Abstract: FR-PO986
Transcriptome-Wide Association Study Identified USP24 as a Kidney Disease Risk Gene
Session Information
- CKD Mechanisms: From Mendel to Mars
November 03, 2023 | Location: Exhibit Hall, Pennsylvania Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: CKD (Non-Dialysis)
- 2303 CKD (Non-Dialysis): Mechanisms
Authors
- Hattori, Keita, Nagoya Daigaku Daigakuin Igakukei Kenkyuka Igakubu, Nagoya, Aichi, Japan
- Tsubota, Shoma, Nagoya Daigaku Daigakuin Igakukei Kenkyuka Igakubu, Nagoya, Aichi, Japan
- Hagita, Junichiro, Nagoya Daigaku Daigakuin Igakukei Kenkyuka Igakubu, Nagoya, Aichi, Japan
- Doke, Tomohito, Nagoya Daigaku Daigakuin Igakukei Kenkyuka Igakubu, Nagoya, Aichi, Japan
- Maruyama, Shoichi, Nagoya Daigaku, Nagoya, Aichi, Japan
Background
Established transcriptome- wide association study (TWAS) have shown lower USP24 expression in kidneys associated with higher eGFR. USP24 has been shown to deubiquitinates proteins associated with apoptosis, DNA repair, and inflammation in tumor cells. However, the role of USP24 on kidney diseases is not well described. We believe the elucidation of the function of USP24 on kidneys help to achieve the future precision medicine.
Methods
LocusZoom was used to visualize single nucleotide polymorphisms (SNPs). Correlated gene expression and pathway analysis was examined using the database of around 400 human kidneys. An established single-cell database was used to annotate cell types expressing USP24. Immunostaining of USP24 with renal tubule markers was examined in kidneys from humans and various mice models CRISPR-CAS9 system was used to generate tubule-specific USP24 deletion mice. Immunoprecipitation analysis was attempted for exploring protein-protein interaction.
Results
The SNPs highly associated with eGFR and USP24 expression in kidneys were located near the promotor regions, and these SNPs had strong linkage disequilibrium (r>0.8). The alternative allele of top SNP (rs17413465) showed a positive Z-score for eGFR GWAS, and negative beta value with USP24 expression in kidney eQTL, indicating higher USP24 expression associated with lower eGFR. Kidney single-cell data showed higher USP24 expression in renal tubule cells compared to non-tubule cells. Double immunofluorescent staining of USP24 with tubule marker, KSP validated the expression of USP24 in renal tubules. Gene correlation analysis in a large scale of human kidney samples showed enrichment of genes correlated with USP24 expression in biological pathways related to chromatin modification, and DNA repair, consistent with the previous reports. Successful insertion of the floxed allele next to USP24 with the CRISPR-CAS9 system was confirmed by genotyping PCR. The cloning of USP24 from cultured mice renal tubules and insertion of HaloTag to the C-terminal of USP24 was confirmed by subsequent DNA sequence.
Conclusion
Multi-omics analysis and experimental analysis suggested lower expression of USP24 in renal tubules might protect from kidney dysfunction by modulating chromatin status and DNA repair.