Differential expression profiles and bioinformatics analysis of tRNA-derived small RNAs in epicardial fat of patients with atrial fibrillation

Abstract

The exact processes underlying atrial fibrillation (AF) are still unclear. It has been suggested that epicardial adipose tissue (EAT) may contribute to arrhythmias and can release various bioactive molecules, including exosomes containing tRNA-derived small RNAs (tsRNAs). Numerous studies have indicated that these tsRNAs can significantly affect key cellular functions. However, there is currently no research investigating the relationship between tsRNAs from EAT and AF. In order to explore the regulatory mechanisms of tsRNAs from EAT associated with AF, we conducted RNA-sequencing analysis on EAT samples collected from 6 AF patients and 6 control subjects with sinus rhythm. Our analysis revealed an upregulation of 146 tsRNAs and a downregulation of 126 tsRNAs in AF. Furthermore, we randomly selected four tsRNAs (tRF-SeC-TCA-001, tiRNA-Gly-CCC-003, tRF-Gly-GCC-002, and tRF-Tyr-GTA-007) for validation using quantitative reverse transcription-polymerase chain reaction. Following this, bioinformatic analyses revealed that the target genes of these tsRNAs were prominently involved in the regulation of cell adhesion and various cellular processes mediated by plasma membrane adhesion molecules. Additionally, based on KEGG analysis, it was suggested that the majority of these target genes might contribute to the pathogenesis of AF through processes such as glycosaminoglycan biosynthesis, AMP-activated protein kinase activity, and the insulin signaling pathway. Our results elucidate changes in the expression profiles of tsRNAs within EAT samples obtained from AF patients, and they forecast potential target genes and interactions between tsRNAs and mRNA within EAT that could contribute to the pathogenesis of AF.

Keywords: Atrial fibrillation; Bioinformatics; Epicardial fat; Sequencing; tRFs & tiRNAs.

Fig. 1

Study design illustration. qRT‒PCR, quantitative reverse transcription-polymerase chain reaction.

Fig. 2

tsRNA expression level analysis. (A) Principle component analysis. The PCA results show a distinguishable tRF & tiRNA spectrum in the epicardial fat depot between atrial fibrillation and sinus rhythm. (B) Scatter plots of differentially expressed tsRNAs. tRFs & tiRNAs above the top line (red dots, upregulation) or below the bottom line (green dots, downregulation) indicate more than a 1.5-fold change between the two compared groups. Grey dots indicate nondifferentially expressed tRFs & tiRNAs. (C) The hierarchical clustering heatmap for tRFs and tiRNAs in the two groups. (D) The volcano plots of differentially expressed tsRNAs. Red/green circles indicate statistically significant differentially expressed tRFs & tiRNAs with fold changes of no less than 1.5 and p values ≤ 0.05 (red: upregulated; green: downregulated). Grey circles indicate nondifferentially expressed tRFs & tiRNAs.

Fig. 3

Analysis of tsRNA subtypes. (A) Venn diagram based on the number of commonly and specifically expressed tRFs and tiRNAs. (B) Venn diagram based on the number of known and detected tRFs and tiRNAs. (C–D) Pie charts of the distribution of subtypes of tRFs & tiRNAs of epicardial adipose tissue in atrial fibrillation (C) and sinus rhythm (D). (E–F) The number of subtypes of tRFs and tiRNAs against tRNA isodecoders in the two groups. (G–H) The frequency of subtype versus length of tRFs and tiRNAs in the two groups.

Fig. 4

Validation by qRT‒PCR in human epicardial adipose tissue of atrial fibrillation and control. AF, atrial fibrillation. Mean ± SEM (n = 6). *P < 0.05.

Fig. 5

The network of candidate tsRNAs and potential target mRNAs. All results have a threshold of ≥1.5-fold change.

Fig. 6

GO enrichment analysis of target mRNAs of the four candidate tsRNAs. (A) Bar plot with enrichment score: top ten enriched items in three domains. (B–D) Dot plot with gene ratio values of the top ten enriched items in biological processes (B), cellular components (C) and molecular functions (D).

Fig. 7

KEGG pathway analysis of target mRNAs of the four candidate tsRNAs. (A) Pathway bar plot with enrichment score values of the top ten significantly enriched signalling pathways. (B) Dotplot with gene ratio values of the top ten significantly enriched signalling pathways.