Abstract
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.