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Biology subjects

van der Peet, M.

Publications and source records attributed to van der Peet, M..

3 recordsLinked to original sources

Reduced triacylglycerols and lipid droplets are associated with resilience to Alzheimers disease

IntroductionWhile it has become clear that alterations in lipid metabolism are associated with AD, it is unclear how they contribute to both cognitive decline and the pathophysiology of AD. MethodsWe performed lipidomics and activity-based protein profiling in the frontal cortex of control, AD and resilient donors, i.e. individuals with AD pathology without cognitive decline. Subsequently we integrated these data using multi-omics factor analysis and correlated the multi-omics profiles to disease and clinical parameters. ResultsThe most pronounced alterations in lipids were in the {omega}6-derived oxylipins, which were particularly increased in the AD patients. Both triacylglycerols (TAGs) and lipid droplets were more abundant in the AD donors compared to the resilient donors. Enzyme activities showed a similar direction in the AD and resilient donors, including decreased activity of ABHD6. Multi-omics factor analysis showed that increased oxylipins, loss of inhibitory cells, synaptic genes and genes related to the inflammatory response were associated with A{beta} plaque load in both AD and resilient donors. ConclusionOur multi-omics data show a response associated with A{beta} load shared among AD and resilient donors and, for the first time, reduced lipid droplets in resilient donors.

neuroscience↗

mzQuality: A tool for quality monitoring and reporting of targeted mass spectrometry measurements

Analyzing metabolites using mass spectrometry can offer valuable insight into an individuals health or disease status. However, various sources of experimental variation can affect the data, making robust quality control essential. In this context, we introduce mzQuality, a user-friendly software tool designed to evaluate and correct technical variations in mass spectrometry-based metabolomics data. MzQuality offers key quality control features, such as batch correction, outlier identification, and analysis of signal-to-noise ratios. It supports any peak-integrated processed data independent of vendor software and does not require the user to have any programming skills. We demonstrate the functionality of mzQuality with a data set of 419 samples measured across six batches, in which mzQuality effectively minimized experimental variation, ensuring the datas readiness for statistical analysis and biological interpretation. With customizable settings, mzQuality can be seamlessly integrated into research workflows to produce more accurate and reproducible metabolomics data.

bioinformatics↗

CellEKT: A robust chemical proteomics workflow to profile cellular target engagement of kinase inhibitors

The human genome encodes 518 protein kinases that are pivotal for drug discovery in various therapeutic areas such as cancer and autoimmune disorders. The majority of kinase inhibitors target the conserved ATP-binding pocket, making it difficult to develop selective inhibitors. To characterize and prioritize kinase-inhibiting drug candidates, efficient methods are desired to determine target engagement across the cellular kinome. In this study, we present CellEKT (Cellular Endogenous Kinase Targeting), an optimized and robust chemical proteomics platform for investigating cellular target engagement of endogenously expressed kinases using the sulfonyl fluoride-based probe XO44 and two new probes ALX005 and ALX011. The optimized workflow enabled the determination of the kinome interaction landscape of covalent and non-covalent drugs across over 300 kinases, expressed as half maximum inhibitory concentration (IC50), which were validated using distinct platforms like phosphoproteomics and NanoBRET. With CellEKT, target engagement profiles were linked to their substrate space. CellEKT has the ability to decrypt drug actions and to guide the discovery and development of drugs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/616061v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@5dd891org.highwire.dtl.DTLVardef@1353379org.highwire.dtl.DTLVardef@1c67382org.highwire.dtl.DTLVardef@1c964eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗