Screening for key genes associated with invasive ductal carcinoma of the breast via microarray data analysis

Abstract

ABSTRACT. The aim of this study was to identify key genes related to invasive ductal carcinoma (IDC) of the breast by analyzing gene expression data with bioinformatic tools. Microarray data set GSE31138 was downloaded from Gene Expression Omnibus, including 3 breast cancer tissue samples and 3 normal controls. Differentially expressed genes (DEGs) between breast cancer and normal control were screened out (FDR < 0.05 and |logFC| > 2). Coexpression between genes was examined with String, and a network was then constructed. Relevant pathways and diseases were retrieved with KOBAS. A total of 56 DEGs were obtained in the IDC of the breast compared with normal controls. A gene coexpression network including 27 pairs of genes was constructed and all the genes in the network were upregulated. Further study indicated that most of the genes in the coexpression network were enriched in ECM-receptor interaction (COL4A2, FN1, and HMMR) and nucleotide excision repair (CETN2 and PCNA) pathways, and that the most significantly related disease was autoimmune lymphoproliferative syndromes. A number of DEGs were acquired through comparative analysis of gene expression data. These findings are beneficial in promoting the understanding of the molecular mechanisms in breast cancer. More importantly, some key genes were revealed via gene coexpression network analysis, which could be potential biomarkers for IDC of the breast.

Extracellular Matrix–receptor Interaction Signaling Genes Associated with Inferior Breast Cancer Survival

“…As presented in Figure 1C, these DEGs were significantly enriched in 19 signaling pathways: the ECM-receptor interaction signaling pathway (p<0.001), malaria (p=0.013), staphylococcus aureus infection (p=0.002), lysosome (p=0.003), ABC transporters (p=0.003), focal adhesion (p=0.005), the PPAR signaling pathway (p=0.01), axon guidance (p=0.011), regulation of lipolysis in adipocytes (p=0.012), protein digestion and absorption (p=0.016), phagosome (p=0.019), hematopoietic cell lineage (p=0.036), biosynthesis of amino acids (p=0.047), the PI3K-Akt signaling pathway (p=0.058), proteoglycans in cancer (p=0.064), the Rap1 signaling pathway (p=0.088), the adipocytokine signaling pathway (p=0.092), biosynthesis of antibiotics (p=0.093), and the AMPK signaling pathway (p=0.095). Among them, the ECM-receptor interaction signaling pathway plays a crucial role in modulating breast cancer metastasis (14)(15)(16). Therefore, DEGs in the ECMreceptor interaction signaling pathway were prioritized for further examination in this study.…”

siRNA-Mediated suppression of collagen type iv alpha 2 (COL4A2) mRNA inhibits triple-negative breast cancer cell proliferation and migration

“…A recent study performed in the breast cancer cell line MCF-7 revealed that the reduction of COL4A2 mRNA levels by miR-29b may contribute to the invasiveness of MCF-7 cells [25]. It has been postulated that extracellular matrix-related COL4A2 is associated with breast cancer and may be a potential biomarker for early diagnosis and therapy of breast cancer [26]. All of the aforementioned studies suggest that COL4A2 may play a role in the pathogenesis of cancer, notably breast cancer.…”

Identification of potential biomarkers and candidate small molecule drugs in glioblastoma

“…Accumulating evidences demonstrated that CETN2 was identified in various types of cancers. Huan et al revealed that CETN2 was associated with invasive ductal carcinoma of the breast, and might be potential biomarker for breast cancer [ 29 ]. It was reported that the down-regulated of CETN2 might have tumor suppressive function in bladder cancer [ 30 ].…”