scholarly journals Identification of Aloperine as an anti-apoptotic Bcl2 protein inhibitor in glioma cells

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7652 ◽  
Author(s):  
Zhijie Xu ◽  
Xiang Wang ◽  
Xi Chen ◽  
Shuangshuang Zeng ◽  
Long Qian ◽  
...  
Keyword(s):  
Cell Lines ◽  
Glioma Cells ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Analysis Tool ◽  
Limited Information ◽  
Human Glioma ◽  
Bcl2 Protein

Objective Aloperine (ALO), an alkaloid isolated from the leaves of Sophora alopecuroides, has been suggested to exhibit anti-inflammatory and anti-tumor properties and is traditionally used to treat various human diseases, including cancer. However, limited information is available about the mechanisms that determine the anti-tumor activities of ALO. Methods Herein, through comprehensive bioinformatics methods and in vitro functional analyses, we evaluated the detailed anti-tumor mechanisms of ALO. Results Using the databases Bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine and PubChem Project, we identified the potential targets of ALO. A protein–protein interaction network was constructed to determine the relationship among these probable targets. Functional enrichment analysis revealed that ALO is potentially involved in the induction of apoptosis. In addition, molecular docking demonstrated that ALO expectedly docks into the active pocket of the Bcl2 protein, suggesting Bcl2 as a direct target of ALO. Moreover, western blot and qPCR analysis showed that ALO downregulated Bcl2 expression in human glioma cell lines, SK-N-AS and U118. Using flow cytometry methods, we further confirmed that ALO significantly promotes apoptosis in SK-N-AS and U118 cell lines, similar to the effect induced by ABT-737, a well-known Bcl2 inhibitor. In addition, Bcl-2 overexpression could rescue ALO-induced Bcl-2 inhibition and suppress pro-apoptotic effects in glioma cells. Conclusion Taken together, these findings suggest that the natural agent ALO effectively enhances apoptosis by acting as a potential Bcl2 inhibitor in human glioma cells.

scholarly journals Identification of Latent Diagnostic Biomarkers and Biological Pathways in Dermatomyositis Based on WGCNA

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Shaxi Ouyang ◽  
Yifang Liu ◽  
Changjuan Xiao ◽  
Qinghua Zeng ◽  
Xun Luo ◽  
...  
Keyword(s):  
Cell Lines ◽  
Differentially Expressed Gene ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Receptor Interaction ◽  
Interferon Α ◽  
Pathway Enrichment Analysis ◽  
Oligoadenylate Synthetase

Introduction. Dermatomyositis (DM) is a chronic autoimmune disease of predominantly lymphocytic infiltration mainly involving the transverse muscle. Its pathogenesis is remaining unknown. This research is designed to probe the latent pathogenesis of dermatomyositis, identify potential biomarkers, and reveal the pathogenesis of dermatomyositis through information biology analysis of gene chips. Methods. In this study, we utilised the GSE14287 and GSE11971 datasets rooted in the Gene Expression Omnibus (GEO) databank, which included a total of 62 DM samples and 9 normal samples. The datasets were combined, and the differentially expressed gene sets were subjected to weighted gene coexpression network analysis, and the hub gene was screened using a protein interaction network from genes in modules highly correlated with dermatomyositis progression. Results. A total of 3 key genes—myxovirus resistance-2 (MX2), oligoadenylate synthetase 1 (OAS1), and oligoadenylate synthetase 2 (OAS2)—were identified in combination with cell line samples, and the expressions of the 3 genes were verified separately. The results showed that MX2, OAS1, and OAS2 were highly expressed in LPS-treated cell lines compared to normal cell lines. The results of pathway enrichment analysis of the genes indicated that all 3 genes were enriched in the cytosolic DNA signalling and cytokine and cytokine receptor interaction signalling pathways; the results of functional enrichment analysis showed that all 3 were enriched in interferon-α response and interferon-γ response functions. Conclusions. This is important for the study of the pathogenesis and objective treatment of dermatomyositis and provides important reference information for the targeted therapy of dermatomyositis.

DNA methylation profile of liver of mice conceived by in vitro fertilization

2021 ◽  
pp. 1-9
Author(s):  
Saúl Lira-Albarrán ◽  
Xiaowei Liu ◽  
Seok Hee Lee ◽  
Paolo Rinaudo
Keyword(s):  
Dna Methylation ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Global Dna Methylation ◽  
Analysis Tool ◽  
Gene Promoters ◽  
Vitro Fertilization ◽  
Natural Mating

Abstract Offspring generated by in vitro fertilization (IVF) are believed to be healthy but display a possible predisposition to chronic diseases, like hypertension and glucose intolerance. Since epigenetic changes are believed to underlie such phenotype, this study aimed at describing global DNA methylation changes in the liver of adult mice generated by natural mating (FB group) or by IVF. Embryos were generated by IVF or natural mating. At 30 weeks of age, mice were sacrificed. The liver was removed, and global DNA methylation was assessed using whole-genome bisulfite sequencing (WGBS). Genomic Regions for Enrichment Analysis Tool (GREAT) and G:Profilerβ were used to identify differentially methylated regions (DMRs) and for functional enrichment analysis. Overrepresented gene ontology terms were summarized with REVIGO, while canonical pathways (CPs) were identified with Ingenuity® Pathway Analysis. Overall, 2692 DMRs (4.91%) were different between the groups. The majority of DMRs (84.92%) were hypomethylated in the IVF group. Surprisingly, only 0.16% of CpG islands were differentially methylated and only a few DMRs were located on known gene promoters (n = 283) or enhancers (n = 190). Notably, the long-interspersed element (LINE), short-interspersed element (SINE), and long terminal repeat (LTR1) transposable elements showed reduced methylation (P < 0.05) in IVF livers. Cellular metabolic process, hepatic fibrosis, and insulin receptor signaling were some of the principal biological processes and CPs modified by IVF. In summary, IVF modifies the DNA methylation signature in the adult liver, resulting in hypomethylation of genes involved in metabolism and gene transcription regulation. These findings may shed light on the mechanisms underlying the developmental origin of health and disease.

scholarly journals MicroRNA-585 inhibits human glioma cell proliferation by directly targeting MDM2

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Wangsheng Chen ◽  
Lan Hong ◽  
Changlong Hou ◽  
Yibin Wang ◽  
Fei Wang ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Cell Lines ◽  
Glioma Cell ◽  
Glioma Cells ◽  
Human Glioma ◽  
Human Glioma Cells ◽  
Human Glioma Cell ◽  
Glioma Cell Proliferation

Abstract Background MicroRNAs (miRNAs) are important regulators for cancer cell proliferation. miR-585 has been shown to inhibit the proliferation of several types of cancer, however, little is known about its role in human glioma cells. Methods miR-585 levels in human glioma clinical samples and cell lines were examined by quantitative real-time PCR (qRT-PCR) analysis. Cell proliferation was measured by Cell Counting Kit-8 (CCK-8) and EdU incorporation assays in vitro. For in vivo investigations, U251 cells were intracranially inoculated in BALB/c nude mice and xenografted tumors were visualized by magnetic resonance imaging (MRI). Results miR-585 expression is downregulated in human glioma tissues and cell lines compared with non-cancerous counterparts. Additionally, miR-585 overexpression inhibits and its knockdown promotes human glioma cell proliferation in vitro. Moreover, miR-585 overexpression also inhibits the growth of glioma xenografts in vivo, suggesting that miR-585 may act as a tumor suppressor to inhibit the proliferation of human glioma. Furthermore, miR-585 directly targets and decreases the expression of oncoprotein murine double minute 2 (MDM2). More importantly, the restoration of MDM2 via enforced overexpression markedly rescues miR-585 inhibitory effect on human glioma cell proliferation, thus demonstrating that targeting MDM2 is a critical mechanism by which miR-585 inhibits human glioma cell proliferation. Conclusions Our study unveils the anti-proliferative role of miR-585 in human glioma cells, and also implicates its potential application in clinical therapy.

scholarly journals Identification of potential biomarkers for abdominal pain in IBS patients by bioinformatics approach

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhongyuan Lin ◽  
Yimin Wang ◽  
Shiqing Lin ◽  
Decheng Liu ◽  
Guohui Mo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Irritable Bowel Syndrome ◽  
Abdominal Pain ◽  
Gastrointestinal Disease ◽  
Rectal Mucosa ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Irritable Bowel ◽  
Potential Biomarkers

Abstract Background Irritable bowel syndrome (IBS) is the most common functional gastrointestinal disease characterized by chronic abdominal discomfort and pain. The mechanisms of abdominal pain, as a relevant symptom, in IBS are still unclear. We aimed to explore the key genes and neurobiological changes specially involved in abdominal pain in IBS. Methods Gene expression data (GSE36701) was downloaded from Gene Expression Omnibus database. Fifty-three rectal mucosa samples from 27 irritable bowel syndrome with diarrhea (IBS-D) patients and 40 samples from 21 healthy volunteers as controls were included. Differentially expressed genes (DEGs) between two groups were identified using the GEO2R online tool. Functional enrichment analysis of DEGs was performed on the DAVID database. Then a protein–protein interaction network was constructed and visualized using STRING database and Cytoscape. Results The microarray analysis demonstrated a subset of genes (CCKBR, CCL13, ACPP, BDKRB2, GRPR, SLC1A2, NPFF, P2RX4, TRPA1, CCKBR, TLX2, MRGPRX3, PAX2, CXCR1) specially involved in pain transmission. Among these genes, we identified GRPR, NPFF and TRPA1 genes as potential biomarkers for irritating abdominal pain of IBS patients. Conclusions Overexpression of certain pain-related genes (GRPR, NPFF and TRPA1) may contribute to chronic visceral hypersensitivity, therefore be partly responsible for recurrent abdominal pain or discomfort in IBS patients. Several synapses modification and biological process of psychological distress may be risk factors of IBS.

scholarly journals Investigation and Functional Enrichment Analysis of the Human Host Interaction Network with Common Gram-Negative Respiratory Pathogens Predicts Possible Association with Lung Adenocarcinoma

2021 ◽  
Vol 28 (1) ◽  
pp. 20-33
Author(s):  
Lydia-Eirini Giannakou ◽  
Athanasios-Stefanos Giannopoulos ◽  
Chrissi Hatzoglou ◽  
Konstantinos I. Gourgoulianis ◽  
Erasmia Rouka ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Cell Junctions ◽  
Respiratory Pathogens ◽  
Gram Negative ◽  
Human Proteins ◽  
Apoptotic Pathways

Haemophilus influenzae (Hi), Moraxella catarrhalis (MorCa) and Pseudomonas aeruginosa (Psa) are three of the most common gram-negative bacteria responsible for human respiratory diseases. In this study, we aimed to identify, using the functional enrichment analysis (FEA), the human gene interaction network with the aforementioned bacteria in order to elucidate the full spectrum of induced pathogenicity. The Human Pathogen Interaction Database (HPIDB 3.0) was used to identify the human proteins that interact with the three pathogens. FEA was performed via the ToppFun tool of the ToppGene Suite and the GeneCodis database so as to identify enriched gene ontologies (GO) of biological processes (BP), cellular components (CC) and diseases. In total, 11 human proteins were found to interact with the bacterial pathogens. FEA of BP GOs revealed associations with mitochondrial membrane permeability relative to apoptotic pathways. FEA of CC GOs revealed associations with focal adhesion, cell junctions and exosomes. The most significantly enriched annotations in diseases and pathways were lung adenocarcinoma and cell cycle, respectively. Our results suggest that the Hi, MorCa and Psa pathogens could be related to the pathogenesis and/or progression of lung adenocarcinoma via the targeting of the epithelial cellular junctions and the subsequent deregulation of the cell adhesion and apoptotic pathways. These hypotheses should be experimentally validated.

Metastasis tumor-associated protein-2 knockdown suppresses the proliferation and invasion of human glioma cells in vitro and in vivo

2014 ◽  
Vol 120 (2) ◽  
pp. 273-281 ◽  
Author(s):  
Chun-Yuan Cheng ◽  
Ying-Erh Chou ◽  
Chung-Po Ko ◽  
Shun-Fa Yang ◽  
Shu-Ching Hsieh ◽  
...  
Keyword(s):  
Glioma Cells ◽  
Human Glioma ◽  
Human Glioma Cells ◽  
Proliferation And Invasion

P13.23 Study of migration characteristics of human glioma cells in vitro

2021 ◽  
Vol 23 (Supplement_2) ◽  
pp. ii37-ii38
Author(s):  
G Pavlova ◽  
S Pavlova ◽  
S Drozd ◽  
E Savchenko ◽  
L Zakharova ◽  
...  
Keyword(s):  
Cell Cultures ◽  
Proliferative Activity ◽  
Average Rate ◽  
Glioma Cells ◽  
Human Glioma ◽  
Human Gliomas ◽  
Migration Activity ◽  
Tumor Invasiveness ◽  
Grade Iii

Abstract BACKGROUND Gliomas are still one of the most aggressive human cancers, and even despite modern therapeutic approaches, the prognosis for patients with this disease is not favorable. It is known that glioma cells are capable of local invasiveness, when glioma cells migrate into healthy brain tissue. A lack of any definite markers, characterizing migrating glioma cells and allowing them to be distinguished from healthy brain cells, requires a thorough investigation. In case it would be possible to characterize invasive glioma cells, then a development of targeted therapy could be feasible. MATERIAL AND METHODS Cell cultures of human gliomas Gr II, III and IV were developed with 5 cultures for each Grade. MTT, RT-PCR, Western and Nosern blot, transcriptome analysis were applied. RESULTS Three cultures of human gliomas had a high degree of migration, within the range of 6% - 14%. These cultures were developed from gliomas of Grade III and Grade IV, and with IDH1- (minus) phenotype. Moreover, cell cultures with IDH1 + (plus) phenotype had a low migration rate within 1%. An intensity of migration correlated with the degree of malignancy, and an average rate decreased with a decrease of the Grade. Moreover, an analysis of the proliferative activity of cell cultures of human gliomas of various degrees of malignancy did not reveal a relationship with a migratory properties of cultures. A number of actively proliferating cultures did not show high migration, while cultures with medium proliferative activity could show a high level of migration. The low level of proliferation of cultures of gliomas of Grade II and I at the beginning of cultivation, in some cases, subsequently increased, but an inherent low migration activity did not change. In actively migrating cultures, a significant decrease in the expression of Sox2 and Nestin is detected. A positive correlation was found between migration abilities of human glioma cell culture cells and the marker Ki67, GFAP, Sox2, and Oct4. The difference was statistically significant by the one-sided Mann-Whitney test. CONCLUSION Conclusions: Cell cultures derived from glioma tumor tissue can be used to predict invasive properties of the tumor. High tumor invasiveness is characteristic for Grade III and Grade IV, and with IDH1- (minus) phenotype, and it also correlates with elevated expression of GFAP, Sox2 and Oct4The reported study was funded by RFBR according to the research project № 18-29-01012 and by the Ministry of Science and Higher Education of the Russian Federation, grant number 075-15-2020-809 (13.1902.21.0030).

scholarly journals The Mechanism Study of Xiao-Xian-Xiong Decoction in the Treatment of Atherosclerosis with Network Pharmacology

2020 ◽  
Author(s):  
Liucheng Xiao ◽  
Zonghuan Li ◽  
Chongyuan Fan ◽  
Chenggong Zhu ◽  
Xingyu Ma ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Signaling Pathway ◽  
Mapk Pathway ◽  
Enrichment Analysis ◽  
Foam Cells ◽  
Functional Enrichment ◽  
Network Pharmacology ◽  
Mechanism Study ◽  
Ppi Networks

Abstract Background: Xiao-Xian-Xiong decoction is a useful formula in the treatment of atherosclerosis in traditional Chinese medicine. In this study, we aimed to investigate the function of Xiao-Xian-Xiong decoction in the treatment of atherosclerosis. Methods: In this study, we conducted the method of network pharmacology and molecular docking to discover the mechanism of Xiao-Xian-Xiong decoction against atherosclerosis. Then, we validated the function of Xiao-Xian-Xiong decoction in atherosclerosis in vitro. We investigated the function and mechanism of Xiao-Xian-Xiong decoction in RAW264.7 macrophage-derived foam cells.Results: We identified 213 targets of Xiao-Xian-Xiong decoction and 331 targets of atherosclerosis. The PPI networks of Xiao-Xian-Xiong decoction and atherosclerosis were constructed. Furthermore, the two PPI networks were merged and the core PPI network was obtained. Then, functional enrichment analysis was conducted with GO and KEGG signaling pathway analysis. KEGG analysis indicated Xiao-Xian-Xiong decoction was correlated with ubiquitin mediated proteolysis pathway, PI3K-AKT pathway, MAPK pathway, Notch signaling pathway, and TGF-β signaling pathway. At last, we validated the function of Xiao-Xian-Xiong decoction with atherosclerosis in vitro. Xiao-Xian-Xiong decoction reduced lipid accumulation and promoted the outflow of cholesterol in RAW264.7-derived foam cells. Xiao-Xian-Xiong decoction increased the expression of ABCA1 and ABCG1 protein in foam cells. ABCA1 and ABCG1 were related with regulation of the inflammatory pathway and cell proliferation in atherosclerosis.Conclusions: Combined the mechanism of available treatments of atherosclerosis, we inferred Xiao-Xian-Xiong decoction could alleviate atherosclerosis by inhibiting inflammatory response and cell proliferation.

scholarly journals RPNs Levels are Prognostic and Diagnostic Markers for Hepatocellular Carcinoma

2021 ◽  
Author(s):  
Wangyang zheng ◽  
Yuling Zheng ◽  
Xue Bai ◽  
Yongxu Zhou ◽  
Liang Yu ◽  
...  
Keyword(s):  
Western Blot ◽  
Cell Lines ◽  
Mammalian Cells ◽  
Tumor Grade ◽  
Ubiquitin Proteasome System ◽  
Functional Enrichment ◽  
Migration And Invasion ◽  
Regulatory Subunits ◽  
Hcc Cells

Abstract Background: Ribophorin family (RPNs) are important regulatory subunits of the proteasome. By influencing Ubiquitin-proteasome system activity, RPNs are responsible for almost all processes of physiology and pathology of mammalian cells. Nevertheless, little is known about the role of RPNs in HCC.Methods: In this work, using the online databases Oncomine, UCSC, Kaplan-Meier Plotter, UALCAN, cBioPortal, TIMER2, GeneMANIA,and STRING, we first evaluated the expression, diagnostic, prognostic, genetic alteration, immunity, gene network, and functional enrichment of RPNs in HCC. QPCR and western blot were used to detect RPN6 and RPN9 expressions in HCC tissues and cell lines. Then we performed studies to eveulated their functions in HCC cells proliferation, migration, and invasion in vitro. Results: All RPNs were surprisingly consistently upregulated in HCC tissues. Moreover, RPNs expression pattern is correlated with HCC tumor grade. RPN2, RPN3, RPN6, RPN9, RPN10, RPN11, and RPN12 have robust values in HCC diagnose. Then, survival analysis revealed that high expression of RPN1, RPN2, RPN4, RPN5, RPN6, RPN9, and RPN11were correlated with unfavorable HCC overall survival. Functional enrichment for RPNs, indicated that RPNs have many potential biosynthesis activities expert for UPS functions. Western blot, and qRT-PCR further verified these results in HCC tissues and cell lines. The silencing of RPN6 and RPN9 significantly influenced HCC cells' proliferation, migration, and invasion in vitro.Conclusions: RPN families functions as an important oncogene in HCC. RPN6 and RPN9 have the potential to be potential biomarkers and targets for HCC.

Sign in / Sign up

Export Citation Format

Share Document