Abstract
Dysregulated mRNA splicing is involved in the pathogenesis of many diseases including cancer, neurodegenerative diseases, and muscular dystrophies such as myotonic dystrophy type 1 (DM1). Comprehensive assessment of dysregulated splicing on the transcriptome and proteome level have been methodologically challenging, and thus investigations have often been targeting only few genes.
Here, we performed a large-scale coordinated transcriptomic and proteomic analysis to characterize a DM1 mouse model (HSALR) in comparison to wild-type. Our integrative proteogenomics approach comprised gene- and splicing-level assessments for mRNAs and proteins. It recapitulated many known instances of aberrant mRNA splicing in DM1 and identified new ones. It enabled the design and targeting of splicing-specific peptides and confirmed the translation of known instances of aberrantly spliced disease-related genes (e.g. Atp2a1, Bin1, Ryr1), complemented by novel findings (e.g. Ywhae, Flnc, Svil). Comparative analysis of large-scale mRNA and protein expression data showed remarkable agreement of differential patterns between disease and wild-type on both the gene and especially the splicing level.
We hence believe that our work is suitable as a model for a robust and scalable integrative proteogenomic strategy. This strategy provides investigative approaches, advances our understanding of the disease biology of splicing-based disorders, and helps establish robust splicing-specific biomarkers.
Competing Interest Statement
All authors except E.M.S. are employees of Novartis, and some hold Novartis stock. E.M.S. declares no conflicts.
Abbreviation list
- DM1
- Myotonic Dystrophy, type 1
- WT
- wild-type
- Tx
- Transcriptomics
- Px
- Proteomics
- GE
- Gene Expression
- DGE
- Differential Gene Expression
- DAS
- Differential Alternative Splicing
- RNA-seq
- high-throughput mRNA sequencing
- FPKM
- Fragments Per Kilobase of transcript per Million mapped reads (RNA-seq analysis)
- FC
- fold change
- MS
- Mass Spectrometry
- HPLC
- High-Performance Liquid Chromatography
- DDA
- Data-Dependent Acquisition
- TMT
- Tandem Mass Tag
- PRM
- Parallel Reaction Monitoring