Title Promoter Affiliations Abstract "Interpretable models for integrative single-cell spatial transcriptomics" "Yvan Saeys" "Department of Applied Mathematics, Computer Science and Statistics" "Within the booming field of single-cell omics analysis, spatial transcriptomics is becoming more and more popular. Being awarded method of the year 2020 by Nature, it has a bright future ahead. The method will put us a step closer to understanding the spatial organization of cells in tissues, and how the organization influences cell function. At this point, no spatially aware transcriptome-wide method has reached single-cell level yet, complicating the data analysis. The first step in this project will be to overcome this hurdle. Different types of single-cell omics data can shed a complimentary light on a tissue, but current methods can't go beyond the integration of two data modalities. Variational autoencoder based methods, creating joint latent spaces, seem suitable for this problem, but their black-box nature is a limitation. In this project, novel machine learning model frameworks that can integrate multiple data modalities (single-cell RNAseq, CITE-Seq, and spatial transcriptomics) and result in biologically interpretable latent spaces, will be built. The framework will be flexible and easily adapted to new technological developments in the spatial transcriptomics field. The variables in the interpretable latent space can be linked to specific cellular aspects. This will allow the study of correlations between those aspects, and answering more complex biological research questions." "Harnessing single-cell and spatial transcriptomics to uncover novel insights into the pathological events that trigger the progression of acute-on-chronic liver failure" "Schalk Van der Merwe" Hepatology "ACLF is a clinically important syndrome that develops in patients with decompensated cirrhosis. This distinct disease entity is characterized by a rapid deterioration of liver function, the development of organ failure and an extremely high short-term mortality. Currently, no therapy exists and ACLF is managed by organ support and treatment of the precipitating event. Important to note is that patients with ACLF exhibit an immunological paradox whereby they feature a hyperinflammatory state on the one hand and a co-existing phase of immunoparesis and infection susceptibility, on the other hand. Understanding the molecular mechanisms that tips the balance towards dampening inappropriate systemic inflammation and reinstating effective antibacterial function, would be crucial to extend patient survival. Here we aim to compose a comprehensive transcriptional map of hepatic (immune) cells and their microanatomical location that underlie ACLF immune dysfunction. We further aim to validate- the identified targets in independent patient cohorts or in murine models mimicking the ACLF syndrome. A success in this project will have groundbreaking impact on shedding light on the pathogenesis of ACLF." "Harnessing Single-Cell and Spatial Transcriptomics to Uncover Novel Insights into Intestinal Barrier Breach in Cirrhosis" "Schalk Van der Merwe" "Hepatology, Translational Research in GastroIntestinal Disorders" "Cirrhosis is the end result of chronic liver diseases and its pathophysiology is paired with a progressive breach of the intestinal barrier. Herein, we address the fundamental question on how the intestinal barrier fails in cirrhosis. We will apply single-cell RNA-sequencing to survey the transcriptional landscape of epithelial and immune cells from control and cirrhosis patients to map cellular and molecular perturbations associated with disease. Furthermore, we will dissect cell-cell interactions in the intestinal mucosa of healthy and diseased subjects by spatial multi-omics. Ultimately, we will validate cellular and molecular pathways identified. We anticipate unveiling fundamental mechanisms underlying intestinal barrier disruption and enteric bacterial translocation in patients with cirrhosis, thereby providing novel translational strategies aiming to abrogate the high mortality rate associated with this disease." "Transcriptomics to identify genetic determinants involved in scrotal hernia in pigs" "Nadine Buys" "Animal and Human Health Engineering (A2H)" "Scrotal hernia in pigs is a congenital defect which causes both loss in animal welfare and economic losses. It has been demonstrated that a genetic component is involved. In this project we aim to characterize the genetic determinants of this defect, thereby helping in the implementation of a genetic selection method against the defect in two boar lines . Genomic and transcriptomic analyses of affected and non-affected piglets will be performed on data from a backcross enrichment experiment. In this way, important functional variants involved in scrotal hernia can be identified. Ultimately, a breeding strategy can be implemented that leads to a reduction of the occurrence of this defect." "Harnessing single-cell and spatial transcriptomics to uncover novel insights into the pathological events that trigger the progression of acute-on-chronic liver failure" "Schalk Van der Merwe" "Laboratory of Growth Control and Cancer Research (VIB-KU Leuven), Hepatology" "ACLF is een klinisch belangrijk syndroom dat zich ontwikkelt bij patiënten met gedecompenseerde cirrose. Deze ziekte-entiteit wordt gekenmerkt door een snelle verslechtering van de leverfunctie, de ontwikkeling van orgaanfalen en een hoge mortaliteit. Momenteel bestaat er geen therapie en de enige behandelingsoptie voor ACLF is orgaan ondersteuning en behandeling van de uitlokkende gebeurtenis. Patiënten met ACLF vertonen enerzijds een hyperinflammatoire toestand en anderzijds een gelijktijdig bestaande fase van immuun dysfunctie en infectiegevoeligheid. Een beter inzicht in de moleculaire mechanismen die de balans omslaan naar het dempen van ongepaste systemische ontstekingen en het herstellen van antibacteriële functies, zou cruciaal zijn om de overleving van de patiënt te verlengen. Hier streven we ernaar een uitgebreide transcriptionele kaart samen te stellen van lever (immun) cellen en hun microanatomische locatie die aan de basis liggen van ACLFimmuundisfunctie. We streven er verder naar om de geïdentificeerde doelwitten te valideren in onafhankelijke patiëntencohorten of in muizenmodellen die het ACLF-syndroom nabootsen. Een succes in dit project zal een baanbrekende impact hebben op het verwerpen van inzichten over de pathogenese van ACLF." "Combining transcriptomics, epigenetics and in vivo CRISPR screens to unravel the cell-cell communication within the steady-state liver module (deLiver-CRISPR)" "Martin Guilliams" "Department of Biomedical molecular biology" "The liver is mainly constituted of hepatocytes, sinusoidal endothelial cells, stellate cells and macrophages called Kupffer cells (KCs). Together, these 4 cells represent 90% of all liver cells. Tissue-resident macrophages were long considered to only play a role in immune defense, but it is now clear that macrophages are essential for tissue homeostasis. Transcriptomic profiling has revealed that each tissue-resident macrophage expresses a unique gene expression profile. Little is known however about the precise cell-cell circuits that underlie the tissue-specific imprinting of macrophages. We hypothesize that the cell-cell circuits between the 4 main liver cells not only forms the blueprint of liver homeostasis, but that perturbations in these cell-cell interactions will lead to the development of liver diseases. Thus, the deLIVER-CRISPR project aims to elucidate how endothelial cells, stellate cells and hepatocytes imprint the KC identity, but also how, in turn, KCs influence the functional specialization of the other liver sinusoidal cells. We will use cutting-edge technologies, including CUT&RUN, snATAC-seq, in vivo CRISPR screens and spatial transcriptomics to unravel the key cell-cell interactions between these cells. Deciphering the reciprocal cell-cell interactions by which liver cells imprint the sinusoidal identity on one another in vivo is not only key to understand liver biology, it also paves the way for the development of in vitro liver organoids." "An AI-driven study of mRNA subcellular localization using highly-multiplexed super-resolution in situ transcriptomics" "Alejandro Sifrim" "Department of Human Genetics, Laboratory of Reproductive Genomics" "The localization of mRNA molecules within a cell plays a crucial role in many fundamental biological processes such as cell migration, polarization, and differentiation. However, this post-transcriptional phenomenon has been understudied due to technological limitations, where only few genes could be assayed. Recently, novel technologies have been proposed for highly-multiplexed, subcellular-resolution in situ assaying of transcripts. Here we propose the application of such cutting-edge technologies on well-described biological models (fruit fly, intestinal enterocyte polarization, axonic and dendritic growth in the brain, human and mouse embryo development) to perform a large-scale study of RNA localization patterns, their molecular actors and functional consequences. To achieve this, we propose the development of novel computational analysis strategies for the automated characterization of spatial expression patterns using deep convolutional autoencoder neural networks. This will allow us to describe known and novel genes which rely on specific localization to perform their function, providing deeper insights into the molecular biology of the studied models." "SpatialConnect: linking tissue biology to the new era of single-cell spatial transcriptomics" "Martin Guilliams" "Department of Applied Mathematics, Computer Science and Statistics, Department of Translational Physiology, Infectiology and Public Health, Department of Diagnostic Sciences, Department of Biomedical molecular biology, Department of Internal Medicine and Pediatrics, Department of Biomolecular Medicine, Department of Plant Biotechnology and Bioinformatics, Department of Basic and Applied Medical Sciences" "The novel single-cell technologies allow to determine the genetic profile of each individual cell per organ. This way, researchers have recently identified novel cell types and activation states that correlate with disease progression or specific developmental stages. However, these techniques are carried out on digested tissue samples and don’t give any information on the precise location of cells. Unfortunately, to fully understand how cellular biology functions, one needs to position the cells in their spatial context. For any cell type, in any species, one needs to know which cells are in the vicinity of the cell of interest. Localising cell types is typically done by antibody-based staining and microscopy. Unfortunately, antibodies are not always available to study specific cell types. Luckily, spatial transcriptomic techniques can now determine the spatial expression of multiple RNA molecules in parallel. As this methodology is based on universal RNA detection, it is applicable across all species: in humans, mammals and plants. The next frontier in single-cell biology is therefore to resolve the precise spatial location of each single cell, so that we can finally understand the tissue architecture for each organ and identify the local cell-cell circuits that control cell fate and functional specialization in health and disease across species. With the SpatialConnect consortium we will build a cutting-edge spatial transcriptomics infrastructure at the Ghent University." "Seed dormancy in grasses: transcriptomics and genetic interaction mapping" "Koen Geuten" "Molecular Biotechnology of Plants and Micro-organisms" "Seed germination initiates the plant life cycle. In the wild this needs to be aligned with optimal environmental conditions. In the field this should not occur prematurely while still attached to the plant, but uniformly after sowing. Germination is regulated through an adaptive postponing process called seed dormancy. In crops, an ideal pattern of dormancy is strong dormancy, which is quickly lost after harvest. While we know that a conserved core mechanism controls dormancy, involving the hormonal balance between abscisic and gibberellic acid, the upstream pathways and the molecular mechanisms at play are not well understood. Yet the genetic regulation of seed dormancy in temperate grasses is highly relevant because they include the temperate cereal crops. These crops mostly lost dormancy through domestication. When germination occurs on the mother plant, this is called pre-harvest sprouting and this significantly affects the quality of the resulting flour. This quality is quantified using the Hagberg falling number in bread wheat. Crops like wheat and barley are not straightforward to use in genetic studies because of the complexity of their genomes. We therefore propose to study the genetics of seed dormancy in the temperate model grass Brachypodium for which accessions show strong dormancy and strong variation in dormancy. Specifically, we propose that the PhD student (1) characterises the transcriptome while dormancy is established or released, (2) orders known genes into pathways through CRISPR genetic interaction mapping. These approaches will provide basic knowledge about seed dormancy in temperate grasses and leads to control this trait in cereal crops." "Transcriptomics in CKD-MBD; On the road to precision medicine" "Pieter Evenepoel" "Nephrology and Renal Transplantation Research Group" "Brief background Chronic kidney disease (CKD) is a common health problem affecting 10-15% of the population. Patients with CKD suffer multiple metabolic complications, among them mineral and bone disorders (MBD). CKD-MBD results in excessive morbidity and mortality due to fractures and cardiovascular disease. Progress within the field of renal bone disease (commonly referred to as renal osteodystrophy [ROD]) is hampered by a lack of validated non-invasive diagnostic tools, as well as an incomplete understanding of the pathophysiology involved. These obstacles need to be overcome in order to establish evidence-based treatment and improve patient outcomes. This project seeks to advance the field by an in-depth investigation into the role of transcriptomics for diagnosis, prognosis, and novel treatment targets for MBD in CKD. Approach This project consists of four separate steps of discovery, validation, exploration, and clinical translation. During the discovery phase, I will identify transcriptomic signatures of clinical bone phenotypes using patient tissue and plasma samples (WP1). As a second step, I will validate my findings by investigating the effects of interventions known to induce changes in bone metabolism on our identified transcriptomic signatures (WP2), using both experimental animal models and relevant patient cohorts. As a novel and explorative study, I will investigate contributions of inter-organ cross-talk between gut and bone (WP3). Lastly, to ensure clinical translation, I will determine the usefulness of my findings for diagnostics and outcome prediction utilizing data from an international biobank and registry with long-term patient follow-up (WP4). Benefit This project aims to deliver both direct clinical utility and novel insight in this field. miRNA transcriptome analysis may not only identify novel risk biomarkers, but also provide new molecular clues potentially amenable to therapeutic targeting, and thus advance precision medicine by informing on diagnosis, prognosis and optimal treatment choices. A main deliverable of this project is to identify a transcriptomic signature in plasma for the evaluation of bone turnover (‘the liquid biopsy’); which may directly obsolete the need for an invasive bone biopsy. By providing insight into molecular pathophysiology, and exploring inter-organ cross-talk, this study will inform on novel pathways potentially amenable to therapeutic targeting."