Research Winnok De Vos

Abstract

Recent evidence suggests that inflammation in the gut can contribute to neurodegeneration and worsen the progression of Alzheimer's Disease (AD). Our own research has unveiled that bacterial amyloids produced by the gut's microbiome trigger a strong immune response in the gastrointestinal system and that serum amyloid SAA3 is a key regulator in kickstarting a series of inflammatory reactions. Because SAA3 can penetrate the blood-brain barrier and is found in higher levels in AD patients, we believe it may play a vital role in the harmful communication between the gut and the brain. Our project is therefore aimed at investigating the mechanisms through which SAA3 activates immune cells (particularly the glia) in the enteric and the central nervous system. This way we intend to further our understanding of pathogenic gut-brain communication and offer critical new insights into AD development.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Despite technological improvements, drug discovery programs have become less successful and more expensive over time. This can in part be attributed to the rigid implementation of sub-optimal preclinical screening platforms that mainly use simple cell cultures, and toxicity and pharmacokinetics experiments with animal models. Organoids are the promise of next-generation model systems for preclinical research. The main roadblocks for organoid adoption are their lack of reproducibility and the absence of technology to characterise them in depth. We believe that robust and reproducible organoid production and analysis can only be guaranteed when organoids are characterized in toto with cellular resolution. With this project, we intend to develop a pipeline for fast cellular phenotyping of intact organoids and prepare for launching a spin-off company that offers this as a service platform to the pharma and biotech industry.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Sijbers Jan
• Fellow: Van De Looverbosch Tim

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Particle therapy is a promising treatment for patients with solid tumors near sensitive organs or radiation-resistant tumors. However, the induced DNA damage is complex and not well understood, precluding reliable biodosimetry in terms of individual radiation sensitivity. And while microscopy is the gold standard for gauging the level of DNA damage at the single cell level, conventional techniques fail to unravel the exact nature and composition of these clusters. We propose to use fluctuation-enhanced expansion microscopy to gain super-resolved insight in DNA damage clusters. We intend to exploit this technology to quantitatively investigate DNA damage repair pathways and kinetics after exposure to proton and carbon ion irradiation. We will hereby specifically focus on the role of nuclear lamins, as they regulate nuclear architecture, DNA damage repair and mutations in their encoding genes predispose for accelerated aging disease and cancer. Using this highly relevant biological use-case, we expect this work to provide a much more quantitative insight in DNA damage and repair after high LET radiation. This should in turn help build better predictive biophysical models that aid in clinical treatment planning based on patient's individual radiation sensitivity.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Within the classical drug discovery pipeline, early target selection and compound validation are based on simple readouts from technologies that average across large populations of cells. This strategy negates much of the total information content in the biological sample at hand, causing selection bias and attrition of promising leads. High-content microscopy holds large potential for refined mode-of-action (MoA) analysis of pharmaco-genomic perturbations. An especially information-rich readout can be obtained with Cell Painting (CP), a pipeline that is implemented in our lab and consists of automated microscopy and morphological analysis of cells stained with inexpensive fluorescent dyes. The resulting cell phenotypic signatures can be used to predict the MoA of compound treatments with high fidelity. However, by design, predictions are limited to known MoA encountered in the dataset. Furthermore, confounding factors, such as experimental noise and intercellular heterogeneity may obscure relevant biological properties. Hence, we envision a more comprehensive MoA documentation by adding a complementary information layer based on transcriptomics of the same cell culture at hand. To this end, we have teamed up with the OncoRNA lab of Prof. Mestdagh (University of Ghent), who has developed a cost-effective platform for parallelized shotgun transcriptomics, which offers high genome coverage. Together, we intend to deploy the combination of CP and transcriptomics for systematic gene silencing screens based on CRISPRi technology. As proof-of-concept, we will perform a targeted knockdown screen for a set of genes with known MoA in a panel of disease-relevant cell lines. By associating specific genes with simultaneous changes in cell morphology and gene expression profile, we aim to establish an enrichment analysis that allows unbiased MoA prediction. We will offer this platform as a service to biotechnology and pharmaceutical companies seeking to enhance their preclinical R&D lines. At the same time, we will build biological data capital, with which we intend to redesign the target discovery process and position ourselves in the vanguard of data-driven biotech at the European level.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Van De Looverbosch Tim

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Flanders Bioimaging (FBI) is an inter-university consortium of advanced light microscopy and biomedical imaging core facilities conceived to integrate, optimize and coordinate the state-ofthe- art imaging infrastructure and expertise in Flanders. Its primary aim is to provide European research access to cutting-edge spearpoint imaging applications at each site via membership of EuroBioImaging, a landmark European Research Infrastructure Consortium. Relying on a track record of scientific collaboration and public-private partnerships, FBI will provide end-to-end solutions, supporting investigators with study design, novel modes of access (e.g., sample shipping, virtual microscopy…), development of novel imaging techniques, advanced image analysis, and training in all aspects from data collection to analysis and interpretation. Workflows developed within FBI comply with FAIR data management principles and internal quality control efforts assure standardized and reliable service. FBI will raise the efficiency of imaging infrastructure exploitation, accelerate technological development and consolidate the leading international position of Flanders in bio-imaging.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Stroobants Sigrid

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The cerebral organoid is an emerging model system with high potential for both fundamental and applied neuroscience research. However, batch-to-batch variability and the inability to characterize these specimens at the cellular level with high throughput, hampers their integration in an industrial setting. With this project, we intend to develop a pipeline that enables unbiased cellular phenotyping of intact cerebral organoids by using a combination of multiplex fluorescent labelling, light-sheet microscopy, and deep learning. Our approach builds on the concept that cells can be accurately identified by means of sheer morphological information. First, we will perfection cell profiling in co-cultures of different brain cell lines by training machine learning-based classifiers. Then, we will translate the concept to 3D, using spheroids from the same cells. To this end, we will render the staining compatible with chemical clearing and conceive a sample mounting procedure for serial, isotropic image acquisition. Finally, we will deploy the optimized method to recognize cell type and state in iPSC-derived cerebral organoids that have been challenged with selected compounds or seeded with glioblastoma cells. The approach will add to a more standardized quality-control of organoids and will facilitate the adoption of this model in drug-screening pipelines. Ultimately, this will boost the translatability of preclinical research and lower attrition rates in late-stage clinical trials.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Ponsaerts Peter
• Fellow: De Beuckeleer Sarah

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Identification of disease mechanisms and novel therapeutic targets relies on the use of cell culture and animal models. While the former are overly simplified, the latter are not human and ethically contested. Suboptimal models at the discovery side will inevitably lead to a steep loss of leads in clinical trials. With the advent of human induced pluripotent stem cell technology, it has now become possible to generate organoids that more faithfully capture part of the heterogeneity and three-dimensional context of human tissue. Several research labs at the University of Antwerp (UA) recognize their potential and have therefore implemented a variety of human patient-derived organoid cultures, in particular for neuroscientific research lines. However, batch-to-batch variability and the inability to characterize these specimens at the cellular level with high-throughput, hamper their integration in a routine screening setting. Therefore, we have the ambition to develop an end-to-end solution that enables unbiased cellular phenotyping of intact neuro-organoids by using a combination of fluorescent labelling, advanced microscopy, and artificial intelligence (AI).

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Ponsaerts Peter
• Co-promoter: Sijbers Jan
• Co-promoter: Timmerman Vincent
• Co-promoter: Weckhuysen Sarah

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The Antwerp Centre for Advanced Microscopy (ACAM) provides high-end service for visualizing biological samples from the nano- to the mesoscale. Its mission is to be the go-to hub for demanding microscopy-oriented work and to exploit its quantitative imaging expertise to foster research excellence at the University of Antwerp. To do so, ACAM assists with project planning, sample preparation, microscope selection and use, image analysis and visualization, and data interpretation. ACAM manages 10 advanced microscope systems, a server for image data warehousing and several workstations for image analysis. High-dimensional imaging is a major focus with light sheet microscopy, ultrafast live cell imaging and high-throughput screening as flagship technologies. Next to novel hardware acquisition and maintenance, ACAM develops its own software algorithms and evaluates experimental accessory setups. Routine training and thematic courses are organized to assure apt knowledge transfer regarding new technologies, optimal equipment usage and experimental reproducibility. ACAM pursues an open science policy and invests in making its data adhere to FAIR data principles. By combining breadth and depth in offered technology, and by keeping the pulse of the rapidly developing imaging field, ACAM aims at empowering researchers to perform science with high impact.

Researcher(s)

• Promoter: Timmermans Jean-Pierre
• Co-promoter: De Vos Winnok
• Co-promoter: Kumar-Singh Samir
• Co-promoter: Pintelon Isabel

Research team(s)

• Laboratory of cell biology and histology

Project website

Project type(s)

• Research Project

Abstract

Dilated cardiomyopathy is the primary cause of heart transplants worldwide. Hereditary variants of the disease are driven by mutations in the LMNA gene, which encodes A-type lamins, structural components of the nuclear envelope (NE). The pleiotropic nature of lamins and the limited availability of patient material complicate the identification of pathological processes underlying heart failure. We and others have shown that lamin perturbations predispose cells for nuclear dysmorphy and rupture, which compromises cell homeostasis and elicits DNA damage. We hypothesize that this so-called NE stress represents a common hallmark of cardiac laminopathies. Hence, we intend to gauge the impact of pathogenic lamin variants on this process in a cellular model that is relevant to the disease. To this end, we will generate induced pluripotent stem cell-derived cardiomyocytes from cardiac patient fibroblasts harboring diverse LMNA mutations. In these cells, we will quantify structural defects of the NE and its susceptibility to rupture with advanced microscopy. In addition, we will perform a comparative transcriptomics experiment to reveal gene regulatory programs that accompany NE stress and evaluate the influence of two major NE stress elicitors by pharmacological modulation. This way, we intend to expose the role of NE stress in the development of cardiac laminopathies and unveil potential leads for its therapeutic targeting.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Defects in the microtubule associated protein tau typify a range of neurodegenerative disorders termed tauopathies, which includes Alzheimer's disease. Recent studies point to the potential involvement of cellular senescence, an irreversible non-proliferative state, associated with inflammatory cytokine secretion, in disease development. However, the causality, timing, and afflicted cell types remain poorly characterized. The goal of this project is to define the exact causal relationship between senescence and tauopathy development in a human context. To achieve this, I intend to produce human iPSC-derived brain organoids that contain the three major cell types of the brain (neurons, astrocytes, or microglia) and assess the emergence of senescence therein using deep coverage microscopy and single cell sequencing. Once a cell-specific senescence signature has been established, I will measure its penetrance in mutant organoids that recapitulate the hallmarks of tau pathology. Finally, I will evaluate whether senescence-targeting compounds modulate tau pathology and influence organoid condition. Together, this work should allow defining whether senescence is a driving factor in human tau pathology development and unveil its potential as druggable node.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Ponsaerts Peter
• Fellow: Van den Daele Johanna

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Detection of transudated antibodies in female genital secretions, washed away with the first fraction of urine – i.e. first-void (FV) urine –, has been confirmed. In addition, vaccine-induced HPV antibodies have been detected in FV urine of women using different immunoassays. Although good correlations between paired FV urine and serum samples have been observed, urinary antibody titres are at least 1000-fold lower than serum antibody titres. To be able to distinguish between both vaccinated vs. not-vaccinated and seroconverted unvaccinated vs. non-seroconverted unvaccinated women using FV urine, antibody yield and assay sensitivity need to be increased. The first step in our process to upgrade the detection of HPV-specific antibodies in FV urine, will be the production of HPV pseudovirions (PsV) for the quadrivalent vaccine types (HPV6, 11, 16, 18) to be used in a highly sensitive immunoassay (WP1). These PsV will be used to create HPV conformational monoclonal antibodies (mAbs) in mice using the hybridoma technology (WP2.1). These mAbs will be made type-specific by desensitisation for all other included HPV PsV types before immunisation with the HPV PsV type of interest. To evaluate the quality of the produced mAbs, a DELFIA time-resolved fluorescence (TRF) assay will be developed using the created PsV. In addition, the neutralizing abilities of the generated mAbs will be assessed using our in-house pseudovirion based neutralisation assay (WP2.2). The produced PsV and mAbs will then be used in a multiplex competitive highly sensitive ELISA using the TRF technology (WP3). It is clear that monitoring neutralizing HPV antibodies non-invasively by using FV urine samples has major advantages since it (i) is an easy to collect non-invasive sample, (ii) can also provide information about the infection by applying parallel DNA testing and, (iii) is suitability for at-home sampling (currently boosted by the COVID-19 pandemic). If successful, the created assay provides a very useful and almost unique tool to monitor neutralizing HPV antibodies. With only limited adaptations, the developed assay will be compatible with serum samples as well. Since there are limited HPV immunoassays available overall, and currently only one other assay (cLIA) detects specifically neutralizing antibodies, this assay will be of great value. In addition, the validated pseudovirions and HPV type-specific neutralizing mAbs will generate substantial interest and wide applications in the field.

Researcher(s)

• Promoter: Vorsters Alex
• Co-promoter: Delputte Peter
• Co-promoter: De Vos Winnok

Research team(s)

• Centre for the Evaluation of Vaccination (CEV)

Project type(s)

• Research Project

Abstract

IMARK capitalizes on the deeply rooted expertise in biomedical imaging at the University of Antwerp to push the boundaries of precision medicine. By resolving molecular and structural patterns in space and time, IMARK aims at expediting biomarker discovery and development. To this end, it unites research groups with complementary knowledge and tools that cover all aspects of imaging-centred fundamental research, preclinical validation and clinical evaluation. IMARK harbours high-end infrastructure for electron and light microscopy, mass spectrometry imaging, magnetic resonance imaging, computed tomography, positron emission tomography and single-photon emission computed tomography. Moreover, IMARK members actively develop correlative approaches that involve multiple imaging modalities to enrich information content, and conceive dedicated image analysis pipelines to obtain robust, quantitative readouts. This unique blend of technologies places IMARK in an excellent position as preferential partner for public-private collaborations and offers strategic advantage for expanding the flourishing IP portfolio. The major application fields of the consortium are neuroscience and oncology. With partners from the Antwerp University Hospital and University Psychiatric Centre Duffel, there is direct access to patient data/samples and potential for translational studies.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Baets Jonathan
• Co-promoter: Baggerman Geert
• Co-promoter: Bogers John-Paul
• Co-promoter: Keliris Georgios A.
• Co-promoter: Kumar-Singh Samir
• Co-promoter: Mertens Inge
• Co-promoter: Morrens Manuel
• Co-promoter: Staelens Steven
• Co-promoter: Stroobants Sigrid
• Co-promoter: Timmerman Vincent
• Co-promoter: Timmermans Jean-Pierre
• Co-promoter: Verhaeghe Jeroen
• Co-promoter: Verhoye Marleen
• Fellow: Lanens Dirk
• Fellow: Prasad Aparna

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Pluripotent stem cell (PSC) technology is increasingly gaining interest for modelling diseases and developing precision therapeutics. However, the immaturity and heterogeneity of PSC-derived cell populations impinge on the reproducibility and preclude their use for comparative and diagnostic analyses. Recognizing these caveats for their own human induced (hi)PSC-based research, the Laboratories of Experimental Hematology, Cardiogenetics and Cell Biology and Histology have teamed up to develop a pipeline that enables accurate phenotypic staging of hiPSC-derived cell culture models. Specifically, to create mature and standardized 2D and 3D-models for cardiomyocyte cultures and brain organoids, our consortium proposes to optimize the culture conditions and refine the interrogation methods. Longitudinal follow-up and validation of functional activity in the differentiation products will be achieved by means of high-throughput multi-electrode array recordings and live cell calcium and voltage imaging. In parallel, cellular heterogeneity will be mapped with quantitative immunofluorescence and transcriptome analyses. The correlation of functional and molecular readouts will allow establishing a biomarker panel for mature hiPSC-derived cardiomyocyte models and brain organoids. Thus, with this work, we intend to develop more reproducible models and to allow selecting only those with the highest functional maturity, a prerequisite for our future stem cell research aimed at studying and treating neuro-inflammatory and cardiogenetic disorders.

Researcher(s)

• Promoter: Ponsaerts Peter
• Co-promoter: De Vos Winnok
• Co-promoter: Loeys Bart

Research team(s)

• Laboratory for Experimental Hematology (LEH)

Project type(s)

• Research Project

Abstract

Crucial insights in cell and developmental biology have been gained by virtue of live cell imaging technology. Along with a growing complexity of cellular models and the finesse with which they can be genetically engineered, comes a demand for more advanced microscopy. In brief, modern comprehensive cell systems research (cellomics) requires light-efficient, intelligent and interactive imaging modalities. To address this shared need, our consortium has identified a state-of-the art platform that allows ultrafast, yet minimally invasive imaging of small to medium-sized biological samples (from single cells to organoids) at high resolution, so as to capture dynamic events that range in timescale from voltage fluctuations to successive cell divisions. To only focus on those events that are truly of interest, and thereby boost throughput, the system is equipped with online image recognition capabilities. Finally, to allow targeted perturbations such as local damage induction or optogenetic switching, small regions can be selectively illuminated in the field of view. With this level of control, it will become possible to interrogate (sub-)cellular processes with unprecedented detail. The platform readily finds applications in diverse frontline research fields including neuroscience, cardiovascular research and infectious diseases, rendering it an indispensable asset for the applicants, the microscopy core facility and the University of Antwerp.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Caljon Guy
• Co-promoter: De Meyer Guido
• Co-promoter: Jordanova Albena
• Co-promoter: Rademakers Rosa
• Co-promoter: Timmerman Vincent
• Co-promoter: Timmermans Jean-Pierre
• Co-promoter: Vissenberg Kris
• Co-promoter: Weckhuysen Sarah

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Neuropathological research is an interdisciplinary field, in which imaging and image-guided interventions have become indispensable. However, the rapid proliferation of ever-more inquisitive technologies and the different scales at which they operate have created a bottleneck at the level of integration, a) of the diverse image data sets, and b) of multimodal image information with omics-based and clinical repositories. To meet a growing demand for holistic interpretation of multi-scale (molecule, cell, organ(oid), organism) and multi-layered (imaging, omics, chemo-physical) information on (dys)function of the central and peripheral nervous system, we have conceived μNEURO, a consortium comprising eight established teams with complementary expertise in neurology, biomedical and microscopic imaging, electrophysiology, functional genomics and advanced data analysis. The goal of μNEURO is to expedite neuropathological research and identify pathogenic mechanisms in neurodevelopmental and -degenerative disorders (e.g., Alzheimer's Disease, epilepsy, Charcot-Marie-Tooth disease) on a cell-to-organism wide scale. Processing large spatiotemporally resolved image data sets and cross-correlating multimodal images with targeted perturbations takes center stage. Furthermore, inclusion of (pre)clinical teams will accelerate translation to a clinical setting and allow scrutinizing clinical cases with animal and cellular models. As knowledge-hub for neuro-oriented image-omics, μNEURO will foster advances for the University and community including i) novel insights in molecular pathways of nervous system disorders; ii) novel tools and models that facilitate comprehensive experimentation and integrative analysis; iii) improved translational pipeline for discovery and validation of novel biomarkers and therapeutic compounds; iv) improved visibility, collaboration and international weight fueling competitive advantage for large multi-partner research projects.

Researcher(s)

• Promoter: Sijbers Jan
• Co-promoter: Baets Jonathan
• Co-promoter: Cras Patrick
• Co-promoter: De Vos Winnok
• Co-promoter: Giugliano Michele
• Co-promoter: Kumar-Singh Samir
• Co-promoter: Staelens Steven
• Co-promoter: Stroobants Sigrid
• Co-promoter: Timmerman Vincent
• Co-promoter: Timmermans Jean-Pierre
• Co-promoter: Verhoye Marleen
• Co-promoter: Weckhuysen Sarah

Research team(s)

• Vision lab

Project type(s)

• Research Project

Abstract

The aim of this network initiative is to exploit collective interest and complementary expertise to enhance insight in the pathophysiological mechanisms of disorders of which we hypothesise they have common ground in the GI tract. We will investigate key areas of uncertainty regarding the exact role of intestinal barrier function (the microbiome, the epithelial barrier and the mucosal immune system) in the different gut-organ-axes and associated pathologies.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Identification of novel therapeutic compounds relies on the use of cell culture and animal models. While the former are overly simplified, the latter are not human and ethically contested. Suboptimal models at the discovery side will inevitably lead to a steep loss of leads in clinical trials. With the advent of human induced pluripotent stem cell (iPSC) technology, it has now become possible to generate organoids that more faithfully capture part of the heterogeneity and three-dimensional context of human tissue. However, the complexity and optical inaccessibility of such tissue mimics hamper their adoption in a routine screening setting. We intend to develop a pipeline that will allow in-depth characterization of organoids. Concretely, we will combine our expertise in advanced microscopy and deep learning to enable ultrafast, high-quality imaging and subsequent cellular phenotyping of organoids. As two case studies with industrial relevance, we will use this pipeline to discriminate cell states in tumor spheroids and cell types in neuro-organoids. Once established, our approach will find a ready market with pharmaceutical and clinical R&D laboratories that wish to test their compound libraries on a physiologically relevant model, in particular in the oncology and neuroscience fields. In addition, it will foster an improved quality control of tissue mimics in the context of regenerative medicine.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Sijbers Jan

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Recent evidence points to microglia, the central nervous system-resident macrophages, as mediators of synapse degeneration in AD. Our project aims to pinpoint the exact contribution of microglia to synapse (dys-)function by deploying an in vitro chimeric OSC platform as physiological model for functional studies of iPSC-derived human microglia, and by analysing the contribution of different microglia subpopulations to synaptic pruning in health and AD. This study will provide new hints on the protective/detrimental role of human microglial subpopulations and will be key to developing AD therapies that are capable of fine-tuning microglial composition in the beneficial direction.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The major aim of this project is to characterize the response of microglia towards tau pathology and to assess the influence they might have on disease progression. To do this in an unbiased and comprehensive manner, we will perform a longitudinal experiment in which we will analyze the transcriptome of individual microglial cells from selected brain regions of a tauopathy mouse model. This work may expose novel molecular targets that could serve for early detection or therapeutic interventions in the context of AD and other neurodegenerative disorders.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The nuclear lamina is a critical regulator of nuclear structure and function. Defects in its major constituent proteins, A-type lamins, cause diseases known as laminopathies. Our group has discovered that laminopathy cells experience transient ruptures of the nuclear envelope, leading to illegitimate exchange of proteins between the cytoplasm and the nucleus. This feature contributes significantly to disease development in laminopathies, but also plays a key role in cancer. However, little is known about the underlying mechanisms. Considering its medical potential, we want to pinpoint the drivers of rupture induction and repair in a systematic manner. Using a combined strategy of molecular profiling and deep coverage microscopy we will further our understanding of the rapidly expanding tree of laminopathies, and may expose new therapeutic entry points with relevance for an even broader spectrum of lamin-associated disorders.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: Houthaeve Gaëlle

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Delivering compounds into cells is a ubiquitous requirement for fundamental life science research and cell-based clinical applications. Since cells are protected from the outside world by their plasma membrane, it requires sophisticated technology to deliver compounds across this barrier without causing toxicity. Photoporation is emerging as a powerful technology to achieve exactly this. It relies on laser illumination of plasmonic nanoparticles that have been added to cells. Absorption of the laser energy by the nanoparticles causes the plasma membrane to become permeable by local heating or pressure effects, allowing external compounds to diffuse into the cells. While it has been amply demonstrated that photoporation does not cause acute cytotoxicity, it remains unknown how it affects cell physiology at the short and longer term. Yet, this information is crucial to safely implement the technology in different settings. Therefore, we will unravel the cellular response to photoporation. We will thereby analyse early downstream events such as the activation of membrane repair pathways and induction of cellular stress levels, as well as more persistent changes in gene expression and genome integrity. The fundamental insights from these studies will provide a solid basis for making photoporation a standard transfection technology that can be used with confidence. At the same time, it will help devise strategies to reduce or exploit potential side effects of photoporation.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Flanders BioImaging (FBI) is an interuniversity consortium dedicated to biomedical imaging and advanced light microscopy, that was set up to integrate, optimize, rationalize and coordinate available imaging infrastructure in Flanders.

Researcher(s)

• Promoter: Stroobants Sigrid
• Co-promoter: De Vos Winnok

Research team(s)

• Molecular Imaging and Radiology (MIRA)

Project type(s)

• Research Project

Abstract

Altered nuclear shape is a defining feature of cancer cells, but the relationship with pathology development remains elusive. Recent observations indicate that nuclear dysmorphy correlates with an enhanced propensity of nuclei to rupture. Such ruptures transiently perturb nuclear compartmentalization but also provoke DNA damage. Thus, nuclear dysmorphy and fragility – jointly referred to as nuclear envelope (NE) stress – may contribute to genome instability and thereby represent a novel emerging hallmark of cancer. To better understand the contribution of NE stress to the carcinogenic process, I propose to systematically investigate the short- and long-term molecular consequences. To this end, I intend to analyze the population-level changes in the transcriptome as well as in the genome upon targeted, temporary disruption of nuclear compartmentalisation. This way, I expect to generate a comprehensive view on the impact of NE stress on cell fate. In extensu, this work may also lead to the identification of novel synthetic lethal targets that could be exploited in clinical applications.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The nuclear lamina is a critical regulator of nuclear structure and function. Defects in its major constituent proteins, A-type lamins, cause diseases known as laminopathies. Laminopathy patient cells experience transient ruptures of the nuclear envelope, leading to uncoordinated exchange of proteins between the cytoplasm and the nucleus. This feature contributes significantly to disease development in laminopathies, but also plays a key role in cancer. However, as yet, little is known about the underlying mechanisms. We want to pinpoint the drivers of rupture induction and repair in a systematic manner. To this end, we will perform a gene-silencing screen that is based on live-cell imaging, using transient loss of nuclear compartmentalization as prime readout. To bypass the unpredictable nature of spontaneous ruptures, we will also optimize methods to mechanically induce ruptures. Putative hits that arise from the primary (spontaneous ruptures) and secondary screen (induced ruptures) will be validated and characterized by location proteomics and co-immunoprecipitation experiments. This functional genomics approach will further our understanding of laminopathy development, and may expose new therapeutic entry points with relevance for the broad spectrum of lamin-associated disorders.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: Marques Leal Ana Sofia

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The goal of this project is to ehicidate the contribution of AQP4-mediated glymphatic function in AD development and to screen for compounds or conditions that modulate AQP4-driven pathways. To do so, we will develop and exploit innovative cell culture and manipulation techniques and use advanced 3D imaging paradigms to characterize humanized mouse models.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Developing novel neuroprotective and/or immune-modulating therapeutic strategies for almost every neurological disease or trauma requires, both for academia and pharmaceutical industry, the existence of robust in vitro cell culture models to mimic disease-associated pathological events. Unfortunately, a complex interplay between multiple central nervous system (CNS) cell types and multiple cell types from the body's peripheral immune system, cannot be easily recapitulated by currently used 2-dimensional (2D) co-culture assays. It is exactly therefore that successful pre-clinical experimental efficacy has proved to be very difficult to translate into clinical benefit, and as a consequence there is an increasing gap in knowledge and progress between bench and bed side. One highly promising novel approach to improve the predictive power of in vitro human neuro-immune research consists in developing modular 3D brain organoids that resemble brain tissue at the structural, cellular and functional level. Within this project we aim to develop and optimize a new method for generating isogenic 3D brain organoids, comprising human pluripotent stem cell (hPSC)-derived neurons, astrocytes and microglia. Furthermore, hPSC-derived astrocytes and endothelial cells will be used to create a blood-brain-barrier model for physical separation of hPSC-derived macrophages from the generated human 3D brain organoids. Together, this integrated cell system will represent a powerful new 3D human neuro-immune cell culture paradigm. Within this multidisciplinary IOF-SBO project, the methodological approach to generate 3D brain organoids, combined with the experience in the field of clinical research and the availability of patient samples, is truly unique and will - in first instance - highly contribute to the field of in vitro cerebrovascular disease modelling and treatment validation. Furthermore, our aims to install an integrated 3D brain organoid technology platform at the University of Antwerp, will - given the current scientific and economic interests – allow for both short-term and long-term valorisation of our combined efforts, with both intellectual (PhD-theses, A1 publications) as well as financial (contract research) revenues.

Researcher(s)

• Promoter: Ponsaerts Peter
• Co-promoter: De Vos Winnok
• Co-promoter: Jorens Philippe
• Co-promoter: Timmermans Jean-Pierre
• Co-promoter: Wouters An

Research team(s)

• Laboratory for Experimental Hematology (LEH)

Project type(s)

• Research Project

Abstract

Since a few years, evidence is growing that a disease process affecting the central nervous system (CNS) can also involve its enteric counterpart (ENS) and vice-versa. Indeed, various neurodegenerative disorders are accompanied or even preceded by gastrointestinal malfunctions. This relationship is well-documented for prion diseases and Parkinson's disease, but has not yet been scrutinized for Alzheimer's disease (AD), a devastating neurodegenerative disorder that is typified by a progressive and debilitating cognitive decline. A defining feature of AD is the accumulation of misfolded amyloid-beta peptides. Considering that the CNS and ENS are highly interconnected, the gut microbiome produces amyloids that can cross-seed polymerization, and inflammation promotes amyloid build-up, it is highly conceivable that the gut is a vulnerable node for amyloid-driven degeneration. Yet, the mechanisms underlying cellular processing of amyloids in the ENS are poorly characterized. Hence, with this research project, we will investigate the entry routes, spreading behaviour and cellular effects of microbial and host-derived amyloid proteins in the ENS. Using innovative imaging technologies and well-defined molecular characterization methods, this work will provide a solid basis for refining the gut-brain axis theory in the context of AD and will open novel avenues for both fundamental and clinical research with relevance for a broad range of proteopathic neurodegenerative diseases.

Researcher(s)

• Promoter: Timmermans Jean-Pierre
• Co-promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Alzheimer's disease (AD) currently affects 1 in 9 individuals over 65 years of age but its prevalence will only rise against the background of a steadily greying population. With no cure currently available and diagnosis relying on the assessment of late-stage cognitive decline, it is imperative that novel early medical entry points are explored through original fundamental research. Recent insights suggest that the gut may be a vulnerable node for amyloid-driven neurodegeneration. That is why we want to define the origin, entry routes and spreading behaviour of amyloid proteins in the enteric nervous system (ENS). Using innovative imaging technologies and well-defined molecular analyses, we will shed light on a novel gut-brain relationship with relevance for future (pre-)clinical research. As the gut represents a unique, minimally invasive window to assess neuropathology, our work may spark the development of early biomarkers that directly report on disease progression in AD-patients. Moreover, confirming the notion that microbial-derived amyloids could represent a putative trigger for pathology may cause a paradigm shift for AD therapy."

Researcher(s)

• Promoter: Timmermans Jean-Pierre
• Co-promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Despite being the most prevalent form of dementia in the world, there still is no cure for Alzheimer's disease (AD). A breakthrough in the development of therapies can only be achieved by generating new insights in the mechanisms that underlie disease development. Although it has become clear that AD is characterized by the progressive accumulation of aberrant proteins in the brain, it is not yet known to what extent their spread correlates with detrimental cellular effects, such as the loss of neuronal connections. This requires an integrated approach that can grasp the functional and structural changes with high resolution in the intact brain through time. No such technology exists as yet. That is why we will combine two sophisticated whole-brain imaging technologies to follow up a well-characterized mouse model for AD during different stages of the disease. Whilst alive, we will monitor brain function - specifically, the connections between brain regions - using an advanced MRI-based technique. Then, we will visualize the structure of the exact same brains at the cellular level using a newly developed microscopy technique that relies on rendering tissue optically transparent. The combination of both into multimodal AD brain maps (or briefly, MADMAPS) will provide unprecedented detail in the neurodegenerative process and allow for correlating functional changes with microscopic defects. On the longer term, the same approach will enhance the reproducibility and reliability of preclinical therapeutic studies by enabling distribution analyses and efficacy tests of disease-modifying compounds.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Biomarkers for radiation exposure are important for a number of reasons. With a growing nuclear threat, the identification of efficient biomarkers for radiation exposure that enable fast triage of exposed individuals is becoming increasingly important. Likewise, the identification of robust biomarkers of radiosensitivity should help tuning current tumor radiotherapies to more personalized schemes. Current golden standard methods for biodosimetry such as cytogenetics assays fall short in several aspects related to emergencies, in that their analysis is very laborious, time-consuming and expensive and therefore not amenable for fast screening of large cohorts. In the last decade, gene expression signatures have emerged as potential biomarkers that could be useful for the abovementioned purposes1–6. We have recently taken this research a step further with the identification of exon expression signatures as robust radiation biomarkers7 which are more sensitive than gene signatures, and therefore more suitable in the case of low-dose exposures. One of the main disadvantages of classical mRNA biomarkers is their inherent instability. Circular RNAs (circRNAs) are a recently described class of non-coding RNA molecules9,10, of which the expression varies according to the cell/tissue-type and developmental timing11–16. Due to their covalently closed circular structure, circRNAs are resistant to exonuclease degradation, and therefore remarkably stable17. This, together with observations that circRNAs are highly abundant in blood cells18 and furthermore enriched in exosomes from human serum19 gives them a very high potential as biomarkers in general, and radiation biomarkers in particular. Hence, in this PhD project, we will identify circRNA biomarkers for radiation exposure and radiosensitivity and characterize the functions of the most promising ones.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Laukens Kris

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Long-term adaptations of the brain, such as memory formation, rely on a delicate dialogue between neurons that is typified by intensive remodeling of both cellular and nuclear morphology. Recent observations suggest an important role for B-type lamins in neurodevelopment. We suspect that lamins interfere with neuronal plasticity via their architectural function in the nucleus. However, the exact mechanisms remain to be determined. Using a combined strategy of molecular profiling and deep imaging approaches, we aim at exposing a novel link between lamins and neuronal function. This way, we intend to further our understanding of a new phenotypical branch in the rapidly expanding tree of laminopathies and identify potential novel biomarkers or drug targets with relevance for the even larger spectrum of neurodevelopmental disorders.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: Verschuuren Marlies

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The nuclear lamina is a critical regulator of nuclear structure and function. Defects in its major constituent proteins, A-type lamins, cause diseases known as laminopathies. Our group has discovered that laminopathy cells experience transient ruptures of the nuclear envelope, leading to illegitimate exchange of proteins between the cytoplasm and the nucleus. This feature contributes significantly to disease development in laminopathies, but also plays a key role in cancer. However, little is known about the underlying mechanisms. Considering its medical potential, we want to pinpoint the drivers of rupture induction and repair in a systematic manner. Using a combined strategy of molecular profiling and deep coverage microscopy we will further our understanding of the rapidly expanding tree of laminopathies, and may expose new therapeutic entry points with relevance for an even broader spectrum of lamin-associated disorders.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: Houthaeve Gaëlle

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

This project aims at developing and implementing novel optogenetic tools and genetically-encoded reporters of synaptic activity in combination with computational tools to quantitatively assess synaptic function. This way, we will establish a next-generation of in vitro high-throughput assays to study the effects of neuropathology on synaptic function and also to screen for novel disease-modifying molecules.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Many neurodegenerative diseases are typified by molecular infectivity, with aggregates spreading through interconnected neuronal networks. As yet, it is not clear how such pathological aggregates spread beyond the initial sites of impairment and how this correlates with local neurodegenerative features, such as the onset of neuroinflammation and associated synaptic and neuronal loss. Monitoring the spatiotemporal spreading pattern of pathological aggregates and associated neurodegenerative features requires a methodology for accurately following up the evolution of disease manifestations within the brain, and this with cellular detail. To this end, we intend to optimise and exploit a nondestructive, high-resolution microscopic imaging approach, based on chemical clearing and light sheet microscopy, to visualise the intact neurodegenerative brain.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The nuclear lamina is a critical regulator of nuclear structure and function. Defects in its major protein constituents, the A-type lamins, cause a spectrum of diseases referred to as laminopathies. We have discovered that laminopathy patient cells repetitively experience transient ruptures of the nuclear envelope, leading to illegitimate exchange of proteins between the cytoplasm and the nucleus. This feature contributes significantly to disease development in laminopathies, and may also play an important role in aging and cancer. However, as yet, little is known about the underlying mechanisms. Using a combined strategy of molecular profiling and deep imaging, we aim at unveiling the major pathways that govern nuclear compartmentalization. This way, we intend to further our understanding of the rapidly expanding tree of laminopathies, and identify new therapeutic entry points with relevance for an even broader spectrum of lamin-related disorders.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: Houthaeve Gaëlle

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The application concerns an innovative microscopy platform for visualizing cells, tissue specimen and living small model organisms in three dimensions at unprecedented speed and with excellent resolution and contrast. As a unique feature, the platform is equipped with a light-sheet module, which is based on an orthogonal configuration of laser-generated, micrometer-thin plane illumination and sensitive one-shot detection. Seamless integration with confocal modalities enables imaging the same sample from the micro- to the mesoscale. The device has a broad application radius in the neurosciences domain inter alia for studying neurodegeneration and -regeneration (e.g. whole brain imaging, optogenetics); but it also has direct utility in various other fields such as cardiovascular research (e.g. plaque formation and stability), plant developmental research (e.g. protein localization during plant growth) and ecotoxicology (e.g. teratogenicity and developmental defects in zebrafish). Furthermore, its modular construction will enable adaptation and targeted expansion for future imaging needs.

Researcher(s)

• Promoter: Timmermans Jean-Pierre
• Co-promoter: Adriaensen Dirk
• Co-promoter: De Meyer Guido
• Co-promoter: De Vos Winnok
• Co-promoter: D'Haese Patrick
• Co-promoter: Giugliano Michele
• Co-promoter: Jordanova Albena
• Co-promoter: Keliris Georgios A.
• Co-promoter: Knapen Dries
• Co-promoter: Maudsley Stuart
• Co-promoter: Ponsaerts Peter
• Co-promoter: Timmerman Vincent
• Co-promoter: Vissenberg Kris

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Chemoresistance is a major impediment to succesful treatment of a growing number of cancer entitites. Circumventing this phenomenon demands highly selective and efficient targeting of cancer-specific pathways. We have recently discovered that MYC(N)-driven tumors show strong upregulation of genes involved in replicative stress-induced DNA damage repair. We thereby identified FOXM1 as a central regulator. Our data suggest that FOXM1 driven DDR is an important determinant in the acquired drug resistance program. In this project we aim at confirming the pivotal role of FOXM1 in drug resistance and dissecting its pathway by integrating knowledge from molecular data sets from patients, primary cell cultures and zebrafish models. This way, we expect to identify novel targets for therapeutic intervention of aggressive or resistant tumors. Once we have established the most vulnerable targets, we will resort to semi-high-throughput screens for pinpointing the most suitable compounds. Subsequently, focused testing of drug combinations on model organisms will prove their in vivo performance and should result in the inclusion of the optimal formulation in phase I clinical trials on patients with highly resistant tumors. Thus, the goal of this project is to devise new and less toxic therapeutic strategies for more efficient killing of tumors and for use in patients in which conventional methods no longer show effect. We thereby consider different MYC(N)- driven tumor types such as neuroblastoma, medulloblastoma, T-cel acute lymphoblastic leukemia and Burkitt lymphoma, emphasising the translational value of our findings.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Long-term adaptations of the brain, such as memory formation, rely on a delicate dialogue between neurons that is typified by intensive remodeling of both cellular and nuclear morphology. Recent observations suggest an important role for B-type lamins in neurodevelopment. We suspect that lamins interfere with neuronal plasticity via their architectural function in the nucleus. However, the exact mechanisms remain to be determined. Using a combined strategy of molecular profiling and deep imaging approaches, we aim at exposing a novel link between lamins and neuronal function. This way, we intend to further our understanding of a new phenotypical branch in the rapidly expanding tree of laminopathies and identify potential novel biomarkers or drug targets with relevance for the even larger spectrum of neurodevelopmental disorders.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: Verschuuren Marlies

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

In the framework of this project, a method will be established for automated and standardized microscopic evaluation of large numbers of biological samples. Protocols will be tailored for histological tissue preparations and for cell cultures. To this end, a combination of optics, robotics and bio-image informatics will be used.

Researcher(s)

• Promoter: De Vos Winnok
• Co-promoter: Bogers John-Paul
• Co-promoter: Kumar-Singh Samir
• Co-promoter: Maudsley Stuart
• Co-promoter: Timmerman Vincent
• Co-promoter: Van Der Linden Annemie

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand the client. UA provides the client research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Laminopathies are orphan diseases caused by mutations in the LMNA gene, which encodes A-type lamins. Recent evidence suggests that lamin defects cause abnormal nucleocytoplasmic compartmentalization. This feature is prone to contribute significantly to disease development in laminopathies, and may also play an important role in aging and certain cancers. With an eye on its medical potential, we want to expose the exact underpinnings of defective compartmentalization.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: Robijns Joke

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The aim of this project is to establish a method for mapping neurodegenerative processes in mouse models, using a combination of tissue clearing, advanced fluorescence microscopy and image processing. This project represents a formal research agreement between UA and on the other hand IWT. UA provides the IWT research results under the conditions stipulated in this contract.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

In this project, we will establish and benchmark a whole-brain imaging approach to monitor spreading of neurodegenerative protein aggregates; in other words, we wish to establish 4D reference maps of neurodegenerative pathologies. To this end, we will combine state-of-the-art tissue clearing strategies with advanced light microscopy and image informatics.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Neuronal communication depends on remodelling of cellular and nuclear morphology. Lamins, architectural proteins of the nucleus, have recently been implicated in neurodevelopmental disorders. To uncover their role in neuronal (dys-) function, we will monitor in vitro neuronal networks upon chemical or genetic perturbation of lamins, by exploiting high-content morphological analyses and live cell calcium imaging.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

Colorectal cancer (CRC) is one of the most lethal cancer types in the world. The major culprit in CRC development is considered to be the Western diet; the consumption of red and processed meat gaining particular attention in this context. To assess the potentially adverse effects of meat uptake we propose a cytometric strategy, based on a multiparametric cyto- and genotoxicity analysis of colon cell cultures that are incubated with in vitro digested meat extracts. Using a top-down approach, we will systematically compare the impact of different meat types on cell viability, morphology, stress and DNA damage in cell monolayers, as well as more complex, but physiologically more relevant cellular models, such as differentiated and 3D cell cultures. Finally, using this setup, we will assess the potentially beneficial impact of co-administrating specific antioxidants or food extracts. The proposed research will provide fundamental insights in the causal relationship of red meat consumption and CRC development and give the first clues towards potential countermeasures. This will provide nutrition community with valuable information to refine their recommendations on red meat consumption, and help the meat industry in tuning their production and processing protocols.

Researcher(s)

• Promoter: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project

Abstract

The techniques for monitoring and manipulating cells have reached a level of maturity that allows them to be implemented in high-level biological research. The promotor wants to grasp this momentum and raise the standard in modern microscopy technology while connecting cellular phenotypes with disease development. From a biological perspective, it is the goal to elucidate the mechanisms underlying cellular dysfunction in the context of genetic diseases, termed laminopathies. This research field is of particular importance because these pathologies show highly diverse manifestations and they magnify features of widespread degenerative processes like human aging. At the cellular level, all laminopathies demonstrate problems with the nuclear lamina, a structure that physically supports the cell nucleus.

Researcher(s)

• Promoter: De Vos Winnok
• Fellow: De Vos Winnok

Research team(s)

• Laboratory of cell biology and histology

Project type(s)

• Research Project