Biology subjects

van Kasteren, S. I.

Publications and source records attributed to van Kasteren, S. I..

4 recordsLinked to original sources

bioRxiv2026

Physiological fatty acid uptake reveals spatial and systemic constraints on nutrient accessibility in vivo

Immune cells rely on exogenous fatty acids (FA) for membrane synthesis, bioenergetics and signalling, yet current approaches cannot accurately quantify physiological FA uptake in vivo. Here, we use cyclopropene-tagged fatty acids (cpFA) that, unlike existing FA-uptake tools, are taken up by physiologically relevant mechanisms. We measure FA uptake at single-cell resolution in vivo and uncover a previously unappreciated distinction between nutrient uptake capacity and nutrient accessibility. Although arachidonic acid exhibits the highest uptake capacity ex vivo across immune populations, it displays limited tissue accessibility in vivo, whereas palmitate is broadly accessible. In vivo nutrient-uptake measurements reveal that tissue architecture shapes nutrient accessibility, with spatial constraints in the spleen and exclusion of circulating FA, but not amino acids, from the thymus. Together, these findings identify nutrient accessibility as a distinct layer of metabolic regulation and reveal that immune-cell metabolism is shaped by spatial and systemic constraints on nutrient access HighlightsO_LINutrient accessibility is a distinct layer of metabolic regulation C_LIO_LIPhysiological FA uptake differs from ex vivo uptake capacity C_LIO_LISpatial and systemic factors govern fatty-acid accessibility C_LIO_LITissue context shapes immune-cell metabolism in vivo C_LI In briefUsing bioorthogonal FA to quantify physiological nutrient uptake in vivo, Wang et al. show that nutrient accessibility is distinct from nutrient uptake capacity. Tissue architecture and systemic FA distribution create spatial constraints on nutrient access, revealing an underappreciated layer of metabolic regulation in immune cells.

immunology↗

bioRxiv2024

Using BONCAT To Dissect The Proteome Of S. aureus Persisters

Bacterial persisters are a subpopulation of cells that exhibit a transient non-susceptible phenotype in the presence of bactericidal antibiotic concentrations. This phenotype can lead to the survival and regrowth of bacteria after treatment, resulting in relapse of infections. As such, it is also a contributing factor to antibacterial resistance. Multiple processes are believed to cause persister formation, yet identifying the proteins expressed during the induction of the persister state has been difficult, because the persister-state is rare, transient and does not lead to genetic changes. In this study, we used Bio-Orthogonal Non-Canonical Amino Acid Tagging (BONCAT) to label, and retrieve, the proteome expressed during the persister state for different strains of methicillin-resistant Staphylococcus aureus. After incubating antibiotic-exposed bacteria with the methionine ortholog L-azidohomoalanine to label the proteins of persister cells, we retrieved labeled proteins using click chemistry-pulldown methodology. Analysis of the retrieved proteome fraction of Methicillin resistant Staphylococcus aureus (MRSA) and Vancomycin resistant Staphylococcus aureus (VRSA) under challenge with {beta}-lactam and fluoroquinolone antibiotics with Label Free Quantification - Liquid chromatography mass spectrometry (LFQ-LCMS) based proteomics reveals the upregulation of proteins involved in stringent response, cell wall biosynthesis, purine metabolism, ppGpp biosynthesis, two component systems (TCS), lipid metabolism, ABC transporters, D-alanine biosynthesis and L-proline degradation. Conversely, we observed a decline of proteins associated with amino acid biosynthesis and degradation, protein biosynthesis, protein modification, and carbohydrate metabolism, among others. These findings indicate that modification of translational activity in persister cells enables bacterial cells to induce an active defense to survive antibiotic pressure.

microbiology↗

bioRxiv2020

Single Cell Analysis of Regions of Interest (SCARI) using a novel photoswitchable tag

The functional activity and differentiation potential of cells is determined by their interaction with surrounding cells. Approaches that allow the unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a trade-off between spatial resolution and cell profiling depth. Here, we developed a photoswitch-based technology that allows the isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran)-cage coupled to nanobodies allowed photoswitching of cells in areas of interest with low-intensity violet light and without detectable phototoxicity. Single cell RNA sequencing of spatially defined CD8+ T cells was used to exemplify the feasibility of identifying location-dependent cell states at the single cell level. Finally, we demonstrate the efficient labeling and photoswitching of cells in live primary human tumor tissue. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples.

bioengineering↗

bioRxiv2018

Bioorthogonal Antigens Allow The Study Of Intracellular Processing And Presentation Of Post-Translationally Modified Antigens

Proteolysis is fundamental to many biological processes. In the immune system, it underpins the activation of the adaptive immune response: degradation of antigenic material into short peptides and presentation thereof on major histocompatibility complexes, leads to activation of T-cells. This initiates the adaptive immune response against many pathogens.

immunology↗