Identification of Differentially Expressed Genes as Potential Therapeutic and Prognostic Targets for Breast Cancer Based on Bioinformatics

Background: Breast cancer (BC) is one of the most common malignant tumors in women. There is an urgent need to explore the key genes responsible for the prognosis of BC. The aim of this study was to screen out differentially expressed genes (DEGs) in BC and to provide reliable prognosis prediction. DEGs related to prognosis of BC were identified and verified as markers for predicting BC prognosis.Methods: Two data sets GSE22820 and GSE29431 were selected from the Gene Expression Omnibus (GEO) database and the DEGs were screened by the online tool of GEO2R and visualized by the volcano maps. The bioinformatics software of database for annotation, visualization, and integrated discovery (DAVID) was used to annotate associated functions of DEGs. Search tool for the retrieval of interacting genes/proteins (STRING) was used to construct the protein-protein interaction (PPI) networks which were visualized by Cytoscape software. Afterward, the data from The Cancer Genome Atlas (TCGA) were used for multivari-ate Cox regression analysis and Kaplan-Meier (K-M) survival analysis was used to identify prognosis-related key genes. The immortalized breast epithelial cell line MCF10A and BC cell line MCF7 were purchased and exploited to verify the differential expression of selected hub genes through real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) and western blot. The expressions of prognostic-related genes were regulated through transfecting MCF7 cells, followed by exploring the effects of prognosis-related genes. The cell proliferation was determined by assays of colony formation. The cell counting kit (CCK)-8 and the cell migration were evaluated by the tests of transwell and cell scratch. The flow cytometry of Annexin V-PE and 7-AAD double stained cells was used for measuring cell apoptosis. Results: The bioinformatics analysis indicated that 969 DEGs were found in GSE22820, out of which 421 genes were over-expressed and 548 genes were under-expressed. In GSE29431, 724 DEGs were found, out of which 109 genes were over-expressed and 615 genes were under-expressed. GSE22820, GSE29431, and Co-DEGs are involved in mitotic nuclear division, regulation of angiogenesis, connective tissue development, muscle organ development, glucose metabolic process, and hexose metabolic process. Genes of peroxisome proliferator-activated receptor alpha (PPARA), peroxisome proliferator-activated receptor gamma (PPARG), lipoprotein lipase (LPL), leptin (LEP), insulin like growth factor 1 (IGF1), type I collagen alpha 1 (COL1A1), Fibronectin (FN)1, and anillin (ANLN) were identified as hub genes, and ANLN, PPARA, PPARG, and LPL were verified for having effect on prognosis of BC. The upregulation of PPARA and PPARG, and the downregulation of ANLN and LPL restrained both proliferation and migration and induced apoptosis of BC cells.Conclusions: PPARA, PPARG, LPL, LEP, IGF1, COL1A1, FN1, and ANLN were identified as hub genes and ANLN, PPARA, PPARG, and LPL could affect the development of BC by inhibiting proliferation and migration and promoting apoptosis of cancer cells.