Research Officer Murdoch Childrens Research Institute, United States
Abstract: Cardiovascular disease accounts for one-third of deaths worldwide, yet the molecular mechanisms underlying a healthy heart and its dysfunction in disease remain incompletely understood. While genetic factors play a significant role, the limited contribution of mutations in the coding genome has shifted the focus toward non-coding regulatory elements. Alternative polyadenylation (APA) is a co-transcriptional mechanism that modifies the 3' untranslated regions (UTR) of mRNA, thereby influencing mRNA stability, localisation, translation, and subsequent protein localisation and function. Emerging evidence highlights that APA significantly affects cardiac gene regulation and may present novel therapeutic opportunities for combating heart disease and dysfunction. To characterise normal APA signatures in cardiac genes, we analysed snRNA-seq data from the Human Heart Cell Atlas using PolyApiper, an innovative tool for detecting APA from scRNA-seq data. Our analysis identified 7,864 genes expressing alternative 3'UTR isoforms and 550 genes undergoing differential APA between atrial and ventricular cardiomyocytes. Extending this investigation to hearts with dilated cardiomyopathy, which exhibit activation of the fetal gene program, we found 6,564 genes subject to APA in cardiomyocytes. These findings also enabled us to prioritise genes for in vitro studies based on 3'UTR isoform expression. For instance, we observed that longer 3'UTRs of the TBX5 gene were associated with reduced mRNA levels, resulting in decreased protein expression. These insights advance our understanding of how APA regulates gene expression and protein function in the healthy heart and reveal how its dysregulation contributes to cardiovascular disease.
