Impact of monocyte differentiation and intracellular infection on processing and presentation of autoantigen D I S S E R T A T I O N zur Erlangung des akademischen Grades Doctor of Philosophy (Ph.D.) eingereicht an der Lebenswissenschaftlichen Fakultät der Humboldt-Universität zu Berlin Von Lydon Wainaina Nyambura Präsidentin der Humboldt-Universität zu Berlin Prof. Dr.-Ing. Dr. Sabine Kunst Dekan der Lebenswissenschaftlichen Fakultät der Humboldt-Universität zu Berlin Prof. Dr. rer. nat. Bernhard Grimm Gutachter/innen 1. Dr. rer. nat. Michal Or-Guil 2. Prof. Dr. rer. nat. Peter Walden 3. Prof. Dr. rer. nat. Paul Wrede Tag der mündlichen Prüfung: 27th April 2018 Acknowledgment I am grateful to my PhD Supervisor Prof. Peter Walden not only for his pivotal guidance and support, but also for the opportunity to join his research group at Charité- Universitätsmedizin Berlin a few years ago, and for his input in my continuous growth in the field of research. I am thankful to Dr. Michal Or-Guil my PhD Supervisor based at Systems Immunology Lab at the Department of Biology, Humboldt University, Berlin, for her great guidance and support. My appreciation goes to Prof. Peter Walden research group members for the constructive discussions, support and great company. I also appreciate Deutscher Akademischer Austauschdienst (DAAD) for the PhD Scholarship award and Charité International Welcome Center for their help in matters pertaining to Ausländerbehörde. Last but not least, I am very grateful to my family members and friends for their encouragement, support and prayers. II III Abstract Dendritic cells (DCs) and macrophages are specialized antigen presenting cells that process self and foreign antigens and present them to T cells via major histocompatibility complex molecules, human leukocyte antigens (HLA) in humans, for induction of tolerance or initiation of T cell-mediated immune responses. Related to differentiation state, they have specific phenotypes and functions, and varied interactions with pathogens herein exemplified by Leishmania donovani (LD) that parasitize macrophages and propagate within their phagolysosomes. The impact of the differentiation state and intracellular infection on antigen processing and presentation by HLA class I remained undefined. To gain insight, we analyzed and compared the HLA-I self peptidomes of MUTZ3 cell line-derived human immature and mature DCs, and THP1 cell line-derived LD-infected and none-infected macrophages by liquid chromatography-tandem mass spectrometry (LC-MS/MS), as well as proteasome compositions by quantitative RT-PCR, and HLA expression and cell activation states by flow cytometry. We found that the HLA I-presented self-peptidomes of the cells in the different states were heterogeneous and individualized, dominated by nonapeptides with similar HLA binding affinities and anchor residues. They were sampled from source proteins of almost all subcellular locations and from proteins involved in various cellular functions in similar proportion including tumour-associated antigens (TAAs). The persistence of LD within the macrophage, did not affect macrophage activation. However, its impact was observed in self-peptidome heterogeneity, HLA binding affinities, anchor residue preferences, source protein peptide sampling (including TAAs) and HLA and proteasome expression. Keywords: antigen processing/presentation, dendritic cells, macrophages, Leishmania donovani, major histocompatibility complex, mass spectrometry, peptidome IV V Zusammenfassung Dendritische Zellen (DCs) und Makrophagen sind spezialisierte antigenpräsentierende Zellen, die eigene und fremde Antigene prozessieren und mittels Haupthistokompatibilitätsmoleküle, humane Leukozytenantige (HLA) im Menschen, T-Zellen präsentieren, um Toleranzen zu induzieren oder T-Zell-vermittelte Immunantworten zu initiieren. Abhängig von ihrer Differenzierung haben sie spezifische Phänotypen und Funktionen undunterschiedliche Interaktionen mit Pathogenen, in dieser Arbeit durch Leishmania donovani (LD) repräsentiert, welche in Phagolysosomen der Makrophagen propagieren. Der Einfluss der Differenzierungszustände und von intrazelluläre Infektionen auf die Antigenprozessierung und -präsentation waren weitgehend undefiniert. Um hier Einblick zu gewinnen, haben wir die HLA-I-präsentierten Selbstpeptidome von menschlichen unreifen und reifen DCs, die aus der MUTZ3-Zelllinie generiert wurden, und LD-infizierte bzw. nicht-infizierte aus der THP1- Zelllinie generierte Makrophagen mittels Flüssigchromatographie-Tandem- Massenspektrometrie (LC-MS/MS), sowie die Proteasom-Zusammensetzung per RT-PCR und die HLA-Expression und Aktivierungszustände der Zellen per Durchflusszytometrie analysiert und verglichen. Wir fanden, dass die HLA-I-Selbstpeptidome der Zellen heterogen und individualisiert waren, von Nonapeptiden dominiert wurden und ähnliche HLA- Bindungsaffinitäten und Ankerreste aufwiesen. Sie stammten aus Quellenproteinen aus fast allen subzellulären Lokalisationen und mit unterschiedlichen zellulären Funktionen in ähnlichen Anteilen und schlossen Tumor-assoziierter Antigene (TAAs) ein. Die Persistenz der LD hatte keinen Einfluß auf den Aktivierungszustand der Makrophagen, verursachte aber eine weitgehende Veränderungen des Peptidoms, der HLA-Bindungsaffinitäten und Ankerreste, der Quellproteine einschließlich TAAs und der HLA- und Proteasom-Expression. Stichwörter: Antigenprozessierung / -präsentation, dendritische Zellen, Makrophagen, Leishmania donovani, Haupthistokompatibilitätskomplex, Massenspektrometrie, Peptidom VI VII Abbreviation ANN Artificial neural networks APC Antigen presenting cell CD 34+ Pluripotent stem cells CD Cluster of differentiation CD4+ Cluster of differentiation 4 CD8+ Cluster of differentiation 8 CHAPS 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate CID Collision-induced dissociation CTLs Cytotoxic T cells DC Dendritic cells ECD Electron-capture dissociation ELISpot Enzyme-linked immunosorbent spot ER Endoplasmic reticulum ERAAP Endoplasmic reticulum amino peptidase associated with antigen processing ESI Electrospray ionization ETD Electron-transfer dissociation GM-CSF Granulocyte-macrophage colony stimulating factor HLA Human leukocyte antigen HPLC High performance liquid chromatography hTERT Human telomerase reverse transcriptase IEDB Immune epitope database IL-4 Interleukin-4 KDa Kilo dalton LARP1 La-related protein 1 LC- MS/MS liquid chromatography tandem mass spectrometry VIII LD Leishmania donovani LMP2 Proteasome subunit beta type-9 LMP7 Proteasome subunit beta type-8 M/z Mass to charge ratio MBOA7 Lysophospholipid acytransferase 7 MECL1 Proteasome subunit beta type-10 MHC Major histocompatibility complex MS Mass spectrometry MS/MS Tandem mass spectrometry MUTZ3 Cytokine-dependent CD34+ human acute myeloid leukaemia cell line MUTZ3 iDC MUTZ3 derived immature dendritic cells MUTZ3 mDC MUTZ3 derived mature dendritic cells PDB Protein database PI Propidium iodide PININ 140 kDa nuclear and cell adhesion-related phosphoprotein PRAME Preferentially expressed antigen in melanoma PSME3 Proteasome activator complex subunit 3 RHAMM Receptor for hyaluronic acid–mediated motility ROS1 Proto-oncogene tyrosine-protein kinase ROS RPMI Roswell park memorial institute medium TAAs Tumour associated antigens TAP Transporter associated with antigen processing TBS Tris-buffered saline TFA Trifluoroacetic acid THP1 Human monocytic cell line derived from an acute monocytic leukemia patient THP1MФ THP1 derived macrophages IX THP1MФi THP1 derived macrophages infected with Leishmania donovani THP1MФiy THP1 derived macrophages infected with YFP transfected Leishmania donovani TRRAP Transformation/transcription domain-associated protein UHRF1 E3 ubiquitin-protein ligase UHRF1 URP2 Femitin family homolog 3 WT1 Wilms tumor protein YFP Yellow fluorescent protein Amino acids one and three letter code Ala A Alanine Gly G Glycine Pro P Proline Arg R Arginine His H Histidine Ser S Serine Asn N Asparagine Ile I Isoleucine Thr T Threonine Asp D Aspatic acid Leu L Leucine Trp W Tryptophan Cys C Cysteine Lys K Lysine Tyr Y Tyrosine Gln Q Glutamine Met M Methionine Val V Valine Glu E Glutamic acid Phe F Phenylalanine X XI Table of Contents Acknowledgment ..................................................................................................................... II Abstract ................................................................................................................................... IV Zusammenfassung .................................................................................................................. VI Abbreviation ........................................................................................................................ VIII Table of Contents ................................................................................................................. XII 1. Introduction ....................................................................................................................... 1 I.1 The immune system ..................................................................................................... 1 I.2 The major histocompatibility complex ........................................................................ 3 I.3 Peptide binding to MHC class I molecules ................................................................. 5 I.4 Antigen processing and presentation ........................................................................... 6 I.5 Leishmania, infection