Nanostring CosMx 980-plex RNA profiling of human kidney biopsy and nephrectomy

The human kidneys are comprised of multiple different cell types in a complex anatomical arragemnt that is optimal for their key functions such as waste removal, regulation of fluid and electrolyte homeostasis and production of hormones. In chronic kidney disease (CKD) this arrangement is disrupted with de-differentiation and atrophy of epithelial cells, recruitment of immune cells and activation of myofibroblasts to produce excess scarring. A better understanding of cellular phenotypes, complex intercellular communication and intracellular signaling pathways that promote CKD could lead to development of novel therapies. We applied single-cell spatial transcriptomics (CosMx Spatial molecular imaging) to human kidney biopy and nephrectomy samples from patients with IgA nephropathy (n=6), minimal change disease (n=3) and advanced pyelonephritis (n=4). FFPE biopsy or nephrectomy samples with IgA nephropathy (n=6), minimal change disease (n=3) and advanced pyelonephritis (n=4) were profiled using the Nanostring CosMx. A total of 980 transcripts were targeted. PanCK, CD45 and CD3 and DAPI were used for cell visualisation. 3 biopsy or 4 nephrectomy samples were adhered to the same microscope slide and profiled in the same run. Slides were prepared and imaged according to manufacturer protocols.