Introduction: Ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) represent distinct stages in breast cancer progression, and accurate differentiation between them is crucial for clinical management, prognosis, and therapeutic decision-making. As the disease progresses from the DCIS stage to IDC, the expression levels of certain genes undergo significant alterations, which can be used to differentiate between DCIS and IDC. In this study, key genes involved in invasiveness were identified using bioinformatics tools.
Methods: The raw gene count files of the GSE47462 dataset were downloaded from the GEO database. Subsequently, counts for 9 DCIS samples and 14 IDC samples were extracted and analyzed using the DESeq2 package in the R program. Genes with differentially expressed levels (adjusted P-values <0.05 and ∣log2FoldChange∣>1) were imported into the STRING database, and a protein-protein interaction (PPI) network was constructed. Network analysis was then performed in Cytoscape 3.10.3, and hub genes were identified.
Results: In total, 38 downregulated genes and 95 upregulated genes were identified in the IDC group compared to the DCIS group. The highest level of expression was associated with the KLKP1 gene (log2FoldChange = 4.32), while the lowest level of expression was observed in the SLC5A8 gene (log2FoldChange = -4.51). The PPI network analysis results were sorted based on degree and betweenness centrality. Findings revealed that the FN1 gene, which is an upregulated gene in IDC, displayed the highest centrality values (degree centrality = 30, betweenness centrality = 0.53), confirming its role as a hub gene.
Conclusion: The findings highlight FN1 as a hub gene in IDC progression and invasiveness. The FN1 gene may serve as a potential candidate for both the diagnosis and treatment of IDC.
Keywords: DCIS, IDC, breast cancer, Network analysis, FN1 gene