Altered Expression of LINC00511 and LINC01028 Could Disorder the Apoptosis Process in Breast Cancer: Integrative Bioinformatics Analysis and Experimental Confir

Background: NME1 is a crucial gene in the proliferation, cancer survival, and differentiation processes. The abnormal changes in the expression of NME1 could cause disturbance in the mentioned processes and lead the normal cells to different abnormalities, including cancer. Breast cancer is the most frequently diagnosed cancer in women and ranks second among causes for cancer related death in women. In this study, the expression pattern of NME1 and the two lncRNAs that have possible interaction with NME1 (LINC01028 and LINC00528) had been evaluated In the Isfahan breast cancer (BC) patients.

Methods and results: Microarray, pathway enrichment, Gene Ontology, RNA and Protein interaction, and co-expression analyses were performed to find novel integrated genes, proteins, and RNAs (coding and non-coding) in the BC patients, based on the bioinformatics tools (R programming language and online databases). After finding novel genes and RNAs, a real-time PCR experiment was performed to evaluate the accurate relative expression of found RNAs in the Isfahan human breast cancer samples. Bioinformatics analyses revealed that NME1 protein could regulate apoptotic-related proteins. Also, based on ENCORI and microarray data analysis, the expression of NME1 and LINC00511 (FC: 6.49, FDR< 0.0001) have a significant up-regulation in the BC samples. Also, LINC01028 had a significantly low expression in the mentioned datasets (FC: 0.08, FDR< 0.0001). A real-time PCR experiment validated the bioinformatics results. Based on the experiment, NME1 (LogFC: 2.664, P. Value< 0.0001) and LINC00511 (LogFC: 2.058, P …