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Kidney Week

Abstract: FR-OR002

Single-Cell Transcriptomics Reveals Direct Target Genes Regulated by Pkd1 in Mouse Kidneys

Session Information

Category: Genetic Diseases of the Kidneys

  • 1001 Genetic Diseases of the Kidneys: Cystic


  • Li, Xiaoyan, Mayo Clinic, Rochester, Minnesota, United States
  • Ding, Hao, Mayo Clinic, Rochester, Minnesota, United States
  • Zhou, Xia, University of Kansas Medical Center, Kansas City, Kansas, United States
  • Calvet, James P., University of Kansas Medical Center, Kansas City, Kansas, United States
  • Li, Xiaogang, Mayo Clinic, Rochester, Minnesota, United States

While PKD gene mutations are known to be responsible for ADPKD, no study has yet been performed to tour the kidneys cell-by-cell to identify genes that are directly and significantly regulated by PKD mutations in individual kidney cells, and to address whether PKD mutation in a specific renal cell type affects gene expression profiles in neighboring cells with wildtype PKD genes. The recently developed technique of single-cell transcriptome analysis (scRNA-seq) can be used to monitor global gene regulation in thousands of individual cells at the same stage of the disease in the same kidney, to provide insights into the mechanisms that determine how PKD gene deletion results in cystogenesis.


We performed scRNA-seq with kidneys from Pkd1flox/flox:Pkhd1-Cre (Pkd1-cKO) mice, in which the Pkd1 gene is selectively deleted in collecting ducts, and Pkd1flox/flox (Pkd1-WT) mice collected at postnatal day 7 (PN7) (before cyst initiation), day 14 (PN14) (after cyst onset) and day 21 (PN21) (later stage of cyst formation) (n ≥ 3 per group) to investigate the dynamic gene transcription profiles of each individual renal cell.


Our scRNA-seq analysis indicated that the gene transcription profiles are affected in several PKD associated signaling pathways and in pathways not previously studied in PKD in collecting duct (CD) cells with Pkd1 deletion. In addition, we found that the specific markers for principal cells (PCs) of the collecting duct, Aqp2 and Hsd11b2, were upregulated in Pkd1 knockout CD cell clusters, and the cell numbers of these clusters were also increased compared to the Pkd1-WT CD cluster, whereas the cell numbers of the clusters of intercalated cells (ICs) (marked by Atp6v1g3 and Atp6v0d2) were decreased, suggesting that loss of Pkd1 increases the transition of CD cells from ICs to PCs, possibly leading to renal metabolic acidosis and high blood pressure. Interestingly, we found that deletion of Pkd1 did not affect the expression levels of Pkd2 in most cell clusters, including the CD cell cluster. However, deletion of Pkd1 in CD cells did affect the gene expression profiles in cell clusters of neighboring cells.


Deletion of Pkd1 in collecting duct cells promotes cyst formation by affecting signaling pathways in CD cells and neighboring cells but not Pkd2 gene transcription in most cell clusters.


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