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RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
Published on: February 13, 2013
The molecular complexity of deep vein thrombosis was preliminarily explored based on the ceRNA network, scRNA-seq and
Bao-Ze Pan1, Qing-Yu Luo1, Ming-Jun Jiang1
1Department of Vascular Surgery, The Second Affiliated Hospital, Hengyang Medical School, University of South China, No.35, Jiefang Road, Hengyang, Hunan Province, 421001, People's Republic of China.
Background:
Deep vein thrombosis (DVT) is a prevalent peripheral vascular disease that is frequently accompanied by significant complications. However, the complexity and diversity of its pathogenesis have resulted in a lack of in-depth understanding of relevant regulatory targets. The objective of this study was to identify the highly distinctive genes associated with DVT, and to investigate their intricacies.
Methods:
In this study, a comprehensive transcriptomic analysis was conducted on blood samples from 4 DVT patients and 6 healthy subjects from an internal test set, employing established standard procedures. Differential (diff) circular RNAs (circRNAs), diff microRNAs (miRNAs) and diff messenger RNAs (mRNAs) associated with DVT were identified to construct a competing endogenous RNA (ceRNA) network model, and node mRNAs were identified in an external validation set (n = 14). Furthermore, a topological analysis was conducted by using 7 protein-protein interaction (PPI) network algorithms. Concurrently, AlphaFold 2 was employed for three-dimensional prediction and assessment of the molecular structure. The comparative toxicology genomics database (CTD) was employed to assess the interconnectivity between these genes. Subsequently, single-cell RNA sequencing (scRNA-seq) was conducted on blood samples from 3 DVT patients and 3 healthy subjects, following the standard protocol, to ascertain the cellular localization of gene expression and the role of core pathways.
Results:
A whole-transcriptome analysis identified a total of 406 diff circRNAs, 29 diff miRNAs and 154 diff mRNAs. Concurrently, a total of 6 circRNAs, 5 miRNAs and 16 mRNAs were incorporated into the ceRNA network models (a total of 6 node mRNAs were identified differentially). A total of 5 hub genes (including JAK2, CD36, TNFSF13B, TLR7 and PARP9) were identified by 7 PPI network algorithms. The structure and function of the above genes are adequately described by the AlphaFold 2 and CTD interference scores. A total of 7 cell types were identified by scRNA-seq, and there were obvious differences in the localization of genes and the role of core pathways in different cells.
Conclusions:
JAK2, CD36, TNFSF13B, TLR7 and PARP9 were identified as potential regulatory target genes for the pathophysiological process of DVT. Additionally, hsa_circ_0095124/hsa-miR-3074-5p/TNFSF13B is a potential regulatory pathway for DVT.
Insights
This study identifies five key genes (JAK2, CD36, TNFSF13B, TLR7, PARP9) as potential targets for deep vein thrombosis (DVT). A specific regulatory pathway involving circRNA, miRNA, and TNFSF13B is also highlighted for DVT.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Deep vein thrombosis (DVT) is a common vascular disease with complex pathogenesis and limited understanding of regulatory targets.
- Identifying novel molecular targets is crucial for understanding DVT complications.
Purpose of the Study:
- To identify distinctive genes associated with DVT.
- To investigate the intricate regulatory mechanisms underlying DVT.
Main Methods:
- Comprehensive transcriptomic analysis of circRNAs, miRNAs, and mRNAs in DVT patients and healthy controls.
- Construction of a competing endogenous RNA (ceRNA) network model.
- Protein-protein interaction (PPI) network analysis, AlphaFold 2 structure prediction, and Comparative Toxicogenomics Database (CTD) assessment.
- Single-cell RNA sequencing (scRNA-seq) to determine cellular gene expression localization and pathway roles.
Main Results:
- Identification of 406 differentially expressed circRNAs, 29 miRNAs, and 154 mRNAs.
- Construction of ceRNA networks revealing key interactions.
- Five hub genes (JAK2, CD36, TNFSF13B, TLR7, PARP9) identified through PPI network analysis.
- scRNA-seq revealed distinct gene expression patterns and pathway roles across different cell types.
Conclusions:
- JAK2, CD36, TNFSF13B, TLR7, and PARP9 are proposed as potential regulatory targets for DVT.
- The pathway hsa_circ_0095124/hsa-miR-3074-5p/TNFSF13B is identified as a potential regulator in DVT pathogenesis.
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