Principles of Spatial Transcriptomics Analysis: A Practical Walk-Through in Kidney Tissue

Abstract

Spatial transcriptomic technologies capture genome-wide readouts across biological tissue space. Moreover, recent advances in this technology, including Slide-seqV2, have achieved spatial transcriptomic data collection at a near-single cell resolution. To-date, a repertoire of computational tools has been developed to discern cell type classes given the transcriptomic profiles of tissue coordinates. Upon applying these tools, we can explore the spatial patterns of distinct cell types and characterize how genes are spatially expressed within different cell type contexts. The kidney is one organ whose function relies upon spatially defined structures consisting of distinct cellular makeup. Thus, the application of Slide-seqV2 to kidney tissue has enabled us to elucidate spatially characteristic cellular and genetic profiles at a scale that remains largely unexplored. Here, we review spatial transcriptomic technologies, as well as computational approaches for cell type mapping and spatial cell type and transcriptomic characterizations. We take kidney tissue as an example to demonstrate how the technologies are applied, while considering the nuances of this architecturally complex tissue.

Keywords: kidney spatial transcriptomics; kidney transcriptomics; slide-seq; slide-seqV2; spatial transcriptomics.

FIGURE 1

Mapped cell types in human and mouse kidney tissue. In Slide-seqV2, a 10 μm cryosection of kidney tissue is melted onto an array containing 10 μm beads which bind to messenger RNA. Once library preparation is complete, spatially barcoded cDNA corresponding to each bead is assigned a cell identity using Seurat transfer learning. Example mouse, human cortex, and human medulla tissue with all cell types mapped are shown. Individual mappings of podocytes, proximal tubules, and thick ascending limbs are shown for the mouse and human cortex arrays, while vascular smooth muscle, collecting duct principal cell, and thick ascending limb are shown for the human medulla array. Scale bars = 500 μm.