NR2E3 gene networks are associated with AHR signaling pathways
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE79463 | GEO | 2017/10/31
SECONDARY ACCESSION(S): PRJNA315878
REPOSITORIES: GEO
Similar Datasets
Project description:In order to obtain a global picture regarding regulation of p53 in liver cells we used HepG2 hepatoma cells.We created two isogenic sub-cultures of HepG2 cells with altered expression of p53. HepG2 cells were infected with a retroviral vector harboring either small-hairpin RNA targeting p53 (termed HepG2sh-p53) or a non relevant small-hairpin RNA (termed HepG2sh-con). Cells were treated with two different p53 stimulators - Nutlin and AICAR
2012-03-30 | E-GEOD-30137 | biostudies-arrayexpress
Project description:In order to obtain a global picture regarding regulation of p53 in liver cells we used HepG2 hepatoma cells.We created two isogenic sub-cultures of HepG2 cells with altered expression of p53. HepG2 cells were infected with a retroviral vector harboring either small-hairpin RNA targeting p53 (termed HepG2sh-p53) or a non relevant small-hairpin RNA (termed HepG2sh-con).
2012-03-31 | GSE30137 | GEO
Project description:Poly(A) binding protein interacting protein 1 (PAIP1) is a translation regulator and also regulate the decay of mRNA. PAIP1 has also been reported to be a marker of increased invasive potential of liver cancer. However, the underlying molecular mechanism of PAIP1 in liver cancer is still unclear. Here, the gene expression profile of HepG2 cells transfected with PAIP1 shRNA (shPAIP1) was compared with cells transfected with empty vector (shCtrl). The results showed that shPAIP1 extensively affects the transcriptional level of 893 genes in HepG2 cells. In particular, GO analysis showed that a large number of up-regulated genes were annotated with terms including cell cycle and WNT receptor signaling pathway. The down-regulated genes were enriched in some pathways including immune response and inflammatory response. qPCR confirmed that PAIP1 knockdown significantly negatively or positively affected the expression of selected DEGs including interleukin-10 signaling pathway genes in HepG2 cells. Expression analysis of TCGA revealed that PAIP1 had positive correlations with IL1R2 and PTAFR in liver tumor tissue, respectively. Our results demonstrated that PAIP1 was not only a translation regulator, but also a transcription regulator in liver cancer. Thus, our study provides important cues for further study on the regulatory mechanism of PAIP1 in liver cancer
2023-03-12 | GSE185866 | GEO
Project description:In colorectal cancer, p53 is commonly inactivated, associated with chemo-resistance, and marks the transition from non-invasive to invasive disease. Cancers, including colorectal cancer, are thought to be diseases of aberrant stem cell populations, as stem cells are able to self-renew, making them long-lived enough to acquire mutations necessary to manifest the disease. We have shown that extracts from sweet sorghum stalk components eliminate colon cancer stem cells (CCSC) in a partial p53-dependent fashion. However, the underlying mechanisms are unknown. In the present study, CCSC were transfected with short hairpin-RNA against p53 (CCSC p53 shRNA) and treated with sweet sorghum phenolics extracted from different plant components (dermal layer, leaf, seed head and whole plant). While all components demonstrated anti-proliferative and pro-apoptotic effects in CCSC, phenolics extracted from the dermal layer and seed head were more potent in eliminating CCSC by elevating caspases 3/7 activity, PARP cleavage, and DNA fragmentation in a p53-dependent and p53-independent fashion, respectively. Further investigations revealed that the anti-proliferative and pro-apoptotic effects were associated with decreases in beta-catenin protein levels, and beta-catenin targets cyclin D1, cMyc, and survivin. These results suggest that the anti-proliferative and pro-apoptotic effects of sweet sorghum extracts against human colon cancer stem cells are via suppression of Wnt/beta-catenin pro-survival signaling in a p53-dependent (dermal layer) and partial p53-independent (seed head) fashion. LCMS used to identify phenolic compounds associated with extract activity
2014-05-01 | MTBLS69 | MetaboLights
Project description:While the roles of individual nuclear receptor (NR) in human diseases have been well characterized, interplays among NRs have not been extensively characterized due, in part, to technical difficulties in simultaneously monitoring molecular activities of all 48 NR genes. Using systems-level analysis of publically available gene expression data from NCI-60 cell lines, we uncovered novel interaction between ESR1 and orphan receptor NR2E3. Expression of NR2E3 is significantly associated with expression of ESR1 in NCI-60 cell lines as well as in breast cancer patients. To investigate how NR2E3 gene signatures are globally correlated with ESR1 signaling pathway, we performed microarray after knocking down NR2E3 or ESR1 in MCF-7 cells. Keywords: DNA microarray (Illumina human Ht12 V3) 3 shControl, 3 shNR2E3, 3 siLuc, 3 siESR1
2011-12-22 | E-GEOD-18431 | biostudies-arrayexpress
Project description:Kiaa0101 (p15PAF) was previously observed overexpressed in hepatocelluler carcinoma tissues and promoted tumorigenesis. In order to identify potential biological pathways modulated by Kiaa0101, a lentivirus vector with Kiaa0101 was constructed and transfected into an HepG2 cell line to obtain a stable cell line with high expression of Kiaa0101. Interestingly, all the protein levels of P21, phosphorylated P21, Akt and phosphorylated Akt were induced. Further, gene expression profiles of Kiaa0101 overexpressed hepatocelluler cancer cells were analyzed using the DNA microarray technique. Differentially expressed genes (DEGs) were screened and followed by Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. 1361 genes and 942 genes were upregulated and downregulated, respectively. The most represented enriched GO biological process, cellular component and molecular function categories included DNA-dependent regulation of transcripton, plasma membrane and DNA binding, respectively. KEGG pathway analysis showed that the most significantly expressed genes were linked to pathways in cancer, MAPK signaling pathway and Wnt signaling pathway. Our study provides a comparative transcriptome analysis and revealed the downstream genes and signaling pathways that are possibly involved in Kiaa0101-induced hepatocelluler carcinoma.
2016-12-06 | GSE90877 | GEO
Project description:While the roles of individual nuclear receptor (NR) in human diseases have been well characterized, interplays among NRs have not been extensively characterized due, in part, to technical difficulties in simultaneously monitoring molecular activities of all 48 NR genes. Using systems-level analysis of publically available gene expression data from NCI-60 cell lines, we uncovered novel interaction between ESR1 and orphan receptor NR2E3. Expression of NR2E3 is significantly associated with expression of ESR1 in NCI-60 cell lines as well as in breast cancer patients. To investigate how NR2E3 gene signatures are globally correlated with ESR1 signaling pathway, we performed microarray after knocking down NR2E3 or ESR1 in MCF-7 cells. Keywords: DNA microarray (Illumina human Ht12 V3)
2011-12-22 | GSE18431 | GEO
Project description: Not available
| S-EPMC9044668 | biostudies-literature
Project description:Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related death worldwide. In Egypt, CRC constitutes 4.2% of all cancers with median age is 50 years old.
| 2268489 | ecrin-mdr-crc
Project description:Perpose:We examined here whether SAM, which alters DNA methylation dynamics, interferes with the activity of Methyl-CpG Binding Domain Protein 2(Mbd2). Methods: mRNA of MBD2 knocked down of Skhep1 and HepG2 cells were generated by deep sequencing using Illumina GAIIx. DNA enriched by our designed microarray of MBD2 knocked down Skhep1 and HepG2 cells were also generated by deep sequencing using Illumina GAIIx. ChIP (Chromatin immunoprecipitation) was performed using ChIP-IT Express Kit with MBD2 antibody of SAM treated Skhep1, HepG2 and NorHep cells. concluds: SAM treatment results in reduction and redistribution of Mbd2 binding across genomic features in liver cancer cells, which is different from the response in untransformed liver cells. There is significant overlap between genes whose Mbd2 binding, DNA methylation and transcription are altered by Mbd2 depletion or SAM treatment. These data suggest that Mbd2 has a cancer specific footprint in binding, DNA methylation and transcription in liver cancer cells that is altered by SAM treatment. SAM selective impact on liver cancer cells is partially mediated by altering cancer specific Mbd2 binding. These data provide a molecular rationale for using either SAM or other Mbd2 modulators for treating/preventing liver cancer.
2021-02-10 | GSE166416 | GEO