Induction of apoptosis through ER stress and TP53 in MCF-7 cells by the nanoparticle [Gd@C82(OH)22]n: A systems biology study

The nanoparticle gadolinium endohedral metallofullerenol [Gd@C82(OH)22]n is a new candidate for cancer treatment with low toxicity. However, its anti-cancer mechanisms remain mostly unknown. In this study, we took a systems biology view of the gene expression profiles of human breast cancer cells (MCF-7) and human umbilical vein endothelial cells (ECV304) treated with and without [Gd@C82(OH)22]n, respectively, measured by the Agilent Gene Chip G4112F. To properly analyze these data, we modified a suit of statistical methods we developed. For the first time we applied the sub-sub normalization to Agilent two-color microarrays. Instead of a simple linear regression, we proposed to use a one-knot SPLINE model in the sub-sub normalization to account for nonlinear spatial effects. The parameters estimated by least trimmed squares- and S-estimators show similar normalization results. We made several kinds of inferences by integrating the expression profiles with the bioinformatic knowledge in KEGG pathways, Gene Ontology, JASPAR, and TRANSFAC. In the transcriptional inference, we proposed the BASE2.0 method to infer a transcription factor's up-regulation and down-regulation activities separately. Overall, [Gd@C82(OH)22]n induces more differentiation in MCF-7 cells than in ECV304 cells, particularly in the reduction of protein processing such as protein glucosylation, folding, targeting, exporting, and transporting. Among the KEGG pathways, the ErbB signaling pathway is up-regulated, whereas protein processing in endoplasmic reticulum (ER) is down-regulated. CHOP, a key pro-apoptotic gene downstream of the ER stress pathway, increases to nine folds in MCF-7 cells after treatment. These findings indicate that ER stress may be one important factor that induces apoptosis in MCF-7 cells after [Gd@C82(OH)22]n treatment. The expression profiles of genes associated with ER stress and apoptosis are statistically consistent with other profiles reported in the literature, such as those of HEK293T and MCF-7 cells induced by the miR-23a∼27a∼24-2 cluster. Furthermore, one of the inferred regulatory mechanisms comprises the apoptosis network centered around TP53, whose effective regulation of apoptosis is somehow reestablished after [Gd@C82(OH)22]n treatment. These results elucidate the application and development of [Gd@C82(OH)22]n and other fullerene derivates.