Computational identification and validation of alternative splicing in ZSF1 rat RNA-seq data, a preclinical model for type 2 diabetic nephropathy

Abstract

Obese ZSF1 rats exhibit spontaneous time-dependent diabetic nephropathy and are considered to be a highly relevant animal model of progressive human diabetic kidney disease. We previously identified gene expression changes between disease and control animals across six time points from 12 to 41 weeks. In this study, the same data were analysed at the isoform and exon levels to reveal additional disease mechanisms that may be governed by alternative splicing. Our analyses identified alternative splicing patterns in genes that may be implicated in disease pathogenesis (such as Shc1, Serpinc1, Epb4.1l5, and Il-33), which would have been overlooked in standard gene-level analysis. The alternatively spliced genes were enriched in pathways related to cell adhesion, cell–cell interactions/junctions, and cytoskeleton signalling, whereas the differentially expressed genes were enriched in pathways related to immune response, G protein-coupled receptor, and cAMP signalling. Our findings indicate that additional mechanistic insights can be gained from exon- and isoform-level data analyses over standard gene-level analysis. Considering alternative splicing is poorly conserved between rodents and humans, it is noted that this work is not translational, but the point holds true that additional insights can be gained from alternative splicing analysis of RNA-seq data.

Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and Therapeutics

“…Recent advances in high-throughput screening (HTS) technologies covering whole-genome and -exome sequencing, such as RNA sequencing (RNA-seq), have greatly contributed to improving the diagnosis and treatment of human diseases. Particularly, RNA-seq currently represents one of the most powerful tools to investigate AS at the genome-wide level [134][135][136][137][138][139]. Compared with gene expression microarrays, also designed to sample AS events on a genome scale, RNA-seq exhibits various potential advantages, including the ability of estimating the abundance of known and novel alternative transcripts, and providing better resolution, deeper coverage, and higher accuracy [139].…”

“…On the other hand, most standard RNA-seq-based analyses have mainly focused on changes in gene expression level, thus lacking information about slight differences in alternative isoform usage and exon inclusion or exclusion. The importance of investigating AS profiles in RNA-seq data was recently highlighted by a study in a preclinical model of progressive diabetic nephropathy [135]. Using the isoform-and exon-level analysis of RNA-seq data, the authors identified AS patterns in genes implicated in disease pathogenesis, such as SHC1, SERPINC1, EPB4.1L5, and IL-33, which would have been overlooked by standard gene-level analysis.…”

RNA Sequencing to Explore Dominant Isoform Switch During CCR6+ Memory T Cell Activation

“…Their study indicates that isoform switches with predicted functional consequences are common and important in dysfunctional cells, which in turn means that expression change should be analyzed at the isoform level. Our previous study also demonstrated additional mechanistic insights can be gained through interrogation of AS in addition to conventional gene-level analysis of RNA-seq data 22 . Most recently, Kahraman et al have analyzed isoform-speci c protein-protein interaction disruptions in 1,209 cancer samples covering 27 different cancer types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project, and identi ed a number of cancer-speci c Most Dominant Transcripts (cMDT) 23 .…”

Construction of prognostic predictor by comprehensive analyzing alternative splicing events for colon adenocarcinoma

“…Exonic regions of the pre-mRNA are spliced together, and intronic regions are removed to form the final mRNA products. There is increasing evidence that the transcript variants of a gene may have opposing roles and that widespread splicing disorders are one of the molecular markers of tumorigenesis and participate in many oncogenic processes, including proliferation, invasion and metastasis, apoptosis, hypoxia, metabolism, angiogenesis, and immune escape [ 6 , 7 ].…”