Kidney Week

Abstract: FR-PO943

Single Cell Transcriptional Profiling of Kidney Organoids Identifies a Novel Gene Activation Signal in Human Glomerular Disease

Session Information

• Development, Stem Cells, Regenerative Medicine - II
  October 26, 2018 | Location: Exhibit Hall, San Diego Convention Center
  Abstract Time: 10:00 AM - 12:00 PM

Category: Development, Stem Cells, and Regenerative Medicine

• 501 Development, Stem Cells, and Regenerative Medicine: Basic

Authors

• Harder, Jennifer L., University of Michigan, Ann Arbor, Michigan, United States

Jennifer L. Harder,

• Menon, Rajasree, University of Michigan, Ann Arbor, Michigan, United States

Rajasree Menon,

• Otto, Edgar A., University of Michigan, Ann Arbor, Michigan, United States

Edgar A. Otto,

• Zhou, Jian, Princeton University, Princeton, New Jersey, United States

Jian Zhou,

• Eddy, Sean, University of Michigan, Ann Arbor, Michigan, United States

Sean Eddy,

• Nair, Viji, University of Michigan, Ann Arbor, Michigan, United States

Viji Nair,

• Hodgin, Jeffrey B., The University of Michigan, Ann Arbor, Michigan, United States

Jeffrey B. Hodgin,

• Wiggins, Roger C., University of Michigan Health System, Ann Arbor, Michigan, United States

Roger C. Wiggins,

• Troyanskaya, Olga, Princeton University, Princeton, New Jersey, United States

Olga Troyanskaya,

• Freedman, Benjamin S., University of Washington, Seattle, Washington, United States

Benjamin S. Freedman,

• Kretzler, Matthias, U.Michigan, Ann Arbor, Michigan, United States

Matthias Kretzler,

Background

Proposed mechanisms for podocyte (PC) compensation in kidney disease include dedifferentiation and non-PC transdifferentiation. Identifying genes expressed during PC development may reveal novel aspects of pathogenesis and progression of glomerular disease. Analysis of developing human kidneys is limited by availability and relative rarity of PCs in tissue. Kidney organoids generated from human stem cells offer a novel ex vivo system to explore gene expression during PC development.

Methods

We generated kidney organoids from human stem cells and performed single cell RNA sequencing. Over 10,000 transcriptomes were combined and clustered using an unsupervised algorithm. Single cell transcriptomes from organoids and developing human kidneys were combined to create developmental trajectories for multiple cell lineages originating from central progenitors. Genes expressed uniquely in cell clusters were identified and expression was quantified in bulk transcriptomic data from microdissected glomeruli isolated from humans with kidney disease (ERCB) and analyzed relative to eGFR and proteinuria.

Results

Cell clustering revealed two putative groups of PCs. Trajectory analysis confirmed both groups mapped to the same cell lineage expressing NPHS2 but separated along the spectrum into early and mature. Early and mature clusters uniquely expressed 69 and 169 genes respectively. The cumulative expression score for the early (but not mature) PC gene set was significantly upregulated (p<0.01) in diseased glomerular tissue relative to living donors. Intriguingly, the early PC set contained genes previously unrecognized as being involved in kidney disease including LYPD1 and PRSS23, each of which correlated with proteinuria and inversely correlated with eGFR.

Conclusion

Developing PCs in kidney organoids express a group of genes that are not expressed in later stage PCs. Expression of these genes in the human adult glomerulus is associated with the presence of kidney disease, suggesting reactivation of a developmental transcriptional program in cells in the glomerulus. This approach identifies the beneficial role of single cell transcriptional profiling of kidney organoids in identification of novel biomarkers of kidney disease.

Funding

• NIDDK Support