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

## TL;DR

This study identifies six genes linked to blood clot formation in the heart of patients with atrial fibrillation, offering insights into disease mechanisms and potential biomarkers.

## Contribution

The study identifies six novel candidate genes associated with thrombus formation in atrial fibrillation patients.

## Key findings

- RNA sequencing identified 27 differentially expressed genes in left atrial appendage tissue with and without thrombus.
- DIRAS3 expression was positively associated with fibrosis and NT-proBNP levels, while CYP26B1 and TUBA3D showed distinct correlations with NT-proBNP.
- Six key genes—DIRAS3, CYP26B1, PRG4, ITLN1, FKBP5, and TUBA3D—were identified as potentially involved in thrombus pathogenesis.

## 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,|log2(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.

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.

The online version contains supplementary material available at 10.1007/s11239-025-03184-1.

We investigated candidate genes associated with left atrial appendage thrombus (LAAT) in patients with atrial fibrillation using RNA sequencing of left atrial appendage tissue obtained during cardiac surgery. RNA sequencing analysis identified six key genes potentially associated with LAAT: DIRAS3, CYP26B1, PRG4, ITLN1, FKBP5, and TUBA3D. Among them, DIRAS3expression showed a positive correlation with both the degree of fibrosis and NT-proBNP levels. CYP26B1 expression was positively correlated with NT-proBNP, whereas TUBA3D expression was negatively correlated. This transcriptomic approach provides valuable insight into the pathogenesis of LAAT formation and the identification of potential biomarkers. Further research is needed to validate these findings and assess their clinical implications.

We investigated candidate genes associated with left atrial appendage thrombus (LAAT) in patients with atrial fibrillation using RNA sequencing of left atrial appendage tissue obtained during cardiac surgery.

RNA sequencing analysis identified six key genes potentially associated with LAAT: DIRAS3, CYP26B1, PRG4, ITLN1, FKBP5, and TUBA3D.

Among them, DIRAS3expression showed a positive correlation with both the degree of fibrosis and NT-proBNP levels. CYP26B1 expression was positively correlated with NT-proBNP, whereas TUBA3D expression was negatively correlated.

This transcriptomic approach provides valuable insight into the pathogenesis of LAAT formation and the identification of potential biomarkers. Further research is needed to validate these findings and assess their clinical implications.

The online version contains supplementary material available at 10.1007/s11239-025-03184-1.