Abstract: SA-PO135

Alternative Splice Isoforms in Human Diabetic Kidney Disease (DKD)

Session Information

Category: Diabetes

  • 503 Diabetes Mellitus and Obesity: Translational

Authors

  • Menon, Rajasree, University of Michigan, Ann Arbor, Michigan, United States
  • Nair, Viji, University of Michigan, Ann Arbor, Michigan, United States
  • Godfrey, Brad A., University of Michigan, Ann Arbor, Michigan, United States
  • Eichinger, Felix H., University of Michigan, Ann Arbor, Michigan, United States
  • Guan, Yuanfang, University of Michigan, Ann Arbor, Michigan, United States
  • Caramori, Maria Luiza A., University of Minnesota, Minneapolis, Minnesota, United States
  • Mauer, Michael, University of Minnesota, Minneapolis, Minnesota, United States
  • Kretzler, Matthias, University of Michigan, Ann Arbor, Michigan, United States
Background

mRNA transcript splice isoforms add a substantial complexity to gene regulation, but their expression and differentiated function have not been explored in renal disease. The goal of this study was to identify whether or not alternative splice isoforms were expressed in biopsy tissues from patients with diabetes.

Methods

TruSeq RNA Access based mRNA-Sequencing was performed on research kidney biopsy samples from 10 living kidney donors and 18 research volunteers with Type 1 diabetes (T1D) followed by weighted correlation network analysis (WGCNA) of the top 5,000 highly expressed variable transcripts. T1D patients were classified as fast-(n=10) and slow-progressors (n=8) for DKD. Alternative splice isoforms, defined by UniProt annotation, had to be differentially expressed (FDR< 0.3) between T1D and controls and to be contained in modules associated with disease progression. As alternative splice isoforms are poorly annotated, an integrated analysis using structure, function and motif predictions was performed and non-canonical isoforms with differential regulation and function from their canonical isoforms were further studied.

Results

39 protein coding transcripts contained in three WGCNA modules were differentially expressed. EGF signaling, extra-cellular matrix and epithelial differentiation were among the top enriched processes. The protein products of 9 of these 39 transcripts are annotated as alternative /non-canonical isoforms. Analysis of the non-canonical isoform 3 of ATF3 was predicted to be involved in type I interferon and cell-substrate junction assembly compared to the canonical isoform. Consistent with this prediction, expression of the non-canonical, but not of the canonical ATF3 isoform, correlated highly with DUSP1 and EGR1 transcripts, known to be regulated by type I interferon. Structure predictions of the ATF3 isoform showed structural differences with RMSD of 3.5 from that of the canonical form with part of the basic leucine zipper domain missing in isoform 3 of ATF3.

Conclusion

We have identified alternative splice isoforms with substantial differential regulation and function prediction associated with key progression pathways in DKD, opening an analytical window to address the complexity of the transcriptome in renal disease.

Funding

  • NIDDK Support