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Integrated Transcriptome-wide Profiling and Protein Structure Analysis of Pathogenic Genes in Venous Thromboembolism

Yan Che, Jing Ding, Yan Zhang

Back ground: Genetic factors are considered to determine the balance of the coagulation and anticoagulation processes, yet the genetic variants related to Venous Thromboembolism (VTE) remain unclear. This study aimed to investigate the potential molecular mechanisms and pathogenic mutations associated with VTE by determining VTE-related Differentially Expressed Genes (DEGs) by transcriptome-wide profiling and assaying protein structure in VTE.

Methods: Two gene expression datasets, GSE48000 and GSE19151, were accessed from the Gene Expression Omnibus (GEO) database to obtain gene expression data associated with VTE. We identified the DEGs between VTE patients and healthy people using R and performed functional enrichment analysis, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Then, Whole-Exome Sequencing (WES) was performed for 25 VTE patients and 17 normal cases, and the structural locations of pathogenic missense mutations were identified using pyMOL. Finally, DGIdb database was used to select candidate drugs for the treatment of VTE.

Results: A total of 232 DEGs were identified from the GEO database. The significant function of these DEGs was mostly involved in RNA catabolic process and ribosome pathway. Notably, the results of WES for DEGs and protein structure analysis showed that Histamine N-Methyltransferase (HNMT) (chr2: 138759649 C>T, rs11558538) may be a main predisposing factor for VTE. In addition, Amodiaquine, Harmaline, Aspirin, Metoprine, Dabigatran, and Diphenhydramine were screened for VTE therapy.

Conclusion: The results showed that HNMT (chr2: 138759649 C>T, rs11558538) may be potential target for the diagnosis and treatment of VTE.