RNA-seq analyses for control and nicotinamide treated TNBC cells

In this study, we investigated how nicotinamide (NAM) affects cellular metabolism in TNBC cells and also such altered cellular metabolism by NAM is linked to cytotoxic functions through an integrated analysis of proteome and transcriptome data generated from three different TNBC cell lines, BT20, MB468, and MB231. By analyzing mRNA-seq data from control and NAM treated TNBC cells (3 replicates in each of 3 cell lines), we identified differentially expressed genes (DEGs), and associated cellular process. The up-regulated genes were associated with the processes related to cell death (programmed cell death, autophagy, and apoptotic mitochondrial changes) and mitochondria (organization, pH reduction/oxidation-reduction/NADP metabolism, response to starvation, respiratory chain, and lipid/oxoacid metabolism). On the other hand, the processes related to immune response (NF-kB and MAPK signaling, cell adhesion/migration, and response to cytokine) and cell proliferation were down-regulated consistently in the three TNBC cells. Overall design: BT20/NAM treated BT20/ MDA-MB-468/NAM treated MDA-MB-468