In contrast, spatial transcriptomic platforms enable measurement of whole-transcriptome mRNA expression of thousands of genes superimposed upon histological information from the same tissue section. Single-cell and single-nuclear sequencing afford indirect spatial localization. However, spatial anchoring is essential to understanding the relationship between cells and structures within specific renal microenvironments. Recently, single-cell and single-nuclear sequencing have proved major breakthroughs in the creation of a molecular atlas of the kidney ( 2– 5) by defining the transcriptomic signatures of specific cells within the kidney. Furthermore, AKI differentially affects the kidney’s diverse array of cells ( 1). This is partially due to the diverse renal milieu of heterogeneous cell types (epithelial, endothelial, fibroblast, vascular smooth muscle, resident immune, and infiltrating immune cells) that interact with each other within a cosmos of unique microenvironments. Despite important advances in understanding this disease, the pathogenesis of AKI at the cellular and molecular levels remains incompletely understood. Developing therapeutic targets to treat AKI requires a better grasp of its molecular pathogenesis. IntroductionĪcute kidney injury (AKI) is a devastating disease with a negative effect on morbidity and mortality. Spatial transcriptomic sequencing complemented single-cell sequencing by uncovering mechanisms driving immune cell infiltration and detection of relevant cell subpopulations. The regional distribution of these immune cells was validated with multiplexed CO-Detection by indEXing (CODEX) immunofluorescence. In the CLP model, infiltrating macrophages dominated the outer cortical signature, and Mdk was identified as a corresponding chemotactic factor.
Atf3 was identified as a chemotactic factor in S3 proximal tubules. Neutrophils infiltrated the renal medulla in the ischemia model.
Using single-cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. Localized regions of reduced overall expression were associated with injury pathways. To study the implications of AKI on transcript expression, we then characterized the spatial transcriptomic signature of 2 murine AKI models: ischemia/reperfusion injury (IRI) and cecal ligation puncture (CLP). The predicted cell-type spots corresponded with the underlying histopathology. We first optimized coordination of spatial transcriptomics and single-nuclear sequencing data sets, mapping 30 dominant cell types to a human nephrectomy.
However, the spatial distribution of acute kidney injury (AKI) is regional and affects cells heterogeneously. Single-cell sequencing studies have characterized the transcriptomic signature of cell types within the kidney.
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