Identification of Early Transcriptional Markers of Autosomal Dominant Polycystic Kidney Disease Cystic Epithelial Cells

Study objective: Mechanisms driving autosomal dominant polycystic kidney disease (ADPKD) cystogenesis, a hallmark of this lethal monogenic disease, are not well understood and reliable biomarkers are scarce. We sought to explore transcriptional changes in ADPKD models with suppressed and non-suppressed cystic phenotype to explore mechanisms driving ADPKD cystogenesis and identify potential biomarkers in disease progression. Hypothesis: Early-stage kidneys from a model in which cystic disease is suppressed by expression of the polycystin-1 C-terminal tail (CTT), a 200 amino acid portion of the larger polycystin-1 protein that is dysregulated in ADPKD, exhibit a differential transcriptional profile from early-stage kidneys in a non-suppressed model. Methodology: Orthologous doxycycline-inducible Pkd1fl/fl;Pax8rtTA;Teto-Cre ADPKD C57BL/6N mouse models expressing CTT ( Pkd1-KO+CTT) or not ( Pkd1-KO) were induced between 4-6 weeks and aged to 10 weeks. We performed single cell RNA sequencing (scRNA-seq) with single cell kidney suspensions from biological replicates that were pooled and processed for cDNA synthesis and library preparation with 10X Chromium technology. Reads were aligned using the 10X Genomics CellRanger pipeline and further processed using the gene cell-inverse cell frequency (gf-icf) pipeline. Data: Clusters corresponding to tubule segments were identified using established annotations. Several novel clusters defined by expression of multiple markers, including Jarid2, Tmtc2, and Filip1l, were identified in the Pkd1-KO model. These clusters were sparsely populated in Pkd1-KO+CTT samples, suggesting that they may correspond to cyst epithelial cells that are suppressed by CTT expression. Each of these novel clusters included cells whose markers identified them from distinct tubule segments (e.g. Sglt2, Umod, S100g), suggesting that cells of different segments are clustered together by virtue of sharing the putative cyst cell transcriptional signature. Importantly, at 10 weeks there are no significant differences in disease endpoints such as kidney weight to body weight, serum creatinine, blood urea nitrogen, or kidney morphology between the Pkd1-KO+CTT and Pkd1-KO models, suggesting that the cells assigned to the cystic epithelial cell clusters exhibit early identifiable differences in transcriptional programming. Summary of results: scRNA-seq at an early timepoint reveals novel transcriptional makers of putative cystic epithelial cells. The protein expression levels of individual markers are being assessed. Conclusions: These results suggest that there are epithelial cells early in disease progression exhibiting a unique transcriptional signature that may elucidate the mechanisms of cyst formation and that may provide new candidate biomarkers. This work was funded in part by the NIH F31 DK135356 (VR), NIH RC2 DK120534-01 (MJC), PR191158 Department of Defense (MJC), and PKD 905682 Foundation for Research in Polycystic Kidney Disease Research Grant (MJC). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.