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Duijl, T.T. van 2023

Quantitative protein mass spectrometry for kidney injury biomarker translation towards the clinical laboratory

Doctoral Thesis

some documents under embargo until 2025-06-08

This thesis describes the development and evaluation of a new laboratory tool to improve early kidney injury diagnosis. In the first part, we define the unmet clinical needs in the clinical care... Show moreThis thesis describes the development and evaluation of a new laboratory tool to improve early kidney injury diagnosis. In the first part, we define the unmet clinical needs in the clinical care pathways in kidney injury, by a questionnaire and s literature review to summarize current state-of-the-art diagnostics. The second part of this thesis comprises the analytical phase of test development. Liquid-chromatography (LC) coupled to tandem MS was chosen as analytical platform for protein-based kidney injury biomarker quantitation from human urine specimens. The third part of this thesis covers aspects of the postanalytical phase of medical test development, which included the establishment of reference intervals and clinical observational cohort studies. Elevated levels of the studied kidney injury biomarkers, and their combined signatures, were associated with acute kidney injury induced by ischemia-reperfusion injury after kidney transplantation, but not with stable chronic kidney disease. In a general perspective, this thesis highlights the role of quantitative protein mass spectrometry for biomarker translation from research towards the clinical laboratory. Show less

Faquih, T.O. 2023

Multi-omics in research: epidemiology, methodology, and advanced data analysis

Doctoral Thesis

open access

Metabolomics, proteomics, and genomics analyses provide profound insight into human biology and disease pathophysiology. In this thesis, we explored the methodological challenges facing these OMICs... Show moreMetabolomics, proteomics, and genomics analyses provide profound insight into human biology and disease pathophysiology. In this thesis, we explored the methodological challenges facing these OMICs technologies and illustrated their applications in epidemiological studies. In part one, we focused on some of the methodological challenges facing OMICs research. These challenges included handling missing data in metabolomics, measurement agreement between high throughput proteomic measurements with standard clinical measurements, and challenges in developing prediction models using metabolomic data. The second part of this thesis addressed various epidemiological research questions by utilizing genomic data and metabolomics measurements (Metabolon and Nightingale platforms) and using advanced data analysis methods. These studies provided important insights into the associations between metabolites and hepatic triglyceride content, the associations of between the size of cytosine-adenine-guanine nucleotide repeats in the huntingtin gene with metabolomic profile, and the associations of the man-made per- and polyfluoroalkyl substances (PFAS) with metabolite levels. Show less

Bergeijk, D.A. van 2022

Ecology and genomics of Actinobacteria and their specialised metabolism

Doctoral Thesis

open access

Filamentous Actinobacteria, such as Streptomyces, produce a plethora of chemically diverse bioactive metabolites that have found applications across medicine, agriculture and biotechnology. Yet,... Show moreFilamentous Actinobacteria, such as Streptomyces, produce a plethora of chemically diverse bioactive metabolites that have found applications across medicine, agriculture and biotechnology. Yet, the vast majority of the biosynthetic potential of Actinobacteria remains uncharacterised, largely because their biosynthetic gene clusters (BGCs) are poorly expressed in the laboratory, preventing the discovery of the cognate natural products. Additionally, only a narrow band of environments and a few taxonomic groups have been explored for gifted Actinobacteria. In this thesis different approaches are described, wherein we combined drug discovery with ecology, aimed at accessing the full potential of Actinobacteria. Bioactive Actinobacteria were isolated from a faecal sample of a 28,000-year-old-mammoth and their taxonomic and metabolic diversity was analysed. Furthermore, the effect of human stress hormones on the production of antibiotics by Streptomyces was investigated, resulting in the discovery of adrenaline as elicitor of siderophore production. This was later shown to be caused by the adrenaline analog catechol, which is ubiquitous in nature. Catechol also elicited the production of angucycline glycosides, well known for their therapeutic potential as anticancer and antibiotic compounds. Lastly, zebrafish were used as an in vivo model to explore the bioactive and functional potential of Actinobacteria within the animal microbiome. Show less

Huijbers, A. 2022

Improving diagnostic, prognostic and predictive biomarkers in colorectal cancer: the role of proteomics and stromatogenesis

Doctoral Thesis

open access

This thesis highlights, firstly, the importance of early CRC detection by presenting results of a CRC diagnostic proteomic biomarker signature with high discriminative power. Secondly, a strong... Show moreThis thesis highlights, firstly, the importance of early CRC detection by presenting results of a CRC diagnostic proteomic biomarker signature with high discriminative power. Secondly, a strong robust, independent prognostic tumor stroma ratio (TSR) biomarker, which confirms to be of important clinical value. The TSR has the ability to stratify colon cancer patients according to their prognostic outcome in a highly reproducible and low-cost manner. It has shown to link patients with a high intra tumor stromal content and a worse prognosis. Literature shows a wealth of evidence that supports this prognostic value in CRC as well as in other cancers. This PhD research therefore concludes that it should be implemented in the official guidelines of the TNM classification to improve stratification for CRC patients in daily routine pathological evaluation. The prospective, international, multicentre UNITED study will hopefully overcome the last hurdle for this clinical implementation. Lastly, this thesis offers more insight in the elusiveness of the tumor microenvironment and stromatogenesis that contributes to the aggressiveness of some CRC tumors. The biological differences, interconnections and changes in the microenvironment presented give multiple leads for further research and new personalized treatment possibilities. Show less

Sampadi, B. 2021

Dose-dependent and compound-specific phospho-signalling responses after (geno)toxic treatment

Doctoral Thesis

open access

Genotoxic stressors may induce various types of DNA damage triggering the activation of the DNA damage response. However, the dose-dependency and the drug compound-specificity of the activated... Show moreGenotoxic stressors may induce various types of DNA damage triggering the activation of the DNA damage response. However, the dose-dependency and the drug compound-specificity of the activated responses are unclear. Here, I first investigated the phospho-signalling responses induced by four chemical stressors with distinct modes of action and uncovered that, at equitoxic doses, even two ‘similar’ DNA damaging agents induced discrete and complex phosphorylation signalling cascades. Next, I investigated the ionising radiation (IR) dose-dependent responses using multi-omics and systems analyses to investigate the molecular and cellular responses to low and high doses of IR. I uncovered that the IR induced molecular responses have different dose-effect relationships. A minor part of the phosphorylation signalling and transcription involved in the DSB-related responses displayed a linear dose-effect relationship. Contrastingly, the reactive oxygen species (ROS) production-related molecular and cellular responses and DNA replication stress revealed complex dose-response relationships. LD uniquely activates ROS-related responses at multiple molecular levels, including proteome, phosphoproteome, nascent transcriptome and metabolome. Further work will be required to determine how these differences in molecular and cellular responses observed over hours after low and high doses impact the risk for cancer development that occurs over months and years. Show less

Berg, P.R. van den 2021

Gene regulation in embryonic development

Doctoral Thesis

open access

The human body consists of hundreds, perhaps thousands of different types of cells, each with different morphologies and functions, despite having the same genome. This diversity is created by gene... Show moreThe human body consists of hundreds, perhaps thousands of different types of cells, each with different morphologies and functions, despite having the same genome. This diversity is created by gene regulation, a set of mechanisms that determine, which genes are used to make proteins and which genes are kept silent. During embryonic development, gene are turned on and off in a tightly orchestrated manner, to make sure that the right cell type is created at the right time and place.In this thesis we report several studies pertaining to gene regulation in embryonic development. Each of the four chapters will cover a different layer of the gene regulation toolbox: gene inactivation by DNA methylation, transcriptional regulation in the developing kidney, regulation of protein turnover and translational regulation through micro-RNAs. Together, these studies provide a refined understanding of the crucial role of gene regulation for embryonic development. Show less

Boer, C. de 2021

Inhibitors and probes targeting endo-glycosidases

Doctoral Thesis

open access

The chemical synthesis of inhibitors and probes targeting endo-glycosidases.

Du, C. 2020

Multi-omics studies of the control of growth and antibiotic production of streptomyces

Doctoral Thesis

open access

Actinobacteria are Gram-positive bacteria that have a complex multicellular life cycle and are well known for their ability to produce a wide range of bioactive natural products (NPs). High... Show moreActinobacteria are Gram-positive bacteria that have a complex multicellular life cycle and are well known for their ability to produce a wide range of bioactive natural products (NPs). High throughput screening has failed to deliver the new antibiotics we so desperately need to combat multidrug-resistant pathogens. Therefore, new systematic approaches are needed to further explore the rich potential of Actinobacteria. The work described in this thesis entails systems biology approaches consisting of technologies such as proteomics, genomics, metabolomics and DNA binding studies. These were then applied to identify the biosynthetic gene clusters (BGCs) that are responsible for the production of novel antibiotics. Small molecules were thereby used as elicitors to activate the expression of cryptic BGCs in Streptomyces roseifaciens. Furthermore, S. coelicolor M1152 that was optimized for heterologous expression of antibiotics, was analysed for changes in protein expression, to understand which changes correlate to optimal antibiotic production. Finally, the role of the nucleoid associated protein SCO1839 in development and antibiotic production was studied. Chip-seq technology showed that it binds to thousands of DNA sequences on the S. coelicolor chromosome, which contain the motif GATC. I hope that this thesis contributes to utilizing multi-dimensional ‘omics approaches to answer major biological questions. Show less

Koenders, S.T.A. 2020

Visualization of vitamin A metabolism

Doctoral Thesis

open access

Vitamin A or retinol is essential in embryonic development, the visual cycle and the immune system. Vitamin A is converted to retinoic acid (RA) by aldehyde dehydrogenases (ALDHs). The family of... Show moreVitamin A or retinol is essential in embryonic development, the visual cycle and the immune system. Vitamin A is converted to retinoic acid (RA) by aldehyde dehydrogenases (ALDHs). The family of ALDHs consists of 19 members, three of which (ALDH1A1, ALDH1A2 andALDH1A3) have retinal as their preferred substrate. Due to a lack of selective and potent inhibitors for these enzymes, it is difficult to study their individual contribution to Vitamin A metabolism in biological systems.Therefore an activity-based probe based on the chemical structure of retinal has been synthesized to enable activity-based protein profiling (ABPP) of ALDHs. The probe covalently binds to the catalytic cysteine of ALDH enzymes which can then be visualized on gel or analyzed by proteomics using ligation chemistry.After biological evaluation of the probe this chemical tool has been used to study the influence of individual ALDH enzymes on the mucosal immune system and to determine the ALDH profile of several breast cancer cell lines. Thus showcasing its use to study Vitamin A metabolism in a wide variety of biological settings including but not limited to: immunology, cancer and (cancer) stem cells. Show less

Orsi Loureiro de Andrade, F. 2020

Emerging risk factors for venous thromboembolism: The role of commonly prescribed drugs for cardiovascular disease and inflammatory disorders

Doctoral Thesis

open access

The aim of this thesis is to identify emerging risk factors for VTE. To achieve this goal, we describe the supposedly causal role of statin and glucocorticoid use (i.e. two drugs that can influence... Show moreThe aim of this thesis is to identify emerging risk factors for VTE. To achieve this goal, we describe the supposedly causal role of statin and glucocorticoid use (i.e. two drugs that can influence inflammation) with changes in hemostasis and VTE risk. Systemic glucocorticoid use increases the relative risk of first VTE by more than three-fold and confers an 5% absolute risk of recurrent VTE per year. On the other hand, rosuvastatin use may reduce the risk of first VTE by 40%. Although the mechanisms behind this association are not fully elucidated, this thesis shows that rosuvastatin is capable of decreasing the thrombin generation potential by 10% in patients with a prior VTE. This thesis has shown that both statins and systemic glucocorticoids can affect the risk of VTE, improving the knowledge on the influence of these two commonly prescribed drugs on VTE pathophysiology. These findings have the potential to further refine the assessment of VTE risk since they highlight that the use of these drugs should be considered when evaluating the risk of VTE. Finally, this thesis provides insight into new therapeutic approaches since the results underscore that treatment strategies on VTE prevention in patients already taken statins, which may be sufficient for VTE prevention, are lacking. Treatment strategies to prevent glucocorticoid-associated VTE are also needed. Show less

Kaisar, M.M. 2017

Tracking helminths : from molecular diagnostics to mechanisms behind immune polarization

Doctoral Thesis

open access

Parasitic helminths are important organisms to study because their infections have both adverse and beneficial effects on the human host. Helminth infections are considered a burden, as these... Show moreParasitic helminths are important organisms to study because their infections have both adverse and beneficial effects on the human host. Helminth infections are considered a burden, as these infections cause significant morbidity in a large proportion worldwide. However, helminth infections, by means of their ability to modify host immune responses can also provide protection against inflammatory diseases (inflammatory bowel disease, diabetes, and asthma). It is important to better understand the underlying mechanisms of these Yin (positive) and Yang (negative) consequences of helminth infections. The general objective of this thesis is to track helminths at different levels. On the one hand to improve the detection of helminth infections, essential for the studying helminths and the interaction with their human host. Moreover, a more sensitive diagnostics is instrumental for monitoring the distribution of helminth infections and to evaluate the helminth infections elimination program. On the other hand, to understand the mechanistic insights of the interplay between helminths and the host immune system results in priming of Th2 and regulatory T cell responses. This could contribute to the identification of targeted pathways to manipulate immune responses, as part of developing therapeutics to treat inflammatory disorders characterized by deregulated Th2 and/or Treg responses. Show less

Welker, F. 2017

The palaeoproteomic identification of pleistocene hominin skeletal remains

Doctoral Thesis

open access

The Middle to Upper Palaeolithic transition in Europe witnesses the local replacement of Neanderthals by Anatomically Modern Humans. During this period several “transitional” technocomplexes are... Show moreThe Middle to Upper Palaeolithic transition in Europe witnesses the local replacement of Neanderthals by Anatomically Modern Humans. During this period several “transitional” technocomplexes are present that seem to combine behavioural characteristics from both the preceding Middle and following Upper Palaeolithic. These technocomplexes therefore play a critical role in our understanding of Neanderthal behavior, cognition and extinction, the dispersal of AMHs into Europe, and the interactions between Neanderthals and AMHs. Unfortunately, biological remains of the hominins responsible for the transitional technocomplexes are notoriously scarce. This dissertation proposes to utilize recent advances in mass spectrometry to identify additional hominin specimens through ZooMS screening and shotgun proteomics. Novel approaches towards de novo/error-tolerant proteomic analysis in Pleistocene contexts were developed and tested, allowing phylogenetic analysis of ancient protein sequences from now-extinct Mammalian species and hominin populations. ZooMS screening is shown to be highly successful for all included Châtelperronian sites. The discovery of additional hominin specimens at one archaeological site allowed demonstrating that ancient protein sequences can be used to differentiate between hominin populations, in this case indicating a Neanderthal affiliation. As a result, palaeoproteomics now allows studying the evolutionary relationships between hominin individuals based on ancient protein sequences. Show less

Baggelaar, M.P. 2017

Activity-based protein profiling of diacylglycerol lipases

Doctoral Thesis

open access

Diacylglycerol lipase (DAGL)-α and -β are enzymes responsible for the biosynthesis of the endocannabinoid 2-arachidonoylglycerol. Selective and reversible inhibitors are required to study the... Show moreDiacylglycerol lipase (DAGL)-α and -β are enzymes responsible for the biosynthesis of the endocannabinoid 2-arachidonoylglycerol. Selective and reversible inhibitors are required to study the function of DAGLs in neuronal cells in an acute and temporal fashion. The work described in this thesis has led to the identification of an activity-based probe (ABP) for DAGL-α. This ABP was instrumental for the identification of a new class of highly selective DAGL inhibitors.

These novel inhibitors can be used to investigate the role of the diacylglycerol lipases in metabolic syndrome and neurodegenerative diseases such a Parkinson’s disease, Alzheimer’s disease and Multiple Sclerosis.

Show less

Velstra, B. 2016

Mass spectrometry based protein profiling : taking the steps towards clinical application

Doctoral Thesis

open access

In this thesis mass spectrometry based protein profiling was applied as a new biomarker screening modality and it was evaluated whether or not this could be translated into early detection... Show more In this thesis mass spectrometry based protein profiling was applied as a new biomarker screening modality and it was evaluated whether or not this could be translated into early detection of breast cancer and pancreatic cancer. The status of breast cancer screening by proteomic profiling is discussed. Which steps have already been made? What is essential to implement this techniques in a clinical setting? Furthermore, the new protein profiling screening methods for pancreatic cancers are evaluated. Future studies will be suggested that are needed to translate this promising biomarker into a clinical application. Show less

Heemskerk, Anthonius Adrianus Maria 2016

Exploring the proteome by CE-ESI-MS

Doctoral Thesis

open access

Recent developments in the coupling of liquid phase separations and mass spectrometry have yielded some new source designs for electrospray ionization. The research in this thesis covers the... Show moreRecent developments in the coupling of liquid phase separations and mass spectrometry have yielded some new source designs for electrospray ionization. The research in this thesis covers the application of a newly developed electrospray ionization source design and it's application for the coupling of capillary electrophoresis to mass spectrometry. The initial chapters cover improvements in sensitivity and separation power in capillary electrophoresis mass spectrometry (CE-MS) by allowing electrospray at ultra low flow rates and therefore optimal ionization and separation conditions. We showed strong complementarity of this CE-MS system with reversed phase liquid chromatography in the identification of peptides and proteins from e.coli digests. Finally a sample preparation method for peptide and protein identification from laser micro-dissected tissue samples from human kidneys was developed. It was shown that a few hundred proteins could be identified from amounts of material representative of one full human glomerulus. On the whole great strides were made in development of strategies employing CE-MS for proteomics analysis. Show less

Treffers, Emma Elisabeth 2015

A +RNA virus diptych : Chikungunya virus-host interactions and arteriviral programmed ribosomal frameshifting

Doctoral Thesis

open access

In part 1 of the thesis quantitative proteomics was used to determine changes in abundance and phosphorylation status of host proteins during infection with the human pathogen chikungunya virus ... Show moreIn part 1 of the thesis quantitative proteomics was used to determine changes in abundance and phosphorylation status of host proteins during infection with the human pathogen chikungunya virus (CHIKV). Several proteins were identified that may be specifically downregulated during CHIKV infection to create a suitable environment for viral replication. eEF2 was identified as a factor that becomes strongly phosphorylated during infection with several viruses which may be a mechanism to stall translation in response to viral infection. In part 2 of the thesis the discovery of a novel and unusual -2/-1 programmed ribosomal frameshifting (PRF) mechanism is described that is used during translation of the nonstructural open reading frame of the economically important porcine reproductive and respiratory syndrome virus (PRRSV). This mechanism relies on a slippery site and stimulatory RNA signal in the PRRSV genome and is stimulated by the viral protein nsp1beta and host poly (C) binding proteins 1 and 2. Frameshifting results in the synthesis of two previously unidentified proteins, nsp2 TF (-2 PRF) and nsp2N (-1 PRF). Virus mutants that can no longer make the frameshift products are attenuated and may be used for vaccine development. Show less

Hendriks, I.A. 2014

Global and site-specific characterization of the SUMO proteome by mass spectrometry

Doctoral Thesis

open access

SUMOylation is a reversible lysine post-translational modification critical for eukaryotic life, and involved in many diseases such as cancer. This thesis describes five years of research into... Show moreSUMOylation is a reversible lysine post-translational modification critical for eukaryotic life, and involved in many diseases such as cancer. This thesis describes five years of research into SUMOylation using cutting edge high-resolution mass spectrometry, at the system-wide level and in an unbiased manner. Various novel and highly efficient methods for purifying SUMOylation from complex samples are described, and validated through mass spectrometry. Overall, we report an unprecedented number of SUMOylation sites, shed light on the dynamic nature of SUMOylation in response to various cellular treatments and stress conditions, and provide an unsurpassed level of depth through extensive bio-informatics analysis. Show less

Zhu, H. 2014

Environmental and metabolomic study of antibiotic production by actinomycetes

Doctoral Thesis

open access

This thesis may be regarded as a concept work, to see how feasible drug discovery approaches still are. For this, a strain collection was built up consisting of actinomycetes from soil in the... Show moreThis thesis may be regarded as a concept work, to see how feasible drug discovery approaches still are. For this, a strain collection was built up consisting of actinomycetes from soil in the Qinling and Himalaya mountains, which were subsequently tested for antibiotic production against multi-drug resistant clinical isolates. This resulted in close to 100 strains that showed strong antimicrobial activity, which were then analyzed in more detail. Two of the strains were subjected to extensive NMR-based metabolomics assisted by mass spectrometry, and several known and also novel antimicrobial compounds were elucidated. Finally, we also focused on the antibiotic activity of volatile organic compounds (VOCs) Show less

Mostovenko, E. 2013

Towards high throughput and spatiotemporal proteomics : analytical workflows and quantitative label-free mass spectrometry

Doctoral Thesis

open access

A large part of modern biology is dedicated to the functional annotation and interpretation of genetic information and its influence on the subject__s phenotype. Proteomics describes the state of... Show moreA large part of modern biology is dedicated to the functional annotation and interpretation of genetic information and its influence on the subject__s phenotype. Proteomics describes the state of the system from the perspective of expression, structure, localization, interaction and function of the proteins. It is a complex field which requires a combination of various disciplines such as cellular biology and biochemistry for sample preparation, analytical chemistry for sample measurement and bioinformatics for the processing of data. Different chapters of this thesis illustrate various aspects of the proteomics pipeline and emphasize the importance and connection between them. Therefore the information in this dissertation can be divided into three major parts depicting these aspects of a proteomics experiment. First, sample preparation for proteomics has been addressed through two studies aimed at decreasing sample complexity and increasing proteome coverage. The second part is dedicated mostly to the technical step of the mass spectrometry measurement and the analysis of obtained spectra. The final part describes example- and proof-of-principle applications. Show less

Willems, S.M. 2011

Molecular genetic aspects and characterization of the extracellular matrix of myxoid tumours of soft tissue

Doctoral Thesis

open access

Myxoid tumours of soft tissues are a heterogeneous group of mesenchymal origin characterized by their so-called myxoid extracellular matrix. although their histological overlap, their clinical... Show moreMyxoid tumours of soft tissues are a heterogeneous group of mesenchymal origin characterized by their so-called myxoid extracellular matrix. although their histological overlap, their clinical behaviour ranges form benign to malignant. In this thesis we studied the exact nature and possible function of the components of the myxoid matrix using a broad range of techniques (including (immuno)histochemistry and (imaging) mass spectrometry. Furthermore, we studied the molecular (cyto)genetic aberrations in different myxoid soft tissue tumours, using direct sequence analysis and COBRA FISH. Show less

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