Alternative Splicing in CKD
November 02, 2023 | 04:48 PM - 04:57 PM
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Alternative Splicing in CKD
- CKD Mechanisms: Prediction, Propagation, and Prevention
November 02, 2023 | Location: Room 119, Pennsylvania Convention Center
Abstract Time: 04:48 PM - 04:57 PM
Category: CKD (Non-Dialysis)
- 2303 CKD (Non-Dialysis): Mechanisms
- Mohandes, Samer, University of Pennsylvania, Philadelphia, Pennsylvania, United States
- Susztak, Katalin, University of Pennsylvania, Philadelphia, Pennsylvania, United States
Samer Mohandes, MD
Alternative splicing (AS) is a process that can lead to variable genotype expression. The primary forms are exon skipping, intron inclusion, alternative 5’ and 3’ splice sites. The role of alternative splicing of VEGF has been shown to play an important role in chronic kidney disease (CKD) development, however a comprehensive assessment of AS events in CKD has not been undertaken yet.
Human kidney tissue (n=410) was collected from nephrectomies of healthy subjects and patients with diabetic or hypertensive CKD. Clinical demographics information was collected via honest broker and histopathology was analyzed in an unbiased manner. RNA was extracted from the tubular compartment and sequenced. RNA-seq reads were aligned to the human genome using STAR v 2.7.3. Outliers identified by Mahalanobis distance. Aligned BAM files were sorted and indexed using Samtools v1.17 and junctions were extracted using Regtools v 1.0. Differential splicing for was analyzed separately using leafcutter v 0.2.7 and adjusted for age, sex, race and RNA quality indices (RNA integrity number, 5’-3’bias, %ribosomal genes, total reads).
When comparing healthy samples to those with eGFR of less than 60 cc/min/1.73m2 (CKD stage 3-5), we identified 31 intron cluster alternative splicing events at an adjusted p-value of 0.05. 26 of these were previously annotated. Pathway analysis using gene ontology (GO) terms showed enrichment for cell death and metabolic pathway. When comparing samples with less than 10% fibrosis to those with greater than 10% fibrosis, we identified 239 alternative differential splicing clusters. 233 of these were previously annotated. Pathway analysis using GO terms demonstrated these genes were enriched in the metabolic and immune pathways.
Large number of differential splicing events were observed in CKD compared to controls with enrichment in the metabolic and immune pathway genes.
(CKD vs control)
|No. of Significant Differentially Spliced Genes||Top Genes||Top pathway enrichment by GO terms|
|GFR <60 ml/min/1.73m2||146 vs 264||31||RAB11FIP3|
|Regulation of cell death|
Negative regulation of cell death
Generation of precursor metabolites and energy
|Interstitial Fibrosis |
|170 vs 240||239||RPS24|
|Small molecule metabolic process|
Organic acid metabolic process
Positive regulation of immune system
Positive regulation of leukocyte migration