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Regulation of Type I Interferons in Health and Autoimmune Disease

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Regulation of Type I Interferons in Health and Autoimmune Disease Regulation of type I interferons in health and autoimmune disease Antonios Psarras Submitted in accordance with the requirements for the degree of Doctor of Philosophy (PhD) University of Leeds Leeds Institute of Rheumatic and Musculoskeletal Medicine September 2018 i Intellectual property and publication statements The candidate confirms that the work submitted is his own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. Chapter 1 includes data from a jointly-authored publication: Psarras A, Emery P, Vital EM. Type I interferon-mediated autoimmune diseases: pathogenesis, diagnosis and targeted therapy. Rheumatology (Oxford). 2017;56(10):1662-75. Psarras A performed the review of literature, critically appraised scientific evidences of the relevant topics and led the writing of the manuscripts. Emery revised the manuscripts for important intellectual content and final approval of the manuscript. Chapter 3 includes data from two jointly-authored publications: El-Sherbiny YM*, Psarras A*, Yusof MYM, Hensor EMA, Tooze R, Doody G, et al. A novel two-score system for interferon status segregates autoimmune diseases and correlates with clinical features. Sci Rep. 2018;8(1):5793. *joint first author El-Sherbiny YM, Emery P, and Vital EM performed conception and design of research, data interpretation and writing the manuscript; El-Sherbiny YM, Md Yusof MY, Wittmann M, and Vital EM designed the research and recruited patients and clinical ii interpretation of the study; Tooze R and Doody G performed B cell design, analysis and interpretation, and writing the manuscript; El-Sherbiny YM, Md Yusof MY, Mohamed AAA, and Psarras A performed flow cytometry analysis and interpretation; El-Sherbiny YM and Psarras A performed gene expression analysis; Hensor EMA performed statistical and factor analysis method development and nanoparticle characterization; Psarras A, McGonagle D, and Vital EM performed data interpretation and writing the manuscript. Md Yusof MY*, Psarras A*, El-Sherbiny YM, Hensor EMA, Dutton K, Ul-Hassan S, et al. Prediction of autoimmune connective tissue disease in an at-risk cohort: prognostic value of a novel two-score system for interferon status. Ann Rheum Dis. 2018;77(10):1432-9. *joint first author Md Yusof MY, Psarras A and Vital EM: substantial contributions to the conception or design of the work, or the acquisition, analysis or interpretation of data, drafting the work or revising it critically for important intellectual content, final approval of the version published and agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. El-Sherbiny YM, Hensor EMA, Dutton K, Ul-Hassan S, Shalbaf M, Alase AA, Wittmann M and Emery P: substantial contributions to the conception or design of the work, or the acquisition, analysis or interpretation of data, drafting the work or revising it critically for important intellectual content and final approval of the version published. iii This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Antonios Psarras to be identified as Author of this work has been asserted by him in accordance with the Copyright, Designs and Patents Act 1988. © 2018 The University of Leeds and Antonios Psarras iv Acknowledgements I would like to thank Dr Edward Vital, Prof Paul Emery and Dr Miriam Wittmann, my supervisors at Leeds Institute of Rheumatic and Musculoskeletal Medicine, for their guidance and endless support for my PhD thesis and my personal career development. I would also like to express my gratitude to Prof George Tsokos at Beth Israel Deaconess Medical Center, who kindly supervised the work I carried out in his lab at Harvard Medical School in 2017 for my PhD thesis. I am especially indebted to the consultants Prof Paul Emery, Dr Edward Vital, Prof Maya Buch, Dr Shouvik Dass, Prof Mark Goodfield, Dr Emma Dunn, Dr John Bamford, specialist registrars Dr Md Yuzaiful Md Yusof, Dr Andrew Barr, Dr Lesley-Anne Bissell, clinical trial coordinator Huma Cassamoali and clinical trial assistant Sabina Khan as well as nurses and healthcare assistants for their services at the Leeds Connective Tissue Disease and Vasculitis Clinic. Registering patients to research cohorts and collecting biological samples on weekly basis would have not been made possible without their endless assistance and valuable contribution. I would also like to thank Diane Corscadden and Katie Mbara at Chapel Allerton Hospital for collecting and sending any patient samples to St. James’s University Hospital. I am grateful to Dr Elizabeth Hensor, who helped with statistical analysis performing the factor analysis, Dr Mohammad Shalbaf, who performed the tissue sectioning of skin biopsies and Dr Adewonuola Alase, who helped with in situ hybridization of the skin and in vitro culturing of human skin cells. I would also like to mention Dr Yasser El-Sherbiny, post-doctoral fellow, and Zoe Wigston, research technician, for their valuable help in the lab. Special thanks to Adam Davison and Liz Straszynski from v Flow Cytometry and Imaging facility in Wellcome Trust Brenner Building for providing induction courses in flow cytometry and confocal microscopy as well as facility’s precious service in cell sorting. I am also indebted to Next Generation Sequencing Facility for performing and analysing the RNA-sequencing data from the samples given, especially Dr Ian Carr, lecturer in medical bioinformatics, Dr Agne Antanaviciute, bioinformatician, and Ummey Hany, technical specialist, for their major contribution to the project. In addition to all contributors above, I would like to express my special thanks and respect to all researchers at University of Leeds and Harvard Medical School I have shared my data and scientific thoughts with, but more importantly, to all the patients that without their actual contribution I would not have been able to perform my experiments and investigate basic mechanisms of human autoimmunity. I would like to express my gratitude to the University of Leeds for enabling me to undertake the current PhD by supporting me with University of Leeds 110 Anniversary Research Scholarship in the research theme “Immunology, Inflammation & Infection”. Moreover, I would like to special mention the Erdheim Travel Scholarship awarded by the School of Medicine at Leeds and the Summer Placement Award Scheme awarded by the British Society for Immunology, which provided financial support during my research visit at Harvard Medical School in Boston, USA. Last but not least, I would like to thank my beloved family and friends for their endless support, love and patience throughout all these years of hard work and scientific challenges that enabled me to submit this PhD thesis. vi List of publications and presentations arising from this thesis Original articles: El-Sherbiny YM*, Psarras A*, et al. A novel two-score system for interferon status segregates autoimmune diseases and correlates with clinical features. Sci Rep. 2018;8(1):5793. *joint first author Md Yusof MY*, Psarras A*, et al. Prediction of autoimmune connective tissue disease in an at-risk cohort: prognostic value of a novel two-score system for interferon status. Ann Rheum Dis. 2018;77(10):1432-9. *joint first author Review articles: Psarras A, et al. Type I interferon-mediated autoimmune diseases: pathogenesis, diagnosis and targeted therapy. Rheumatology (Oxford). 2017;56(10):1662-75. Oral presentations: Psarras A, et al. The role of skin tissue in initiation of Systemic Lupus Erythematosus. Annual Northern and Yorkshire Rheumatology Meeting, York (UK), September 2018. Psarras A, et al. Type I interferon is produced by non-haematopoietic tissue cells but not pDCs in preclinical autoimmunity and SLE. Annual European League Against Rheumatism (EULAR) Congress, Madrid (Spain), June 2018. vii Psarras A, et al. Prediction of connective tissue disease in at-risk cohort using a novel interferon-stimulated gene expression score. Annual Congress of Japanese College of Rheumatology (JCR), Tokyo (Japan), April 2018. Psarras A, et al. Type I interferon regulation in preclinical and established autoimmunity. Annual Northern and Yorkshire Rheumatology Meeting, York (UK), September 2017. Psarras A, et al. Towards prevention of Systemic Lupus Erythematosus: predicting disease and identification of therapeutic targets. 7th NIHR Infrastructure Doctoral Research Training Camp, Ashridge Business School (UK), July 2016. Psarras A, et al. Distinct subsets of interferon-stimulated genes are associated with incomplete and established systemic lupus erythematosus. 36th European Workshop for Rheumatology Research, York (UK), february 2016. Poster presentations: Psarras A, et al. TNf-α regulates plasmacytoid dendritic cells by suppressing IfN-α production and enhancing Th1 and Th17 cell differentiation. Annual European League Against Rheumatism (EULAR) Congress, Madrid (Spain), June 2018. Psarras A, et al. TNf-α is a major regulator of human plasmacytoid dendritic cells by promoting a functional drift to antigen presentation. Annual Congress of British Society for
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