Gene expression profile in the atrial fibrillation patient hearts across seven heart regions
Atrial fibrillation (AF) is the most frequent persistent arrhythmia, and many genes have been reported as a causal gene candidate for AF. However, most transcriptome analyses of AF have limited to the atrial samples and have not evaluated by multiple cardiac regions. In this study, we analyzed the expression levels of protein-coding and long noncoding RNAs (lncRNAs) in six different cardiac regions by RNA-seq. Surprisingly, the most changed region in gene expression by the presence of AF was the pulmonary vein (PV), not the atria. Upon analysis of these significant genes, the ion channel-related gene set was significantly enriched. In addition, cancer-related lncRNAs was up-regulated in PV in AF. A Co-expression network analysis could detect the functional gene clusters. In particular, the functional coupling between the lncRNA FOXCUT and transcription factor FOXC1 are known to be involved in process of the epithelial-mesenchymal transition in cancer tissues. Thus, they may also play an aggravating role in the pathogenesis of AF. In the least, this study suggests that (1) RNA alteration is most intense in PVs and (2) post-acquired gene regulation, such as the FOXCUT-FOXC1 axis, may contribute to the progression of AF. Overall design: High-througput sequence was demonstrated with NovaSeq 6000 (Illumina). First, extracted RNAs were purified by poly(A) capture. Resultant mRNAs were then fragmented and reverse-transcribed into single-stranded complementary DNAs (cDNAs). Subsequently, cDNAs were double-stranded by a DNA polymerase. During the polymerase reactions, deoxy UTP (dUTP) were mixed in nucleotide materials. Both ends of double-stranded DNA (ds DNA) were ligated to a 13 bp adapter sequence. Next, the ds DNAs were subjected to PCR amplification for the multi-sized DNA library preparation. NovaSeq Control software v1.4.0 analyzed the sequencing runs and tag sequences classified each read in the raw sequencing data. A total of 21 RNA-seq data were used for three samples each of sinoatrial node (SAN), left atrium (LA), right atrium (RA), left ventriclle (LV), right ventricle (RV), pulmonary vein (PV), and left atrial appendage (LAA), LV, pulmonary vein (PV). fastp software (version 0.12.4) was used for Read quality control and adapter removal. Reads were aligned using STAR software (version 2.7.0a).