CODEX Multiplex Imaging Uncovers Unique Cell Types, States, and Niches in Health and Disease
- Technology-Based Approaches in Nephrology
November 03, 2022 | Location: W308, Orange County Convention Center‚ West Building
Abstract Time: 04:57 PM - 05:06 PM
Category: Pathology and Lab Medicine
- 1700 Pathology and Lab Medicine
- Barwinska, Daria, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Sabo, Angela R., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Winfree, Seth, University of Nebraska Medical Center, Omaha, Nebraska, United States
- Gulbronson, Connor J., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Eadon, Michael T., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Williams, James C., Indiana University School of Medicine, Indianapolis, Indiana, United States
- El-Achkar, Tarek M., Indiana University School of Medicine, Indianapolis, Indiana, United States
Group or Team Name
Co-Detection by indEXing (CODEX) multiplex imaging is a new and powerful tool for imaging many protein markers on one tissue specimen. A challenge in applying this technology on human kidney tissue is to establish a robust analytical pipeline to analyze the resultant multidimensional large-scale data and compare multiple datasets.
We imaged human cortical tissue from healthy reference and renal disease (AKI, Lupus, CKD, IgA) specimens with 38 different antibodies, including epithelial, immune, and injury markers. Segmentation of nuclei and unsupervised analysis, classification and visualization were performed using a customized open-source software tool: Volumetric Tissue Exploration and Analysis (VTEA). Additional analysis to combine datasets in a single analytical space was performed using R and visualized in VTEA. We also performed cell centric neighborhood analysis to define spatially relevant cell niches.
In healthy tissue, unsupervised clustering and classification of cell types not only identified the major structures in the renal cortex, but also unique subsets of both proximal tubules (PTs) and thick ascending limbs (TALs). PTs were consistently found to have a unique subset that was positive for THY1 (CD90), which is a marker of cell differentiation. PT and TALs cells also showed a subset that was positive for PROM1 (CD133), which is a marker associated with repair. Immune cell clusters were defined using various markers such as CD45, CD68, CD11C, CD206, CD20 and CD3. In kidney disease, we observed a marked alteration in the abundance and distribution of epithelial and immune cell subtypes. Neighborhood analysis showed unique cell niches that were altered in disease. Specifically, cell niches enriched in THY1+ PTs were markedly diminished, whereas immune-rich niches expanded with disease.
We established a unique analytical pipeline for CODEX multiplexed imaging data that can be utilized to define various cell types in the human kidney in health and disease and compare between specimens. Our findings highlight unique cell niches and uncover alteration of specialized epithelial and immune cell types with disease, thereby identifying potential novel targets for therapy.
- NIDDK Support