Cancer immunotherapy has experienced remarkable advances in the last decades. Striking clinical responses have been achieved for several solid cancers, particularly cancer types with a high... Show moreCancer immunotherapy has experienced remarkable advances in the last decades. Striking clinical responses have been achieved for several solid cancers, particularly cancer types with a high mutation burden, which placed tumour-mutated antigens (neoantigens) centre stage as targets of tumour immunity and cancer immunotherapy. Neoantigens can be presented in complex with HLA molecules on the tumour cell surface, where T cells with the correct specificity can recognize the neoantigen as ‘non-self’ which will trigger killing of the tumour cell by the T cell. In theory, cancers with a low/moderate mutation burden that present neoantigens in complex with HLA class molecules could still be eligible for T cell-mediated immunotherapy. This thesis, describes the finding that neoantigen-specific T cells are present in mismatch-repair proficient (MMR-p) colorectal cancer patients, a low mutation burden cancer type. Moreover, CD39 and CD103 were found as cell surface markers that pinpoint the T cell population that contains the neoantigen-specific T cells. In addition, subsequent metastasis of a melanoma patient cohort were studied and revealed that also at advanced, late-stage disease, neoantigen-directed T cell therapy is, in theory, still applicable. Taken together, the studies reveal potential for the development of neoantigen-directed cancer immunotherapy for a broader patient population. Show less
Epithelial-mesenchymal plasticity (EMP) and tumor cell migration play an important role in cancer progression, and an improved understanding of the mechanisms underlying these concepts is essential... Show moreEpithelial-mesenchymal plasticity (EMP) and tumor cell migration play an important role in cancer progression, and an improved understanding of the mechanisms underlying these concepts is essential for developing new targeted approaches. In this thesis, we studied these mechanisms using mathematical and computational approaches.First, we summarized and reviewed previous computational approaches that have been used to decipher EMP regulation. We then created mathematical models to explore (1) how different regulatory networks can explain epithelial-mesenchymal transition (EMT) in different cell contexts, and (2) how EMP and immune regulation can interact to cause tumor immunoevasion.Next, we studied the role of cell density in migration characteristics of triple-negative breast cancer cell lines by using a combined experimental and computational approach. We show how clustering and pseudopodial dynamics, potentially influenced by EMT-related factors, can alter the migratory behavior of these cell lines.Jointly, our work has shown that computational modeling can be used to test hypotheses based on experimental data, and generate testable hypotheses, making it a valuable addition to wet-lab experiments. Importantly, we identified mechanisms related to potential therapeutic targets, hopefully leading to improved targeted therapies and reduced cancer mortality. Show less
Immune checkpoint therapies that aim to (re)activate the immune response against cancer cells have shown promising results in a variety of tumor types. Yet, a large fraction of cancer patients does... Show moreImmune checkpoint therapies that aim to (re)activate the immune response against cancer cells have shown promising results in a variety of tumor types. Yet, a large fraction of cancer patients does not benefit from these therapies. While the presence of a substantial number of immune cells, and in particular T cells, in the tumor is generally related with a better clinical response to checkpoint therapies, the T cells in the tumor are diverse in their capacity to eliminate the tumor. In order to improve treatment outcome of cancer patients, we require a better understanding of the roles of different T cells in the response (and resistance) to immune checkpoint therapy. The development of single cell profiling technologies has provided us with a powerful tool to analyze the state and functionality of individual cells. In this thesis, I have used single cell profiling methods in combination with innovative experimental technologies to unravel the diversity of T cells in human tumors and define the changes in the profiles of T cells that occur in response to treatment with immune checkpoint therapy to dissect which T cells are important for therapy response. Show less
All cellular organisms contain genomic DNA which provides the instructions for their correct development and functioning. Damage to this DNA may interfere with critical cellular processes such as... Show moreAll cellular organisms contain genomic DNA which provides the instructions for their correct development and functioning. Damage to this DNA may interfere with critical cellular processes such as transcription and replication and has the potential to drive mutagenesis. In turn, this may underlie inherited disorders and accelerate progression of diseases such as cancer and neurodegenerative disorders. The protection of cells and organisms against these devastating effects of DNA damage relies on the DNA damage response (DDR), which comprises a complex network of signaling and repair pathways that coordinate the sensing, signaling and repair of DNA lesions while accommodating suitable adjustments in for instance chromatin structure and cell cycle progression. Not only does the DDR dictate the appropriate repair pathway for several types of DNA damage, including DNA double-strand breaks (DSB), it also modulates replication fork surveillance mechanisms in response to DNA replication stress (RS). While many core proteins have been studied in detail, the full repertoire of factors involved in these pathways remains unknown. Clearly, extending our knowledge on regulators of the DDR will contribute to our understanding of the development, and possibly the treatment, of the numerous disorders that are associated with defects in the DDR. The research described in this thesis has successfully identified and characterized novel factors in DSB repair and the RS response. Show less
The spindle-assembly checkpoint (SAC) is a safety mechanism which secures accurate chromosome segregation during mitosis. BUB1, a serine/threonine kinase, is one of the proteins involved in this... Show moreThe spindle-assembly checkpoint (SAC) is a safety mechanism which secures accurate chromosome segregation during mitosis. BUB1, a serine/threonine kinase, is one of the proteins involved in this checkpoint and its inhibition is thought to have therapeutic potential for the treatment of cancer. Although the exact role of BUB1 in the SAC remains controversial, inhibition of its kinase function has previously been shown to reduce tumor size in mouse xenograft models when combined with paclitaxel. The research described in this thesis aimed to develop novel BUB1 kinase inhibitors for which high-throughput screening was used as starting point for drug discovery. Medicinal chemistry efforts were performed to improve potency after which the obtained inhibitors were further evaluated in cellular assays. In addition, the development of a cellular BUB1 target engagement assay is described. Hit optimization led to the discovery of two lead compounds with good physicochemical properties, subnanomolar affinity for BUB1, good cellular BUB1 target engagement, acceptable selectivity over other kinases and a favorable in vitro ADME profile. Show less
G protein-coupled receptors (GPCRs), one of the largest families of membrane proteins, are responsive to a diverse set of physiological endogenous ligands including hormones and neurotransmitters.... Show moreG protein-coupled receptors (GPCRs), one of the largest families of membrane proteins, are responsive to a diverse set of physiological endogenous ligands including hormones and neurotransmitters. Due to the various GPCR ligand binding domains present on GPCRs and their sensitivities to a diverse array of ligands, these proteins have shown to be very ‘druggable’ as they are the main target for an estimated 30% of approved drugs. A growing body of evidence shows a prominent role of GPCRs in all phases of cancer with a mutation frequency of approximately 20% in all cancers. Mutations occurring in GPCRs can severely alter their normal function and may ultimately convert their physiological and pathological roles. One particular class of rhodopsin-like GPCRs included in this thesis are the adenosine receptors (ARs). Due to the accumulation of adenosine in the tumor microenvironment, all four subtypes of ARs might be targets for the development of novel approaches for the treatment of cancer. For each of the four subtypes, a number of somatic mutations have been identified in patient isolates. In this thesis, we examined them on receptor activation and ligand binding using reference adenosine receptor ligands, and determined the impact mutations have on these pharmacological readouts. Show less
T cell exhaustion is a state of T cell hypofunction arising during persistent viral infections and cancer. Recent advances in the field of immunology uncover the roles of cytokines in regulating T... Show moreT cell exhaustion is a state of T cell hypofunction arising during persistent viral infections and cancer. Recent advances in the field of immunology uncover the roles of cytokines in regulating T cell responses. Using LCMV Clone-13 as a model of persistent viral infection, this thesis investigates the roles of IL-27 and IFN-I in regulating T cells during infection. In addition, the thesis explores the potential of JAK inhibitor in rescuing T cell exhaustion during persistent viral infection and cancer. Show less
Het onderzoek beschreven in dit proefschrift is gericht op de identificatie en karakterisering van regulatoren en/of effectoren van TGF-β-signalering en TGF-β-geïnduceerde EMT in pancreas-, long-... Show moreHet onderzoek beschreven in dit proefschrift is gericht op de identificatie en karakterisering van regulatoren en/of effectoren van TGF-β-signalering en TGF-β-geïnduceerde EMT in pancreas-, long- en borstkankertypes. Deze nieuw geïdentificeerde componenten en mechanismen kunnen worden onderzocht voor de ontwikkeling van geneesmiddelen voor kankertherapie. Show less
Death in all types of melanomas is generally caused by metastasis. Uveal melanoma (UM) is the most common intraocular melanoma, there are currently no (patient-derived) animal models that... Show moreDeath in all types of melanomas is generally caused by metastasis. Uveal melanoma (UM) is the most common intraocular melanoma, there are currently no (patient-derived) animal models that faithfully recapitulate metastatic dissemination of UM. Here we generate embryonic zebrafish models for both the primary and disseminated stage of ocular melanoma. In doing so we can recapitulate the etiology of cancer in its totality. Subsequently, we developed a patient-derived zebrafish xenograft (zf-PDX) model, using spheroid cultures generated from metastatic and primary UM tissues. Harnessing this versatile model, we reveal high sensitivity of circulating UM cells to ferroptosis induction in vivo by Erastin and RSL3, implicating ferroptosis as a new potential therapy in metastatic UM.Increased melanin levels in cutaneous melanoma are associated with decreased patient survival. Melanin levels in primary uveal melanoma patient cells positively correlate with their metastatic potential in zebrafish. Modulation of melanin levels of pan-melanoma cells results in enhanced/reduced metastatic potential upon increased or decreased melanin levels, respectively. Melanin depletion sensitizes melanoma cells to ferroptosis inducers in zebrafish leading to a decreased metastatic burden. Collectively, our data identify melanin biosynthetic enzymes as potential future target to treat melanoma and show that melanin protects metastasizing melanoma cells from ferroptosis. Show less
Despite the interest and success in immunotherapy, our current understanding of how the immune activation balance – on the macro level – and the expression of receptors and their ligands – on the... Show moreDespite the interest and success in immunotherapy, our current understanding of how the immune activation balance – on the macro level – and the expression of receptors and their ligands – on the micro level – shape health and disease is still limited. By identifying novel regulatory networks that dictate immune cell activity in physiologically relevant settings, well-designed pooled genetic screens could offer a relevant approach to address this knowledge gap. Genetic screens have become a powerful tool to identifygenes that affect the response and phenotype of a cell in an unbiased manner.In this thesis, I aimed to identify regulators of immune cell activation in the context of cancer through a combination of in vitro and in vivo genetic screens and genetically modified mouse models. Specifically, this was achieved by both 1) using genetic screening technologies to identify novel cancer cell-expressed inhibitory ligands or regulatorsof immune-modulating ligands in an unbiased manner, and 2) investigating the effect of these regulators on the cellular components and signaling pathways that constitute the local tumor microenvironment and potentially dictate anti-tumor efficacy. Show less
Being confronted with cancer is a life-changing event, with major impact to well-being, quality of life and relationships. Cancer treatments and outcomes have improved, but possess the potential to... Show moreBeing confronted with cancer is a life-changing event, with major impact to well-being, quality of life and relationships. Cancer treatments and outcomes have improved, but possess the potential to impair reproductive and sexual function. International guidelines highlight the importance of timely discussion of sexual function and fertility deterioration resulting from treatments. In spite of these developments, practice behaviour and attitudes of health professionals have been reported to vary.The first part of this thesis demonstrates barriers among oncology professionals in the Netherlands in discussing sexual function during daily practice. In general, consensus exists regarding responsibility for addressing sexual dysfunction. Despite, the implementation of discussing sexual function as a standard of care is not carried out structural.Part two describes practice routines concerning the counselling on impaired fertility and fertility preservation for cancer patients of reproductive age. Medical oncologists and oncology nurses both reported discussing the impact of treatment on fertility. However, it was not performed in all cases and depending on factors like educational level, experience, type of hospital, prognosis and chances of fertility recovery.Furthermore, testicular cancer patients were evaluated on specific items concerning the discussion, referral and process of semen cryopreservation. Long term reproductive concerns were identified among survivors. Show less
This thesis aims to gain a better understanding of NER, to elucidate new molecular mechanisms and proteins that orchestrate how DNA repair is carried out on genomic DNA that is tightly packed in... Show moreThis thesis aims to gain a better understanding of NER, to elucidate new molecular mechanisms and proteins that orchestrate how DNA repair is carried out on genomic DNA that is tightly packed in chromatin inside the living cell. It is important to obtain a better clinical picture of how inherited defects in DNA repair genes shapes phenotypes in patients with DNA repair-deficiency disorders. Show less
Tumor heterogeneity favors tumor tissue to survive and resist drugs, leading to the failure of chemotherapeutic agents to induce a therapeutic response. In addition, the absorption mechanisms,... Show moreTumor heterogeneity favors tumor tissue to survive and resist drugs, leading to the failure of chemotherapeutic agents to induce a therapeutic response. In addition, the absorption mechanisms, metabolism and excretion of chemotherapeutic drugs, which are commonly used for cancer patients and the lack of specific targeting of these drugs can cause adverse effects on treated patients. Thus, the general objective of this thesis is to investigate the biological activity of targeted poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) as a drug delivery system (DDS) for carvedilol (CVDL) or oxaliplatin (OXA), in vitro and in vivo, to treat colorectal cancer (CRC). DDSs were formulated to achieve this goal. In chapters 2, 3 and 4, our studies were discussed in detail on the formulations and characterizations of NPs as DDSs with ideal characteristics to increase the therapeutic range of drugs at the tumor site. As well as the biological evaluation of these DDS when its anti-inflammatory activity (Chapter 2) and its antitumor activity in vitro (Chapters 2, 3 and 4) and in vivo (Chapters 3 and 4). Taken together, all the DDSs studied in this thesis were able to improve the chemotherapeutic efficiency of the drugs studied in Chapters 2, 3 and 4. Show less
Upon infection or vaccination, naïve CD8+ T cells clonally expand and differentiate into antigen-specific effector cell populations, which turn into phenotypically diverse memory CD8+ T cell... Show moreUpon infection or vaccination, naïve CD8+ T cells clonally expand and differentiate into antigen-specific effector cell populations, which turn into phenotypically diverse memory CD8+ T cell subsets that differ in their cytokine polyfunctionality, cytolytic capacity and homing properties. The circulating memory CD8+ T cell pool can be largely classified in two major subsets: effector memory T (TEM) and central memory T (TCM) cells. Contrary to the classical view that lymphocytes continuously recirculate, tissue-resident memory T (TRM) cells have been discovered as cells with the unique ability to reside in tissues with limited recirculation through the blood. Antigen-specific CD8+ TRM cells are induced upon antigen encounter and localize to many different tissues, including barrier tissues, where they play a crucial role in protection against infectious and malignant disease. Within these major circulating and resident T cell subsets a variety of phenotypes and functions exists. However, the development of the heterogeneous populations of memory T cells is not fully understood. In this thesis we dissect the development and heterogeneity of antigen-specific circulating and tissue-resident CD8+ T cells upon vaccination and infection, study their protective capacity in infectious and malignant disease and use this information to improve vaccination and immunotherapeutic strategies. Show less
Biomarker molecules are analyzed in clinical tests to diagnose a disease, but often these test lack sensitivity or specificity. Also, for many diseases there is not even a blood based test... Show moreBiomarker molecules are analyzed in clinical tests to diagnose a disease, but often these test lack sensitivity or specificity. Also, for many diseases there is not even a blood based test available, while blood collection is relatively low invasive. For breast- and pancreatic cancer, there are several proteins that could potentially serve as biomarkers in blood, but these are not yet specific enough to use for diagnostic testing. Further research on other types of biomarkers may therefore be a valuable addition to eventually be able to develop a blood test. Methods for glycosylation profiling from serum and dried bloodspots with mass spectrometry were developed and applied to pancreatic- and breast cancer biomarker studies. Differences were found between profiles of healthy and sick persons for pancreatic cancer, but no clear differences were seen for breast cancer. This is probably due to the many different forms of breast cancer which result in different profiles. In the future, combining different types of markers from serum might ensure that differences between healthy and sick, between different diseases and between types of disease can be identified. This could lead to the development of a blood test for the early detection of cancer and other diseases. Show less
This thesis addresses current treatment strategies in older cancer patients, as well as the consequences of these decisions for clinical outcomes. In addition, this thesis investigated the value of... Show moreThis thesis addresses current treatment strategies in older cancer patients, as well as the consequences of these decisions for clinical outcomes. In addition, this thesis investigated the value of frailty assessment in different cancer populations and described the implementation of a multidisciplinary team approach in frail older cancer patients. Show less
As HLA Class I expression is an important target for cytotoxic T cells but an in inhibitor of NKcells, we were interested in the regulation of its expression.We review HLA expression in UM, how it... Show moreAs HLA Class I expression is an important target for cytotoxic T cells but an in inhibitor of NKcells, we were interested in the regulation of its expression.We review HLA expression in UM, how it is involved in the inflammatory phenotype, how it is regulated and how putative treatments might be effective in its expression.We investigate the potential role of the NFkB pathway in the regulation of inflammation in UM and its potential association with HLA Class I expression.In order to increase our understanding for the reason behind the elevated HLA Class I expression in UM tumours, we investigate the involvement of epigenetics. We focus on a set of epigenetic enzymes called histone deacetylases and report that these regulators are highly expressed in Monosomy 3 UM.We wonder whether HDAC expression is influenced by the presence of infiltrating lymphocytes and macrophages.We focus on miRNA’s as another set of epigenetic regulators of inflammation. We investigate the potential relation of a set of 125 miRNA’s with HLA Class I expression and the presence of an infiltrate in UM and report two patterns of miRNA expression.We study the LAG3 immune checkpoint in UM tumours. As immune checkpoints might be responsible for the T cell exhaustion which is observed in UM, we investigate the involvement of LAG in prognostication and study how LAG3 and its ligands are distributed among different UM tumours. Show less
Immunotherapies for cancer are an emerging class of therapeutic strategies which aim to treat cancer via augmentation of the immune system. Despite significant success of immunotherapies in the... Show moreImmunotherapies for cancer are an emerging class of therapeutic strategies which aim to treat cancer via augmentation of the immune system. Despite significant success of immunotherapies in the past decade, not all patients will respond to these treatments and the reasons why immunotherapies are successful in some patients, but not others, remain incompletely understood. The immune response to cancer is a complex, multistage process, and mathematical and computational models are a useful tool for understanding such complex systems. In this thesis, I develop mathematical and computational models of cytotoxic T lymphocytes (CTLs), who are key players in the immune system due to their ability to recognise, destroy, and provide long lasting protection against malignant or virally infected cells. Show less
Immunotherapy approach to cancer is only benefiting to a minority of patients. In this study, we approach cancer solutions by studying the microenvironment and its immunological signature... Show moreImmunotherapy approach to cancer is only benefiting to a minority of patients. In this study, we approach cancer solutions by studying the microenvironment and its immunological signature throughout the body by focusing on the systemic immunity with new technology like mass cytometry. By highlighting specific immunological patterns in cancer, we were able to associate responsive immune cells and positive outcome, therefore paving the way to improve immunotherapy in cancer. Show less
In this thesis, the researcher developed a nanosystem based on the metallophilic Interaction between cyclometalated complexes. Using this strategy, the researcher achieved efficient photodynamic... Show moreIn this thesis, the researcher developed a nanosystem based on the metallophilic Interaction between cyclometalated complexes. Using this strategy, the researcher achieved efficient photodynamic therapy to several cancers, accompanied by the cell imaging property. Show less
