Type I interferons (IFN-I) are pleiotropic cytokines that were originally identified for their antiviral properties and are now recognized for playing key roles in the defense against a range of... Show moreType I interferons (IFN-I) are pleiotropic cytokines that were originally identified for their antiviral properties and are now recognized for playing key roles in the defense against a range of other microorganisms as well as cancer. Their production should be well-controlled to be of benefit to the host, as excessive or chronic IFN-I expression leads to adverse effects such as immunosuppression or the induction of severe immunopathology.The studies presented in this thesis are aimed at uncovering mechanisms that regulate the production of IFN-I. The obtained knowledge on the involved molecular processes, may aid the development of targeted therapies that enhance or intercept IFN-I responses for maximum host protection while minimizing damage. Show less
The aim of this thesis was to better understand the underlying biology of tumor-immune interactions, especially in the circulation of CRC patients. The focus was primarily on the innate immune... Show moreThe aim of this thesis was to better understand the underlying biology of tumor-immune interactions, especially in the circulation of CRC patients. The focus was primarily on the innate immune system including NK cells, NKT cells, and macrophages. Show less
Replication of positive-stranded RNA viruses requires the activity of proteases that cleave the viral replicase polyproteins. For Middle East respiratory coronavirus (MERS-CoV), the virus-encoded... Show moreReplication of positive-stranded RNA viruses requires the activity of proteases that cleave the viral replicase polyproteins. For Middle East respiratory coronavirus (MERS-CoV), the virus-encoded papain-like protease (PLpro) is one of such proteases. This protease also functions as a deubiquitinating enzyme (DUB) that removes ubiquitin from substrates, most likely to suppress the ubiquitin-dependent activation of the innate immune response. The work described in this thesis provides novel insights in the interaction between PLpro and ubiquitin. The crystal structure of the PLpro-ubiquitin complex facilitated the design of substitutions in PLpro that selectively disrupted its DUB activity. DUB-negative MERS-CoV induced enhanced immune responses compared to wild-type virus, while showing similar replication in infected cells. Relative to wild-type virus, the virulence of DUB-negative MERS-CoV was reduced in mice and earlier, better-regulated immune responses were measured in their lungs. In the search for novel antivirals, ubiquitin sequence variants were selected that bound with very high affinity to MERS-CoV PLpro. Expression of those ubiquitin variants affected the activity of PLpro and concomitantly inhibited virus replication resulting in severely less virus progeny. Collectively, the gained knowledge can be used to design novel coronavirus vaccines or further develop ubiquitin variants as antiviral agents against viruses that encode DUBs. Show less
The disease is characterized by a progressive and largely irreversible decline in lung function, which is associated with long-term airway exposures to cytotoxic particles and gasses, such as... Show moreThe disease is characterized by a progressive and largely irreversible decline in lung function, which is associated with long-term airway exposures to cytotoxic particles and gasses, such as cigarette smoke. Microbial colonization and infections are an important pathophysiological aspect in COPD patients. However, the underlying mechanisms linking smoking with microbial colonization and infections in COPD are incompletely understood. The airway epithelium is the first target of inhaled cigarette smoke. Furthermore, epithelial cells are the first defense lining of the respiratory tract that prevents microbial colonization and infections. Therefore, alterations in host defense and airway epithelial remodeling may contribute to COPD development and progression. In this thesis, studies are presented in which the impact of cigarette smoke exposure and COPD disease status on the innate host defense functions of the airway epithelium are explored. This was done by using cell culture experiments in which the effect of cigarette smoke was examined, or in which epithelial cultures of COPD patients and non-COPD (ex)smokers were compared. Show less
The replication of all positive-stranded RNA viruses of eukaryotes is thought to take place at cytoplasmic membranous replication organelles. One of the most prominent types of viral ROs induced by... Show moreThe replication of all positive-stranded RNA viruses of eukaryotes is thought to take place at cytoplasmic membranous replication organelles. One of the most prominent types of viral ROs induced by a number of these viruses, including coronaviruses and arteriviruses, are double-membrane vesicles (DMVs) that contain viral double-stranded RNA. This thesis discusses the formation of these replication organelles by arteri- and coronaviruses and provides new insights in the viral proteins involved. The ultrastructure of the replication organelles was unravelled using both electron microscopy and tomography. Furthermore, this research described in this thesis also shows that the innate immune system in infected cells can prevent the formation of the membrane structures. Show less
Control of infectious diseases poses continuous challenges for human health. Salmonella bacteria are a major cause of gastrointestinal infections and systemic disease like typhoid fever. We used... Show moreControl of infectious diseases poses continuous challenges for human health. Salmonella bacteria are a major cause of gastrointestinal infections and systemic disease like typhoid fever. We used zebrafish-Salmonella infection models to study host immune responses to Salmonella, particularly focusing on the role of the autophagy machinery. Autophagy and a related process known as Lc3-associated phagocytosis (LAP) trap invading microbes in intracellular vesicles and eventually eliminate them through the lysosomal degradation pathway. We show that macrophages and neutrophils trap Salmonella in Lc3-decorated phagosomes by a process dependent on the host factors Rubicon and NADPH oxidase, which generates anti-bacterial reactive oxygen species. This process could be defined as LAP as it requires some but not all components of the autophagy machinery. Genetic inhibition of LAP and ablation of macrophages resulted in hypersusceptibility to infections with both wild type and attenuated strains, revealing that LAP is an essential line of defense against Salmonella during systemic disease, when macrophages are the main carriers of the infection. Our studies also revealed a novel functional link between the autophagy modulator Dram1 and induction of LAP. This work encourages further studies aimed at the identification of autophagy modulating drugs for host-directed therapy of antibiotic-resistant Salmonella infections. Show less
Persistent infections with high-risk type human papillomaviruses (hrHPVs) can progress to cancer. HrHPVs infect keratinocytes (KCs) and successfully suppress host immunity for up to two years... Show morePersistent infections with high-risk type human papillomaviruses (hrHPVs) can progress to cancer. HrHPVs infect keratinocytes (KCs) and successfully suppress host immunity for up to two years despite the fact that KCs are well equipped to detect and initiate immune responses to invading pathogens. HrHPV interferes with the innate immune response by affecting several signaling pathways that otherwise would prompt anti-viral mechanisms in the host cell. Furthermore, hrHPV interferes with the production of cytokines that are involved in the attraction of immune cells to the infected epithelium. In addition, hrHPV hides itself from the immune system by suppressing the antigen presentation machinery and employs means to hamper the response of KC__s to signals from adaptive immune cells. In this thesis we show that hrHPV attenuates innate immune signaling (Chapter 2) and CD40-mediated (Chapter 3) and IFN_ and/or TNF_-induced (Chapter 4) adaptive immune signaling. HrHPV exploits the cellular proteins UCHL1 (Chapter 2) and IFRD1 (Chapter 4) that act on multiple points in the IRF and NF_B signaling pathways. Moreover, hrHPV downregulates cellular IFITM1 to resist the growth inhibitory effects of IFN_ and/or TNF_ (Chapter 5). Our data provide important new insights on how hrHPV can persist in the face of host immunity. Show less
HPVs need to avoid immune responses of the host in order to establish persistent infection. HPVs achieve this by dampening innate immunity of keratinocytes, the major cell type targeted by HPV. As... Show moreHPVs need to avoid immune responses of the host in order to establish persistent infection. HPVs achieve this by dampening innate immunity of keratinocytes, the major cell type targeted by HPV. As there is reduced production of danger signals including antimicrobial molecules, proinflammatory cytokines and chemokines by keratinocytes, HPV infection remains undetected by the immune system. However, our further data showed that PRR signaling is not completely blocked by hrHPV. Thus, the activation of innate and adaptive immunity at the site of HPV infection is slowed down but not prevented. In order for cancers to grow out they need to suppress the local effector cells. We focused on the role of the PD-1 receptor and its ligands PD-L1 and PD-L2, our data showed that the majority (81%) of the tumors from cervical cancer patients do not express PD-L1. Furthermore, PD-L1 expression was not associated with patient survival. Finally, we presented evidence that the chemokine receptor CXCR7 expression predicts poor disease-free and disease-specific survival in cervical cancer patients. Show less
The work described in this thesis provides novel insights into the structural and (multi)functional characteristics of arterivirus PLP2. This enzyme plays an essential role in the viral replication... Show moreThe work described in this thesis provides novel insights into the structural and (multi)functional characteristics of arterivirus PLP2. This enzyme plays an essential role in the viral replication cycle by cleaving the viral replicase polyproteins. In addition, there were indications that PLP2 is able to influence certain cellular processes by cleaving ubiquitin. We have now shown that PLP2 indeed functions as a deubiquitinating enzyme (DUB) and that this activity is important for the suppression of the innate immune response in the cell. To be able to separate both functions of PLP2 we have solved the crystal structure of this enzyme in complex with ubiquitin. Based on this structure, we were able to design mutations in PLP2 that selectively disrupt the interaction with ubiquitin, without interfering with cleavage of the viral polyproteins. Using these mutants, we have demonstrated for the first time the importance of a viral DUB in the evasion of innate immunity in the context of an infection. The acquired knowledge can now be applied to the design of improved arterivirus vaccines and studies of other viral DUBs, including those encoded by the zoonotic coronaviruses that cause SARS and MERS. Show less
This thesis is focused on the innate immune defence mechanisms responsible for controlling mycobacterial growth after infection. To provide a detailed description of the host__s innate immune... Show moreThis thesis is focused on the innate immune defence mechanisms responsible for controlling mycobacterial growth after infection. To provide a detailed description of the host__s innate immune response to M. marinum infection, zebrafish gene expression levels were analysed by RNA sequencing at various time points during infection and correlated with imaging data of the process of pathogenesis. We demonstrate that the scavenger receptor Marco (macrophage receptor with collagenous structure) is a key player in the rapid phagocytosis of M. marinum and we use gene expression analysis in combination with gene knockdown studies to show that it is also essential in the establishment of an initial transient pro-inflammatory response to M. marinum infection. Once phagocytosed, M. marinum is capable of avoiding killing mechanisms of the host cell and can continue to grow within macrophages. This is the period when Membrane Attack Complex/Perforin proteins are involved in killing intracellular bacteria by their pore-forming activities. We reveal the regulatory mechanisms and function of two macrophage specific genes, mpeg1 and mpeg1.2 (macrophage expressed gene 1.2). The results from this thesis complement knowledge obtained from other model organisms by providing new insights into both counteracting and supporting mechanisms underlying the innate immune response. Show less
High-grade osteosarcoma is a malignant bone tumor with the highest incidence in young patients. In chapter 2, we studied MSCs of osteosarcoma patients and found downregulation of HCLS1 in... Show moreHigh-grade osteosarcoma is a malignant bone tumor with the highest incidence in young patients. In chapter 2, we studied MSCs of osteosarcoma patients and found downregulation of HCLS1 in osteosarcoma patient derived MSCs as compared to healthy donor derived MSCs. Despite almost two years in culture, none of the samples underwent spontaneous transformation. An increase in binucleation was noted upon increasing passage in both osteosarcoma patient and healthy donor derived MSCs. In chapter 3, prognostic factors related to the survival of patients with pulmonary metastasized high-grade osteosarcoma were studied. Higher metastatic tumor burden (i.e. larger number of pulmonary nodules), presence of vital metastases upon resection and male sex were associated with an increased risk of death. In chapter 4 we show that osteosarcoma metastasis seems to be inhibited by the presence of macrophages in the tumor microenvironm ent. In chapters 5 and 6 we show that osteosarcoma cells are sensitive to lysis by both autologous and allogeneic NK cells. Patient derived NK cells can be adequately activated by cytokine treatment with IL-15 (chapter 5) or IFN-_ (chapter 6). Therefore, activation of autologous NK cells (either in vivo or ex vivo) may be efficacious. In conclusion, the activation of innate immune cells such as macrophages and NK cells is a promising new adjuvant treatment strategy to treat patients with high-grade osteosarcoma Show less
Vein graft surgery to treat occlusive arterial disease is a common applied procedure. Each year more than two million vein graft surgeries are performed worldwide. The major drawback of vein... Show moreVein graft surgery to treat occlusive arterial disease is a common applied procedure. Each year more than two million vein graft surgeries are performed worldwide. The major drawback of vein grafting is that within 10 years after vein graft surgery 50-60 % of the vein grafts suffer from patency loss due to thrombosis, intimal hyperplasia formation, accelerated atherosclerosis and rupture. Endogenous factors orchestrate the development and failure of vein grafts. Investigating the role of endogenous constituents on vein graft remodeling can enhance our basic knowledge of the involvement of these factors in vein graft remodeling. By interfering in the function of endogenous factors, as we showed in this thesis, vein graft remodeling can be negatively or positively influenced depending on the factor and strategy used. New therapeutic strategies can be developed based on this knowledge. In this thesis we investigate the role of innate immune components, complement system factors, toll like receptors, mast cells and NK cells and the role of Annexin A5 in vein graft remodeling. Furthermore we explored the role of plaque stability, plaque neovascularization and extracellular matrix remodeling in a hypercholersterolemic mouse vein graft model. Show less
The work presented in this thesis has provided new insights into the mechanisms involved in the regulation of innate immune responses in zebrafish embryos. Furthermore, cell-specific transcriptome... Show moreThe work presented in this thesis has provided new insights into the mechanisms involved in the regulation of innate immune responses in zebrafish embryos. Furthermore, cell-specific transcriptome profiling studies identified novel marker genes for distinguishing immune cell types, which is highly useful information to fulfill the demand for new fluorescent reporter lines and lineage-specific antibodies in the zebrafish model. We have shown that Ptpn6, a protein tyrosine phosphatase homolog of human SHP1, functions as a critical negative regulator, required for a properly balanced innate immune response and for controlling infections with bacterial pathogens. In Salmonella typhimurium infection, ptpn6 deficiency caused a general hyperinduction of pro-inflammatory genes, which was contraproductive as it impaired the infection control. In Mycobacterium marinum infection, a more specific effect of ptpn6 deficiency on matrix metalloproteinase gene expression was found as a major underlying cause of increased bacterial burden. We further concluded that Ptpn6 functions as a much stronger negative regulator than infection-inducible miRNAs of the miR-146 family, which may be involved in more subtle fine-tuning of the innate immune response. Knowledge about the distinct roles of Ptpn6 and miR-146 miRNAs has practical applicability in regard to their potential as therapeutic targets for inflammatory diseases and cancer. Show less
South Asians have a high incidence of diabetes and subsequent cardiovascular and renal complications. Increasing evidence points towards the involvement of the complement system. We found higher... Show moreSouth Asians have a high incidence of diabetes and subsequent cardiovascular and renal complications. Increasing evidence points towards the involvement of the complement system. We found higher levels of both complement C3( the central molecule in the complement cascade) and SC5b-9 (the effector phase of complement activation) in type 2 diabetic South Asians compared to Caucasians. However, neither C3 nor Sc5b-9 predicted cardiovascular events, though higher SC5b-9 levels were associated with renal damage. Mannose binding lectin (MBL, the recognition molecule of the lectin pathway) was studies. A low MBL genotype was associated with cardiovascular events, whiel a high serem MBL level was associated with progressive renal failure. Show less
In the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR)... Show moreIn the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR) family, that are required for pathogen recognition. These receptors detect specific molecular structures of microorganisms and in turn are able to trigger host immune responses. The work described in this thesis focuses on the use of the zebrafish embryo as a model to study the vertebrate immune system in order to gain new insights into the mechanisms of innate immune defence against bacterial infections and TLR signalling. Making use of a Salmonella infection model in combination with microarray technology and gene knock-down studies we were able to thoroughly characterize the embryonic host transcriptome response to a bacterial infection. Furthermore, we have demonstrated important functions for key signalling molecules in the innate immune response, including Tlr5, MyD88 and Traf6 and discovered new downstream targets of the TLR signalling pathway. The data presented here will enable in-depth functional follow-up studies that will provide new insights into the mechanisms of innate immune defence systems. This, in combination with future applications of zebrafish embryo infection models in high-throughput compound screens, holds much promise for the discovery of novel anti-microbial and anti-inflammatory drugs. Show less
Airway epithelial cells are indispensable for the host defense system in the lungs. Various strategies by which epithelial cells protect the lungs against inhaled pathogens have been described. In... Show moreAirway epithelial cells are indispensable for the host defense system in the lungs. Various strategies by which epithelial cells protect the lungs against inhaled pathogens have been described. In spite of that, the molecular mechanisms by which epithelial cells initiate and control the host defense response have not been explored systematically. In this thesis, the molecular mechanisms underlying the initiation and regulation of the early epithelial host defense response in the airways were investigated. Using genomics technology, genes were identified to be associated with the early inflammatory response in airway epithelial cells. Many of the identified genes had previously not been associated with the host defense response against pathogens in the airways. The early epithelial host defense response is rapidly induced and transient of nature and can be divided into two phases. The initial phase is characterized by a stengthening of the physical barrier and is accompanied by the production of immune signaling molecules. In the proceeding phase, production of specialized antimicrobial agents occurs. Striking similarities were found in the molecular mechanisms of host defense in epithelial tissues of the airways and skin. Due to these similarities, genetic alterations in epithelial host defense mechanisms may explain the occurrence of inflammatory disorders at multiple sites of the body at the same time. These observations provide the basis for future investiations to further unravel the molecular mechanisms underlying epithelial host defense, both in the airways and other epithelial tissues. Show less
