Abstract: TH-PO1091
High-Resolution, Multimodal, Large-Scale Three-Dimensional (3D) Mapping of the Kidney Benchmarks Cell Distances and Niche Distributions
Session Information
- Pathology and Lab Medicine
October 22, 2026 | Location: Exhibit Hall A, Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Pathology and Lab Medicine
- 1700 Pathology and Lab Medicine
Authors
- Sabo, Angela R., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Sohail, Mohammad Ahsan, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Ferkowicz, Michael J., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Poudel, Chetan, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Winfree, Seth, QCDx Inc., Farmington, Connecticut, 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
- Eadon, Michael T., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Dagher, Pierre C., Indiana University School of Medicine, Indianapolis, Indiana, United States
- El-Achkar (Ashkar), Tarek M., Indiana University School of Medicine, Indianapolis, Indiana, United States
Background
Kidney tissue can be defined at various scales, ranging from single cell level to functional tissue units (FTUs, e.g. glomeruli, tubules). This unique organization tightly links spatial distribution to complex functions. While the basic organization has been studied in 2D, a spatially anchored, 3D mapping based on protein expression at the cell level is not yet fully established.
Methods
Reference kidney nephrectomies were imaged using techniques spanning all modalities of 3D spatial protein imaging: 1) 3D second harmonic generation and confocal multiplexed fluorescence imaging (8 targets; 50µm section; 12 cell types) 2) 3D highly multiplexed fluorescence imaging of serial sections with post-hoc registration and rendering (45 targets; 40-300 µm total thickness; 30 cell types) 3) highly multiplexed 3D confocal imaging with optical sectioning (18 targets; 50 µm section; 17 cell types) and 4) light sheet microscopy (4 targets; 300 µm section). Cell segmentation was performed, and clustering was implemented in R using Louvian method. Cells were annotated based on average marker intensity. Volume rendering and distances meausurements in 3D were done using Imaris.
Results
The kidney cells and FTU organization including collagen and vessel density distributions were mapped in 3D from cortex to medulla. Distances between various cell types and FTUs were measured and established. Unique spatial associations between resident immune cells and specialized/injured epithelium and vascular structures were defined distinctly in the cortex and medulla across various scales. Tracing of nephron units showed distinct spatial organization in the cortex and a large area of close association and possible lateral contact between thick ascending limbs and glomeruli. The medullary ray in the cortex is the largest area of potential communication between indiviual nephron units. The distribution of cell distances and associations within neighborhoods were shifted when comparing 2D and 3D methods.
Conclusion
By showing unique spatial associations between cells and FTUs, high-resolution, large-scale 3D protein mapping of the kidney provides a platform for understanding physiology and interpreting changes during kidney disease. The provided measurements and estimations could set benchmarks for use in studying kidney tissue and the appropriateness of implimentating 2D vs 3D methodologies.
Funding
- NIDDK Support