Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome

Jianbin Zhang; 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

doi:10.3389/fphys.2019.00278

Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome

Front Physiol. 2019 Mar 19:10:278. doi: 10.3389/fphys.2019.00278. eCollection 2019.

Authors

Jianbin Zhang¹, Qiangqiang Nie^{1

2}, Chaozeng Si³, Cheng Wang⁴, Yang Chen⁵, Weiliang Sun⁶, Lin Pan⁶, Jing Guo⁶, Jie Kong¹, Yiyao Cui¹, Feng Wang², Xueqiang Fan¹, Zhidong Ye¹, Jianyan Wen¹, Peng Liu^{1

2}

Affiliations

¹ Department of Cardiovascular Surgery, China-Japan Friendship Hospital, Beijing, China.
² Department of Cardiovascular Surgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.
³ Department of Operations and Information Management, China-Japan Friendship Hospital, Beijing, China.
⁴ Department of Medicine, Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN, United States.
⁵ MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST, School of Medicine, Tsinghua University, Beijing, China.
⁶ Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China.

Abstract

Objective: Varicose 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.

Methods: We 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.

Results: From 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.

Conclusion: This 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.

Keywords: GBP5; RNA-sequencing; guanylate-binding protein 5; interferon; varicose veins; weight gene co-expression network analysis.