Integrated proteomics and transcriptomics analysis reveals insights into differences in premature mortality associated with disparate pathogenic RBM20 variants

• Published in: Journal of molecular and cellular cardiology 2024-12, Vol.197, p.78-89
• Main Authors: Gregorich, Zachery R., Larson, Eli J., Zhang, Yanghai, Braz, Camila U., Liu, Chunling, Ge, Ying, Guo, Wei
• Format: Article
• Language: English
• Subjects: Adverse remodeling; Animals; Cardiomyopathy, Dilated - genetics; Cardiomyopathy, Dilated - metabolism; Cardiomyopathy, Dilated - pathology; Dilated cardiomyopathy; Gene Expression Profiling; Gene Expression Regulation; Genetic mutations; Humans; Mice; Mitochondria; Multiomics; Phenotype; Premature mortality; Proteomics; Proteomics - methods; RBM20; RNA Splicing - genetics; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Transcriptome
• ISSN: 0022-2828; 1095-8584; 1095-8584
• DOI: 10.1016/j.yjmcc.2024.10.013

Variants in RNA binding motif protein 20 (RBM20) are causative in a severe form of dilated cardiomyopathy referred to as RBM20 cardiomyopathy, yet the mechanisms are unclear. Moreover, the reason(s) for phenotypic heterogeneity in carriers with different pathogenic variants are similarly opaque. To gain insight, we carried out multi-omics analysis, including the first analysis of gene expression changes at the protein level, of mice carrying two different pathogenic variants in the RBM20 nuclear localization signal (NLS). Direct comparison of the phenotypes confirmed greater premature morality in S639G variant carrying mice compared to mice with the S637A variant despite similar cardiac remodeling and dysfunction. Analysis of differentially spliced genes uncovered alterations in the splicing of both RBM20 target genes and non-target genes, including several genes previously implicated in arrhythmia. Global proteomics analysis found that a greater number of proteins were differentially expressed in the hearts of Rbm20S639G mice relative to WT than in Rbm20S637A versus WT. Gene ontology analysis suggested greater mitochondrial dysfunction in Rbm20S639G mice, although direct comparison of protein expression in the hearts of Rbm20S639G versus Rbm20S637A mice failed to identify any significant differences. Similarly, few differences were found by direct comparison of gene expression at the transcript level in Rbm20S639G and Rbm20S637A despite greater coverage. Our data provide a comprehensive overview of gene splicing and expression differences associated with pathogenic variants in RBM20, as well as insights into the molecular underpinnings of phenotypic heterogeneity associated with different dilated cardiomyopathy-associated variants. [Display omitted] •Disparate RBM20 NLS variants causes distinct disease phenotypes.•S639G variant causes greater premature mortality compared to S637.•DSGs in Rbm20S639G versus Rbm20S637A included genes linked to arrhythmia.•Unique Rbm20S639G DEPs implicate mitochondrial dysfunction in phenotype differences.•First protein-level and multi-omics characterization in RBM20 cardiomyopathy.