scholarly journals STAT3 Is the Master Regulator for the Forming of 3D Spheroids of 3T3-L1 Preadipocytes

Cells ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 300
Author(s):  
Hiroshi Ohguro ◽  
Yosuke Ida ◽  
Fumihito Hikage ◽  
Araya Umetsu ◽  
Hanae Ichioka ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cultured Cells ◽  
Binding Protein ◽  
Critical Role ◽  
Enrichment Analysis ◽  
Sequencing Analysis ◽  
Fatty Acid Binding ◽  
Go Enrichment ◽  
Go Enrichment Analysis ◽  
3D Spheroids

To elucidate the currently unknown mechanisms responsible for the diverse biological aspects between two-dimensional (2D) and three-dimensional (3D) cultured 3T3-L1 preadipocytes, RNA-sequencing analyses were performed. During a 7-day culture period, 2D- and 3D-cultured 3T3-L1 cells were subjected to lipid staining by BODIPY, qPCR for adipogenesis related genes, including peroxisome proliferator-activated receptor γ (Pparγ), CCAAT/enhancer-binding protein alpha (Cebpa), Ap2 (fatty acid-binding protein 4; Fabp4), leptin, and AdipoQ (adiponectin), and RNA-sequencing analysis. Differentially expressed genes (DEGs) were detected by next-generation RNA sequencing (RNA-seq) and validated by a quantitative reverse transcription–polymerase chain reaction (qRT–PCR). Bioinformatic analyses were performed on DEGs using a Gene Ontology (GO) enrichment analysis and an Ingenuity Pathway Analysis (IPA). Significant spontaneous adipogenesis was observed in 3D 3T3-L1 spheroids, but not in 2D-cultured cells. The mRNA expression of Pparγ, Cebpa, and Ap2 among the five genes tested were significantly higher in 3D spheroids than in 2D-cultured cells, thus providing support for this conclusion. RNA analysis demonstrated that a total of 826 upregulated and 725 downregulated genes were identified as DEGs. GO enrichment analysis and IPA found 50 possible upstream regulators, and among these, 6 regulators—transforming growth factor β1 (TGFβ1), signal transducer and activator of transcription 3 (STAT3), interleukin 6 (IL6), angiotensinogen (AGT), FOS, and MYC—were, in fact, significantly upregulated. Further analyses of these regulators by causal networks of the top 14 predicted diseases and functions networks (IPA network score indicated more than 30), suggesting that STAT3 was the most critical upstream regulator. The findings presented herein suggest that STAT3 has a critical role in regulating the unique biological properties of 3D spheroids that are produced from 3T3-L1 preadipocytes.

EPA and DHA confer protection against DON-induced endoplasmic reticulum stress and iron imbalance in IPEC-1 cells

2021 ◽  
pp. 1-29
Author(s):  
Jia Lin ◽  
Feifei Huang ◽  
Tianzeng Liang ◽  
Qin Qin ◽  
Qiao Xu ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Er Stress ◽  
Rna Sequencing ◽  
Cell Injury ◽  
Cell Damage ◽  
Binding Protein ◽  
Sequencing Analysis ◽  
Epa And Dha ◽  
Expression Of Genes ◽  
Transferrin Receptor 1

Abstract This study assessed the molecular mechanism of eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA) protection against IPEC-1 cell damage induced by deoxynivalenol (DON). The cells were divided into six groups, including the CON group, the EPA group, the DHA group, the DON group, the EPA+DON group, and the DHA+DON group. RNA sequencing was used to investigate the potential mechanism, and qRT-PCR was employed to verify the expression of selected genes. Changes in ultrastructure were used to estimate pathological changes and endoplasmic reticulum (ER) injury in IPEC-1 cells. Transferrin receptor 1 (TFR1) was tested by ELISA. Fe2+ and malondialdehyde (MDA) contents were estimated by spectrophotometry, and reactive oxygen species (ROS) was assayed by fluorospectrophotometry. RNA sequencing analysis showed that EPA and DHA had a significant effect on the expression of genes involved in ER stress and iron balance during DON-induced cell injury. The results showed that DON increased ER damage, the content of MDA and ROS, the ratio of X-box binding protein 1s (XBP-1s)/X-box binding protein 1u (XBP-1u), the concentration of Fe2+, and the activity of TFR1. However, the results also showed that EPA and DHA decreased the ratio of XBP-1s/XBP-1u to relieve DON-induced ER damage of IPEC-1 cells. Moreover, EPA and DHA (especially DHA) reversed the factors related to iron balance. It can be concluded that EPA and DHA reversed IPEC-1 cell damage induced by DON. DHA has the potential to protect IPEC-1 cells from DON-induced iron imbalance by inhibiting ER stress.

Abstract P347: Retinol-binding Protein 7 (RBP7) is Required for PPARG-mediated Endothelial Protection via Adiponectin

Hypertension ◽  
2016 ◽  
Vol 68 (suppl_1) ◽  
Author(s):  
Chunyan Hu ◽  
Henry L Keen ◽  
Ko-Ting Lu ◽  
Deborah R Davis ◽  
Xuebo Liu ◽  
...  
Keyword(s):  
Endothelial Dysfunction ◽  
Rna Sequencing ◽  
Basilar Artery ◽  
Vascular Function ◽  
Carotid Arteries ◽  
Target Genes ◽  
Binding Protein ◽  
Retinol Binding Protein ◽  
Specific Expression ◽  
Fatty Acid Binding

PPARγ protects against endothelial dysfunction by regulation of unknown target genes. One such target, RBP7, an intracellular fatty acid-binding protein, exhibits endothelium-specific expression, but its effect on vascular function remain unknown. We hypothesize that RBP7 is endothelial protective. We examined vascular responses in basilar artery (pressurized myograph) of RBP7-knockout (KO) and wild type (WT) mice fed normal chow (ND) or high fat diet (HFD) for 8 wks. Endothelium-dependent acetylcholine (ACh)-induced relaxation was significantly impaired in HFD-fed KO mice (ACh, 100μM: 33±7% KO vs 83±10% WT, p<0.05), but not in ND-fed groups. This response was ameliorated by pre-incubation with superoxide scavenger tempol (1mM) or PEG-superoxide dismutase (100 U/ml). Mean arterial pressure (measured by radiotelemetry), body weight, hepatic steatosis, fasting glucose, glucose tolerance, and insulin sensitivity were similar in HFD-fed KO and WT mice. To identify targets downstream of RBP7, RNA-Sequencing was performed on carotid arteries from 8-week HFD-fed WT and KO mice as well as ND-fed age-matched littermates. Adiponectin (AdipoQ), a PPARγ target, was increased ~6-fold in HFD-fed WT mice, a response that was markedly blunted in KO mice. RNA sequencing was confirmed by qPCR. There was no difference in plasma AdipoQ. AdipoQ protein is expressed in endothelial cells of carotid arteries and its level of expression was increased in HFD-fed WT but not KO mice (AdipoQ/CD31: 1.14±0.1 WT-HFD vs 0.82±0.1 WT-ND, p<0.05; 0.79±0.1 KO-HFD vs 0.81±0.04 KO-ND). This led us to hypothesize that AdipoQ is involved in RBP7-mediated endothelial protection. Incubation of basilar artery with mouse full-length AdipoQ protein (5 μg/mL, 4 hours) significantly ameliorated endothelial dysfunction (ACh, 100 μM: 56±6% AdipoQ+KO vs 26±3% KO, p<0.05) and blunted carotid artery superoxide production in HFD-fed KO mice. AdipoQ also protects against endothelial dysfunction caused by subpressor Ang-II in KO mice. We conclude that RBP7 protects the endothelium from oxidative stress-induced dysfunction through an AdipoQ-dependent mechanism. Our evidence suggests RBP7 is an essential cofactor for activation of some PPARγ target genes in the endothelium.

scholarly journals Comprehensive biological information analysis of PTEN gene in pan-cancer

2021 ◽  
Author(s):  
Hang Zhang ◽  
Wenhan Zhou ◽  
Xiaoyi Yang ◽  
Shuzhan Wen ◽  
Baicheng Zhao ◽  
...  
Keyword(s):  
3D Structure ◽  
Enrichment Analysis ◽  
Biological Information ◽  
Pten Gene ◽  
Clinical Prognosis ◽  
Regulatory Pathways ◽  
Go Enrichment ◽  
Go Enrichment Analysis ◽  
Pan Cancer ◽  
Low Expression

Abstract Background PTEN is a multifunctional tumor suppressor gene mutating at high frequency in a variety of cancers. However, its expression in pan-cancer, correlated genes, survival prognosis, and regulatory pathways are not completely described. Here, we aimed to conduct a comprehensive analysis from the above perspectives in order to provide reference for clinical application. Methods we studied the expression levels in cancers by using data from TCGA and GTEx database. Obtain expression box plot from UALCAN database. Perform mutation analysis on the cBioportal website. Obtain correlation genes on the GEPIA website. Construct protein network and perform KEGG and GO enrichment analysis on the STRING database. Perform prognostic analysis on the Kaplan-Meier Plotter website. We also performed transcription factor prediction on the PROMO database and performed RNA-RNA association and RNA-protein interaction on the RNAup Web server and RPISEq. The gene 3D structure, protein sequence and conserved domain were obtained in NCBI respectively. Results PTEN was underexpressed in all cancers we studied. It was closely related to the clinical stage of tumors, suggesting PTEN may involved in cancer development and progression. The mutations of PTEN were present in a variety of cancers, most of which were truncation mutations and missense mutations. Among cancers (KIRC, LUAD, THYM, UCEC, Gastric Cancer, Liver Cancer, Lung Cancer, Breast Cancer), patients with low expression of PTEN had a shorter OS time and poorer OS prognosis. The low expression of PTEN can cause the deterioration of RFS in certain cancers (TGCT, UCEC, LIHC, LUAD, THCA), suggesting that the expression of PTEN was related to the clinical prognosis. Our study identified genes correlated with PTEN and performed GO enrichment analysis on 100 PTEN-related genes obtained from the GEPIA website. Conclusions The understanding of PTEN gene and the in-depth exploration of its related regulatory pathways may provide insight for the discovery of tumor-specific biomarkers and clinical potential therapeutic targets.

Transcriptome Signatures Reveal Candidate Key Genes in the Peripheral Blood Mononuclear Cells of Patients With Coronary Artery Disease

2020 ◽  
Author(s):  
Vijayakrishna Kolur ◽  
Basavaraj Vastrad ◽  
Chanabasayya Vastrad ◽  
Iranna Kotturshetti ◽  
Anandkumar Tengli
Keyword(s):  
Coronary Artery Disease ◽  
Gene Ontology ◽  
Coronary Artery ◽  
Regulatory Network ◽  
Target Gene ◽  
Enrichment Analysis ◽  
Hub Genes ◽  
Go Enrichment ◽  
Artery Disease ◽  
Go Enrichment Analysis

Abstract BackgroundCoronary artery disease (CAD) is one of the most common disorders in the cardiovascular system. This study aims to explore potential signaling pathways and important biomarkers that drive CAD development. MethodsThe CAD GEO Dataset GSE113079 was featured to screen differentially expressed genes (DEGs). The pathway and Gene Ontology (GO) enrichment analysis of DEGs were analyzed using the ToppGene. We screened hub and target genes from protein-protein interaction (PPI) networks, target gene - miRNA regulatory network and target gene - TF regulatory network, and Cytoscape software. Validations of hub genes were performed to evaluate their potential prognostic and diagnostic value for CAD. Results1,036 DEGs were captured according to screening criteria (525upregulated genes and 511downregulated genes). Pathway and Gene Ontology (GO) enrichment analysis of DEGs revealed that these up and down regulated genes are mainly enriched in thyronamine and iodothyronamine metabolism, cytokine-cytokine receptor interaction, nervous system process, cell cycle and nuclear membrane. Hub genes were validated to find out potential prognostic biomarkers, diagnostic biomarkers and novel therapeutic target for CAD. ConclusionsIn summary, our findings discovered pivotal gene expression signatures and signaling pathways in the progression of CAD. CAPN13, ACTBL2, ERBB3, GATA4, GNB4, NOTCH2, EXOSC10, RNF2, PSMA1 and PRKAA1 might contribute to the progression of CAD, which could have potential as biomarkers or therapeutic targets for CAD.

scholarly journals Mining Featured Biomarkers Linked with Epithelial Ovarian Cancer Based on Bioinformatics

Diagnostics ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 39
Author(s):  
◽  
Chanabasayya Vastrad ◽  
◽  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Target Gene ◽  
Enrichment Analysis ◽  
Microrna Target ◽  
Pathway Enrichment ◽  
Protein Protein Interaction ◽  
Go Enrichment ◽  
Gene Regulatory ◽  
Go Enrichment Analysis

: Epithelial ovarian cancer (EOC) is the18th most common cancer worldwide and the 8th most common in women. The aim of this study was to diagnose the potential importance of, as well as novel genes linked with, EOC and to provide valid biological information for further research. The gene expression profiles of E-MTAB-3706 which contained four high-grade ovarian epithelial cancer samples, four normal fallopian tube samples and four normal ovarian epithelium samples were downloaded from the ArrayExpress database. Pathway enrichment and Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) were performed, and protein-protein interaction (PPI) network, microRNA-target gene regulatory network and TFs (transcription factors ) -target gene regulatory network for up- and down-regulated were analyzed using Cytoscape. In total, 552 DEGs were found, including 276 up-regulated and 276 down-regulated DEGs. Pathway enrichment analysis demonstrated that most DEGs were significantly enriched in chemical carcinogenesis, urea cycle, cell adhesion molecules and creatine biosynthesis. GO enrichment analysis showed that most DEGs were significantly enriched in translation, nucleosome, extracellular matrix organization and extracellular matrix. From protein-protein interaction network (PPI) analysis, modules, microRNA-target gene regulatory network and TFs-target gene regulatory network for up- and down-regulated, and the top hub genes such as E2F4, SRPK2, A2M, CDH1, MAP1LC3A, UCHL1, HLA-C (major histocompatibility complex, class I, C) , VAT1, ECM1 and SNRPN (small nuclear ribonucleoprotein polypeptide N) were associated in pathogenesis of EOC. The high expression levels of the hub genes such as CEBPD (CCAAT enhancer binding protein delta) and MID2 in stages 3 and 4 were validated in the TCGA (The Cancer Genome Atlas) database. CEBPD andMID2 were associated with the worst overall survival rates in EOC. In conclusion, the current study diagnosed DEGs between normal and EOC samples, which could improve our understanding of the molecular mechanisms in the progression of EOC. These new key biomarkers might be used as therapeutic targets for EOC.

scholarly journals A Network Pharmacology Approach to Explore the Pharmacological Mechanism of Xiaoyao Powder on Anovulatory Infertility

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Huiping Liu ◽  
Liuting Zeng ◽  
Kailin Yang ◽  
Guomin Zhang
Keyword(s):  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Active Compounds ◽  
Pharmacological Mechanism ◽  
Go Enrichment ◽  
Human Proteins ◽  
Network Pictures ◽  
Go Enrichment Analysis ◽  
Anovulatory Infertility

Aim.To explore the pharmacological mechanism of Xiaoyao powder (XYP) on anovulatory infertility by a network pharmacology approach.Method.Collect XYP’s active compounds by traditional Chinese medicine (TCM) databases, and input them into PharmMapper to get their targets. Then note these targets by Kyoto Encyclopedia of Genes and Genomes (KEGG) and filter out targets that can be noted by human signal pathway. Get the information of modern pharmacology of active compounds and recipe’s traditional effects through databases. Acquire infertility targets by Therapeutic Target Database (TTD). Collect the interactions of all the targets and other human proteins via String and INACT. Put all the targets into the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to do GO enrichment analysis. Finally, draw the network by Cytoscape by the information above.Result.Six network pictures and two GO enrichment analysis pictures are visualized.Conclusion.According to this network pharmacology approach some signal pathways of XYP acting on infertility are found for the first time. Some biological processes can also be identified as XYP’s effects on anovulatory infertility. We believe that evaluating the efficacy of TCM recipes and uncovering the pharmacological mechanism on a systematic level will be a significant method for future studies.

scholarly journals The DOMINO web-server for active module identification analysis

2021 ◽  
Author(s):  
Hagai Levi ◽  
Nima Rahmanian ◽  
Ran Elkon ◽  
Ron Shamir
Keyword(s):  
Gene Network ◽  
Enrichment Analysis ◽  
Molecular Processes ◽  
Activity Profile ◽  
Module Identification ◽  
Go Enrichment ◽  
Downstream Analysis ◽  
User Friendly ◽  
Identification Analysis ◽  
Go Enrichment Analysis

Active module identification (AMI) is an essential step in many omics analyses. Such algorithms receive a gene network and a gene activity profile as input and report subnetworks that show significant over-representation of accrued activity signal ("active modules"). Such modules can point out key molecular processes in the analyzed biological conditions. We recently introduced a novel AMI algorithm called DOMINO, and demonstrated that it detects active modules that capture biological signals with markedly improved rate of empirical validation. Here, we provide an online server that executes DOMINO, making it more accessible and user-friendly. To help the interpretation of solutions, the server provides GO enrichment analysis, module visualizations, and accessible output formats for customized downstream analysis. It also enables running DOMINO with various gene identifiers of different organisms. The server is available at http://domino.cs.tau.ac.il. Its codebase is available at https://github.com/Shamir-Lab.

scholarly journals Analysis of small RNA changes in different Brassica napus synthetic allopolyploids

2019 ◽  
Author(s):  
Yunxiao Wei ◽  
Fei Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Differential Expression ◽  
Small Rna ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Small Rna Sequencing ◽  
Go Enrichment ◽  
Polyploid Formation ◽  
Differentially Expressed Mirnas ◽  
New Perspective ◽  
Go Enrichment Analysis

Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for solving the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective of small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.

scholarly journals Systematic Analyses of the Expression, Function, and Prognostic Value of CCNBs in Breast Caner

2021 ◽  
Author(s):  
Xinyu Liu ◽  
Yuqi Tang ◽  
Shuang Wang ◽  
Shutong Liu ◽  
Chenglin Li ◽  
...  
Keyword(s):  
Prognostic Value ◽  
Enrichment Analysis ◽  
Good Prognosis ◽  
Interactive Analysis ◽  
Kaplan Meier ◽  
Go Enrichment ◽  
Level Function ◽  
Go Enrichment Analysis ◽  
Kaplan Meier Plotter ◽  
Breast Caner

Abstract Background Cyclin B (CCNB) family plays key roles in the cell cycle, cell division and proliferation. Three members of CCNB family have been identified, including CCNB1, CCNB2 and CCNB3. Many studies have explored the roles of CCNBs in the tumorigenesis and pathogenesis of different types of cancer. However, the expression level, function, and prognostic value of CCNBs in breast caner (BC) are still unclear.Methods We explored the specific alterations of CCNBs in BC and predicted their prognostic value for BC patients. Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier plotter, cBioPortal, STRING, Database for Annotation,Visualization and Integrated Discovery (DAVID) databases were used for above analyses.Results We found that CCNB1 amd CCNB2 were significantly overexpressed in BC compared with normal samples, but not CCNB3. Survival analysis showed that upregulated CCNB1 and CCNB2 expression levels were associated with poor prognosis of BC patients, while high CCNB3 expression was related to good prognosis for BC patients. Furthermore, gene oncology (GO) enrichment analysis was performed to reveal the functions of CCNBs and the interacted genes related to CCNBs. In addition, hsa-miR-139-5p and has-miR-944 were identified to be potentially involved in the regulation of CCNB1.Conclusion Our study suggests that CCNB1, CCNB2 are potential targets of precise therapy for BC patients and that CCNB3 is a novel biomarker for the good prognosis of BC patients.

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