Abstract: FR-OR57
A Spatial Atlas of the Human Kidneys of Cell Types and Functional Tissue Units Identified in Highly Multiplexed Immunofluorescence Images
Session Information
- Kidney Pathology: From Classic Clinicopathologic Studies to Computational Pathology
November 03, 2023 | Location: Room 109, Pennsylvania Convention Center
Abstract Time: 05:24 PM - 05:33 PM
Category: Pathology and Lab Medicine
- 1800 Pathology and Lab Medicine
Authors
- Winfree, Seth, University of Nebraska Medical Center, Omaha, Nebraska, United States
- Sabo, Angela R., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Barwinska, Daria, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Cheng, Ying-Hua, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Bowen, William S., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Ferkowicz, Michael J., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Melo Ferreira, Ricardo, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Kaushal, Madhurima, Washington University in St Louis, St Louis, Missouri, United States
- Gaut, Joseph, Washington University in St Louis, St Louis, Missouri, United States
- Eadon, Michael T., Indiana University School of Medicine, Indianapolis, Indiana, United States
- El-Achkar, Tarek M., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Jain, Sanjay, Washington University in St Louis, St Louis, Missouri, United States
Background
Kidney tissue can be defined at the cell level and at the level of unique functional tissue units (FTUs, e.g. glomeruli and tubules). FTUs are tightly linked to the spatial organization of the kidney. Several single cell transcriptomic atlases have been developed for the kidney, but a spatially anchored comprehensive atlas for cell types and FTUs based on protein expression has yet to be described.
Methods
Mesoscale sequential sections from reference kidney tissue spanning from cortex to papilla were imaged using Fusion-Phenocycler, a mesoscale highly multiplexed fluorescence imaging platform. 40 markers were used to identify major cell types (epithelial, immune, endothelial), states (stress, repair, cycling) and FTUs. An analytical pipeline was developed to perform image registration, followed by cell and FTU segmentation, labeling, mapping, and neighborhood definition.
Results
Over 4 million cells from 5 donors and 18 tissue sections were incorporated in the analytical pipeline, which resulted in the identification of over 30 cell types distributed across the kidney and localized in structures that align with FTU ontologies. A cell-based neighborhood analysis captured tubular niches unique to the renal cortex and outer or inner stripe of the medulla. This spatial segregation was complemented with interstitial niches unique to the cortex or medulla. FTU segmentations mapped the major FTUs of the kidney, including vasculature, glomeruli, several tubules and interstitium. Using sequential sections interrogated with Fusion-Phenocycler, FTU segmentation were used to generate 3D models of renal FTUs highlighting the 3D arrangement of kidney FTUs.
Conclusion
We establish a reference mesoscale spatial atlas to define anatomically and functionally distinct compartments of the kidney with single cells and FTUs. This work begins to define: 1) the 3D relationship of FTUs, including the relationship between vasculature and tubules, 2) a comprehensive map of cell-types in the human kidney and their organization into FTUs and the how cellular niches vary across the kidney. This atlas provides a cellularly resolved and spatially anchored reference to understand kidney function in health and disease.
Funding
- Other NIH Support