Kidney Single-cell Transcriptomes Predict Spatial Corticomedullary Gene Expression and Tissue Osmolality Gradients.

Area of Science:

• Renal physiology
• Single-cell transcriptomics
• Spatial transcriptomics

Background:

• Single-cell transcriptomics offers insights into cell types, gene expression, and spatial information within tissues.
• Kidney cells exist within an osmolality gradient from cortex to medulla, potentially influencing their transcriptomes and spatial arrangement.

Purpose of the Study:

• To investigate the utility of single-cell transcriptomics for reconstructing spatial organization of kidney cells.
• To analyze gene expression patterns along the corticomedullary axis, particularly osmo-responsive genes.
• To compare transcriptomic data between wild-type and Grhl2 knockout mice to assess phenotypic impact.

Main Methods:

• Performed single-cell or single-nuclei mRNA sequencing on dissociated mouse kidneys and dissected medullary regions.
• Employed computational methods to predict cell spatial ordering and quantify osmo-responsive gene expression.
• Utilized in situ hybridization for validating spatial gene expression predictions.

Main Results:

• Single-cell transcriptomics enabled approximate reconstruction of kidney tubule cell spatial positions and prediction of corticomedullary gene expression.
• Observed gradual spatial gene expression changes and identified osmo-responsive genes following the physiological osmolality gradient.
• Found flattened expression gradients of osmo-responsive genes in Grhl2 knockout mice, correlating with reduced medullary osmolality.

Conclusions:

• Single-cell transcriptomics effectively predicts spatial gene expression along the kidney's corticomedullary axis.
• Quantification of osmotically regulated genes using this method aids in predicting physiological phenotypes.
• The study demonstrates the power of single-cell transcriptomics in dissecting kidney architecture and function.