Abstract: FR-PO124
Transcript Isoform Switching in Sepsis-Induced AKI
Session Information
- AKI: Mechanisms - II
November 04, 2022 | Location: Exhibit Hall, Orange County Convention Center‚ West Building
Abstract Time: 10:00 AM - 12:00 PM
Category: Acute Kidney Injury
- 103 AKI: Mechanisms
Authors
- Zollman, Amy, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Halim, Arvin, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Myslinski, Jered, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Dagher, Pierre C., Indiana University School of Medicine, Indianapolis, Indiana, United States
- Hato, Takashi, Indiana University School of Medicine, Indianapolis, Indiana, United States
Background
In a subset of patients with sepsis-induced AKI, recovery of kidney function is observed. Understanding how such recovery unfolds will aid the development of targeted therapy. We have previously identified that translation shutdown is a hallmark of late phase sepsis. In a reversible model of endotoxemia, this late phase of sepsis is also a crucial transition period where tissue recovery begins. Notably, a set of genes are found to be highly resistant to translation shutdown. These resistant genes are enriched in pathways involved in RNA splicing. Thus, to examine the role of RNA splicing in tissue recovery, we performed long-read sequencing and analyzed temporal changes in RNA isoforms.
Methods
Reversible AKI was induced in mice by 5 mg/kg LPS iv. Kidneys were harvested at various time points. Full-length transcripts were prepared following the Nanopore protocol (SQK-DCS109) and sequenced on GridION.
Results
During the early course of endotoxemia, no significant changes were observed in the composition of RNA isoforms. In contrast, during late phases of endotoxemia (16–30 hrs), hundreds of genes exhibited distinct isoform switches. The emergence of isoform switches occurred during translation shutdown and the resultant alternative isoforms persisted throughout the recovery phase. Exon skipping and alternative exon ending were the 2 dominant modes of alternative splicing. Moreover, we found a number of very short isoforms consisting of a canonical first exon and a cryptic polyadenylated exon that originated from a first intron. Importantly, these short isoforms outnumbered their corresponding conventional protein coding isoforms. Because these short isoforms lack sufficient lengths of open reading frame (<100 nt), they are predicted to fail in generating proteins. Thus, we surmise that the preponderance of short isoforms could serve as a novel endogenous gene downregulation mechanism. Indeed, we found that crucial stress-response genes including p53 exhibited this short isoform switch, thus effectively leading to downregulation of functional p53. Such isoform switch could permit cells to exit cell cycle arrest and promote tissue recovery in sepsis.
Conclusion
Transcript isoform switching is pervasive during the recovery phase of septic AKI. The genesis of the very short isoforms may have functional importance in controlling the expression of stress-response genes.
Funding
- NIDDK Support