Alternative Splicing of Serum Response Factor Reveals Isoform-Specific Remodeling in Cardiac Diseases

• Published in: Genes Vol. 16; no. 8; p. 947
• Main Authors: Abdi, Sayed Aliul Hasan, Azhar, Gohar, Zhang, Xiaomin, Sharma, Shakshi, Hafeez, Mohib, Wei, Jeanne Y.
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 11.08.2025; MDPI
• Subjects: Alternative splicing; Alternative Splicing - genetics; Analysis; Cardiomyopathy; Cardiovascular disease; Cardiovascular diseases; Congestive heart failure; Coronary artery disease; Correlation analysis; Datasets; Dilated cardiomyopathy; Exons; Gene expression; Genes; Genomes; Heart; Heart diseases; Heart Diseases - genetics; Heart Diseases - metabolism; Heart Diseases - pathology; Heart failure; Heart Failure - genetics; Humans; Ischemia; Lipid metabolism; Multivariate analysis; Protein Isoforms - genetics; Proteins; Proteomics; RNA; RNA Splicing Factors - genetics; Serum response factor; Serum Response Factor - genetics; Serum Response Factor - metabolism; Splicing factors; Therapeutic targets; Transcriptome; Transcriptomes; Transcriptomics; cardiovascular disease; serum response factor; RNA-seq; alternative splicing
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes16080947

Background: Alternative splicing is an important mechanism of transcriptomic and proteomic diversity and is progressively involved in cardiovascular disease (CVD) pathogenesis. Serum response factor (SRF), a critical transcription factor in cardiac development and function, may itself undergo splicing regulation, potentially altering its function in disease states. Objective: The objective of this study is to identify SRF-associated alternative splicing events in cardiac pathological conditions and examine regulatory interactions with splicing factors using RNA-seq data. Methods: Three human heart RNA-seq databases (PRJNA198165, PRJNA477855, PRJNA678360) were used, comprising various cardiac conditions like non-ischemic cardiomyopathy (NICM), ischemic cardiomyopathy (ICM), dilated cardiomyopathy (DCM), and heart failure with reduced ejection fraction (HFrEF), with and without left ventricular assist device (LVAD) support. Splicing events were identified using the rMATS tool, and correlation analyses were performed between SRF and predicted splicing factors. Functional enrichment of SRF-correlated genes was assessed via Gene Ontology (GO) and KEGG pathways. Results: The skipped exon (SE) events were the predominant splicing type across all datasets. SRF chr6, including (Exon 2, 43,173,847–43,174,113), (Exon 4, 43,176,548–43,176,667), and (Exon 5, 43,178,294-43,178,485), were most frequently involved in SE and mutually exclusive exon (MXE) events across multiple heart failure subtypes. Correlation analysis revealed strong positive associations between SRF and several splicing factors (HNRNPL, HNRNPD, SRSF5, and SRSF8). GO and KEGG analyses revealed enrichment of muscle development, sarcomere structure, lipid metabolism, and immune signaling pathways. Conclusions: Our study shows that SRF is subject to extensive alternative splicing in heart failure, particularly at Exon 2 and Exon 5, suggesting isoform-specific roles in cardiac remodeling. The strong co-expression with specific splicing factors delineates a regulatory axis that may explain the pathological transcriptome in cardiomyopathy. These findings provide a foundation for exploring splicing-based biomarkers and therapeutic targets in cardiac pathology for SRF.