Cross-Model Single-Cell and Spatial Atlas Reveals the Involvement of Spp1 in the Progression of PKD

Background: Hallmarks of polycystic kidney disease (PKD) have been recognized for several decades. However, it has been difficult to generate a detailed list of genes enriched specifically in cystic niches due to the inability to isolate purely cystic epithelial populations from in vitro and in vivo models. Further, the lack of spatial orientation in single cell RNA sequencing (scRNAseq) has made it difficult to identify intra- and- inter- cellular signaling networks between cystic epithelium and stromal cells. Methods: In this study, we analyzed scRNAseq data from six different mouse models of PKD, along with spatial transcriptomic data from two mouse models of PKD. We generated an integrated cross model atlas to unbiasedly analyze the stromal cell landscape of cystic kidneys. Results: Using this atlas, we identified multiple clusters of tubular epithelium that were enriched in PKD, and the differential gene expression observed in these clusters appeared to be driven primarily by the rate of disease progression and cystic status of the animal. We found Spp1 signaling was upregulated in cystic niches in PKD using both scRNAseq data and spatial analysis, with multiple signaling interaction partners predicted including fibroblasts and immune cells. We tested the functional importance of Spp1 using two PKD mouse models deficient in Spp1; we found that loss of Spp1 resulted in worsened PKD severity in the Ift88 model, whereas disease parameters improved in the Pkd1RC/RC mouse model of disease. To understand these disparate effects, we analyzed Spp1 expression and signaling in the two models using our scRNAseq atlas. Our data suggests these disparate effects might be due to differences in the cell types receiving the ligand, the receptors present, or the cell types expressing Spp1. Lastly, we identified enriched Spp1 signaling in scRNAseq data from autosomal dominant PKD (ADPKD) patients, confirming the conservation of this pathway in human disease. Conclusion: In summary, our atlas can be used to identify and test the importance of intra- and- intercellular signaling networks that are present between tubular epithelial cells, stromal cells, and immune cells, as well as their relevance to patients with cystic kidney disease. Funding: Private Foundation Support