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Profiling of the full-length transcriptome in abdominal aortic aneurysm using nanopore-based direct RNA sequencing.
Xin, Hai; He, Xingqiang; Li, Jun; Guan, Xiaomei; Liu, Xukui; Wang, Yuewei; Niu, Liyuan; Qiu, Deqiang; Wu, Xuejun; Wang, Haofu.
Afiliación
  • Xin H; Department of Vascular Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, People's Republic of China.
  • He X; Department of Cardiology, Xijing Hospital, Fourth Military Medical University, 169 West Changle Road, Xi'an 710032, People's Republic of China.
  • Li J; Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China.
  • Guan X; Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China.
  • Liu X; Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China.
  • Wang Y; Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China.
  • Niu L; Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China.
  • Qiu D; Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China.
  • Wu X; Department of Vascular Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, People's Republic of China.
  • Wang H; Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China.
Open Biol ; 12(2): 210172, 2022 02.
Article en En | MEDLINE | ID: mdl-35104432
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aneurisma de la Aorta Abdominal / Perfilación de la Expresión Génica / Secuenciación de Nucleótidos de Alto Rendimiento / Transcriptoma Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Revista: Open Biol Año: 2022 Tipo del documento: Article Pais de publicación: Reino Unido
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aneurisma de la Aorta Abdominal / Perfilación de la Expresión Génica / Secuenciación de Nucleótidos de Alto Rendimiento / Transcriptoma Tipo de estudio: Prognostic_studies Límite: Humans Idioma: En Revista: Open Biol Año: 2022 Tipo del documento: Article Pais de publicación: Reino Unido