Profiling APOL1 Nephropathy Risk Variants in Genome-Edited Kidney Organoids with Single-Cell Transcriptomics

Esther Liu, Behram Radmanesh, Byungha H. Chung, Michael David Donnan, Dan Yi, Amal Dadi, Kelly D. Smith, Jonathan Himmelfarb, Mingyao Li, Benjamin S. Freedman, Jennie Lin*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Background DNA variants in APOL1 associate with kidney disease, but the pathophysiologic mechanisms remain incompletely understood. Model organisms lack the APOL1 gene, limiting the degree to which disease states can be recapitulated. Here we present single-cell RNA sequencing (scRNA-seq) of genome-edited human kidney organoids as a platform for profiling effects of APOL1 risk variants in diverse nephron cell types. Methods We performed footprint-free CRISPR-Cas9 genome editing of human induced pluripotent stem cells (iPSCs) to knock in APOL1 high-risk G1 variants at the native genomic locus. iPSCs were differentiated into kidney organoids, treated with vehicle, IFN-γ, or the combination of IFN-γ and tunicamycin, and analyzed with scRNA-seq to profile cell-specific changes in differential gene expression patterns, compared with isogenic G0 controls. Results Both G0 and G1 iPSCs differentiated into kidney organoids containing nephron-like structures with glomerular epithelial cells, proximal tubules, distal tubules, and endothelial cells. Organoids expressed detectable APOL1 only after exposure to IFN-γ. scRNA-seq revealed cell type-specific differences in G1 organoid response to APOL1 induction. Additional stress of tunicamycin exposure led to increased glomerular epithelial cell dedifferentiation in G1 organoids. Conclusions Single-cell transcriptomic profiling of human genome-edited kidney organoids expressing APOL1 risk variants provides a novel platform for studying the pathophysiology of APOL1-mediated kidney disease.

Original languageEnglish (US)
Pages (from-to)203-215
Number of pages13
Issue number3
StatePublished - Mar 1 2020


  • APOL1
  • Basic Science
  • endoplasmic reticulum stress
  • focal and segmental glomerulosclerosis
  • functional genomics
  • Genetics
  • genome editing
  • induced pluripotent stem cells
  • nephron progenitor cells
  • organoids

ASJC Scopus subject areas

  • Nephrology
  • Medicine (miscellaneous)


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