Differential Splice Isoform and Gene Expression in Pediatric Genetic Cardiomyopathies

Background: In the recent past, extensive data on gene and protein expression in the hearts of adult patients have been collected. These data include a wide array of information on diseased myocardium and more limited datasets on nonfailing hearts. However, in pediatric patients, these mechanisms—particularly in nonfailing and genotype-positive hearts—remain largely unexplored, primarily due to a lack of pediatric myocardium. Such data would be helpful for deepening our understanding of the mechanisms underlying heart failure in children.

Methods: We isolated total RNA from the left ventricles (LV) of 3 pediatric nonfailing donors (aged 5–16 years) and 10 adults (aged >25 years), alongside 24 genotype-positive failing patients (aged 2 months–18 years). Among the failing patients, nine carry mutations in TNNC1, TNNT2, or TNNI3. Following RNA isolation, the myocardial samples were sequenced using both Nanopore and Illumina technologies. The data were then bioinformatically analyzed to assess differential gene expression and alternative splicing. Before these analyses, all samples underwent whole exome sequencing (WES) or cardiac gene panel screening to exclude pathogenic genotypes in nonfailing donor hearts and identify disease-causing mutations in failing hearts.

Results: We observed significant changes in the gene expression of the troponin complex, associated with mutations in the troponin genes. Notably, there was increased expression of cardiac isoforms of TnI and TnC TNNI3, TNNC1, and the slow-skeletal isoform of TnT TNNT1, suggesting a genotype-associated gene expression pattern that was absent from patients with other pathogenic variants. Additionally, we identified 33 genes, including TPM3 and MYL12A, with differential expression between nonfailing adults and children. Moreover, we found several novel splice isoforms, including a new splice isoform of TPM2, β-Tropomyosin, which was present across all patients. We also discovered genes with alternative splicing patterns that vary between children and adults, such as CLCN6, a chloride-gated voltage channel, and FHL1, a zinc-finger protein.

Conclusion: Our findings reveal distinct molecular differences in patients with troponin mutations, uncovering unique gene expression patterns that are not present in other types of cardiomyopathies. Additionally, we identified significant gene expression differences between the pediatric and adult myocardium. These insights could pave the way for more targeted and effective treatments.

Publikationsverlauf

Artikel online veröffentlicht:
11. Februar 2025