Transcriptome Reprogramming in Heart Failure: The Hidden Splicing Code

Heart failure remains a major cause of morbidity and mortality that is associated with myocardial changes in metabolism, contractile function, and molecular remodeling. Cardiomyopathies comprise a diverse group of disorders that can be triggered by various external and internal stressors. This review aims to cover the underlying molecular mechanism driving heart failure progression, at the level of alternative splicing.

Alternative splicing is a fundamental mechanism that expands transcriptomic diversity through the differential inclusion or exclusion of exons. This process enables a single gene to generate multiple mRNA isoforms, thereby fine-tuning gene function in a context-dependent manner. Splicing outcomes are determined by a highly coordinated regulatory network, including cis-acting splicing elements, transcriptional kinetics, and trans-regulatory RNA-binding proteins, which together form a dynamic "splicing code" that responds to physiological and pathological stresses. In the heart, alternative splicing regulates cardiac cell homeostasis and normal physiological function. Dysregulated alternative splicing has been increasingly recognized as a key contributor to cardiovascular diseases, particularly in the context of sarcomere gene isoform switching. However, emerging evidence suggests that cardiomyopathies arising from distinct etiologies including dilated, ischemic, and cardiometabolic disorder are associated with unique splicing programs. Here, we provide a comprehensive overview of the regulatory mechanisms governing alternative splicing in the heart, with a particular emphasis on disease-specific splicing events across different forms of cardiomyopathy. We further discuss recent advances in targeting aberrant splicing for therapies as well as novel splicing analysis platforms, highlighting the potential of RNA-based strategies to modulate splicing in heart failure.