Profiling of the full-length transcriptome in abdominal aortic aneurysm using nanopore-based direct RNA sequencing

• Published in: Open biology Vol. 12; no. 2; p. 210172
• Main Authors: Xin, Hai, He, Xingqiang, Li, Jun, Guan, Xiaomei, Liu, Xukui, Wang, Yuewei, Niu, Liyuan, Qiu, Deqiang, Wu, Xuejun, Wang, Haofu
• Format: Journal Article
• Language: English
• Published: England The Royal Society 01.02.2022
• Subjects: abdominal aortic aneurysm; alternative polyadenylation; Alternative Splicing; Aortic Aneurysm, Abdominal - diagnosis; Aortic Aneurysm, Abdominal - genetics; Biomarkers; Computational Biology - methods; Gene Expression Profiling - methods; Gene Expression Regulation; High-Throughput Nucleotide Sequencing - methods; Humans; lncRNAs; Microsatellite Repeats; nanopore-based RNA sequencing; Transcriptome; lncRNAs; nanopore-based RNA sequencing; alternative splicing; abdominal aortic aneurysm; alternative polyadenylation
• DOI: 10.1098/rsob.210172
• ISSN: 2046-2441

Abdominal aortic aneurysm (AAA) is a common and serious disease with a high mortality rate, but its genetic determinants have not been fully identified. In this feasibility study, we aimed to elucidate the transcriptome profile of AAA and further reveal its molecular mechanisms through the Oxford Nanopore Technologies (ONT) MinION platform. Overall, 9574 novel transcripts and 781 genes were identified by comparing and analysing the redundant-removed transcripts of all samples with known reference genome annotations. We characterized the alternative splicing, alternative polyadenylation events and simple sequence repeat (SSR) loci information based on full-length transcriptome data, which would help us further understand the genome annotation and gene structure of AAA. Moreover, we proved that ONT methods were suitable for the identification of lncRNAs via identifying the comprehensive expression profile of lncRNAs in AAA. The results of differentially expressed transcript (DET) analysis showed that a total of 7044 transcripts were differentially expressed, of which 4278 were upregulated and 2766 were downregulated among two groups. In the KEGG analysis, 4071 annotated DETs were involved in human diseases, organismal systems and environmental information processing. These pilot findings might provide novel insights into the pathogenesis of AAA and provide new ideas for the optimization of personalized treatment of AAA, which is worthy of further study in subsequent studies.