Title Abstract "Gene expression profiles as biomarkers in human biomonitoring: the study of temporal variation in gene expression and relationships with exposure and effects of environmental pollution" "As part of a preventive environment and health, there is a strong need for the development of new biomarkers of exposure and / or effects of environmental pollutants, which already give an indication of possible health effects at an early stage. Measuring gene expression in peripheral blood using microarray is an attractive concept. The underlying hypothesis is that circulating blood reflects the physiological response of an organism, and that these blood cells, lymphocytes and, more specifically, to adjust their transcriptome (gene expression profile) as a function of the state of health of the host. Monitoring gene expression profiles is therefore seen as a promising approach for the identification of sensitive biomarkers in a human biomonitoring program. This study aims to contribute to the identification of sensitive markers of adverse effects already indicate health effects at an early stage. In a first work package (WP1), a literature study was made of the capabilities and difficulties in the use as a biomarker gene expression in the human-environmental biomonitoring, and the potential benefits over traditional biomarkers. A major requirement to use gene expression in biomonitoring is that the normal transcriptional variability documented. It is important to characterize the variation at the population level, but also temporal variation at the individual level. Only if such background values U+200BU+200Bare known, can be obtained by gene expression after exposure to pollutants ascertain whether a significant increase or decrease of gene expression. In this study, the stability of gene expression in blood was in function of time was examined using data from a study population of healthy adults. Short and long-term variability in gene expression has been described and analyzed in work package 2. The emphasis on seasonality and the influence of gender. In the third part (WP 3) the impact of polluentblootstelling was examined for gene expression. The policy usefulness of gene expression profiles in the context of a human biomonitoring is discussed in monitoring network WP4. The study indicated that in an environment-health context, gene expression monitoring is promising but not yet so far developed for clinical applications. The technology appears to be robust but there is a constant evolution on th field of data processing and interpretation. The short-term and seasonal variability of individual genes was documented in a study of healthy young adults. Exposure-response relationships were observed at which the response was found often genus specific. The technology is used in a biomonitoring context as ""early warning signal"" for complex exposure, but the interpretation of the meaning of health requires further follow-up" "Development of a cell motility gene expression signature to confront with the gene expression profile of inflammatory breast carcinoma." "Molecular Imaging, Pathology, Radiotherapy & Oncology (MIPRO)" "This project represents a formal research agreement between UA and on the other hand UZA. UA provides UZA research results mentioned in the title of the project under the conditions as stipulated in this contract." "Gene duplicability and gene expression changes following gene and genome duplication" "Yves Van de Peer" "Department of Plant Biotechnology and Bioinformatics" "Gene and genome duplications are important processes that lead to novel functions and an overall increase in biological complexity. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that genes in certain functional categories are more amenable to survive duplication events than others. Although gene duplicate retention may be explained by various types of selection as well as by neutral evolution, it has been suggested that changes in gene expression could be linked, or even could be a prerequisite, for the retention of duplicated genes. However, how changes in gene expression following duplication would affect the retention of duplicated genes (i.e. duplicability) remains unknown. Because genes with different duplicabilities may show different changes in expression in response to duplications, the proposed research proposal aims at better understanding the link between changes in gene expression and gene duplicability following gene and genome duplication. We will make use of a large collection of omics datasets in angiosperms to pinpoint the evolutionary forces that apply to duplicated genes. We believe that obtaining a deep understanding in a widespread and important evolutionary process such as gene duplication will improve our knowledge of the role of duplication in evolution and its impacts on (plant) fitness, adaptation, and survival." "INFERENCE. Scalable screening platform for predicting the mode-of-action of gene perturbations based on Integrated Functional Enrichment analysis of gene expREssion aNd CEll phenotypic readouts." "Winnok De Vos" "Ghent University, Laboratory of cell biology and histology" "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." "Deciphering gene regulatory networks and cis-regulatory codes in Drosophila through a combination of genetic perturbations, digital gene expression, and bioinformatics." "Stein Aerts" "Laboratory of Computational Biology (VIB-KU Leuven)" "Gene regulation is fundamental to the execution of developmental programs, the generation of cellular and evolutionary diversity, and the aetiology of disease. Recent advances in regulatory genomics have provided insight into some aspects of transcriptional regulation, but the overall knowledge of the genomic cis-regulatory code and the emerging transcriptional networks, remains sparse. The aims of this research project are to unravel transcriptional networks and to elucidate novel aspects of the syntax and semantics of cis-regulatory logic through an integrated computaitonal end experimental approach. Using Drosophila eye development as a model system, and taking advantage of recent progress both in digital gene expression technologies and in Drosophila genetics, we will construct a compendium of transcriptome perturbations throughout the developing compound eye. Next, we will dissect this compendium in silico to predict direct regulatory interactions between transcription factors and target enhancers, and validate the predictions in vivo through enhancer-reporter assays. Novel methods realized in this project on a model system will deliver a basis for regulatory data modelling and extrapolation that is necessary to overcome the prohibitive number of experimental conditions that currently hinders the annotation of the regulatory genome in human." "Antibiotic tolerance in Escherichia coli: functional characterisation and single-cell analysis of stochastic gene expression of a new persistence gene." "Jan Michiels" "Centre of Microbial and Plant Genetics, Molecular Imaging and Photonics, NUMA, Numerical Analysis and Applied Mathematics Section" "Persistence is the phenomenon in which a fraction of an isogenic bacterial population is insensitive to extremely high antibiotics concentrations. In contrast to resistant bacteria, persisters will give rise to a population with the same antibiotics usceptibility as the original population upon inoculation in fresh medium. This persister fraction is held responsible for the resurging of infections after treatment with antibiotics. Even though the phenomenon was first described over 60 years ago, the cause of persistence as well as the precise physiological nature of these cells remains unclear. This has prevented the development of therapies specifically targeting persisters. We wish to identify proteins affecting persistence using a combined molecular and microscopic analysis." "Histological and gene expression profile in muscles of children with cerebral palsy and impact of Botulinum toxin treatment" "Ghislaine Gayan-Ramirez" "Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Research Group for Neurorehabilitation (eNRGy)" "Cerebral palsy, which is caused by a non-progressive lesion in the developing brain, represents the single largest cause of childhood disability. It is primary characterized by neural deficits and secondly by musculoskeletal problems that progress with age. Most treatments for cerebral palsy children are directed at the muscle but are hindered by insufficient knowledge on the histological and gene expression profile of the muscle alterations seen in these children especially at young ages. There is also no database on growing healthy children regarding muscle microscopic properties (e.g. fiber size and proportion) that could serve as reference values for comparison. Moreover, recent concerns have raised that intramuscular botulinum toxin type A, the first-line intervention to treat focal spasticity in these children, may compromise muscle size and quality. In this project, gene expression profile and histological assessment with a specific focus on muscle growth, extracellular matrix components and neuromuscular junction will be first addressed in children with cerebral palsy and aged-matched healthy children at different ages. Potential relations between these data and macroscopic muscle alterations (e.g. muscle volume and cross-sectional area) and neuromuscular symptoms (e.g. spasticity) will be determined to eventually define specific CP phenotypes. In addition, histological data in healthy children will be used to build a database for reference values. Second, the time course of the muscle changes occurring after botulinum toxin type A injection will be followed in the same CP child while determining histological and gene expression profile and by comparing these data to age-matched healthy children. Muscle samples of two different muscles will be collected in CP and healthy children using the sonographically guided percutaneous needle microbiopsy technique. The PhD project involves collection and handling of the muscle biopsies, fine-tuning of the protocols, performing the analysis of the muscle samples and interpreting the results in relation to the clinical symptoms. Measurements include: 1) Histology staining with immunofluorescence on muscle slice and quantification with a fluorescence microscope; 2) Gene and protein expression on muscle homogenate using general molecular biology techniques (RNA and protein extraction, RT2 PCR profiler arrays, qRT-PCR, western blot, protein assays)." "Understanding chromosome conformation, 3D nuclear DNA architecture and gene expression in human embryogenesis at single-cell resolution" "Thierry Voet" "Department of Human Genetics, Woman and Child" "Our understanding of the organisation of DNA present in a cell’s nucleus into higher order structures is rudimentary, but crucial to comprehend varying gene expression and phenotypes of cells in normal and diseased conditions. In particular in the first cell cycles of life following fertilisation drastic changes occur in the DNA architecture of nuclei as well as in gene expression, whereby cells become committed and restricted in contributing to important embryonic tissues. When such processes go awry, this may lead to loss of pregnancy or severe developmental disorders in later foetal or postnatal life.This project aims to develop and apply a novel, state-of-the-art single-cell sequencing method for studying the 3D nuclear DNA architecture as well as the expression of genes, both genome wide and of the same single cell. Application of this technology to whole human embryos in the various stages of development will provide the fundamental basis for understanding how the cells’ nuclear DNA architecture evolves during development within and across embryos, how this process is linked with gene expression and thus cellular differentiation and phenotypes, and how this process is perturbed by the numerical and structural chromosomal anomalies that often accumulate in human embryos. The technology will furthermore be portable to other tissues to understand normal organismal development, disease aetiology and ageing." "An (epi)genetic study of a complex life cycle in a warming world: gene expression patterns across metamorphosis in a damselfly" "Robby Stoks" "Ecology, Evolution and Biodiversity Conservation" "Global temperatures are rapidly rising and species traits are changing to better cope with warming. Species can adjust to warming in a plastic manner or in a genetic manner, yet the contribution of both processes to respond to recent global warming is not clear. Most animals, including damselflies that heavily react to global warming, have a life cycle with a larval stage separated from the adult stage by metamorphosis. These different life stages may inhabit different thermal microhabitats, generating different responses to global warming. The general objective of my project is therefore to advance the knowledge of thermal adaptation and thermal plasticity in animals with a complex life cycle to better understand current and future phenotypic responses to global warming. To this end, I will study Ischnura elegans damselflies from thermally differentiated populations along a latitudinal gradient, which I will experimentally expose to different temperatures in a common environment. I will compare their gene expression patterns both in the larval and in the adult stage and identify genes that are differentially expressed due to a plastic response and due to genetic adaptation. Next, I will screen for environmentally-induced, non-genetic mechanisms contributing to these differences in gene expression across metamorphosis as well as for genetic variation in regulatory regions associated with differentially expressed genes." "Gene expression analyses for the differentiation between viral and bacterial meningitis in children." "Benson Ogunjimi" "Vaccine & Infectious Disease Institute (VAXINFECTIO)" "Rapid detection of bacterial meningitis in children remains an important goal for emergency room doctors and paediatricians. The differentiation between viral and bacterial meningitis in children is mainly based on clinical scoring systems that are, however, neither 100% sensitive nor 100% specific. Additionally, adequate sampling of cerebrospinal fluid (CSF) is not always achievable. Recently, the value of gene expression analyses for infectious diseases has been illustrated in several clinical and experimental settings. Several studies were able to show a difference in gene expression between different types of influenza, between different types of bacterial infections, between tuberculosis and other inflammatory or infectious diseases in African children and between some viral infections and some bacterial infections. However, none of these studies specifically addressed the value of gene expression analyses in differentiating between viral and bacterial meningitis. In this multicentre prospective study, we will use whole blood gene expression analyses to differentiate between viral and bacterial infections in children with meningitis (N = 80). This study will add to the important clinical differentiation between viral and bacterial meningitis in children. Furthermore, we believe that the determination of the gene expression signalling in bacterial (but also viral) meningitis will elucidate the pathophysiology of this disease."