Regulation of vascular endothelial growth factor receptors by Rb and E2F1: role of acetylation

Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets

Background

Altered networks of gene regulation underlie many complex conditions, including cancer. Inferring gene regulatory networks from high-throughput microarray expression data is a fundamental but challenging task in computational systems biology and its translation to genomic medicine. Although diverse computational and statistical approaches have been brought to bear on the gene regulatory network inference problem, their relative strengths and disadvantages remain poorly understood, largely because comparative analyses usually consider only small subsets of methods, use only synthetic data, and/or fail to adopt a common measure of inference quality.

Methods

We report a comprehensive comparative evaluation of nine state-of-the art gene regulatory network inference methods encompassing the main algorithmic approaches (mutual information, correlation, partial correlation, random forests, support vector machines) using 38 simulated datasets and empirical serous papillary ovarian adenocarcinoma expression-microarray data. We then apply the best-performing method to infer normal and cancer networks. We assess the druggability of the proteins encoded by our predicted target genes using the CancerResource and PharmGKB webtools and databases.

Results

We observe large differences in the accuracy with which these methods predict the underlying gene regulatory network depending on features of the data, network size, topology, experiment type, and parameter settings. Applying the best-performing method (the supervised method SIRENE) to the serous papillary ovarian adenocarcinoma dataset, we infer and rank regulatory interactions, some previously reported and others novel. For selected novel interactions we propose testable mechanistic models linking gene regulation to cancer. Using network analysis and visualization, we uncover cross-regulation of angiogenesis-specific genes through three key transcription factors in normal and cancer conditions. Druggabilty analysis of proteins encoded by the 10 highest-confidence target genes, and by 15 genes with differential regulation in normal and cancer conditions, reveals 75% to be potential drug targets.

Conclusions

Our study represents a concrete application of gene regulatory network inference to ovarian cancer, demonstrating the complete cycle of computational systems biology research, from genome-scale data analysis via network inference, evaluation of methods, to the generation of novel testable hypotheses, their prioritization for experimental validation, and discovery of potential drug targets.

Nicotine-mediated induction of E-selectin in aortic endothelial cells requires Src kinase and E2F1 transcriptional activity

Smoking is highly correlated with enhanced likelihood of atherosclerosis by inducing endothelial dysfunction. In endothelial cells, various cell-adhesion molecules including E-selectin, are shown to be upregulated upon exposure to nicotine, the addictive component of tobacco smoke; however, the molecular mechanisms underlying this induction are poorly understood. Here we demonstrate that nicotine-induced E-selectin transcription in human aortic endothelial cells (HAECs) could be significantly blocked by α7-nAChR subunit inhibitor, α-BT, Src-kinase inhibitor, PP2, or siRNAs against Src or β-Arrestin-1 (β-Arr1). Further, chromatin immunoprecipitations show that E-selectin is an E2F1 responsive gene and nicotine stimulation results in increased recruitment of E2F1 on E-selectin promoter. Inhibiting E2F1 activity using RRD-251, a disruptor of the Rb-Raf-1 kinase interaction, could significantly inhibit the nicotine-induced recruitment of E2F1 to the E-selectin promoter as well as E-selectin expression. Interestingly, stimulation of HAECs with nicotine results in increased adhesion of U937 monocytic cells to HAECs and could be inhibited by pre-treatment with RRD-251. Similarly, depletion of E2F1 or Src using RNAi blocked the increased adhesion of monocytes to nicotine-stimulated HAECs. These results suggest that nicotine-stimulated adhesion of monocytes to endothelial cells is dependent on the activation of α7-nAChRs, β-Arr1 and cSrc regulated increase in E2F1-mediated transcription of E-selectin gene. Therefore, agents such as RRD-251 that can target activity of E2F1 may have potential therapeutic benefit against cigarette smoke induced atherosclerosis.

Regulation of matrix metalloproteinase genes by E2F transcription factors: Rb-Raf-1 interaction as a novel target for metastatic disease

The retinoblastoma (Rb)-E2F transcriptional regulatory pathway plays a major role in cell-cycle regulation, but its role in invasion and metastasis is less well understood. We find that many genes involved in the invasion of cancer cells, such as matrix metalloproteinases (MMP), have potential E2F-binding sites in their promoters. E2F-binding sites were predicted on all 23 human MMP gene promoters, many of which harbored multiple E2F-binding sites. Studies presented here show that MMP genes such as MMP9, MMP14, and MMP15 which are overexpressed in non-small cell lung cancer, have multiple E2F-binding sites and are regulated by the Rb-E2F pathway. Chromatin immunoprecipitation assays showed the association of E2F1 with the MMP9, MMP14, and MMP15 promoters, and transient transfection experiments showed that these promoters are E2F responsive. Correspondingly, depletion of E2F family members by RNA interference techniques reduced the expression of these genes with a corresponding reduction in collagen degradation activity. Furthermore, activating Rb by inhibiting the interaction of Raf-1 with Rb by using the Rb-Raf-1 disruptor RRD-251 was sufficient to inhibit MMP transcription. This led to reduced invasion and migration of cancer cells in vitro and metastatic foci development in a tail vein lung metastasis model in mice. These results suggest that E2F transcription factors may play a role in promoting metastasis through regulation of MMP genes and that targeting the Rb-Raf-1 interaction is a promising approach for the treatment of metastatic disease.

ARRB1-mediated regulation of E2F target genes in nicotine-induced growth of lung tumors

BACKGROUND

Nicotine induces the proliferation of non-small cell lung cancer (NSCLC) cells via nicotinic acetylcholine receptors and the arrestin, β1 (ARRB1) protein. However, whether ARRB1 translocates to the nucleus upon nicotinic acetylcholine receptor activation and how it regulates growth of human NSCLCs are not known.

METHODS

We investigated nuclear localization of ARRB1 in human NSCLC cell lines (A549 and H1650), normal lung cell lines (NHBE and SAEC), and lung cancer tissue microarray. A549 cells were transfected with ARRB1-specific short hairpin RNA (A549-sh) to knockdown ARRB1 expression, or with empty vector (A549-EV), to examine the role of ARRB1 in the mitogenic and antiapoptotic effects of nicotine, binding of ARRB1 to E2F transcription factors, and the role of ARRB1 in nicotine-induced expression of E2F-regulated survival and proliferative genes cell division cycle 6 homolog (CDC6), thymidylate synthetase (TYMS), and baculoviral IAP repeat-containing 5 (BIRC5). Real-time polymerase chain reaction was performed for quantitative analysis of mRNA expression. Chromatin immunoprecipitation assays were performed on A549 cells and fresh-frozen human NSCLC tumors (n = 8) to examine the binding of ARRB1, E1A binding protein (EP300), and acetylated histone 3 (Ac-H3) on the E2F-regulated genes. All statistical tests were two-sided.

RESULTS

Nicotine induced the nuclear translocation of ARRB1 in NSCLC and normal lung cells, and lung tumor tissues from smokers showed an increased nuclear localization. The mitogenic and antiapoptotic effects of nicotine were reduced in A549-sh cells. Nuclear ARRB1 bound to E2F transcription factors in normal lung cells, NSCLC cells, and tumors. Nicotine treatment induced a statistically significant increased expression of E2F-regulated genes in A549-EV but not in A549-sh cells; the maximum difference being observed in BIRC5 (A549-EV vs A549-sh, mean fold-increase in mRNA level upon nicotine treatment = 20.7-fold, 95% confidence interval = 19.2- to 22.2-fold, vs mean = 0.8-fold, 95% confidence interval= 0.78- to 0.82-fold, P < .001). Furthermore, nicotine induced the binding of ARRB1, EP300, and Ac-H3 on E2F-regulated genes.

CONCLUSION

Nicotine induced the nuclear translocation of ARRB1 and showed increased expression of proliferative and survival genes, thereby contributing to the growth and progression of NSCLCs.

Maternal peripheral blood gene expression in early pregnancy and preeclampsia

We investigated associations of early pregnancy maternal peripheral blood gene expression with preeclampsia. In a nested case control study, gene expression of peripheral blood, collected at 16weeks of gestation on average from 16 women destined to develop preeclampsia and 16 women who had normotensive pregnancies was profiled using Affymetrix GeneChip Arrays. Fold change and Student's T-test analyses were used to compare differential gene expression across the groups. Functions and functional relationships as well as common regulatory sequences of differentially expressed genes were investigated. Genes participating in abnormal placentation (e.g COL1A1), immune/inflammation response (e.g. IKBKB) and cellular development (including cell cycle) (e.g. RBI) were differentially expressed in early pregnancy peripheral blood in preeclampsia. We identified transcription factors (i.e. Sp1, MAZ and MZF1) that may account for co-expression of differentially expressed genes. Preeclampsia is associated with differential gene expression in early pregnancy peripheral blood.