# Integration of spatial and single-nucleus transcriptomics to map gene expression in the developing mouse kidney

## TL;DR

This study combines spatial and single-nucleus RNA sequencing to create a detailed map of gene activity in developing mouse kidneys.

## Contribution

The study introduces KSTAT, a new tool for analyzing spatial gene expression and cell communication in kidney development.

## Key findings

- Significant heterogeneity was found among embryonic kidney pericytes.
- The integration of data provides a high-resolution atlas of gene expression in kidney development.
- KSTAT enables prediction of cell–cell communication and pathway activity.

## Abstract

The kidney is a complex organ requiring tightly coordinated interactions between epithelial, endothelial and mesenchymal cells during development. Congenital kidney defects can result in kidney disease and renal failure, highlighting the importance of understanding kidney formation mechanisms. Advances in RNA sequencing have revealed remarkable cellular heterogeneity, especially in the kidney stroma, although relationships between stromal, epithelial and endothelial cells remain unclear. This study presents a comprehensive gene expression atlas of embryonic and postnatal kidneys, integrating single-nucleus and in situ RNA sequencing data. We developed the Kidney Spatial Transcriptome Analysis Tool (KSTAT), enabling researchers to identify cell locations, predict cell–cell communication and map gene pathway activity. Using KSTAT, we were able to uncover significant heterogeneity among embryonic kidney pericytes, providing an important resource for hypothesis generation and advancing knowledge of kidney development and disease.

Summary: Integration of spatial and single-nucleus RNA-sequencing data enables high-resolution mapping of gene expression and signaling in developing mouse kidney tissue.