RNA sequence analysis of differentially expressed genes in left atrial appendage thrombus

Abstract Cardioembolic stroke is a major complication of atrial fibrillation (AF). We investigated differentially expressed genes (DEGs) in the left atrial appendage (LAA) with and without LAA thrombus (LAAT) using RNA sequencing (RNA-seq). LAA tissue samples were obtained during cardiac surgery. We analyzed samples with LAAT (n = 6) and without LAAT (n = 5). Differential gene expression analysis was conducted to identify significantly altered genes. RNA-seq identified 27 differentially expressed genes (false discovery rate < 0.05,|log 2 (fold change)| >2). Among these, four DEGs— DIRAS3 , CYP26B1 , PRG4 , and ITLN1 —exhibited particularly large fold changes. Protein-protein interaction network analysis revealed two hub genes, FKBP5 and TUBA3D, based on degree (≥ 30) and betweenness centrality (≥ 3000). Quantitative PCR confirmed consistent expression patterns for these genes. Furthermore, consistent results were obtained in another independent set (10 cases with LAAT and 10 cases without LAAT). Linear regression analysis, adjusted for age and gender, showed that DIRAS3 expression was significantly associated with both the fibrosis ratio (β = 2.99, 95% confidence interval [CI] 0.22–5.75, p = 0.034) and NT-proBNP levels (β = 373, 95% CI 238–507, p = 5.71E-08). Additionally, CYP26B1 and TUBA3D expression levels were significantly associated with NT-proBNP (β = 349, 95% CI 23.8–674, p = 0.036; β = -140, 95% CI -272 to -8.81, p = 0.038, respectively). We identified candidate genes potentially involved in LAAT in AF patients through RNA-seq analysis. These findings may elucidate the molecular mechanisms underlying LAAT pathogenesis. Graphical abstract Transcriptomic analysis of LAAT in patients with AF suggested that six genes— DIRAS3 , CYP26B1 , PRG4 , ITLN1 , FKBP5 , and TUBA3D —might be associated with thrombus formation. Among them, DIRAS3 expression was positively associated with both fibrosis ratio and NT-proBNP levels. CYP26B1 expression was also positively associated with NT-proBNP, whereas TUBA3D expression showed a negative association. This transcriptomic approach provides valuable insights into the pathogenesis of LAAT and highlights potential biomarkers for future investigation.