Metabolomics has the potential to play a pivotal role in understanding disease onset and progression, and ultimately personalized treatments. One of its major challenges is its large-scale... Show moreMetabolomics has the potential to play a pivotal role in understanding disease onset and progression, and ultimately personalized treatments. One of its major challenges is its large-scale implementation, which is necessary to deal with the high variability of the metabolome. In this work we have developed tools for automated sample handling and preparation for metabolomics analysis, and bioanalysis in general. The tools are versatile, suitable for high-throughput, and able to deal with sensitive and biomass-limited samples. Sample transfer through segmented-flow can accommodate a wide range of samples and volumes, and can work seamlessly with many downstream processing or analysis. Two sample preparation tools based on droplets; one universal preconcentration tools using controlled evaporation, and one based on simultaneous extraction and enrichment, also provide a versatile interface and can be used to bridge gaps between processing steps. The working principles of these sample handling and preparation tools are universal and can be adapted for specific applications. Show less
In this thesis, we developed new ways to use a technique called electroextraction (EE) to extract charged molecules from one liquid into another using an electric field. We wanted to make EE more... Show moreIn this thesis, we developed new ways to use a technique called electroextraction (EE) to extract charged molecules from one liquid into another using an electric field. We wanted to make EE more practical and easy to use for extracting different types of molecules. We tackled three main challenges: making EE work seamlessly with other techniques, avoiding the need to dilute small samples, and making EE more robust and user-friendly. To do this, we used automation and made use of existing analysis systems. This allowed us to fully take advantage of EE without needing manual processing or dilution. As a result, we were able to expand the range of compounds and types of molecules that EE can extract, and even extract both positively and negatively charged molecules at the same time. Show less
Breast cancer has a high mortality in women worldwide. Tumor cells experience hypoxia, which is accompanied by alterations in cell metabolism and can drive metastasis by triggering an epithelial... Show moreBreast cancer has a high mortality in women worldwide. Tumor cells experience hypoxia, which is accompanied by alterations in cell metabolism and can drive metastasis by triggering an epithelial–mesenchymal transition (EMT) in the tumor cells. Yes-associated protein (YAP) and a transcriptional co-activator with PDZ-binding (TAZ) are two transcriptional co-activators involved in growth, metabolism, and metastasis in cancer. Breast cancer can be divided into different subtypes. One criterium underlying such subtypes is based on the levels of Human Epidermal growth factor Receptor 2 (HER-2), Estrogen Receptor (ER) and Progesterone Receptor (PR). The subtypes include luminal-like (luminal A and luminal B), HER-2 enriched and basal-like (often “triple negative”). Triple negative breast cancer (TNBC) has a lower survival rate due to the lack of therapeutic targets. Fundamental research exploring the molecular mechanisms at work in cancer cells and their response to a hypoxic environment may contribute to insights for future clinical treatment. This thesis focused on profiling breast cancer cells belonging to distinct subtypes under acute and chronic hypoxia, investigating the crosstalk between hypoxia regulated pathways and YAP/TAZ signaling in luminal breast cancer versus TNBC cells, and identification of the potential targets of TAZ in breast cancer cells. Show less
To increase clinical success rate of drugs, a better understanding of drug action mechanism and disease dynamics is required. Metabolomics, which studies small molecules involved in biochemical... Show moreTo increase clinical success rate of drugs, a better understanding of drug action mechanism and disease dynamics is required. Metabolomics, which studies small molecules involved in biochemical processes in organisms, has shown to be a useful tool for this better understanding. In this thesis, we focus on the endocannabinoid system (ECS) and profiling its related metabolic pathways using liquid chromatography - mass spectrometry (LC-MS) based metabolomics techniques. The endocannabinoid system (ECS) is a signaling system involved in multiple physiological and pathological processes. Due to its wide distribution and complex network of metabolic interactions, the development of drugs targeting the ECS has seen high failure rates. To get a better understanding of the behavior of the ECS and related pathways, LC-MS platforms with wide coverage of the major ECS-related metabolites, or with high sensitivity that reaches low levels of metabolites, were developed and optimized. Furthermore, these metabolomics platforms were applied in clinical studies looking into cardiometabolic health, and revealed correlations between endogenous metabolite signaling, cardiometabolic health and the benefits of exercise. Show less
Heterozygous germ-line mutations in BRCA1 and BRCA2 predispose to several types of cancer. Owing to their roles in the error-free repair of DNA double-strand breaks (DSBs) via homologous... Show moreHeterozygous germ-line mutations in BRCA1 and BRCA2 predispose to several types of cancer. Owing to their roles in the error-free repair of DNA double-strand breaks (DSBs) via homologous recombination (HR), lack of BRCA1/2 in these tumors results in DNA damage defects that can be specifically targeted by the inhibition of Poly-(ADP-ribose) polymerase 1 (PARP1). PARP1 is a key sensor of DNA damage and its inhibition has been shown to be synthetically lethal with deficiencies in HR, resulting in the selective killing of BRCA1/2-deficient tumor cells, while sparing BRCA1/2-proficient non-tumor cells. The success of this approach has resulted in the approval of four PARP1 inhibitors (PARPi) for the treatment of ovarian, breast, prostate and pancreatic cancers. However, drug resistance poses a major obstacle as, despite initial responses, patients receiving PARPi often develop resistance to the treatment. Understanding the molecular mechanisms behind PARPi resistance is therefore crucial to identify key determinants of PARPi response and to find combination treatment strategies to overcome resistance to PARPi by preventing, delaying or targeting resistant clones. In this thesis, we expanded our insights into the molecular mechanisms underlying PARPi resistance by conducting functional genetic screens in PARPi-resistance cell lines. Show less
Antimicrobial drugs constitute a fundamental part of modern medicine. The global rise in antimicrobial resistance poses a major threat to global health. Optimising antimicrobial treatment... Show moreAntimicrobial drugs constitute a fundamental part of modern medicine. The global rise in antimicrobial resistance poses a major threat to global health. Optimising antimicrobial treatment strategies in patients offers an important direction to address this challenge. In this thesis, we describe how quantitative characterisation of the drug, the pathogen, and the patients, and how these three factors interact, can help to achieve this goal. To this end, we used a combination of state-of-the-art in silico model-based approaches to analyse and integrate experimental data from in vitro models, and clinical data from healthy volunteers and patients. We developed models describing infection site drug exposure, antimicrobial resistance evolution, and host response biomarker dynamics. We explored the impact of infection on pulmonary pharmacokinetics, evolutionary-based treatment strategies, and the utility host response biomarker for treatment monitoring. The work in this thesis builds towards developing novel strategies to optimise antimicrobial treatments and showcases the importance on interdisciplinary collaborations. Show less
Als gevolg van de grote technologische vooruitgang in de gezondheidszorg worden in toenemende mate gegevens verzameld tijdens de uitvoering van klinische onderzoeken. Het is evenwel essentieel om... Show moreAls gevolg van de grote technologische vooruitgang in de gezondheidszorg worden in toenemende mate gegevens verzameld tijdens de uitvoering van klinische onderzoeken. Het is evenwel essentieel om te beseffen dat gegevens op zich van weinig of geen waarde zijn. Ten behoeve van hun optimale bruikbaarheid dienen gegevens geanalyseerd, geïnterpreteerd en verwerkt te worden. Machine learning-strategieën kunnen hiertoe nuttige en adequate oplossingen bieden. Dit proefschrift bevat machine learning-benaderingen toegepast op verschillende klinische datasets. De klassieke gegevens bestaan uit elektrische signalen van het electrocardiogram (ecg) verkregen bijgezonde proefpersonen, de innovatieve gegevens zijn afkomstig vanmetingen in een rijsimulator, en de opkomende gegevens zijn afgeleid van dna-analyse van de micro-organismen die op de huid voorkomenvan patiënten met huidziekten. We toonden aan dat het aantal ECG’s van invloed was op de nauwkeurigheid van geschatte verlenging van het qt-interval voor alle ingezette qt-correctieformules. Met behulp van SHapley AdditiveexPlanations (shap)-waarden werd de impact van de individuele kenmerken op de voorspelling van fysiologische leeftijd van het hart bepaald. We maakten gebruik van machine learning voor een betere beoordeling van de rijprestaties van bestuurders die medicijnen gebruikten. Tot slot lieten we zien dat de belangrijkste micro-organismen voor discriminatie van seborrroische dermatitis – naast Cutibacterium en Staphylococcus – kwamen relatief weinig voor, waardoor men deze micro-organismen in standaardanalyses eenvoudig over het hoofd kan zien. Daarmee hebben we aangetoond dat machine learning kanworden toegepast op gegevens die zijn afgeleid van klinische onderzoeken om in een vroeg stadium het effect van medicijnen en andere interventies op te sporen en te evalueren. Show less
Solute carrier (SLC) transporters are a large and diverse class of relatively understudied transmembrane proteins. Due to their critical role in cellular homeostasis, physiological processes and... Show moreSolute carrier (SLC) transporters are a large and diverse class of relatively understudied transmembrane proteins. Due to their critical role in cellular homeostasis, physiological processes and disease development, there is a great number of SLCs that have the potential to be viable drug targets for the treatment of disease. Robust assays are required to identify and characterize potential drugs for SLCs, which are often screened in vitro using cell-based or cell-free systems. Conventional assays either require the use of chemical labels, which i) can be invasive and compromise a cell’s physiology, ii) are based on end-point measurements, iii) use cell preparations and/or iv) do not allow screening of a large number of compounds. This thesis presents the development and application of novel label-free assays based on electrical impedance that allow the assessment of functional activity for three human SLCs: the dopamine transporter (DAT, SLC6A3), norepinephrine transporter (NET, SLC6A2) and excitatory amino acid transporters (EAAT, SLC1 family). With the ability to screen and characterize SLC inhibitors, these assays are a new addition to the ever-expanding toolbox for SLC transporters and could prove valuable in drug discovery programs for a wide range of diseases. Show less
In this thesis, we focus on novel proteins/mechanisms that regulate integrin-adhesion mediated mechano-transduction. We characterized the role of integrin α6β4/HD and caskin2 in force generation... Show moreIn this thesis, we focus on novel proteins/mechanisms that regulate integrin-adhesion mediated mechano-transduction. We characterized the role of integrin α6β4/HD and caskin2 in force generation via FA, investigated the underlying crosstalk between adhesions and cytoskeletons. Moreover, we also explored the mechanism that drives the integrin αVβ5 clustering in FCLs, in which cell tension is also involved. Last but not the least, we investigated the role of an unexplored protein, caskin2, in the regulation of cellular mechanics. Show less
Integrins play an essential role in multicellular life by connecting cells to the extracellular matrix. This thesis provides an overview of the distinct types of integrin-containing cell adhesion... Show moreIntegrins play an essential role in multicellular life by connecting cells to the extracellular matrix. This thesis provides an overview of the distinct types of integrin-containing cell adhesion complexes present in epithelial cells. By employing BioID we succesfully characterized the composition of focal adhesions, flat clathrin lattices, and hemidesmosomes. In addition, we investigated the role of different adhesion complexes in (cancer) cell adhesion, migration, polarity, and proliferation and in mechanotransduction. 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
This thesis aimed to investigate core cross-linked polymeric micelles (CCPMs) and expand their potential for the delivery of hydrophobic drugs and co-factors. Applying polypept(o)ides as the... Show moreThis thesis aimed to investigate core cross-linked polymeric micelles (CCPMs) and expand their potential for the delivery of hydrophobic drugs and co-factors. Applying polypept(o)ides as the polymeric platform technology, the fundamental implications of secondary structure formation on ring-opening N-carboxyanhydride (NCA) polymerization and self-assembly were examined and optimized. CCPMs with functional core architectures serving external or disease-related stimuli were developed. To establish robust CCPM production, overcome drug resistance mechanisms, and explore therapeutic agents for immunomodulation, polymer science was combined with organic and inorganic chemistry. Show less
Over several decades, a variety of computational methods for drug discovery have been proposed and applied in practice. With the accumulation of data and the development of machine learning methods... Show moreOver several decades, a variety of computational methods for drug discovery have been proposed and applied in practice. With the accumulation of data and the development of machine learning methods, computational drug design methods have gradually shifted to a new paradigm, i.e. deep learning methods have attracted particular interest in drug design. In this study, a new deep learning-based method (DrugEx) was proposed to design de novo drug-like molecules. It was proven that candidate molecules designed by DrugEx had a larger chemical diversity, and better covered the chemical space of known ligands. In order to address the issue of polypharmacology, the DrugEx algorithm was updated with multi-objective optimization towards multiple targets. The results of its application demonstrated the generation of compounds with a diverse predicted selectivity profile toward multiple targets, offering the potential of high efficacy and lower toxicity. In order to improve its generality, DrugEx was further updated to have the capability of designing molecules based on given scaffolds. We extended the architecture of Transformer to deal with each molecule as a graph. As a proof, its effectiveness in that 100% valid molecules are generated and most of them had predicted high affinity towards A2AAR with given scaffolds. Moreover, GenUI was developed as a visualizion software platform that makes it possible to integrate molecular generators within a feature-rich graphical user interface to facilitate collaboration in the disparate communities interested in computer-aided drug discovery.These studies highlight the overwhelming power of AI methods in drug discovery. Show less
Chemical-induced organ toxicity is a major concern in the development and use of chemicals, including drugs, pesticides, industrial chemicals and cosmetics. In the last decades, the onset and... Show moreChemical-induced organ toxicity is a major concern in the development and use of chemicals, including drugs, pesticides, industrial chemicals and cosmetics. In the last decades, the onset and progression of chemical-induced organ toxicity has been linked amongst others to perturbation of mitochondria.In this work, we set out to further unravel the mechanisms behind mitochondrial toxicity initiated by a chemical insult. More in-depth and biology driven assessment of the onset and progression of mitochondrial perturbation supports the development of relevant prediction tools. We aimed to stimulate the integration of these in vitro and in silico prediction tools in the safety assessment of existing and new chemicals, to allow detailed assessment of mitochondrial fitness upon chemical exposure. Show less
The focus of the described research in this thesis is on the oxidative stress response (Nrf2 pathway). The aim of the research presented in this thesis is to obtain more information concerning... Show moreThe focus of the described research in this thesis is on the oxidative stress response (Nrf2 pathway). The aim of the research presented in this thesis is to obtain more information concerning microRNAs which are involved in the Nrf2 pathway, to determine and evaluate the application of microRNAs for the construction of novel mechanistic biomarkers. Furthermore, we aimed to obtain a better understandingwith respect to the dynamics of the Nrf2 pathway to repeated xenobiotic exposure.To investigate the effect of overexpression of microRNAs on the Nrf2 pathway response in general and in combination with chemical exposure, a microRNA mimic screen was performed. In this screen overexpression of microRNAs was induced by using synthetic microRNA mimics. Since repeated exposure may drive adaptation programs and may lead to different responses between single and repeated exposures. The effect of a second exposure on the dynamics of the Nrf2 pathway activation was conducted. Final, results of a study are shown where a panel of structurally different phenolic compounds were used to demonstrate the proof-of-concept that Nrf2 pathway reporters can successfully be applied as biomarkers to characterize the specific pro-oxidant responses of chemicals. Show less
Barrier function is the natural role of the skin. The lipid matrix present in the outermost layer of the skin, the stratum corneum is important for this function. Barrier impairment and altered... Show moreBarrier function is the natural role of the skin. The lipid matrix present in the outermost layer of the skin, the stratum corneum is important for this function. Barrier impairment and altered lipid composition are observed in several inflammatory skin diseases including atopic dermatitis and psoriasis. However, the relationship between the lipid properties and barrier function is not comprehended.In this project, a lipid model was prepared from synthetic lipids that closely resemble the stratum corneum lipid composition and organization. Subsequently, diseased skin models were developed to mimic various abnormalities in lipid composition observed in atopic dermatitis patients’ skin. Biophysical methods were used to monitor the changes in lipid organization in these models. Diffusion studies and trans-epidermal water loss measurements were performed to monitor the barrier function. This allowed the determination of the changes in lipid properties that were most instrumental in reducing the lipid barrier.This thesis further describes the use of simple skin lipid model membranes incorporating fewer components to provide a detailed insight into the relationship between lipid composition, lipid organization, and the skin barrier. The information gained in this project offers the opportunity to develop a new generation of formulations to treat these patients. Show less
The clinical potential of applying synthetic lethality to cancer treatment is famously demonstrated by the BRCA1/PARP1 paradigm: a tumor specific defect in BRCA1 – a component of the DNA double... Show moreThe clinical potential of applying synthetic lethality to cancer treatment is famously demonstrated by the BRCA1/PARP1 paradigm: a tumor specific defect in BRCA1 – a component of the DNA double-strand break (DSB) repair pathway homologous recombination (HR) – results in a remarkable sensitivity to PARP1 inhibition (PARPi). Despite spectacular initial responses in patients, resistance to PARPi treatment may develop and must be overcome to maximally exploit this interaction in the clinic. Genetically engineered (mouse) model systems have shown that PARPi resistance may arise through inactivation of the 53BP1 pathway. The 53BP1 pathway normally protects DSB ends from resection and the removal of this “brake” restores HR in the absence of BRCA1. However, how the 53BP1 pathway protects DSB ends from resection has remained elusive. In this thesis, advances in 3D tumor organoid culture protocols and CRISPR/Cas9 (screening) technology were applied to identify and validate new components of the 53BP1 pathway that render BRCA1 deficient cells resistant to PARPi upon their loss. Furthermore, a new acquired vulnerability that can be therapeutically exploited to deplete such PARPi resistant cells is described. Together, this thesis provides mechanistic insight in DSB repair and illustrates how such fundamental knowledge may stand at the basis to combat resistance. Show less
Particles are omnipresent in biopharmaceutical products. In protein-based therapeutics such particles are generally associated with impurities, either derived from the drug product itself (e.g.... Show moreParticles are omnipresent in biopharmaceutical products. In protein-based therapeutics such particles are generally associated with impurities, either derived from the drug product itself (e.g. protein aggregates), or from extrinsic contaminations (e.g. cellulose fibers). These impurities can affect product stability, as well as cause adverse effects once introduced into the human body. Particulate impurities are present over a wide range of sizes (from nanometers to millimeters) making them difficult to characterize by using a single method.Novel drug products may also contain particles that act as the active pharmaceutical ingredient (e.g., living cells) or a drug delivery vehicle (e.g., lipid nanoparticles). Unwanted immunotoxicity and inconsistent in vivo functionality can result from particle instability and aggregate formation. Therefore, the efficacy and safety of these therapeutics is dependent on the particle composition, quantity and size distribution.Consequently, well-established methods are required to quantify and characterize particles in the submicron- and micron-size ranges. In this thesis, we developed new approaches which allow for comprehensive characterization of the particle populations present in biopharmaceutical products, both as impurities or as API. Furthermore, the performed work focused on comparing different particle characterization techniques to allow a better understanding of the limitations and strengths of each method applied. Show less
The chemical and structural heterogeneity of toxoid vaccines makes their analysis challenging. However, detailed insights on a molecular level can be obtained by mass spectrometry. Our initial... Show moreThe chemical and structural heterogeneity of toxoid vaccines makes their analysis challenging. However, detailed insights on a molecular level can be obtained by mass spectrometry. Our initial focus was the identification of formaldehyde-induced modifications in diphtheria toxin, which is described in Chapter 2. Subsequently, the methods described in Chapter 2 were applied to study what effects formaldehyde-induced modifications on model proteins have on their susceptibility to enzymatic proteolysis (Chapter 3). During the analysis of these model proteins, unknown formaldehyde-induced modifications were observed. The structural elucidation of these modifications, the discovery of a new type of crosslinks and various other subsequent reaction products are described in Chapter 4. The degradomics analysis described in Chapter 3 was applied to tetanus toxoids to distinguish heat-denaturated toxoids from their original state (Chapter 5). In order to reduce the analysis time and further improve the degradomics approach, an optimized strategy using Tandem Mass Tag multiplexing for the relative quantification of peptides was developed for the analysis of diphtheria toxoids (Chapter 6). Finally, Chapter 7 provides a brief discussion on the results presented in this thesis and offers some perspectives on implementation of the findings for toxoid vaccine development, quality control and further research. Show less
