Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome
ObjectiveVaricose veins are a common problem worldwide and can cause significant impairments in health-related quality of life, but the etiology and pathogenesis remain not well defined. This study aims to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed g...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2019-03-01
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| Series: | Frontiers in Physiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fphys.2019.00278/full |
| _version_ | 1819153824088064000 |
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| author | Jianbin Zhang Qiangqiang Nie Qiangqiang Nie Chaozeng Si Cheng Wang Yang Chen Weiliang Sun Lin Pan Jing Guo Jie Kong Yiyao Cui Feng Wang Xueqiang Fan Zhidong Ye Jianyan Wen Peng Liu Peng Liu |
| author_facet | Jianbin Zhang Qiangqiang Nie Qiangqiang Nie Chaozeng Si Cheng Wang Yang Chen Weiliang Sun Lin Pan Jing Guo Jie Kong Yiyao Cui Feng Wang Xueqiang Fan Zhidong Ye Jianyan Wen Peng Liu Peng Liu |
| author_sort | Jianbin Zhang |
| collection | DOAJ |
| description | ObjectiveVaricose veins are a common problem worldwide and can cause significant impairments in health-related quality of life, but the etiology and pathogenesis remain not well defined. This study aims to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.MethodsWe harvested great saphenous veins (GSV) from patients who underwent coronary artery bypass grafting (CABG) and varicose veins from conventional stripping surgery. RNA-Sequencing (RNA-Seq) technique was used to obtain the complete transcriptomic data of both GSVs from CABG patients and varicose veins. Weighted Gene Co-expression network analysis (WGCNA) and further analyses were then carried out with the aim to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.ResultsFrom January 2015 to December 2016, 7 GSVs from CABG patients and 13 varicose veins were obtained. WGCNA identified 4 modules. In the brown module, gene ontology (GO) analysis showed that the biological processes were focused on response to stimulus, immune response and inflammatory response, etc. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the biological processes were focused on cytokine-cytokine receptor interaction and TNF signaling pathway, etc. In the gray module, GO analysis showed that the biological processes were skeletal myofibril assembly related. The immunohistochemistry staining showed that the expression of ASC, Caspase-1 and NLRP3 were increased in GSVs from CABG patients compared with varicose veins. Histopathological analysis showed that in the varicose veins group, the thickness of vascular wall, tunica intima, tunica media and collagen/smooth muscle ratio were significantly increased, and that the elastic fiber/internal elastic lamina ratio was decreased.ConclusionThis study shows that there are clear differences in transcriptomic information between varicose veins and GSVs from CABG patients. Some inflammatory RNAs are down-regulated in varicose veins compared with GSVs from CABG patients. Skeletal myofibril assembly pathway may play a crucial role in the pathogenesis of varicose veins. Characterization of these RNAs may provide new targets for understanding varicose veins diagnosis, progression, and treatment. |
| first_indexed | 2024-12-22T15:11:19Z |
| format | Article |
| id | doaj.art-f1074db0a44844aa8b6e4203ef25e6e0 |
| institution | Directory Open Access Journal |
| issn | 1664-042X |
| language | English |
| last_indexed | 2024-12-22T15:11:19Z |
| publishDate | 2019-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Physiology |
| spelling | doaj.art-f1074db0a44844aa8b6e4203ef25e6e02022-12-21T18:21:52ZengFrontiers Media S.A.Frontiers in Physiology1664-042X2019-03-011010.3389/fphys.2019.00278436087Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins TranscriptomeJianbin Zhang0Qiangqiang Nie1Qiangqiang Nie2Chaozeng Si3Cheng Wang4Yang Chen5Weiliang Sun6Lin Pan7Jing Guo8Jie Kong9Yiyao Cui10Feng Wang11Xueqiang Fan12Zhidong Ye13Jianyan Wen14Peng Liu15Peng Liu16Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, ChinaDepartment of Operations and Information Management, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Medicine, Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN, United StatesMOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, ChinaInstitute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, ChinaInstitute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, ChinaInstitute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, ChinaDepartment of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, ChinaDepartment of Cardiovascular Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, ChinaObjectiveVaricose veins are a common problem worldwide and can cause significant impairments in health-related quality of life, but the etiology and pathogenesis remain not well defined. This study aims to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.MethodsWe harvested great saphenous veins (GSV) from patients who underwent coronary artery bypass grafting (CABG) and varicose veins from conventional stripping surgery. RNA-Sequencing (RNA-Seq) technique was used to obtain the complete transcriptomic data of both GSVs from CABG patients and varicose veins. Weighted Gene Co-expression network analysis (WGCNA) and further analyses were then carried out with the aim to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.ResultsFrom January 2015 to December 2016, 7 GSVs from CABG patients and 13 varicose veins were obtained. WGCNA identified 4 modules. In the brown module, gene ontology (GO) analysis showed that the biological processes were focused on response to stimulus, immune response and inflammatory response, etc. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the biological processes were focused on cytokine-cytokine receptor interaction and TNF signaling pathway, etc. In the gray module, GO analysis showed that the biological processes were skeletal myofibril assembly related. The immunohistochemistry staining showed that the expression of ASC, Caspase-1 and NLRP3 were increased in GSVs from CABG patients compared with varicose veins. Histopathological analysis showed that in the varicose veins group, the thickness of vascular wall, tunica intima, tunica media and collagen/smooth muscle ratio were significantly increased, and that the elastic fiber/internal elastic lamina ratio was decreased.ConclusionThis study shows that there are clear differences in transcriptomic information between varicose veins and GSVs from CABG patients. Some inflammatory RNAs are down-regulated in varicose veins compared with GSVs from CABG patients. Skeletal myofibril assembly pathway may play a crucial role in the pathogenesis of varicose veins. Characterization of these RNAs may provide new targets for understanding varicose veins diagnosis, progression, and treatment.https://www.frontiersin.org/article/10.3389/fphys.2019.00278/fullweight gene co-expression network analysisRNA-sequencingvaricose veinsinterferonGBP5guanylate-binding protein 5 |
| spellingShingle | Jianbin Zhang Qiangqiang Nie Qiangqiang Nie Chaozeng Si Cheng Wang Yang Chen Weiliang Sun Lin Pan Jing Guo Jie Kong Yiyao Cui Feng Wang Xueqiang Fan Zhidong Ye Jianyan Wen Peng Liu Peng Liu Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome Frontiers in Physiology weight gene co-expression network analysis RNA-sequencing varicose veins interferon GBP5 guanylate-binding protein 5 |
| title | Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome |
| title_full | Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome |
| title_fullStr | Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome |
| title_full_unstemmed | Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome |
| title_short | Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome |
| title_sort | weighted gene co expression network analysis for rna sequencing data of the varicose veins transcriptome |
| topic | weight gene co-expression network analysis RNA-sequencing varicose veins interferon GBP5 guanylate-binding protein 5 |
| url | https://www.frontiersin.org/article/10.3389/fphys.2019.00278/full |
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