The Role of DOCK8 in Human Lymphocytes
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The Role of DOCK8 in Human Lymphocytes Bethany Pillay A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy St Vincent’s Clinical School, Faculty of Medicine UNSW Sydney Immunology Division Garvan Institute of Medical Research Supervisors: Professor Stuart Tangye and Associate Professor Cindy Ma September 2019 Thesis/Dissertation Sheet Surname/Family Name : PILLAY Given Name/s : BETHANY ANN Abbreviation for degree as give in the University : PhD calendar Faculty : MEDICINE School : ST VINCENT’S CLINICAL SCHOOL Thesis Title : THE ROLE OF DOCK8 IN HUMAN LYMPHOCYTES Abstract 350 words maximum: (PLEASE TYPE) Dedicator of cytokinesis 8 (DOCK8) is a guanine nucleotide exchange factor that is highly expressed in lymphocytes and is involved in cytoskeletal rearrangement. Bi-allelic inactivating mutations in DOCK8 cause a combined immunodeficiency which is characterised by severe viral, bacterial and fungal infections, eczema, allergies and impaired humoral responses and which requires haematopoietic stem cell transplant (HSCT) to overcome. However, the cellular defects underlying these clinical symptoms have not been fully investigated. This thesis firstly examines the contribution of the CD4+ T cell compartment to the clinical features of DOCK8 deficiency by using cell cultures of DOCK8-deficient patients. This revealed skewed in vivo differentiation explaining patient susceptibility to infections and their propensity towards allergic conditions. To explore the cellular alterations which enable the clinical improvement of patients following HSCT, a comprehensive study of lymphocyte phenotype and function in DOCK8- deficient patients before and after HSCT was undertaken. This study found key functional differences which provided explanation for resolution of symptoms in patients post HSCT and noted persistent defects which may influence continuing patient care. Furthermore, investigation of a DOCK8-revertant patient allowed for the analysis of both DOCK8-deficient and DOCK8- revertant cells within the same individual and enabled the elucidation of the influence of environment on the identified defects of DOCK8 deficiency. Lastly, the extent of cellular impairment that was due to the involvement of DOCK8 in previously identified signalling pathways was examined with the use of immunodeficiency patients with mutations in DOCK8- related proteins. The findings of this analysis suggested that the outcomes of DOCK8 deficiency were not due solely to the role of DOCK8 in a single signalling pathway. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all property rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstracts International (this is applicable to doctoral theses only). ……………………………………………… ……………………………………..…… ……….……………………...…….… Signature Witness Signature Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years must be made in writing. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. FOR OFFICE USE ONLY Date of completion of requirements for Award: ii iii iv Acknowledgements To my supervisors Stu and Cindy – thank you for agreeing to take me on despite me not having an immunology background. Thanks for all the help along the way and time spent with experiments and meetings and presentations and editing and countless emails to clinicians and collaborators to chase up details and ensure patient samples. To Danielle – thank you for being my first port of call for almost any issue I had (including super gluing things back together) and for the tremendous number of things you do for the lab to make it a better place for us all. To Kat and Geetha – thank you for showing me the ropes and putting up with me following you around and asking constant questions when I first started in the lab and then for agreeing to spend time with me outside the lab as a friend. To my office buddies – thank you Simon for the interesting youtube rabbit holes we went down and thank you to my work wife Julia for being the person I talk to most. To Emily and Frenchie – thank you to my English duo for all their vital words of encouragement and support as well as their friendship along the way. To the rest of the lab – thanks for helping me out when I needed it, all the fun times and listening to my rants. I’m telling you, our tv show “Lab rats” would have been a hit! To level 9 – thanks for always being happy to lend a hand or have a chat. It has been a privilege to be part of the department most obsessed with trivia. To my family and friends – thank you for the support and for knowing to ask just enough questions to show you care but not to hassle me about when I would be finished. To Alex – thank you for not knowing what you were getting into but for hanging in there with me anyway. v vi vii Publications arising from this work Pillay BA, Avery DT, Smart JM, Cole T, Choo S, Chan D, Gray PE, Frith K, Mitchell R, Phan TG, Wong M, Campbell DE, Hsu P, Ziegler JB, Peake J, Alvaro F, Picard C, Bustamante J, Neven B, Cant AJ, Uzel G, Arkwright PD, Casanova JL, Su HC, Freeman AF, Shah N, Hickstein DD, Tangye SG, Ma CS. JCI Insight. 2019; 25(5) Tangye SG, Bucciol G, Casas-Martin J, Pillay B, Ma CS, Moens L, Meyts I. Human inborn errors of the actin cytoskeleton affecting immunity: way beyond WAS and WIP. Immunology Cell Biol. 2019; 97(4):389-402 Béziat V, Li J, Lin JX, Ma CS, Li P, Bousfiha A, Pellier I, Zoghi S, Baris S, Keles S, Gray P, Du N, Wang Y, Zerbib Y, Lévy R, Leclercq T, About F, Lim AI, Rao G, Payne K, Pelham SJ, Avery DT, Deenick EK, Pillay B, Chou J, Guery R, Belkadi A, Guérin A, Migaud M, Rattina V, Ailal F, Benhsaien I, Bouaziz M, Habib T, Chaussabel D, Marr N, El-Benna J, Grimbacher B, Wargon O, Bustamante J, Boisson B, Müller- Fleckenstein I, Fleckenstein B, Chandesris MO, Titeux M, Fraitag S, Alyanakian MA, Leruez-Ville M, Picard C, Meyts I, Di Santo JP, Hovnanian A, Somer A, Ozen A, Rezaei N, Chatila TA, Abel L, Leonard WJ, Tangye SG, Puel A, Casanova JL. Science Immunology. 2018; 3(24) Tangye SG, Pillay B, Randall KL, Avery DT, Phan TG, Gray P, Ziegler JB, Smart JM, Peake J, Arkwright PD, Hambleton S, Orange J, Goodnow CC, Uzel G, Casanova JL, Lugo Reyes SO, Freeman AF, Su HC, Ma CS. Dedicator of cytokinesis8-deficient CD4+ T cells are biased to a TH2 effector fate at the expense of TH1 and TH17 cells. Journal of Allergy and Clinical Immunology. 2017; 139(3):933-949. Presentations arising from this work Biennial meeting of the European Society for Immunodeficiencies, Lisbon, Portugal, 2018 Annual meeting of the Australasian Society for Immunology, Perth, Australia, 2018 ASI NSW branch meeting, Kiama, Australia, 2018 Annual meeting of the Australasian Society for Immunology, Brisbane, Australia, 2017 International Congress of Immunology, Melbourne, Australia, 2016 viii Experiments that were not the sole work of the author All experiments were performed by the author at the Garvan Institute of Medical Research with the following exceptions: Fig 4.8A experiment performed by Danielle Priestley Fig 6.4B-D (WAS and XLT patients) experiment performed by Danielle Priestley ix Abbreviations ABTS 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) AD autosomal dominant ADA adenosine deaminase deficiency APCs antigen presenting cells AR autosomal recessive BCR b cell receptor BSA bovine serum albumin CADD combined annotation dependent depletion CBA cytometric bead array CCR cc chemokine receptor CD cluster of differentiation CDC42 cell division control protein homolog cDNA complementary deoxyribonucleic acid CFSE carboxyfluorescein succinimidyl ester CMC chronic mucocutaneous candidiasis CMV cytomegalovirus CNS central nervous system CNV copy number variations CRISPR/Ca clustered regularly interspaced short palindromic repeats/ CRISPR- s9 associated protein 9 DC dendritic cells DHR dock homology region DMSO dimethyl sulfoxide DNA deoxyribonucleic acid dNTPs deoxynucleoside triphosphate DOCK2 dedicator of cytokinesis 2 DOCK8 dedicator of cytokinesis 8 DTT dithiothreitol EBV Epstein-Barr virus EDTA ethylenediaminetetraacetic acid ELISA enzyme-linked immunosorbent assay FA formaldehyde FACS fluorescence activated cell sorting F-actin filamentous actin FCS fetal calf serum FSC-A forward scatter area FSC-H forward scatter height GC germinal centre GEF guanine exchange factor gof gain of function GvHD graft vs host disease HIES hyper IgE syndrome x HRP horse radish peroxidase HSCT haematopoietic stem cell transplant HSV herpes simplex virus ICAM-1 intercellular adhesion molecule 1 IFN interferon Ig immunoglobulin IL interleukin IS immune synapse IU international units IVIg intravenous immunoglobulin kU/l kilounit antibody per litre kUa/l kilounit of allergen-specific antibody per litre LB luria broth LCL lymphoblastoid cell line LFA-1 lymphocyte function-associated antigen 1 LN lymph nodes lof loss of function