Abstract: SA-PO0636
Transcriptomic Analysis of Multiple CLCN5 Cell Lines Reveals Disruption of Podocyte Cytoskeleton Dynamics and Identifies Potential Therapeutic Targets
Session Information
- Monogenic Kidney Diseases: Tubular and Other
November 08, 2025 | Location: Exhibit Hall, Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Genetic Diseases of the Kidneys
- 1201 Genetic Diseases of the Kidneys: Monogenic Kidney Diseases
Authors
- Lane, Brandon M., Duke University School of Medicine, Durham, North Carolina, United States
- Chryst-Stangl, Megan, Duke University School of Medicine, Durham, North Carolina, United States
- Wu, Guanghong, Duke University School of Medicine, Durham, North Carolina, United States
- Spruill, Caleb R, East Carolina University, Greenville, North Carolina, United States
- Gbadegesin, Rasheed A., Duke University School of Medicine, Durham, North Carolina, United States
Background
Pathogenic variants in the gene encoding Chloride Voltage Gated Channel 5 (CLCN5) are generally associated with Dent disease, a tubular disorder connected to nephrocalcinosis. However, some variants have been reported to produce podocytopathy phenocopies. We have shown that the truncating CLCN5 variant p.Gly400ValfsTer29 causes nephrotic syndrome phenotypes in patients and decreases iPSC-derived podocyte endocytosis and viability. These same phenotypes were observed in immortalized podocyte cell lines with reduced CLCN5 expression, but the exact pathogenic mechanisms are still unknown. To identify disease mechanisms and therapeutic targets, we performed unbiased transcriptomic analysis of patient-derived iPSC podocytes as well as immortalized podocyte cell lines with reduced CLCN5.
Methods
We performed RNA-Seq analysis of immortalized podocyte cell lines with lentiviral shRNA mediated CLCN5 knockdown (KD) and controls as well as patient-derived iPSC podocytes from 2 affected CLCN5 patients and 2 of their unaffected family members. All samples were evaluated in triplicate.
Results
CLCN5 was the most downregulated gene in both patient-derived iPSC podocytes and CLCN5 KD podocytes compared to their respective controls (LogFC of 3.3 and 2.5 and p-values of 1.05E-69 and 1.89E-26 respectively). There were 608 differentially expressed genes in common between iPSC-derived and CLCN5 KD podocytes compared to their respective controls, with 75 having an adjusted p-value less than 0.05. Gene Ontology (GO) pathway analysis of both groups revealed a downregulation of actin cytoskeleton pathways and an upregulation of synaptic membrane and GABA receptor pathways. The top downregulated cytoskeleton genes include SYNPO2L, ACTN1, and MYH9. The top upregulated genes include several GABA receptor, integrin, and cadherin genes.
Conclusion
The downregulation of genes involved in the regulation of actin cytoskeleton regulation in CLCN5 defective podocytes fits well with the known endocytosis defects and provides potential therapeutic targets. The upregulation of alternative chloride channel-related genes is likely a response to the loss of CLCN5 activity and suggests that this may be an additional therapeutic strategy.
Funding
- NIDDK Support