Viral hemorrhagic fever (VHF) is a group of acute diseases caused by highly infectious viruses including Ebola, Lassa, Dengue viruses. Its high mortality rate poses high risk to public health,... Show moreViral hemorrhagic fever (VHF) is a group of acute diseases caused by highly infectious viruses including Ebola, Lassa, Dengue viruses. Its high mortality rate poses high risk to public health, however, studies on VHF have been hampered due to the non-availability of proper models and incomplete knowledge on its mechanism. In order to fill this gap, this thesis presented new bioanalytical, lab-on-chip and single-cell assays to investigate changes in vascular biology and macrophage immunometabolism induced by VHF viruses. Firstly, an organ chip was developed to mimic the hemorrhagic shock syndrome caused by VHF viruses in vitro and test experimental drug candidates. In addition, acoustic force spectroscopy was applied to investigate the effect of Dengue on the cellular viscoelastic properties of endothelial cells at single-cell level. Then, metabolic profiling of endothelial cells and macrophages upon Ebola viral protein exposure was performed on bulk-level. Finally, the immunometabolism of human macrophages upon polarization was investigated by live single-cell metabolomics, setting the stage for future host-pathogen studies at single-cell level. Overall, this thesis will facilitate the understanding of VHF viruses and the development of treatment strategies. More importantly, the technologies developed here expectedly open up opportunities to combat the viruses that threaten global society. Show less
This thesis describes the research that was performed to unravel the function and development of human lymphoid tissue-resident (lt)NK cells in relation to the circulating CD56bright and CD56dim NK... Show moreThis thesis describes the research that was performed to unravel the function and development of human lymphoid tissue-resident (lt)NK cells in relation to the circulating CD56bright and CD56dim NK cells. Two methods, RNA sequencing and flow cytometry, both commonly used in the field of immunology, were employed at the bulk and single-cell level. We highlighted the complexity of single-cell analysis that could potentially lead to misinterpretation, but also the additional value over bulk approaches by uncovering the cellular heterogeneity and developmental trajectories. Finally, our workflow for single-cell analysis was applied on a patient more than 50 years after hematopoietic stem cell transplantation to perform combined analysis of the T cell phenotype and T cell receptor repertoire. Show less
Slenders, L.; Landsmeer, L.P.L.; Cui, K.; Depuydt, M.A.C.; Verwer, M.; Mekke, J.; ... ; Laan, S.W. van den, Mokry, M. 2021
Genome-wide association studies (GWASs) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into... Show moreGenome-wide association studies (GWASs) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into biological mechanisms and targets for drug discovery remains challenging. Intersecting genetic and gene expression data has led to the identification of candidate genes. However, previously studied tissues are often non-diseased and heterogeneous in cell composition, hindering accurate candidate prioritization. Therefore, we analysed single-cell transcriptomics from atherosclerotic plaques for cell-type-specific expression to identify atherosclerosis-associated candidate gene-cell pairs.\nWe applied gene-based analyses using GWAS summary statistics from 46 atherosclerotic and cardiovascular disease, risk factors, and other traits. We then intersected these candidates with single-cell RNA sequencing (scRNA-seq) data to identify genes specific for individual cell (sub)populations in atherosclerotic plaques. The coronary artery disease (CAD) loci demonstrated a prominent signal in plaque smooth muscle cells (SMCs) (SKI, KANK2, and SORT1) P-adj. = 0.0012, and endothelial cells (ECs) (SLC44A1, ATP2B1) P-adj. = 0.0011. Finally, we used liver-derived scRNA-seq data and showed hepatocyte-specific enrichment of genes involved in serum lipid levels.\nWe discovered novel and known gene-cell pairs pointing to new biological mechanisms of atherosclerotic disease. We highlight that loci associated with CAD reveal prominent association levels in mainly plaque SMC and EC populations. We present an intuitive single-cell transcriptomics-driven workflow rooted in human large-scale genetic studies to identify putative candidate genes and affected cells associated with cardiovascular traits. Collectively, our workflow allows for the identification of cell-specific targets relevant for atherosclerosis and can be universally applied to other complex genetic diseases and traits. Show less
Immunotherapy approach to cancer is only benefiting to a minority of patients. In this study, we approach cancer solutions by studying the microenvironment and its immunological signature... Show moreImmunotherapy approach to cancer is only benefiting to a minority of patients. In this study, we approach cancer solutions by studying the microenvironment and its immunological signature throughout the body by focusing on the systemic immunity with new technology like mass cytometry. By highlighting specific immunological patterns in cancer, we were able to associate responsive immune cells and positive outcome, therefore paving the way to improve immunotherapy in cancer. Show less
