Network-Based Analysis Reveals Gene Signature in Tip Cells and Stalk Cells

Background: Angiogenesis occurs during various physiological or pathological processes such as wound healing and tumor growth. Differentiation of vascular endothelial cells into tip cells and stalk cells initiates the formation of new blood vessels. Tip cells and stalk cells are endothelial cells with different biological characteristics and functions. Objective: The aim of this study was to determine the mechanisms of angiogenesis by exploring differences in gene expression of tip cells and stalk cells. Methods: Raw data were retrieved from NCBI Gene Expression Omnibus (GSE19284). Data were reanalyzed using bioinformatics methods that employ robust statistical methods, including identification of differentially expressed genes (DEGs) between the stalk and tip cells, Weighted Gene Correlation Network Analysis (WGCNA), gene ontology and pathway enrichment analysis using DAVID tools, integration of Protein-Protein Interaction (PPI) networks and screening of hub genes. DEGs of stalk and tip cells were grouped as dataset A. Gene modules associated with differentiation of stalk and tip cells screened by WGCNA were named dataset B. Further, we retrieved existing markers of angiogenesis from previous experimental studies on tip and stalk cells which we called dataset C. Intersection of datasets A, B and C was used as a candidate gene. Subsequently, we verified the results applying Quantitative Polymerase Chain Reaction (Q-PCR) to our clinical specimen. In general, the Q-PCR results coincide with the majority of the expression profile. Results: We identified five candidate genes, including ESM1, CXCR4, JAG1, FLT1 and PTK2, and two pathways, including Rap1 signaling pathway and PI3K-Akt signaling pathway in vascular endothelial cells that differentiate into tip cells and stalk cells using bioinformatics analysis. Conclusion: Bioinformatics approaches provide new avenues for basic research in different fields such as angiogenesis. The findings of this study provide new perspectives and a basis for the study of molecular mechanisms of vascular endothelial cell differentiation into stalk and tip cells. Genes and pathways identified in this study are potential biomarkers and therapeutic targets for angiogenesis in the tumor.