Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Xenium]

Spatial transcriptomics (ST) technologies enable the mapping of gene expression to specific regions within tissues. However, current ST platforms present inherent trade-offs between resolution and throughput, which cannot be entirely addressed by a single technology. To unravel the spatiotemporal landscape of gene expression and cellular interactions during kidney injury and repair, we employed an integrated approach combining Xenium's high-resolution in situ sequencing with Visium's whole-transcriptome spatial profiling. Bilateral ischemia-reperfusion injury (IRI) was induced on the kidneys of 8-10 week-old male mice (18 minutes), and control mice underwent sham surgery. Kidneys were harvested at various time points (Sham, 4 hours, 12 hours, 2 days, 14 days, and 42 days) and preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks. Serial tissue sections from these blocks were subjected to parallel Xenium in situ sequencing and Visium whole-transcriptome spatial profiling.