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Gene expression profiling in Venous thromboembolism: Insights from publicly available datasets

Sunanda Arya1, Rashi Khare1, Iti Garg1

  • 1Defence Institute of Physiology and Allied Sciences (DIPAS), Defence Research and Development Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India.

Computational Biology and Chemistry
|October 16, 2024
PubMed

Insights

Venous thromboembolism (VTE) involves complex genetic factors. This study identified key up-regulated genes like MYC and down-regulated genes like MRPL13, offering insights for new diagnostic and therapeutic strategies.

Area of Science:

  • Genomics and Bioinformatics
  • Cardiovascular Disease Research
  • Molecular Biology

Background:

  • Venous thromboembolism (VTE) is a significant global health issue, ranking as the third leading cause of cardiovascular disease.
  • The intricate genetic underpinnings of VTE pathogenesis remain incompletely understood, necessitating further investigation.

Purpose of the Study:

  • To identify critical hub genes and molecular pathways implicated in the development and progression of VTE.
  • To leverage public gene expression data for a comprehensive analysis of VTE-associated genetic mechanisms.

Main Methods:

  • Differential gene expression (DEG) analysis was performed on two VTE patient datasets (GSE48000 and GSE19151) using the GEO2R tool.
  • Bioinformatics tools were employed to compare gene expression profiles between VTE patients and healthy controls.
  • Protein-protein interaction (PPI) network analysis was utilized to identify key hub genes.

Main Results:

  • Analysis revealed 19 up-regulated and 134 down-regulated genes in VTE patients.
  • Significantly enriched pathways included complement and coagulation cascade, B-cell receptor signaling, DNA methylation, and inflammation.
  • Top up-regulated hub genes (MYC, FOS, SGK1, CR2, CXCR4) are linked to vascular integrity, while down-regulated hub genes (MRPL13, MRPL3, MRPL11, RPS29, RPL9) are primarily mitochondrial ribosomal proteins.

Conclusions:

  • This study elucidates significantly enriched pathways and genes crucial for VTE development and prognosis.
  • The identified genetic markers and pathways hold potential for the development of novel diagnostic and therapeutic interventions for VTE management.
Abstract

Keywords:
Deep vein thrombosis (DVT)Differentially Expressed Genes (DEGs)Gene expressionPulmonary embolism (PE)Venous thromboembolism (VTE)

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