Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease

Kidney injury disrupts the intricate renal architecture and triggers
limited regeneration, and injury-invoked inflammation and fibrosis.
Deciphering molecular pathways and cellular interactions driving these
processes is challenging due to the complex renal architecture. Here, we
apply single cell spatial transcriptomics to examine ischemia-reperfusion
injury in the mouse kidney. Spatial transcriptomics reveals
injury-specific and spatially-dependent gene expression patterns in
distinct cellular microenvironments within the kidney and predicts
Clcf1-Crfl1 in a molecular interplay between persistently injured proximal
tubule cells and neighboring fibroblasts. Immune cell types play a
critical role in organ repair. Spatial analysis reveals cellular
microenvironments resembling early tertiary lymphoid structures and
identifies associated molecular pathways. Collectively, this study
supports a focus on molecular interactions in cellular microenvironments
to enhance understanding of injury, repair and disease.