium breve UCC2003 on the transcriptome of neonatal murine IECs. Small IECs from two-week-old neonatal mice administered B. breve UCC2003 or PBS (control) were subjected to global RNA sequencing, and differentially expressed genes, pathways, and affected cell types were determined. We observed extensive regulation of the IEC transcriptome with ∼4,000 genes significantly up-regulated, including key genes linked with epithelial barrier function. Enrichment of cell differentiation pathways was observed, along with an overrepresentation of stem cell marker genes, indicating an increase in the regenerative potential of the epithelial layer. In conclusion, B. breve UCC2003 plays a central role in driving intestinal epithelium homeostatic development during early life and suggests future avenues for next-stage clinical studies.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Agatha Treveil
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Lukas C Harnisch
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Shabhonam Caim
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Charlotte Leclaire
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Douwe van Sinderen
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12YT20, Ireland
| | - Tamas Korcsmaros
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; Chair of Intestinal Microbiome, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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Püngel D, Treveil A, Dalby MJ, Caim S, Colquhoun IJ, Booth C, Ketskemety J, Korcsmaros T, van Sinderen D, Lawson MAE, Hall LJ. Bifidobacterium breve UCC2003 Exopolysaccharide Modulates the Early Life Microbiota by Acting as a Potential Dietary Substrate. Nutrients 2020; 12:E948. [PMID: 32235410 PMCID: PMC7231044 DOI: 10.3390/nu12040948] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/20/2020] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bifidobacterium represents an important early life microbiota member. Specific bifidobacterial components, exopolysaccharides (EPS), positively modulate host responses, with purified EPS also suggested to impact microbe-microbe interactions by acting as a nutrient substrate. Thus, we determined the longitudinal effects of bifidobacterial EPS on microbial communities and metabolite profiles using an infant model colon system. METHODS Differential gene expression and growth characteristics were determined for each strain; Bifidobacterium breve UCC2003 and corresponding isogenic EPS-deletion mutant (B. breve UCC2003del). Model colon vessels were inoculated with B. breve and microbiome dynamics monitored using 16S rRNA sequencing and metabolomics (NMR). RESULTS Transcriptomics of EPS mutant vs. B. breve UCC2003 highlighted discrete differential gene expression (e.g., eps biosynthetic cluster), though overall growth dynamics between strains were unaffected. The EPS-positive vessel had significant shifts in microbiome and metabolite profiles until study end (405 h); with increases of Tyzzerella and Faecalibacterium, and short-chain fatty acids, with further correlations between taxa and metabolites which were not observed within the EPS-negative vessel. CONCLUSIONS These data indicate that B. breve UCC2003 EPS is potentially metabolized by infant microbiota members, leading to differential microbial metabolism and altered metabolite by-products. Overall, these findings may allow development of EPS-specific strategies to promote infant health.
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Affiliation(s)
- Deborah Püngel
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
| | - Agatha Treveil
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
- Earlham Institute, Norwich NR4 7UZ, UK
| | - Matthew J Dalby
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
| | - Shabhonam Caim
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
| | - Ian J Colquhoun
- Analytical Sciences, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (I.J.C.); (C.B.)
| | - Catherine Booth
- Analytical Sciences, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (I.J.C.); (C.B.)
| | - Jennifer Ketskemety
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
| | - Tamas Korcsmaros
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
- Earlham Institute, Norwich NR4 7UZ, UK
| | - Douwe van Sinderen
- APC Microbiome Institute, University College Cork, T12 K8AF Cork, Ireland;
| | - Melissa AE Lawson
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
- Lydia Becker Institute for Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research, Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK
| | - Lindsay J Hall
- Gut Microbes & Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich NR4 7UQ, UK; (D.P.); (A.T.); (M.J.D.); (S.C.); (J.K.); (T.K.)
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
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Jones EJ, Matthews ZJ, Gul L, Sudhakar P, Treveil A, Divekar D, Buck J, Wrzesinski T, Jefferson M, Armstrong SD, Hall LJ, Watson AJM, Carding SR, Haerty W, Di Palma F, Mayer U, Powell PP, Hautefort I, Wileman T, Korcsmaros T. Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Dis Model Mech 2019; 12:dmm.037069. [PMID: 30814064 PMCID: PMC6451430 DOI: 10.1242/dmm.037069] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Paneth cells are key epithelial cells that provide an antimicrobial barrier and maintain integrity of the small-intestinal stem cell niche. Paneth cell abnormalities are unfortunately detrimental to gut health and are often associated with digestive pathologies such as Crohn's disease or infections. Similar alterations are observed in individuals with impaired autophagy, a process that recycles cellular components. The direct effect of autophagy impairment on Paneth cells has not been analysed. To investigate this, we generated a mouse model lacking Atg16l1 specifically in intestinal epithelial cells, making these cells impaired in autophagy. Using three-dimensional intestinal organoids enriched for Paneth cells, we compared the proteomic profiles of wild-type and autophagy-impaired organoids. We used an integrated computational approach combining protein-protein interaction networks, autophagy-targeted proteins and functional information to identify the mechanistic link between autophagy impairment and disrupted pathways. Of the 284 altered proteins, 198 (70%) were more abundant in autophagy-impaired organoids, suggesting reduced protein degradation. Interestingly, these differentially abundant proteins comprised 116 proteins (41%) that are predicted targets of the selective autophagy proteins p62, LC3 and ATG16L1. Our integrative analysis revealed autophagy-mediated mechanisms that degrade key proteins in Paneth cell functions, such as exocytosis, apoptosis and DNA damage repair. Transcriptomic profiling of additional organoids confirmed that 90% of the observed changes upon autophagy alteration have effects at the protein level, not on gene expression. We performed further validation experiments showing differential lysozyme secretion, confirming our computationally inferred downregulation of exocytosis. Our observations could explain how protein-level alterations affect Paneth cell homeostatic functions upon autophagy impairment. This article has an associated First Person interview with the joint first authors of the paper. Editor's choice: Using an integrative approach encompassing intestinal organoid culture, proteomics, transcriptomics and protein-protein interaction networks, we list Paneth cell functions dependent on autophagy.
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Affiliation(s)
- Emily J Jones
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Zoe J Matthews
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Devina Divekar
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jasmine Buck
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Matthew Jefferson
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Stuart D Armstrong
- National Institute of Health Research, University of Liverpool, Liverpool L3 5RF, UK
| | - Lindsay J Hall
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
| | - Alastair J M Watson
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Simon R Carding
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Ulrike Mayer
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Penny P Powell
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Tom Wileman
- Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK.,Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK .,Quadram Institute, Norwich Research Park, Norwich NR4 7UA, UK
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