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Kidney Week

Abstract: FR-PO021

Diverse Immune, Stromal, and Vascular Niches Along the Cortico-Medullary Axis of the Human Kidneys by Integrating 10 Different Modalities Performed on the Same Tissue Block

Session Information

Category: Augmented Intelligence, Digital Health, and Data Science

  • 300 Augmented Intelligence, Digital Health, and Data Science

Authors

  • Winfree, Seth, University of Nebraska Medical Center, Omaha, Nebraska, United States
  • Lake, Blue, Altos Labs Inc, Redwood City, California, United States
  • Melo Ferreira, Ricardo, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Fung, Anthony A., University of California San Diego, La Jolla, California, United States
  • Sabo, Angela R., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Kaushal, Madhurima, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Barwinska, Daria, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Zhang, Bo, University of California San Diego, La Jolla, California, United States
  • Gaut, Joseph, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Zhang, Kun, Altos Labs Inc, Redwood City, California, United States
  • Shi, Lingyan, University of California San Diego, La Jolla, California, 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 School of Medicine, St Louis, Missouri, United States

Group or Team Name

  • HuBMAP.
Background

Methods to delineate cell types and microenvironment using multiple modalities (DNA, RNA, protein and metabolites) across cortico-medullary axis and that are applicable in a clinical setting are needed to understand cellular basis of kidney disease.

Methods

Multimodal assays were performed on same or sequential sections using an innovative freezing and processing method on prechilled metal blocks: 1) 10X multiome (snRNAseq and snATACseq on same cell, 280µm), 2) Light microscopy (5µmH&E, 5µmPAS), 3) 10X VISIUM and H&E (spatial transcriptomics, 10µm), 4) CODEX (40plex antibody panel for nephron, immune, endothelial, stromal and kidney injury, 10µm) and H&E, 5) Label free imaging with Stimulated Raman Scattering (SRS) microscopy on the same section as CODEX to generate lipids, extracellular matrix and pseudo-H&E data. Integration of modalities used molecular, cellular, and morphological bridges across kidney functional tissue units (FTUs).

Results

The tissue processing pipeline was feasible with multiple omic and spatial technologies from the same block at multiple institutions with passing QC for each assay. 10X multiome data from ~200K nuclei (12 donors) identified more than 25 immune, 20 stromal and 20 endothelial cell identities with clear zonation along the cortico-medullary axis. Novel niches of several fibroblast and immune cells were identified using VISIUM integrated with CODEX where 3.9 million cells (5 donors, 30 cell types based) on protein markers showed distinct zonation and higher protein-to-lipid ratio and increased lipid saturation in podocytes and mesangial cells versus distal tubules were seen in CODEX-SRS mapping.

Conclusion

This work outlines the collection and construction of a multimodal atlas of the human kidney from same tissue by 1) Integrating multimodal single cell and FTU spatial map using less than half depth of a kidney biopsy is feasible and compatible in a clinical setting, 2) Identifying zonation of interstitium and vascular cell diversity along the cortico-medullary axis by multiple modalities, 3) RNA-protein-lipid-ECM-histology mapping in millions of cells, neighborhoods and FTUs.

Funding

  • NIDDK Support