Master Regulators of Signaling Pathways: An Application to the Analysis of Gene Regulation in Breast Cancer.

Analysis of gene regulatory networks allows the identification of master transcriptional factors that control specific groups of genes. In this work, we inferred a gene regulatory network from a large dataset of breast cancer samples to identify the master transcriptional factors that control the genes within signal transduction pathways. The focus in a particular subset of relevant genes constitutes an extension of the original Master Regulator Inference Algorithm (MARINa) analysis. This modified version of MARINa utilizes a restricted molecular signature containing genes from the 25 human pathways in KEGG's signal transduction category. Our breast cancer RNAseq expression dataset consists of 881 samples comprising tumors and normal mammary gland tissue. The top 10 master transcriptional factors found to regulate signal transduction pathways in breast cancer we identified are: TSHZ2, HOXA2, MEIS2, HOXA3, HAND2, HOXA5, TBX18, PEG3, GLI2, and CLOCK. The functional enrichment of the regulons of these master transcriptional factors showed an important proportion of processes related to morphogenesis. Our results suggest that, as part of the aberrant regulation of signaling pathways in breast cancer, pathways similar to the regulation of cell differentiation, cardiovascular system development, and vasculature development may be dysregulated and co-opted in favor of tumor development through the action of these transcription factors.

Regulation of LPA receptor function by estrogens.

17beta-Estradiol induced LPA(1) receptor desensitization in C9 cells stably expressing LPA(1) receptors and transiently expressing estrogen receptor alpha. Such desensitization was evidenced by a reduction in lysophosphatidic acid-mediated Ca(2+)mobilization and it was associated to receptor phosphorylation and internalization. These effects of 17beta-estradiol were rapid (taking place over 5 min) and were blocked by the estrogen receptor antagonist ICI 182780. Similarly, inhibitors of phosphoinositide 3-kinase (wortmannin and LY294002) and of protein kinase C (staurosporine and Gö 6976) blocked 17beta-estradiol-induced LPA(1) receptor desensitization and phosphorylation. Confocal microscopy evidenced LPA(1) receptor internalization in response to 17beta-estradiol treatment. Association between LPA(1) receptors and protein kinase C alpha was suggested by co-immunoprecipitation assays. Protein kinase C alpha was associated with LPA(1) receptors in the absence of stimulus and such association further increased in a dynamic fashion in response to 17beta-estradiol. The results demonstrated that in C9 cells estrogens modulate LPA(1) action through estrogen receptor alpha with the participation of protein kinase C alpha and phosphoinositide 3-kinase.