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Xin H, He X, Li J, Guan X, Liu X, Wang Y, Niu L, Qiu D, Wu X, Wang H. Profiling of the full-length transcriptome in abdominal aortic aneurysm using nanopore-based direct RNA sequencing. Open Biol 2022; 12:210172. [PMID: 35104432 PMCID: PMC8807055 DOI: 10.1098/rsob.210172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
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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Affiliation(s)
- Hai Xin
- Department of Vascular Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, People's Republic of China
| | - Xingqiang He
- Department of Cardiology, Xijing Hospital, Fourth Military Medical University, 169 West Changle Road, Xi'an 710032, People's Republic of China
| | - Jun Li
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China
| | - Xiaomei Guan
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China
| | - Xukui Liu
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China
| | - Yuewei Wang
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China
| | - Liyuan Niu
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China
| | - Deqiang Qiu
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China
| | - Xuejun Wu
- Department of Vascular Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, People's Republic of China
| | - Haofu Wang
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, People's Republic of China
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Edvinsson M, Ilbäck NG, Frisk P, Thelin S, Nyström-Rosander C. Trace Element Changes in Thoracic Aortic Dissection. Biol Trace Elem Res 2016; 169:159-63. [PMID: 26152852 DOI: 10.1007/s12011-015-0432-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/29/2015] [Indexed: 01/10/2023]
Abstract
Thoracic aortic dissection is a life-threatening condition with an incompletely understood pathogenesis. Trace elements are essential for the functioning of different processes in the body, including the immune system and associated responses to infection/inflammation. Because inflammation may be part of the pathogenesis of thoracic aortic dissection, we investigated whether trace element changes associated with inflammation occur in serum and tissue samples during the disease. The study included 21 patients undergoing surgery for thoracic aortic dissection, 10 forensic autopsy specimens for tissue controls and 23 healthy blood donors for serum controls. Levels of magnesium (Mg), calcium (Ca), vanadium (V), manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn), arsenic (As), selenium (Se), cadmium (Cd) and mercury (Hg) were measured in the aortic tissue and serum by inductively coupled plasma-mass spectrometry (ICP-MS). In the serum, Ca, V, Cu and Zn decreased, whereas Fe increased. In the tissue, Cu and Zn decreased and Fe tended to increase. The Cu/Zn ratio in the serum, a marker of infection/inflammation, did not change in the patients. Concerning trace element changes in the serum and tissue, our data do not support the hypothesis that inflammation is involved in the pathogenesis of thoracic aortic dissection.
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Affiliation(s)
- Marie Edvinsson
- Department of Medical Sciences, Infectious Diseases, Uppsala University, University Hospital, S-751 85, Uppsala, Sweden.
| | - Nils-Gunnar Ilbäck
- Department of Medical Sciences, Infectious Diseases, Uppsala University, University Hospital, S-751 85, Uppsala, Sweden
- Risk Benefit Assessment Department, National Food Agency, Box 622, 751 26, Uppsala, Sweden
| | - Peter Frisk
- Research in Metal Biology, Rudbeck Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Stefan Thelin
- Department of Surgical Sciences, Thoracic Surgery, Uppsala University, 751 85, Uppsala, Sweden
| | - Christina Nyström-Rosander
- Department of Medical Sciences, Infectious Diseases, Uppsala University, University Hospital, S-751 85, Uppsala, Sweden
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de Assis RM, de Lourdes Higuchi M, Reis MM, Palomino SAP, Crespo Hirata RD, Hirata MH. Involvement of TLR2 and TLR4, <i>Chlamydophila pneumoniae</i> and <i>Mycoplasma pneumoniae</i> in adventitial inflammation of aortic atherosclerotic aneurysm. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/wjcd.2014.41004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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