Development of Dendritic Cells in the Intestine Tamsin Florencia Pamela Zangerle Murray BSc., MRes. A thesis submitted to the College of Medicine, Veterinary and Life Sciences, University of Glasgow in fulfilment of the requirements for the degree of Doctor of Philosophy. May 2016 Institute of Infection, Immunity and Inflammation University of Glasgow 120 University Place Glasgow, G12 8TA Acknowledgements If there is anything in life that maKes you appreciate the support you have, it is doing a PhD…oh and losing a parent! These last few years would not have been possible without the people mentioned below, as well as many more that have given a few words of encouragement along the way. And so, to begin with I must thanK Allan Mowat, my supervisor – it was a slow start for both of us, but I think we got there in the end! ThanK you for all of your advice and support, the amount of your time spent reading and correcting this thesis, and for all of the encouragement you have given. I realise that your support will continue for years to come, and I just hope that I have been an acceptable final PhD student! Thank you to ‘The Mowlings’ (Mowats & Millings) both past and present. Simon Milling, thanK you for being my supervisor in waiting and operating an open doors policy for when I ever needed to speak to you. Charlie, thanK you for passing me the reins, if a little reluctantly, in the final year of your PhD – I learnt a lot from your determination and drive. You set me up in the lab and were there for me when I needed it (most memorably after my first lab meeting). Also, many thanKs for reading over my SIRPα chapter. Calum, you pocKet genius! There was never a moment where you failed to bring a smile to my face, be it with words of encouragement, maKing me remember how to compensate properly, crazy mad joKes, or putting up with my singing. Your patience and guidance will not go unnoticed in the future. Thanks also for reading Chapter 5! Alberto, gracias por su apoyo y amabilidad; y para la comprensión de mis emociones Latina! Thank you to Vuk, Carolyn, Stephanie and Pamela for reading over my chapters and for all of your support over the years, and thank you Carolyn for getting me through some tough times. Ashley Gilmore, Lizzie, Hannah, AshoK, Jennifer, Lotta, Verena, Johannes and AniKa, thanK you for maKing everyday a fun day. ThanKs to everyone in the department, especially Megan MacLeod, for your advice and words of wisdom, as well as giving me courage in meeting speaKers and not fearing that I would talK about my dreams! ThanKs to all the CRF staff for looKing after my timed breeders, as I know they were a bit of a headache. Thank you Diane 2 Vaughan for all of your help in the Flow Facility and putting me forward for the amazing opportunity to go to BD, Erembodegem for the Aria III training course. Thank you Oliver Pabst for the opportunity to do some lovely histology in your lab, though sadly I could never get the technique quite as nice in Glasgow. Thanks also to Lindsay Hall and Christoph Muller for providing me with mice, and thank you Joanne KonKel for employing me as a post-doc before getting the PhD, as well as for your patience over the last few months. I am indebted to Darren MonKton and Olwyn Byron for seeing potential in me and for their continued support as I carried out my Wellcome Trust (to whom I am also grateful) funded PhD. Thank you also to Bill Cushley, for all of our chats and pep talks. You have been a great help through these years. Also, many thanKs to the BSI for providing me with the travel grant that got me my job!! Now to the family: Mum, you are the strongest person I Know. ThanK you for supporting me through the emotional rollercoaster that has been the last five years. If losing Dad so tragically on the day I was awarded this PhD wasn’t bad enough, then the continued battle with grief and the stress of the PhD really did test me, but you were there every step of the way, unwavering and supportive, but more than happy to give me a KicK up the bum when it was required. Papá, te haces un lío con esto bueno y adecuado para mí, pero creo que estaría orgulloso de lo que he logrado en su ausencia. Carise, thanK you for being a great little sister! And to all of my Aunties, Uncles and Cousins and Abuela, both in Europe and Argentina, Knowing you are all there for me has Kept me going. Thanks to the Kennys and Brian as well. ThanK you to all of my friends: Hannah Kelly, my best of friends for your beautiful cynicism and a bed in London when I had conferences to attend, Katie Percival for your charming and sunny smile, Siubhan MacDonald for your calming elegance, and all of my other University of Bristol friends. Matthew LaKins and Amy Sawtell, thanK you for everything. Hannah Wessel, your love has been invaluable; Lizzie Mann, the laughs too much; Ruth McCartney, you are wise beyond your years; and Pamela Wright, you are a star! Thank you also to Marcia Blagg – your friendship has been treasured, and thanKs for your help with my introduction figures. I am sure I have 3 forgotten people, but to you all, I am forever in your debt for giving me the strength to finish the PhD. And finally, Michael Kenny: Thanks for the gin! No really, thank you Mike for putting up with me over the last few years. It can’t have been easy and it must taKe the patience of a saint to deal with me, even on a good day! You Know how much you mean to me and although we have had our own stresses to deal with, you have never stopped supporting or loving me, and for that I am truly grateful. There are no words to thank you enough, so instead of rambling on any further I will leave it there. And now to learn some Spanish, a promise I have made to mi Papa… 4 Table of Contents Acknowledgements ................................................................................................................... 2 List of Tables and Figures ........................................................................................................ 9 Author’s declaration .............................................................................................................. 13 Publication ................................................................................................................................ 14 List of Abbreviations .............................................................................................................. 15 Summary .................................................................................................................................... 18 1 Chapter 1 ............................................................................................................................. 22 General Introduction ............................................................................................................. 22 1.1 Introduction ............................................................................................................................. 23 1.1.1 The gastrointestinal tract .............................................................................................................. 23 1.1.2 The intestinal immune system .................................................................................................... 24 1.1.3 Peyer’s patches and isolated lymphoid follicles .................................................................. 25 1.1.4 Mesenteric lymph nodes ............................................................................................................... 26 1.1.5 Intestinal epithelial cells ................................................................................................................ 27 1.1.6 Lamina Propria .................................................................................................................................. 28 1.1.7 Intestinal microbiota ....................................................................................................................... 30 1.1.8 Active immunity versus tolerance in the intestine ............................................................ 30 1.2 The neonatal intestine .......................................................................................................... 32 1.3 Dendritic cells ......................................................................................................................... 33 1.3.1 How to identify a DC ........................................................................................................................ 34 1.3.2 Dendritic cell subsets ...................................................................................................................... 35 1.3.3 Dendritic cell functions .................................................................................................................. 38 1.4 Development of dendritic cells .......................................................................................... 44 1.4.1 Dendritic cell ontogeny and development ............................................................................. 46 1.5 Intestinal mononuclear phagocytes ................................................................................ 47 1.5.1 Intestinal DC subsets ....................................................................................................................... 48 1.5.2 Functions of Intestinal DC ............................................................................................................. 51 1.5.3 Local conditioning of intestinal dendritic