A comprehensive assessment of VCAN transcriptional expression and evaluation as an effective prognostic biomarker against breast cancer: in silico study

Abstract

Abstract Background The VCAN gene provides instructions for making a protein called versican which is a type of protein known as a proteoglycan. Versican is a key ingredient of the extracellular matrix, and due to its widespread expression in the body, versican is involved in cell adhesion, proliferation, and migration. Mutations or alterations of this protein could result in the disintegration of the fine-tuned molecular machinery which can lead to uncontrolled cell proliferation. Results VCAN is a novel prognostic marker for multiple cancers, and it showed tremendous results on breast cancer prognosis based on the data available on multiple websites. So, we targeted VCAN to analyze the expression and the outcome of breast cancer. This is a server-based study, and the expression of VCAN shows upregulation in breast cancer subtypes as compared to the normal tissue. The promoter methylation analysis suggested that overexpression of VCAN may be due to hypomethylation. Mutation analysis showed a positive correlation with VCAN expression where missense-type mutation has the highest percentage (77.33%), truncating (17.33%), and splice (4%) and somatic mutation frequency is 1.8%. VCAN was closely related to ten different genes and coexpressed with five of the genes among them. Five distinct compounds are linked to the methylation and mutagenesis of VCAN, according to the gene–drug interaction. Conclusions The upregulation of VCAN is closely correlated with promoter methylation and the clinical features of breast cancer patients. The whole study suggests that the breast cancer patient’s survival rate gets lower when the VCAN expression level gets higher. We anticipated that these findings will lead to further improvements in breast cancer prognosis and the significance of VCAN as a biomarker for breast cancer prognosis.

Keywords

• Breast cancer
• Cancer biomarker
• VCAN
• Gene expression
• Bioinformatics