van den Berg, B. M. | Search bioRxiv

bioRxiv2025

Spatial metabolomics reveals persistent localized niche-specific metabolic failure in kidneys following ischemia-reperfusion injury

After acute kidney injury (AKI), the persistence of failed repair proximal tubule (FR-PT) cells is postulated to hamper kidney regeneration and increase the risk of chronic kidney disease. This fibrotic shift likely depends on microenvironmental interactions, which remain largely unstudied. To investigate this, we mapped the spatial metabolic architecture of post-ischemic kidneys using an untargeted semi-quantitative spatial metabolomics (qMSI) approach, integrated with high-resolution spatial transcriptomics. Unsupervised neighborhood clustering of qMSI data revealed distinct microenvironments. Lipidome profiles identified diffusely spread areas with persistent injury markers surrounding FR-PT cells. These niches exhibited decreased linoleic acid and elevated succinic acid levels, even in epithelial cells that appeared otherwise healthy. Corresponding transcriptomic profiles confirmed downregulation of oxidative phosphorylation and fatty acid {beta}-oxidation in these regions. Together, these findings point towards niche-specific metabolic failure and persistent mitochondrial dysfunction in areas considered healthy, underscoring the need to prioritize metabolic resuscitation to prevent long-term consequences of AKI.

biochemistry↗

bioRxiv2024

Spatial quantitative metabolomics enables identification of remote and sustained ipsilateral cortical metabolic reprogramming after stroke

Mass spectrometry imaging (MSI) has become a cornerstone of spatial biology research. However, various factors that are intrinsic to the technology limit quantitative capacity of MSI-based spatial metabolomics and thus reliable interpretation. Here, we developed a quantitative MSI workflow (Q-MSI), based on isotopically 13C-labeled yeast extract as internal standards, to overcome these pitfalls. Using brain and kidney tissue, we demonstrate that this approach allows for (absolute) quantification of hundreds of metabolites and lipids. Applying our workflow to a stroke model allowed us to not only map metabolic remodeling of the infarct and peri-infarct area over time, but also discover hitherto unnoted remote metabolic remodeling in the histologically unaffected ipsilateral sensorimotor cortex. At day 7 post-stroke, increased levels of neuroprotective lysine and reduced excitatory glutamate levels were found compared to the contralateral cortex. By day 28 post-stroke, lysine and glutamate levels had been normalized, while decreased precursor pools of UDP-GlcNAc and linoleate persisted that have previously been associated with vulnerability. Importantly, traditional normalization strategies not employing internal standards were unable to visualize these differences. Using 13C-labeled yeast extracts as a normalization strategy establishes a new paradigm in quantitative MSI-based spatial metabolomics that greatly enhances reliability and interpretive strength.

biochemistry↗