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Abstract: FR-PO159

Comprehensive Transcriptomic Mapping of Baseline and Pathological Human Kidneys at Single-Cell Resolution

Session Information

Category: CKD (Non-Dialysis)

  • 1903 CKD (Non-Dialysis): Mechanisms

Authors

  • Subramanian, Ayshwarya, Broad Institute, Cambridge, Massachusetts, United States
  • Vernon, Katherine Anne, Brigham and Women's Hospital, Boston, Massachusetts, United States
  • Slyper, Michal, Broad Institute, Cambridge, Massachusetts, United States
  • Waldman, Julia, Broad Institute, Cambridge, Massachusetts, United States
  • Keller, Keith H., Brigham and Women's Hospital, Boston, Massachusetts, United States
  • Zhou, Yiming, Brigham and Women's Hospital, Boston, Massachusetts, United States
  • Dionne, Danielle, Broad Institute, Cambridge, Massachusetts, United States
  • Nguyen, Lan Thi, Broad Institute, Cambridge, Massachusetts, United States
  • Weins, Astrid, Brigham and Women's Hospital, Boston, Massachusetts, United States
  • Rosen, Orit, Broad Institute, Cambridge, Massachusetts, United States
  • Regev, Aviv, Broad Institute, Cambridge, Massachusetts, United States
  • Greka, Anna, Harvard Medical School, Boston, Massachusetts, United States

Group or Team Name

  • HCAKidney
Background

The heterogeneity of cell types and states in human tissues pose challenges for precision medicine and targeted therapeutics as not all patients present the same disease phenotype or treatment response. Most of our current understanding of cell-types comes from comprehensive histological observations of surface proteins and other molecules, gathered over the decades. However, recent advances in single cell and spatial genomics, such as single-cell RNA-Seq, now allow us to classify large numbers of individual cells by their profiles. In this study, as part of the Human Cell Atlas initiative, we aim to catalog cell-types in human kidney specimens obtained from healthy donors and patients with kidney diseases.

Methods

Discarded tissue from tumor nephrectomies was subjected to single-cell dissociation or single-nucleus isolation, the latter applicable to frozen tissue as well. Droplet-based single-cell or single nucleus RNA-Seq libraries were prepared, PCR amplified and sequenced. Single-cell profiles were clustered, and clusters were annotated post hoc based on known marker genes.

Results

We identified over 10 known cell-types, from around 2,000 cells from discarded healthy tissue. Recovered cell-types included both renal parenchymal and immune cells. Heterogeneity was observed in collecting duct and proximal tubular cells. Data-driven markers were inferred for the cell-types.

Conclusion

We have established working single-cell dissociation protocols optimized specifically for human kidney specimens with paired reproducible analyses and insights. Proportions of cell-types will be reported with more confidence as we gather more samples, and in comparison with specific disease phenotypes.

Funding

  • Private Foundation Support