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Towards Retinal Repair: Analysis of Photoreceptor Precursor Cells and Their Cell Surface Molecules

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Towards Retinal Repair: Analysis of Photoreceptor Precursor Cells and Their Cell Surface Molecules Towards retinal repair: analysis of photoreceptor precursor cells and their cell surface molecules Ya-Ting Han University College London Institute of Child Health A thesis submitted for the degree of Philosophiae Doctor For the incredible cells that drive me here. ii Acknowledgements I would like to firstly thank my supervisor Prof. Jane Sowden for her consistent support, encouragement and advice throughout my PhD. I still remember when I just started my PhD and wanted some dendritic cells in a control experiment for some even not so exciting markers, Jane instantly contacted her colleagues to provide me these cells. Cases as such are countless. I have been encouraged to develop my own research ideas and Jane has always been supporting. It is through all these that I confidently and happily conducted my studies here. I am very happy that I chose the right supervisor. Thank you, Jane! I would also like to thank my secondary supervisor Prof. Robin Ali for his encouragements throughout, Dr. Janny Morgan for her advice during my PhD upgrade, Prof. Andy Copp, Prof. David Muller, Dr. Kenth Gustafsson, Dr. Andy Stoker, Dr. Juan-Pedro Martinez-Barbera, and Dr. Patrizia Ferretti for helpful discussion and advices. Thanks to Dr. Kevin Mills and Dr. Wendy Heywood for their supports with mass spectrometry, especially Wendy for her unlimited kind and generous help during all my time with mass spectrometry. Thanks to Dan who helped and advised me in molecular cloning. Thanks to Rachael who performed all the injections for cell transplantation. Thanks to Jorn who showed me the techniques when I just entered the lab and helped me with my first cell transplantation. The NrlGFP cell transplantation with cell surface markers was also performed together with him. Thanks to Tassos who advised and helped a lot regarding the shRNA. Thanks to Aoife for sharing with me her cilia antibodies. Thanks to Dr. Siobhan Burns and Dr. Gerben Bouma for providing me the dendritic cells. Thanks to Bertrand and Ayad for training me in confocal imaging and flow cytometry respectively. Friends in the office have made my PhD life much more fun and colourful. Many thanks go to Sara G, Sarah D, Mike, Lily, KP, Vic, Suganthi, Nicola, Barbara, Giulia, Sherry, Sophie, Su, Veronika, and all the people past and present in BDRC. Special thanks go to Meng who has always been beside me: not only for the lovely meals he cooked, but also for the scripts he wrote for me to run microarray analysis and all the discussions he contributed toward my puzzles in research. And special thanks to Leyo who helped nothing but making my life busier……………………………………………………………………………………………………. and merrier... Thanks to Child Health Research Appeal Trust from ICH UCL and Overseas Research Scholarship from UCL for funding my study and life. iii I, Yating Han confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. iv Towards retinal repair: analysis of photoreceptor precursor cells and their cell surface molecules Ya-Ting Han UCL, Institute of Child Health Abstract Photoreceptor cells are the sensory cells of the retina, responsible for detecting light and conducting the signals to secondary neurons. Because they cannot be regenerated, loss of photoreceptor cells leads to irreversible blindness. Cell transplantation with postmitotic photoreceptor precursor cells has been shown as a feasible approach to rescue vision in animal models, but the molecular properties of these transplantation-competent cells are not understood. The aims of this thesis are to 1) determine the properties of photoreceptor precursor cells by transcriptome and proteome analysis; 2) identify cell surface molecules that can be used to isolate these cells from cell mixtures and/or that are important for their migration and correct integration in development and in a transplantation context. Nrl/CrxGFP transgene-labelled photoreceptor precursor cells were separated from other retinal cells by flow cytometry and subjected to microarray and mass spectrometry analysis. Bioinformatics analysis showed that the photoreceptor precursor cells were enriched in expression of genes encoding cell projection proteins. Over 200 cell surface molecule candidates were identified and 32 genes encoding confirmed extracellular domains were expressed > 5-fold higher in photoreceptor precursors than other retinal cells. These included the stem cell marker Prom1 (CD133), which was specifically expressed in photoreceptor cells (particularly on their cilia) throughout development as well as on transplanted photoreceptors. Together with CD73 and CD24, it serves as a specific marker to isolate photoreceptor cells for transplantation. An axon guidance molecule Sema7a was shown to be highly expressed in photoreceptor cells. It co- labels with PlxnC1, rather than the expected receptor Itgb1, in developing retina, as well as transplanted migrating photoreceptor cells. Knockout of Sema7a resulted in retinal holes and abnormal photoreceptor synapse projection indicating a role of Sema7a in outer retina lamination. This study sets the foundation for future work on photoreceptor cell surface molecules in development and retinal repair. v Table of Contents ACKNOWLEDGEMENTS ....................................................................................................... III ABSTRACT ........................................................................................................................... V ABBREVIATION ................................................................................................................... X LIST OF FIGURES ................................................................................................................ XV LIST OF TABLES ............................................................................................................... XVIII 1 INTRODUCTION ............................................................................................................. 1 1.1 EYE STRUCTURE, RETINAL STRUCTURE, PHOTORECEPTOR STRUCTURE............................................ 1 1.2 EYE FORMATION AND DEVELOPMENT, EYE FIELD TFS ................................................................ 3 1.3 RETINAL DEVELOPMENT .................................................................................................... 4 1.4 PHOTORECEPTOR DEVELOPMENT ........................................................................................ 6 1.4.1 FROM PROGENITORS TO PRECURSORS ....................................................................................... 6 1.4.2 FROM PRECURSORS TO MATURE PHOTORECEPTORS ..................................................................... 6 1.5 ROD PHOTORECEPTOR CELLS VS CONE PHOTORECEPTOR CELLS .................................................. 12 1.6 RETINAL DEGENERATION AND CELL TRANSPLANTATION THERAPY ............................................... 16 1.7 WHY SURFACE MOLECULES OF PHOTORECEPTOR CELLS ........................................................... 22 1.8 APPROACHES FOR SCREENING CELL SURFACE MOLECULES ........................................................ 24 1.9 HYPOTHESIS AND AIM .................................................................................................... 25 2 MATERIALS AND METHODS ......................................................................................... 27 2.1 MICE ......................................................................................................................... 27 2.2 DISSECTION OF THE EYE AND THE RETINA............................................................................. 27 2.2.1 DISSECTION AND DISSOCIATION OF RETINAL CELLS ..................................................................... 27 2.2.2 DISSECTION OF EYES FOR EMBEDDING ..................................................................................... 27 2.3 CELL SORTING AND FLOW CYTOMETRY ANALYSIS ................................................................... 28 2.3.1 FLUORESCENCE-ACTIVATED CELL SORTING (FACS) .................................................................... 28 2.3.2 FLOW CYTOMETRY ANALYSIS .................................................................................................. 28 2.4 MICROARRAY AND BIOINFORMATICS ANALYSIS ..................................................................... 31 vi 2.4.1 MICROARRAY QUALITY CONTROL ANALYSIS .............................................................................. 32 2.4.2 FUNCTIONAL BIOINFORMATICS ANALYSIS OF MICROARRAY GENES BY DAVID ................................. 38 2.5 RNA EXTRACTION AND PCR ............................................................................................ 39 2.6 IMMUNOHISTOCHEMISTRY .............................................................................................. 41 2.6.1 IMMUNOHISTOCHEMISTRY OF EYE CRYOSECTIONS ..................................................................... 41 2.6.2 IMMUNOCYTOCHEMISTRY OF DISSOCIATED CELLS ...................................................................... 42 2.6.3 ANTIBODIES AND PEPTIDES .................................................................................................... 42 2.6.4 MICROSCOPY AND IMAGE PROCESSING.................................................................................... 43 2.7 HEMATOXYLIN AND EOSIN STAINING FOR FROZEN SECTIONS .................................................... 46 2.8 WESTERN
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