Analyzing cell type-specific dynamics of metabolism in kidney repair

To overcome the limitations of current metabolic analysis we present an advanced high spatial metabolomics approach using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We show that this method can map cell type-specific dynamic changes in the central carbon metabolism, as well as the contribution of different nutrients to energy metabolism in a complex heterogenous tissue architecture such as the kidney. Combined with multiplexed immunofluorescence staining, we can detect metabolic changes and nutrient partitioning in targeted cell types as demonstrated in a bilateral renal ischemia/reperfusion injury (bIRI) model. Our method was designed to use different 13C-isotope-labeled nutrients that allowed tracing of spatio-temporal incorporation of the 13C-isotopes into the main intermediates of glycolysis and the TCA cycle. We applied a tissue culture system, in which 350 µm-thick vibratome slices of fresh mouse kidney. During incubation, parallel introduction of different 13C-isotope-labeled nutrients to the tissue culture medium at different time points. Negative ion-mode MALDI-MSI at subcellular resolution (i.e. pixel size of 5 × 5 µm2) was applied to detect metabolites and (phospho)lipids from the harvested tissues. The exported and processed datasets are provied here. Due to the large size of all raw data, some ROIs from measured samples are provied here to show information of 13c-labeled metabolites and the quality of spectrum. <br>