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Abstract: SA-OR049

Combined Single Cell Epigenomic and Transcriptomic Analysis of Healthy vs. FSGS Adult Human Kidney

Session Information

Category: Glomerular Diseases

  • 1204 Podocyte Biology

Authors

  • Muto, Yoshiharu, Washington University School of Medicine, St.Louis, Missouri, United States
  • Malone, Andrew F., Washington University School of Medicine, St.Louis, Missouri, United States
  • Wu, Haojia, Washington University School of Medicine, St.Louis, Missouri, United States
  • Kirita, Yuhei, Washington University School of Medicine, St.Louis, Missouri, United States
  • Gaut, Joseph, Washington University School of Medicine, St.Louis, Missouri, United States
  • Humphreys, Benjamin D., Washington University School of Medicine, St.Louis, Missouri, United States
Background

Unraveling the pathogenesis of human FSGS requires a detailed understanding of the distinct cell types, cell specific transcriptomes, chromatin status and cell state changes in healthy and FSGS kidneys. We hypothesized that combined single nucleus RNA-seq and ATAC-seq on a single human biopsy would allow definition of FSGS-specific transcriptional changes and the DNA regulatory variation driving them, at cellular resolution.

Methods

We performed combined scATAC-seq and snRNA-seq on healthy kidney from partial nephrectomy, and on each half of a human kidney biopsy from a 42 year-old transplant patient with new onset proteinuria (2.4g) and preserved renal function (Cr 0.8 mg/dL). Histologic read on the biopsy was FSGS with 30% podocyte foot process effacement by EM. Informatics was by standard workflows.

Results

After quality control, 4,626 cells (8 clusters) and 6,459 cells (13 clusters) were included in the scATAC-seq analysis from the FSGS and healthy kidney, respectively. For snRNA-seq these numbers were 4,672 cells (13 clusters) and 4524 cells (17 clusters). A matrix of cell type specific differentially accessible regions and transcription factor motifs across cell types revealed 580 significantly enriched TF motifs in healthy, and 435 in FSGS. We generated a multimodal, harmonized kidney single cell atlas using all datasets to better understand how transcription and chromatin accessibility are regulated in FSGS. This revealed strong podocyte upregulation of PRKCI, aka atypical PKC, which is required for maintenance of slit diaphragms, and decreased podocyte – mesangial NPNT-ITGA8 signaling in FSGS. The most strongly enriched TF motifs in FSGS endothelium were for ETS family members (ETS1, ETV1,3-5, ELK3-4, ERG), which are downstream of VEGF signaling, whereas snRNA-seq from podocytes showed enhanced VEGFA expression, suggesting active podocyte-endothelial signaling in FSGS.

Conclusion

A multi-omics approach in human FSGS was successfully applied, revealing that that the cell-specific landscape of chromatin accessibility changes dramatically in human FSGS. Combining this epigenome data with snRNA-seq data allows inference of intercellular communication pathways driving disease pathogenesis.

Funding

  • NIDDK Support