Viral infections have been associated with the progression of atherosclerosis and CD8+ T-cells directed against common viruses, such as influenza, Epstein-Barr virus, and cytomegalovirus, have been... Show moreViral infections have been associated with the progression of atherosclerosis and CD8+ T-cells directed against common viruses, such as influenza, Epstein-Barr virus, and cytomegalovirus, have been detected inside human atherosclerotic lesions. These virus-specific CD8+ T-cells have been hypothesized to contribute to the development of atherosclerosis; however, whether they affect disease progression directly remains unclear. In this study, we aimed to characterize the activation status of virus-specific CD8+ T-cells in the atherosclerotic lesion.\nThe presence, clonality, tissue enrichment, and phenotype of virus-associated CD8+ T-cells in atherosclerotic lesions were assessed by exploiting bulk T-cell receptor-β sequencing and single-cell T-cell receptor (α and β) sequencing datasets on human endarterectomy samples and patient-matched blood samples. To investigate if virus-specific CD8+ T-cells can be activated through T-cell receptor stimulation in the atherosclerotic lesion, the immunopeptidome of human plaques was determined.\nVirus-associated CD8+ T-cells accumulated more in the atherosclerotic lesion (mean=2.0%), compared with patient-matched blood samples (mean=1.4%; P=0.05), and were more clonally expanded and tissue enriched in the atherosclerotic lesion in comparison with nonassociated CD8+ T-cells from the lesion. Single-cell T-cell receptor sequencing and flow cytometry revealed that these virus-associated CD8+ T-cells were phenotypically highly similar to other CD8+ T-cells in the lesion and that both exhibited a more activated phenotype compared with circulating T-cells. Interestingly, virus-associated CD8+ T-cells are unlikely to be activated through antigen-specific interactions in the atherosclerotic lesion, as no virus-derived peptides were detected on HLA-I in the lesion.\nThis study suggests that virus-specific CD8+ T-cells are tissue enriched in atherosclerotic lesions; however, their potential contribution to inflammation may involve antigen-independent mechanisms. Show less
Recent advances in our understanding of immunotherapeutic strategies against cancer and the development of improved analysis tools and computing power have led to a highly anticipated progression... Show moreRecent advances in our understanding of immunotherapeutic strategies against cancer and the development of improved analysis tools and computing power have led to a highly anticipated progression of the cancer-vaccine field. The possibilities of personalized approaches to vaccinate patients against tumor-specific antigens by the prediction of MHC-binding peptides are already in clinical studies. Currently, the field is lacking behind in antigen identification tools and optimal delivery of vaccines. The studies in this thesis are divided in two major parts which address these topics. The first part reports a novel approach for the identification of relevant MHC class I and II binding epitopes. With the combined use of exome sequencing and mass-spectrometric analysis, relevant neoantigens were characterized from MHC class I and II in murine and human models. Meanwhile, significant genomic differences were observed in the MC38 murine colorectal cancer model of different sources. The second part shows the development of a molecular approach for the tracking of ligands and peptides to improve our understanding of vaccine delivery. Therefore, bioorthogonal ‘click’ chemistry was applied for in situ ligation of fluorophores to antigen, thus providing a quantification method of processed antigens. Subsequent optimizations were explored into bioorthogonal reactions independent of copper. Show less
MHC class I (MHC-I) molecules present a blueprint of the intracellular proteome to T cells allowing them to control infection or malignant transformation. As a response, pathogens and tumor cells... Show moreMHC class I (MHC-I) molecules present a blueprint of the intracellular proteome to T cells allowing them to control infection or malignant transformation. As a response, pathogens and tumor cells often downmodulate MHC-I mediated antigen presentation to escape from immune surveillance. Although the fundamental rules of antigen presentation are known in detail, the players in this system are not saturated and new modules of regulation have recently been uncovered. Here, we update the understanding of antigen presentation by MHC-I molecules and how this can be exploited by tumors to prevent exposure of the intracellular proteome. This knowledge can provide new ways to improve immune responses against tumors and pathogens. Show less
Kremer, A.N.; Zonneveld, M.I.; Kremer, A.E.; Meijden, E.D. van der; Falkenburg, J.H.F.; Wauben, M.H.M.; ... ; Griffioen, M. 2018
The human herpesvirus Epstein-Barr virus (EBV) is a large DNA virus that infects over 90% of the adult world population. EBV is the causative agent of infectious mononucleosis and EBV infection is... Show moreThe human herpesvirus Epstein-Barr virus (EBV) is a large DNA virus that infects over 90% of the adult world population. EBV is the causative agent of infectious mononucleosis and EBV infection is associated with various malignancies. EBV establishes lifelong infections in immunocompetent hosts. To counteract the host’s immune defence, EBV acquired numerous immune evasion mechanisms. During latency of EBV, viral protein synthesis is limited or absent, making the virus-infected cells virtually invisible to the immune system. Evasion mechanisms of EBV active during primary infection as well as in reactivation are necessary for establishment of latent infection and prolonged replication. Studying viral evasion not only helps to understand EBV, but also the human immune system. Viral molecules interfering with antigen presentation by HLA I and HLA II have been identified previously, but so far, it was unclear how EBV interferes with the lipid antigen-presenting molecule CD1d. The work described in this thesis shows EBV’s mechanism to interfere with cell surface expression of CD1d. Further, a novel immune evasion molecule that obstructs antigen-presentation during the late lytic phase of EBV infection was identified and its working mechanism was unravelled. Understanding viral immune evasion mechanisms may aid in developing therapies for EBV-associated diseases. Show less
The first aim of this thesis was to investigate basic components of the initiation of an allergic response, including the route of sensitization and the cells responsible for the initiation... Show more The first aim of this thesis was to investigate basic components of the initiation of an allergic response, including the route of sensitization and the cells responsible for the initiation of Th2 skewing in allergic subjects. More specifically, both clinical and immunological evidence of food allergy development through cutaneous sensitization were presented in the form of a case study. Furthermore the ability of human basophils to initiate a Th2 response through direct antigen presentation to T cells was investigated. The second aim of this thesis is to investigate the use of current therapies and the development of new therapies for difficult-to-treat allergic diseases. Dominant T-cell epitopes of major peanut allergen proteins were identified and characterized providing the first step in the design of a safe and effective peptide based T cell targeted immunotherapy to treat peanut allergy. Finally, the immunological and clinical efficacy of omalizumab for the treatment of allergic bronchopulmonary aspergillosis was assessed, for the first time, in a randomized placebo-controlled clinical trial. Throughout these studies, basophils played an important role as either the object of investigation or as a tool in diagnosis, allowing determination of the efficacy of existing therapeutics, or assessment of the safety of novel therapies. Show less
The human genome comprises of more than 22.000 genes. These genes encode for proteins playing a role in many general or tissue-specific biological processes, but for many of them the function is... Show moreThe human genome comprises of more than 22.000 genes. These genes encode for proteins playing a role in many general or tissue-specific biological processes, but for many of them the function is not yet unraveled yet. A way to study all the different genes at once in a certain biological process is by genome-wide screening. By considering all genes in a pathway, new players can be identified that would otherwise not have been linked to the studied process. In this thesis, I describe a siRNA-based genome-wide screen used to identify new proteins involved in MHC class II antigen presentation, expression and transport. The data obtained from this screen not only led to the identification of proteins involved in the MHC class II pathway specifically, but we also identified a regulator of a more general process namely intracellular endosome localization. This shows the importance of genome-wide screening in the identification of new players and regulators of certain biological pathways which may be considered as new drug targets to cure diseases. Show less
Rosalia, R.A.; Quakkelaar, E.D.; Redeker, A.; Khan, S.; Camps, M.; Drijfhout, J.W.; ... ; Melief, C.J.M. 2013
Major histocompatibility class II molecules (MHC class II) are one of the key regulators of adaptive immunity because of their specific expression by professional antigen presenting cells (APC).... Show moreMajor histocompatibility class II molecules (MHC class II) are one of the key regulators of adaptive immunity because of their specific expression by professional antigen presenting cells (APC). They present peptides derived from endocytosed material to T helper lymphocytes. Consequently, MHC class II is fundamental in orchestrating both cellular and humoral immune responses. A genetic association of certain MHC class II alleles with autoimmunity has long been established. The molecular mechanisms underlying this association are only poorly understood. An in depth understanding of the antigen presentation pathway by MHC class II is essential for the improvement of current therapies. In this thesis, the tools to arrive at a systems understanding of MHC class II antigen presentation are discussed. What are the advantages and disadvantages of a genome-wide screen? And how can a multi-dimensional, data-integrating approach increase the understanding of the systems biology of MHC class II? Show less
Major Histocompatibility Complex class II (MHC-II) antigen presentation is involved in the regulation of immune responses against infections and tumours and strongly linked to autoimmune diseases.... Show moreMajor Histocompatibility Complex class II (MHC-II) antigen presentation is involved in the regulation of immune responses against infections and tumours and strongly linked to autoimmune diseases. To better understand this process we performed a genome-wide RNAi screen. The effect of downregulation of each human gene on MHC class II expression and antigen loading was analyzed. Genes affecting MHC-II antigen presentation were tested for their involvement in MHC-II transcription and transport. Some genes might function in repositioning MHC-II towards the plasmamembrane upon Dendritic Cell maturation. This was confirmed by silencing these genes in immature Dendritic Cells. The novel GTPase ARF7, ARF7EP and MYO1E play a central role in this transport process. MHC-II antigen loading on intraluminal vesicles of the MHC-II compartment is facilitated by chaperone DM. In a confocal FRET study we investigated whether microdomain-forming tetraspanins CD63 and CD82, interacting with MHC-II and DM, could facilitate the MHC-II/DM interaction. MHC-II and DM preferably interacted with CD63 on the intraluminal vesicles, likely facilitating the MHC-II/DM interaction and antigen loading. MHC-II favoured interactions with CD82 on the limiting- and plasmamembrane suggesting a sorting role for CD82. This knowledge will contribute to development of new methodologies to influence MHC class II presentation in patients. Show less
Major advancements in the understanding of the immune system have provided us with the opportunity for rational design of therapeutic immunological interventions. The notion that dendritic cells ... Show moreMajor advancements in the understanding of the immune system have provided us with the opportunity for rational design of therapeutic immunological interventions. The notion that dendritic cells (DC) play a crucial role in the activation of T lymphocytes has made DC biology of central importance for vaccine development. Accordingly, efficient delivery of antigen to DCs is one of main objectives in vaccine development. In this thesis, antibody-mediated antigen targeting is evaluated as a potential antigen delivery strategy for therapeutic vaccination. Complexes of protein antigen and antigen-specific antibodies are natural formulations that bind to Fc__ receptors. Fc__R ligation on DCs leads to efficient uptake, DC maturation and presentation of the antigen to T lymphocytes. Interaction of Ag-Ab complexes with Fc__Rs on DCs provides a link between the humoral and cellular arms of the immune response. This thesis contains an extensive evaluation of Fc__R-mediated antigen delivery to dendritic cells in the context of T lymphocyte-mediated immunotherapy. In addition, it contains a detailed analysis of Fc__R function on DCs and addresses the kinetics of cross-presentation of antigen after Fc__R-mediated uptake. Show less
This thesis focuses on the generation of MHC ligands and their use in analyzing T cell immunity, both in mouse and men. It is roughly split into two sections: the first part deals specifically with... Show moreThis thesis focuses on the generation of MHC ligands and their use in analyzing T cell immunity, both in mouse and men. It is roughly split into two sections: the first part deals specifically with the rules governing the generation of MHC ligands, while the second part describes technological advances in the use of these MHC ligands to analyze T cell immunity. The first part of this thesis starts with an introduction on antigen presentation, covering both the different mechanisms through which epitopes are generated and the process by which epitopes are presented to T cells. Emphasis lies on the discoveries in this field of the last decade. This introduction is followed by two chapters on the generation of antigenic epitopes. Chapter two describes the analysis of protease activity in the endocytic pathway, while chapter three investigates the antigenic source of epitopes generated during cross-presentation. The second part of this thesis starts with a review on the status of MHC multimer technology as a tool to analyze antigen specific T cell populations. Chapter five then describes a high-throughput approach to generate a vast array of different peptide-MHC complexes for several human MHC alleles, allowing for faster and more complex applications of MHC multimer technology. In the next chapter, the peptide-exchange technology of chapter 5 is used for the development of another novel strategy: multidimensional encoding of peptide-MHC complexes. This chapter describes the development, validation and use of this encoding technique that allows the parallel detection of antigen-specific T cell responses of up to 25 T cell populations in one single sample. Finally, this thesis concludes with a summary and discussion chapter, giving a short overview of the presented data and discussing its relevance in the field of antigen presentation. Show less
This thesis is composed of two parts part one: The study on anti-estrogen resistance and defining criteria a cell has to meet in order to become resistant to anti-estrogenic compounds. part two:... Show moreThis thesis is composed of two parts part one: The study on anti-estrogen resistance and defining criteria a cell has to meet in order to become resistant to anti-estrogenic compounds. part two: the study of antigen-loading, vesicle positioning and costimulation. Show less
Intracellular proteins are degraded by the proteasome. The resulting protein fragments can be regarded as waste, but it is clear that peptides play an important role in several processes, like the... Show moreIntracellular proteins are degraded by the proteasome. The resulting protein fragments can be regarded as waste, but it is clear that peptides play an important role in several processes, like the immune response. Peptides are destroyed very rapidly and irrespectively of their sequence. A peptide's length appeared to be important as the half-life increases when additional amino acids are present at the amino-terminus. As exception dibasic N-terminal peptides appeared to be more stable than other peptides, resulting in overrepresentation by HLA-B27 molecules that bind preferably binds dibasic N-terminal peptides. Cross-presentation of peptides from infected cells by professional antigen presenting cells (APC) is crucial for a proper immune response because they express the required co-stimulatory molecules. The exact mode of antigen transfer is largely unknown, and we describe a novel pathway for cross-presentation, by passive diffusion of peptides through gap junctions from infected cells to APCs Apoptosis-derived antigens have been shown to be a major source of cross-presented antigens. Peptides from apoptotic cells can be presented by the cell itself, or transferred to healthy neighboring cells and be presented by MHC class I molecules of these cells, thereby facilitating cross-presentation, through gap junction mediated intercellular peptide transfer. Show less
