Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease

KEY POINTS: Myofibroblasts and injury repair-related cell types were exclusively observed in polycystic kidney disease and enriched within the cyst microenvironment. Cyst-associated gene signature of 45 genes with decreased expression further away from the cysts was largely related to inflammation. Communication in low-inflamed cystic microdomains related to cellular signaling, morphogenesis, and inflammation in polycystic kidney disease. BACKGROUND: Changes in the cyst microenvironment in polycystic kidney disease (PKD) may drive progressive cyst formation. Bulk-cell and single-cell RNA sequencing have advanced our understanding of altered signaling; however, the lack of spatial information has limited our insights into local gene expression and cellular communication near cysts. METHODS: We used wild-type and Pkd1 -deficient mouse kidneys to generate 10× Genomics Visium Spatial Gene Expression datasets. Using our single-cell mouse kidney atlas and single-cell sequencing data for spot deconvolution, we enhanced resolution and estimated enriched cell types. We analyzed spatial gene expression patterns and used a cyst-centered analysis to identify cyst-associated gene signature. Cell communication near cysts was investigated, identifying key ligand-receptors. Prioritized key factors were validated in tissues. RESULTS: We observed enrichment of fibroblasts, injury repair-related cell types, and diverse immune populations in PKD. Injury repair-related cells were exclusively observed in PKD, predominantly localized within immune cell-dense regions near cysts. These cells collectively contributed to the altered gene expression profile in PKD, including cyst-associated signature genes related to inflammatory processes. Analysis of cellular communication in less-inflamed regions around cysts revealed the involvement of multiple cell types. Key ligand-receptor interactions were associated with cytokine signaling, fibrosis, cellular development, and repair. These included Angpt2 , C3 , Csf1 , Cxcl12 , Il34 , Gas6 , Il16 , Mdk , Mif , Ptn , Sfrp2 , Spp1 , Sdc1 , Tnc , Tnfsf12 , and Wnt5a . In addition, extracellular matrix (ECM) proteins implicated in immune response, ECM remodeling, cell adhesion, and cell signaling were identified, such as Adam9 , Adam10 , Col1a1, Col3a1, Col4a2, Lamb2, Lamc1, Efnb1 , Efnb2 , Thbs1, Thbs2 , and Vcam1 . Immunohistochemistry confirmed expression of Syndecan-1-Collagen IV, Midkine-Integrin β 1, CSF-1, Pleiotrophin, and Tenascin-C in cystic kidneys. CONCLUSIONS: Spatial transcriptomics in PKD revealed enrichment of (myo)fibroblasts, immune, and injury repair-related cells near cysts, creating a (pro)inflammatory and (pro)fibrotic niche. Key ligand-receptor and ECM interactions were identified and validated.