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Abstract: TH-OR001

Osmolarity-Dependent Gene Expression Enables Spatial Resolution of Cells from Whole Kidney Single Cell RNA Data

Session Information

Category: Fluid and Electrolytes

  • 901 Fluid and Electrolytes: Basic

Authors

  • Hinze, Christian, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
  • Karaiskos, Nikos, Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine, Berlin, Germany
  • Boltengagen, Anastasiya, Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine, Berlin, Germany
  • Himmerkus, Nina, Institute of Physiology, CAU, Kiel, Germany
  • Bleich, Markus, Institute of Physiology, CAU, Kiel, Germany
  • Potter, Steven, Cincinnati Children's Hospital, Cincinnati, Ohio, United States
  • Potter, Andrew, Cincinnati Children's Hospital, Cincinnati, Ohio, United States
  • Kocks, Christine, Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine, Berlin, Germany
  • Rajewsky, Nikolaus, Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine, Berlin, Germany
  • Schmidt-Ott, Kai M., Max Delbrueck Center for Molecular Medicine, Berlin, Germany
Background

In whole organ single cell data, spatial information of cells is usually lost but can sometimes be restored if regional marker genes are identifiable. In the kidney, certain cell types exist in regions of different microenvironments along the corticomedullary axis. For instance, cells of the proximal tubule, thick ascending limb or collecting duct extend from the serum-isosmotic renal cortex into the hyperosmotic renal medulla. We hypothesized that differences in regional gene expression between cortex, outer and inner medulla driven by different microenvironments and osmolarity-dependent genes might provide information on the spatial origin of cells in single cell data.

Methods

We obtained mouse kidneys and prepared single cell suspensions of whole kidneys as well as of microdissected cortical, outer and inner medullary tissue and applied single cell RNA sequencing. We assigned cell type information based on known marker genes and systematically analyzed regional gene expression differences and differences in expression of osmolarity-dependent genes (osmogenes) within different tubular cell types. In addition, we developed an unsupervised algorithm based on osmogene expression and used this information to spatially assign cells in whole kidney single cell suspensions.

Results

Our data show that the expression of osmogenes is tubule segment-specific and increases towards the inner medulla. We show that osmogenes are substantial drivers of gene expression differences within a given cell type along the corticomedullary axis. They harbor spatial information especially for tubule cells present in the outer and inner medulla but also to a lesser extent for other cell types. Applying our algorithm to spatially assign whole kidney single cell data reveals an imbalanced composition of regional origin of kidney cells in whole kidney single cell suspensions with a marked underrepresentation of medullary kidney cells.

Conclusion

Osmolarity-dependent genes show cell type-specific regional expression patterns and harbor spatial information of kidney cells. They can be used to spatially assign cells within whole kidney single cell RNA sequencing data and uncover a previously unrecognized regional bias in whole kidney single cell preparations.