Discovery of new candidate biomarkers in Breast cancer tissue by multiomic analysis

During the transition from a normal cell to a tumor cell, in addition to morphological changes and the loss of some essential regulatory functions, a significant change is the ability to modify or reprogram energy metabolism and in fact, metabolism reprogramming has been recognized as a hallmark trait of many, if not all, tumors [Hanahan & Weinberg, 2011). Tumor cells exhibit varying degrees of increased glycolysis, depending on the cell type and growth conditions. About 60% of the ATP in tumor cells is produced through aerobic glycolysis (the Warburg effect), unlike normal cells, where ATP production typically occurs via oxidative phosphorylation (OXPHOS) in the mitochondria.The autonomous oncogenic activation of glycolysis appears to sustain the Warburg effect. However, the higher levels of glycolytic enzymes resulting from this effect may contribute to tumor adaptation through their alternative, non-glycolytic functions. These metabolic differences between tumor and normal tissues could underlie potential therapeutic applications.Alpha Enolase, encoded by the gene ENO1, is a critical enzyme in the glycolytic pathway. It catalyzes the dehydration of 2-phosphoglyceric acid to phosphoenolpyruvate and the reverse reaction during gluconeogenesis. Enolase forms homodimers that catalyze these reactions, with its mechanism of action facilitated by a magnesium ion that binds the substrate to the enzyme in the correct position.The ENO1 gene also encodes for another protein, Myc promoter binding protein-1 (MBP-1), a 37 kDa protein synthesized from the alternative translation of ENO1 mRNA, encoding α-enolase. Both α-enolase and MBP-1 are involved in tumorigenesis, albeit as antagonists. ENO1 is crucial for cell growth, hypoxia tolerance, autoimmune activities, and glycolysis. Conversely, MBP-1 suppresses cell proliferation and the invasive ability of cancer cells. MBP-1 acts, in the nucleus, as a transcriptional repressor of several proto-oncogenes, including c-MYC, HERBB2, COX-2, and FOXP3.Under physiological conditions, the intracellular levels of MBP-1 are considerably lower than those of α-enolase due to differences in their translation efficiency and stability. However, in many cancers, including breast cancer, increased levels of α-enolase are associated with significantly reducing MBP-1 levels.To elucidate the molecular pathways and the gene expression modulations through which MBP-1 inhibits cell growth and to identify potential new targets of MBP-1, transient and stable (using Clontech Tet-On® 3G Inducible Expression System) transfections were performed in various breast cancer cell lines to express MBP-1 fused with a FLAG tag. Western blot analysis was conducted to detect the presence of FLAG-MBP-1 using specific antibodies. Gene expression profiles of MBP1-transfected cells and controls were evaluated by statistical analyses. Pairwise comparison with Gene Set Enrichment Analysis (GSEA), Gene Onthology and pathway enrichment analysis revealed differentially expressed genes involved in diverse biological processes and molecular functions related to proliferation, apoptosis, cell migration and Epithelial Mesenchymal Transition (EMT). Several genes were found to act downstream to MBP1 and some of them may represent a new good prognosis gene signature for the subclass of triple-negative breast cancer (TNBC).