scholarly journals Analysis of Transcription Factor-Related Regulatory Networks Based on Bioinformatics Analysis and Validation in Hepatocellular Carcinoma

2018 ◽  
Vol 2018 ◽  
pp. 1-16 ◽  
Author(s):  
Shui Liu ◽  
Xiaoxiao Yao ◽  
Dan Zhang ◽  
Jiyao Sheng ◽  
Xin Wen ◽  
...  

Hepatocellular carcinoma (HCC) accounts for a significant proportion of liver cancer, which has become the second most common cause of cancer-related mortality worldwide. To investigate the potential mechanisms of invasion and progression of HCC, bioinformatics analysis and validation by qRT-PCR were performed. We found 237 differentially expressed genes (DEGs) including EGR1, FOS, and FOSB, which were three cancer-related transcription factors. Subsequently, we constructed TF-gene network and miRNA-TF-mRNA network based on data obtained from mRNA and miRNA expression profiles for analysis of HCC. We found that 42 key genes from the TF-gene network including EGR1, FOS, and FOSB were most enriched in the p53 signaling pathway. The qRT-PCR data confirmed that mRNA levels of EGR1, FOS, and FOSB all were decreased in HCC tissues. In addition, we confirmed that the mRNA levels of CCNB1, CCNB2, and CHEK1, three key markers of the p53 signaling pathway, were all increased in HCC tissues by bioinformatics analysis and qRT-PCR validation. Therefore, we speculated that miR-181a-5p, which was upregulated in HCC tissues, could regulate FOS and EGR1 to promote the invasion and progression of HCC by p53 signaling pathway. Overall, the study provides support for the possible mechanisms of progression in HCC.

2018 ◽  
Vol 50 (6) ◽  
pp. 2216-2228 ◽  
Author(s):  
Ting Zhang ◽  
Hongmei Wang ◽  
Qiang Li ◽  
Jianliang Fu ◽  
Jiankang Huang ◽  
...  

Background/Aims: This study focused on evaluating the effect of MALAT1 and MDM2 on ischemic stroke through regulation of the p53 signaling pathway. Materials: Bioinformatics analysis was performed to identify abnormally expressed lncRNAs, mRNAs and their associated pathways. Oxygen-glucose deprivation/reoxygenation (OGD/R) in cells and middle cerebral artery occlusion/reperfusion (MCAO/R) in mice were performed to simulate an ischemic stroke environment. Western blot and qRT-PCR were used to examine lncRNA expression and mRNA levels. Fluorescence in situ hybridization (FISH) LncRNA was used to locate mRNA. MTT and flow cytometry were performed to examine cell proliferation and apoptosis. Finally, immunohistochemistry was used to observe the expression of genes in vivo. Results: MALAT1 and MDM2, which exhibit strong expression in stroke tissues, were subjected to bioinformatics analysis, and the p53 pathway was chosen for further study. MALAT1, MDM2 and p53 signaling pathway-related proteins were all up regulated in OGD/R cells. Furthermore, Malat1, Mdm2 and p53 pathway related-proteins were also up regulated in MCAO/R mice. Both MALAT1 and MDM2 were localized in the nuclei. Down regulation of MALAT1 and MDM2 enhanced cell proliferation ability and reduced apoptosis, resulting in decreased infarct size in MCAO/R brains. Conclusion: These results indicate that MALAT1/MDM2/p53 signaling pathway axis may provide more effective clinical therapeutic strategy for patients with ischemic stroke.


Hepatology ◽  
2011 ◽  
Vol 53 (3) ◽  
pp. 843-853 ◽  
Author(s):  
Weili Liu ◽  
Xiaoxing Li ◽  
Eagle S.H. Chu ◽  
Minnie Y.Y. Go ◽  
Lixia Xu ◽  
...  

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4879-4879 ◽  
Author(s):  
Hai Wang ◽  
Chao Xie ◽  
Shiwu Li ◽  
Eva V. George ◽  
Westley H. Reeves ◽  
...  

Abstract A consistent feature of over 100 reported cases of breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is their complex cytogenetic abnormalities, suggesting that genomic instability may drive lymphomagenesis and/or tumor progression. Loss of heterozygosity(LOH) of the TP53 tumor suppressor gene locus on the short arm of chromosome 17 (17p13.1) is a frequent finding. Human p53 plays an important role in cell cycle arrest, DNA repair, and apoptosis and it maintains genome stability by preventing mutations. Recently, three T cell breast lymphoma (TLBR) cell lines were derived from patients’ BIA-ALCL primary tumor biopsy specimens. These cell lines are IL-2 dependent, ALK-negative, CD30+activated cytotoxic T cells closely resembling the original tumor cells. Thus, the cell lines may serve as an important tool for studying this newly recognized disease entity. Because of its rarity, the clinical pathologic features, tumor cell biology, and genetics of BIA-ALCL have yet to be fully defined. Here we tested the hypothesis that the p53 signaling pathway is defective in TLBR cells. We initially examined TP53 transcript expression among the cell lines. By qRT-PCR, p53 transcripts were detected in all three lines, with the highest level in TLBR-2. Next we examined p53 protein expression and p53 activation in response to ultraviolet (UV) or gamma irradiation. By Western blotting, all TLBR cell lines expressed much lower levels of p53 protein following UV irradiation (400 J/m2) than Karpas (ALK+ ALCL) cells and failed to show ATM/ATR-induced phosphorylation of p53 on serine 15, an early indicator of p53 activation. Genetic defects (deletion, mutation) of the p53 coding sequence were not found by Sanger sequencing. Interestingly, a polymorphism at p53 codon 72 (Arg72Pro), a normal variant associated with increased susceptibility to breast cancer, was detected in TLBR-1 and -3 (derived from indolent BIA-ALCL), but not in the aggressive BIA-ALCL line TLBR-2. Thus, TLBR cells exhibit defective regulation of the p53 pathway in response to DNA damage, suggesting that their ability to sense DNA damage or the regulation of p53 stability may be impaired. We next examined the DNA damage sensing pathway upstream of p53 in the presence and absence of the DNA demethylating agent 5-aza-2'-deoxycytidine (AZA, 10µM for 48hrs). In all TLBR lines, ATM and ATR transcripts were expressed at much lower levels (qRT-PCR) than normal, and their expression was not significantly affected by AZA. However, compared with human T cells, CHK2 (phosphorylate P53 at Ser20) transcripts were very low in TLBR-1 and -2, but not in TLBR-3 cells. CHK2 and p21 (the main p53 target gene) transcripts after AZA were greatly increased in TLBR-2, mildly elevated in TLBR-3, and unchanged in TLBR-1 cells, suggesting that DNA methylation of the CHK2 and p21 genes may partly explain the defective p53 signaling in TLBR-2 cells. This was confirmed by detecting of CHK2 phorphrylation only in TLBR-3 cells. Mdm2, a major negative regulator of p53 protein stability, was either normal or low (qRT-PCR), and was unaffected by AZA. However, immunobloting with Mdm2 antibodies revealed increased levels of two isoforms following UV of TLBR-1 and -2, but only the small isoform was expressed in TLBR-3 cells and there was little response to UV treatment. Treatment of TLBR cells with 5 µM Nutlin-3 (Mdm2 antagonist, p53 activator, and apoptosis inducer) inhibited cell growth by 40% at day 5 (MTT assay). We conclude that these three BIA-ALCL derived cell lines share dysregulation of the p53 signaling pathway, which may contribute to the genomic instability characteristic of these BIA-ALCL cases. First two authors have equally contributed to this abstract. Disclosures: No relevant conflicts of interest to declare.


2016 ◽  
Vol 2016 ◽  
pp. 1-21 ◽  
Author(s):  
Qian Mao ◽  
Pin-Hu Zhang ◽  
Jie Yang ◽  
Jin-Di Xu ◽  
Ming Kong ◽  
...  

Ginsenoside F2(F2), a protopanaxdiol type of saponin, was reported to inhibit human gastric cancer cells SGC7901. To better understand the molecular mechanisms of F2, an iTRAQ-based proteomics approach was applied to define protein expression profiles in SGC7901 cells in response to lower dose (20 μM) and shorter duration (12 hour) of F2treatment, compared with previous study. 205 proteins were screened in terms of the change in their expression level which met our predefined criteria. Further bioinformatics and experiments demonstrated that F2treatment downregulated PRR5 and RPS15 and upregulated RPL26, which are implicated in ribosomal protein-p53 signaling pathway. F2also inhibited CISD2, Bcl-xl, and NLRX1, which are associated with autophagic pathway. Furthermore, it was demonstrated that F2treatment increased Atg5, Atg7, Atg10, and PUMA, the critical downstream effectors of ribosomal protein-p53 signaling pathway, and Beclin-1, UVRAG, and AMBRA-1, the important molecules in Bcl-xl/Beclin-1 pathway. The 6 differentially abundant proteins, PRR5, CISD2, Bcl-xl, NLRX1, RPS15, and RPL26, were confirmed by western blot. Taken together, ribosomal protein-p53 signaling pathway and Bcl-xl/Beclin-1 pathway might be the most significantly regulated biological process by F2treatment in SGC7901 cells, which provided valuable insights into the deep understanding of the molecular mechanisms of F2for gastric cancer treatment.


2021 ◽  
Author(s):  
PL Wei ◽  
Yifei Qi ◽  
Yupei Tan ◽  
Dehuai Long ◽  
Wenlong Xing ◽  
...  

Abstract Background Many experiments showed that Notopterygii Rhizoma Et Radix (NRR) can resist arrhythmia, but the mechanism of its action has not clear. Here, we investigated the possible mechanisms of NRR by network pharmacology and molecular docking and verified them experimentally. Methods Active componds and targets of NRR were retrieved by the Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database andAnalysis Platform, SymMap, and the Encyclopedia of Traditional Chinese Medicine (ETCM) databases. Arrhythmia-related targets were acquired from Comparative Toxicogenomics Database (CTD) and GeneCards databases. Overlapping targets of NRR associated with arrhythmia were acquired via Venn diagram. DAVID was applied for GO and KEGG pathway analyses. Cytoscape software and its plug-in were used for PPI network construction, module division and hub nodes screening. AutoDock Vina and qRT-PCR were carried out for validation. Results The 21 active compounds and 57 targets were obtained. Of these, coumarin was the predominant category including 15 components and 31 targets. The 5 key targets of NRR in treating arrhythmia, and these targets are involved in the apoptotic process, extrinsic apoptotic signaling pathway in absence of ligand, endopeptidase activity involved in apoptotic process by cytochrome c. The main pathways are p53 signaling pathway, Hepatitis B and Apoptosis. The results of molecular docking and qRT-PCR display good effect on hub node regulation in NRR treatment. Conclusion NRR plays an important role in anti-apoptotic mediated by modulating p53 signaling pathway, which may provide insight into future research and clinical applications in arrhythmia therapy.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 5330-5330 ◽  
Author(s):  
Fu-Sheng Chou ◽  
Mark Wunderlich ◽  
James C. Mulloy

Abstract A subset of acute myeloid leukemia is caused by the chromosomal translocation (8;21), resulting in the expression of the AML1-ETO (AE) fusion protein. AE expression in human CD34+ umbilical cord blood (UCB) cells causes an expansion of the hematopoietic stem and progenitor cell (HSPC) compartment, but alone does not cause leukemia. We have recently shown that AE represses DNA damage repair genes, resulting in higher mutation frequency as well as p53 activation and increased basal apoptosis. Interestingly, we found that AE expression in CD34+ UCB cells was associated with high Bcl-xL levels, while control cells showed a gradual loss of Bcl-xL protein. Furthermore, expression of AE in aged HSPC that had already downregulated Bcl-xL also led to Bcl-xL protein upregulation. In addition, Bcl-xL protein, but not mRNA, was decreased by pharmacological and RNAi-mediated inhibition of p53 in AE cells and increased by low-intensity γ-irradiation, implying that Bcl-xL turnover may be post-translationally regulated by p53 levels. Bcl-xL knock-down by short-hairpin RNA in AE cells resulted in even higher p53 activity and growth disadvantage, suggesting that AE cells depend largely upon Bcl-xL for survival in the context of p53 activation. AE cells are also more sensitive than long-term cultured UCB cells to GX15-070, a BH3-mimetic drug that binds and inhibits all anti-apoptotic Bcl-2 family proteins. The sensitivity of AE cells to Bcl-xL inhibition and GX15-070 treatment may be due to upregulation of various pro-apoptotic Bcl-2 family proteins. Surprisingly, p53-upregulated modulator of apoptosis (PUMA) mRNA levels were decreased or remained unchanged in association with AE expression, even in the context of an upregulated p53 signaling pathway. Chromatin immunoprecipitation assay revealed that AE binds to and AML1 binding site in the putative promoter of PUMA, in a region distinct from the p53 consensus binding site. Indeed, PUMA expression is increased in response to γ-irradiation in cells expressing AE. This suggests that AE may directly repress PUMA gene expression, but does not prevent p53 binding. Taken together, our data indicate that AE expression may lead to re-establishment of a new balance between the pro-apoptotic signals conveyed by the activated p53 signaling pathway and the pro-survival signals, presumably Bcl-xL upregulation and PUMA repression, within the Bcl-2 family proteins to ensure cell survival and propagation.


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