Transcriptomic Analysis of Pkd2-Deficient Kidneys Shows Altered Metabolic and Cytoskeleton Pathways Similar to Pkd1 Models and Evidence of an Increased Inflammatory Response
- Genetic Diseases: Cystic - Basic
November 03, 2023 | Location: Exhibit Hall, Pennsylvania Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Genetic Diseases of the Kidneys
- 1201 Genetic Diseases of the Kidneys: Cystic
- Outeda, Patricia, Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States
- Menezes, Luis F., National Institutes of Health, Kidney Disease Branch/National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, Maryland, United States
- Basquin, Denis, Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States
- Watnick, Terry J., Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is characterized by fluid-filled cysts and progressive enlargement of the kidney. Mutations in either PKD1 or PKD2 genes, encoding polycystins 1 and 2, are responsible for the disease. Despite advances in understanding polycystins structure and function, how mutations in PKD genes lead to cystogenesis is still unknown. While dozens of studies have investigated the transcriptome of human and mouse PKD1 mutant kidneys, none focused on PKD2 deficient kidneys. Here we report RNAseq from Pkd2 cystic kidneys from a slow progression model.
We induced Pkd2 deletion at P27 (postnatal day 27) in a strain that inactivates Pkd2 in the renal epithelium. We isolated RNA from kidneys at P125 from 10 males and 10 females (5 Pkd2fl/fl; Pax8rtTA-Cre (+) and 5 littermate Pkd2fl/fl; Pax8rtTA-Cre (-) per set) and sequenced using and Illumina NovaSeq 6000 S4 system. Sequence reads were mapped to mm10 mouse genome and counted using STAR. Differential gene expression and pathway analyses were done in R using DESeq2, clusterProfiler and fgsea.
Transcriptomic analysis identified ~1976 significantly differentially expressed (DE) genes (adjusted p < 0.05), of which 622 were only DE in males and 229 in females. In both sexes, injury markers were up-regulated and pathway analyses suggested increased chemokine activity. Gene set enrichment analysis suggested enrichment of up-regulated genes in inflammatory pathways and down-regulated genes in oxidative phosphorylation and fatty acid metabolism, similar to what is observed in Pkd1 knockout kidneys. Approximately 700 DE genes in Pkd2 knockout kidneys were also DE in Pkd1 knockout kidneys. Pathway analysis of DE genes in both Pkd1 and Pkd2 models showed enrichment of genes involved in cytoskeleton, actin biding and encoding proteins in the kinetochore.
The data suggest an increased inflammatory response in Pkd2 knockout kidneys and some of the transcriptional changes previously reported in Pkd1. The presence of injury markers suggests that some of these differences could be secondary to kidney injury. Meta-analysis of Pkd1 and Pkd2 knockout kidneys implicate changes in cytoskeleton and actin signaling as common pathways.