ITRAQ-based Bioinformatics Analysis Reveals the Potential Anticancer Effects of ATP4B in Gastric Cancer

Abstract Background: Gastric cancer (GC) is one of the major malignancies of gastrointestinal tract. Hydrogen-potassium ATPase beta (ATP4B) gene is aberrantly downexpressed in gastric cancer that is associated with worse disease outcome. The objective of this study was to investigate the biological significance of ATP4B in GC carcinogenesis and development. Methods: The expression level of ATP4B was analyzed via clinical tissues and TCGA database. Then, we overexpressed ATP4B in SGC7901 and utilized isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technique validate the ATP4B-regulated proteomics profile alterations. Bioinformatics analysis was performed to evaluate the biological processes of ATP4B in GC. Western blot was used for the verification of significant downstream proteins of ATP4B based on bioinformatics analysis data.Results: We identified 293 differentially expressed proteins between the ATP4B overexpressing and control groups in SGC7901, including 145 upregulated proteins and 148 downregulated proteins. GO enrichment analysis indicated that ATP4B-modulating downstream proteins were primarily related to mitochondria function and metabolism. ATP4B-induced enrichments of biological functions were partly associated with suppressing tumor advancement, illustrating an inhibitory role for ATP4B in the progression of GC. Co-expression interaction network analysis exhibited the significant alterations in p53 and STAT3/NF-κB signaling pathway. Consistently, KEGG pathway analysis showed that DEPs are enriched in cell metabolism and cancer-related signaling pathway. Western blot validated the activation of p53 pathway and the inhibition of NF-κB /CD44 pathway after ATP4B overexpressing in GC cells.Conclusion: ATP4B plays a critical anticancer effect by regulating p53/NF-κΒ/mitochondrial pathway. Our data suggested a novel role and mechanism for ATP4B in GC progression.

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Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Simiao Powder on Knee Osteoarthritis

BioMed Research International ◽

10.1155/2020/6971503 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

Author(s):

Zhengquan Huang ◽

Xiaoqing Shi ◽

Xiaochen Li ◽

Li Zhang ◽

Peng Wu ◽

...

Keyword(s):

Molecular Docking ◽

Knee Osteoarthritis ◽

Signaling Pathway ◽

Protein Interaction ◽

Cell Metabolism ◽

Interaction Network ◽

Enrichment Analysis ◽

Network Pharmacology ◽

Active Components ◽

Discovery Studio

Objective. To explore the molecular mechanism of Simiao powder in the treatment of knee osteoarthritis. Methods. Based on oral bioavailability and drug-likeness, the main active components of Simiao powder were screened using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). GeneCard, OMIM, DisGeNET, DrugBank, PharmGkb, and the Therapeutic Target Database were used to establish target databases for knee osteoarthritis. Cytoscape software was used to construct a visual interactive network diagram of “active ingredient - action target – disease.” The STRING database was used to construct a protein interaction network and analyze related protein interaction relationships. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) biological process enrichment analysis were performed on the core targets. Additionally, Discovery Studio software was used for molecular docking verification of active pharmaceutical ingredients and disease targets. Results. Thirty-seven active components of Simiao powder were screened, including 106 common targets. The results of network analysis showed that the targets were mainly involved in regulating biological processes such as cell metabolism and apoptosis. Simiao powder components were predicted to exert their therapeutic effect on the AGE-RAGE signaling pathway in diabetic complications, IL-17 signaling pathway, TNF signaling pathway, Toll-like receptor signaling pathway, and HIF-1 signaling pathway. The molecular docking results showed that the active components of Simiao powder had a good match with the targets of IL1B, MMP9, CXCL8, MAPK8, JUN, IL6, MAPK1, EGF, VEGFA, AKT1, and PTGS2. Conclusion. Simiao powder has multisystem, multicomponent, and multitarget characteristics in treating knee osteoarthritis. Its possible mechanism of action includes inhibiting the inflammatory response, regulating immune function, and resisting oxidative stress to control the occurrence and development of the disease. Quercetin, wogonin, kaempferol, beta-sitosterol, and other active ingredients may be the material basis for the treatment of knee osteoarthritis.

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ANXA1 Induces Oxaliplatin Resistance of Gastric Cancer through Autophagy by Targeting PI3K/AKT/mTOR

10.21203/rs.3.rs-895675/v1 ◽

2021 ◽

Author(s):

Jun Ren ◽

Qing Zhi Hu ◽

Ming Geng Niu ◽

Jie Xia ◽

Xing Wang ◽

...

Keyword(s):

Gastric Cancer ◽

Western Blot ◽

Signaling Pathway ◽

Enrichment Analysis ◽

Mtor Signaling ◽

Gene Set Enrichment Analysis ◽

Rna Seq ◽

Mtor Signaling Pathway

Abstract Background: Resistance to oxaliplatin (OXA) is a major cause of recurrence in gastric cancer (GC) patients. ANXA1 has been found to participate in the regulation of diverse cellular functions in a variety of cell types including anti-inflammatory processes. We aimed to investigate the role of ANXA1 in autophagy and chemoresistance of GC cells. Methods: To identify the genes that regulate oxaliplatin resistance, we used RNA-seq to profile gene expression within oxaliplatin resistant GC and parental cells. Immunohistochemical and RT-qPCR was performed to detect ANXA1 expression in tissues of 2 cohorts of GC patients who received OXA-based chemotherapy. The chemoresistant effects of ANXA1 were assessed by cell viability, apoptosis, and autophagy assays. The effects of ANXA1 on autophagy were assessed by mRFP-GFP-LC3 and western blot. Gene set enrichment analysis (GSEA) and western blot was performed to detect the activity of PI3K/AKT/mTOR signaling under the regulation of ANXA1.Results: Based on RNA-seq profiling, ANXA1 was selected as a candidate that was upregulated in oxaliplatin resistant GC cells. Furthermore, we discovered that ANXA1 is upregulated in chemo-resistant GC tissues. Knockdown of ANXA1, via inhibiting autophagy, enhanced the sensitivity of OXA-resistant GC cells to OXA in vitro and in vivo. Mechanically, we identified that PI3K/AKT/mTOR signaling pathway was activated in the ANXA1 stably knockdown AGS/OXA cells, which leads to the down-regulation of autophagy.Conclusions: ANXA1 functions as a chemoresistant gene in GC cells by targeting the PI3K/AKT/mTOR signaling pathway and might be a prognostic predictor for GC patients who receive OXA-based chemotherapy.

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Bioinformatics Analysis and Identification of Potential Biomarkers in Gastric Cancer

10.21203/rs.3.rs-111288/v1 ◽

2020 ◽

Author(s):

Jingdi Yang ◽

Bo Peng ◽

Xianzheng Qin ◽

Tian Zhou

Keyword(s):

Gene Expression ◽

Gastric Cancer ◽

Differentially Expressed Genes ◽

Bioinformatics Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Hub Genes ◽

Protein Protein Interaction ◽

Protein Protein Interaction Network

Abstract Background: Although the morbidity and mortality of gastric cancer are declining, gastric cancer is still one of the most common causes of death. Early detection of gastric cancer is of great help to improve the survival rate, but the existing biomarkers are not sensitive to diagnose early gastric cancer. The aim of this study is to identify the novel biomarkers for gastric cancer.Methods: Three gene expression profiles (GSE27342, GSE63089, GSE33335) were downloaded from Gene Expression Omnibus database to select differentially expressed genes. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were performed to explore the biological functions of differentially expressed genes. Cytoscape was utilized to construct protein-protein interaction network and hub genes were analyzed by plugin cytoHubba of Cytoscape. Furthermore, Gene Expression Profiling Interactive Analysis and Kaplan-Meier plotter were used to verify the identified hub genes.Results: 35 overlapping differentially expressed genes were screened from gene expression datasets, which consisted of 11 up-regulated genes and 24 down-regulated genes. Gene Ontology functional enrichment analysis revealed that differentially expressed genes were significantly enriched in digestion, regulation of biological quality, response to hormone and steroid hormone, and homeostatic process. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed differentially expressed genes were enriched in the secretion of gastric acid and collecting duct acid, leukocyte transendothelial migration and ECM-receptor interaction. According to protein-protein interaction network, 10 hub genes were identified by Maximal Clique Centrality method.Conclusion: By using bioinformatics analysis, COL1A1, BGN, THY1, TFF2 and SST were identified as the potential biomarkers for early detection of gastric cancer.

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Bioinformatics Analysis Identifies CPZ as a Tumor Immunology Biomarker For Gastric Cancer

Current Bioinformatics ◽

10.2174/1574893615999200707145643 ◽

2020 ◽

Vol 15 ◽

Author(s):

Yuan Gu ◽

Ying Gao ◽

Xiaodan Tang ◽

Huizhong Xia ◽

Kunhe Shi

Keyword(s):

Gastric Cancer ◽

T Cells ◽

Signaling Pathway ◽

Tumor Immunology ◽

Bioinformatics Analysis ◽

Human Cancer ◽

Disease Free Survival ◽

Kaplan Meier ◽

Potential Biomarker ◽

Pathway Regulation

Background: Gastric cancer (GC) is one of the most common malignancies worldwide. However, the biomarkers for the prognosis and diagnosis of Gastric cancer were still need. Objective: The present study aimed to evaluate whether CPZ could be a potential biomarker for GC. Method: Kaplan-Meier plotter (http://kmplot.com/analysis/) was used to determine the correlation between CPZ expression and overall survival (OS) and disease-free survival (DFS) time in GC [9]. We analyzed CPZ expression in different types of cancer and the correlation of CPZ expression with the abundance of immune infiltrates, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, via gene modules using TIMER Database. Results: The present study identified that CPZ was overexpressed in multiple types of human cancer, including Gastric cancer. We found that overexpression of CPZ correlates to the poor prognosis of patients with STAD. Furthermore, our analyses show that immune infiltration levels and diverse immune marker sets are correlated with levels of CPZ expression in STAD. Bioinformatics analysis revealed that CPZ was involved in regulating multiple pathways, including PI3K-Akt signaling pathway, cGMP-PKG signaling pathway, Rap1 signaling pathway, TGF-beta signaling pathway, regulation of cell adhesion, extracellular matrix organization, collagen fibril organization, collagen catabolic process. Conclusion: This study for the first time provides useful information to understand the potential roles of CPZ in tumor immunology and validate it to be a potential biomarker for GC.

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Bioinformatics analysis of the prognosis and biological significance of VCAN in gastric cancer

Immunity Inflammation and Disease ◽

10.1002/iid3.414 ◽

2021 ◽

Author(s):

Xiao‐yan Huang ◽

Jin‐jian Liu ◽

Xiong Liu ◽

Yao‐hui Wang ◽

Wei Xiang

Keyword(s):

Gastric Cancer ◽

Bioinformatics Analysis ◽

Biological Significance

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CENPF/CDK1 Signaling Pathway Enhances the Progression of Adrenocortical Carcinoma by Regulating the G2/M-phase Cell Cycle

10.21203/rs.3.rs-1012618/v1 ◽

2021 ◽

Author(s):

Yugang Huang ◽

Dan Li ◽

Li Wang ◽

Xiaomin Su ◽

Xian-bin Tang

Keyword(s):

Cell Cycle ◽

Signaling Pathway ◽

Adrenocortical Carcinoma ◽

Immune Cell ◽

Interaction Network ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Phase Cell ◽

Aberrant Expression ◽

M Phase

Abstract Adrenocortical carcinoma (ACC) is an aggressive and rare malignant tumor and prone to local invasion and metastasis. While, overexpressed Centromere Protein F (CENPF) is closely related to oncogenesis of various neoplasms, including ACC. However, the prognosis and exact biological function of CENPF in ACC remains largely unclear. In present essay, the expression of CENPF in human ACC samples, GEO and TCGA databases depicted that CENPF were overtly hyper-expressed in ACC patients and positively correlated with tumor stage. The aberrant expression of CENPF was significantly correlated with unfavorable overall survival (OS) in ACC patients. Then, the application of gene-set enrichment analysis (GSEA) declared that CENPF was mainly involved in the G2/M-phase mediated cell cycle and p53 signaling pathway. Further, a small RNA interference experiment was conducted to demonstrate that the interaction between CENPF and CDK1 enhanced the G2/M-phase transition of mitosis, cell proliferation and might induce p53 mediated anti-tumor effect in human ACC cell line, SW13 cells. Lastly, two available therapeutic strategies, including immunotherapy and chemotherapy, have been further probed. Immune infiltration analysis highlighted that ACC patients with high CENPF expression harbored significantly different immune cell populations, and high TMB/MSI score. Then, the gene-drug interaction network stated that CENPF inhibitors, such as Cisplatin, Sunitinib, and Etoposide, might serve as potential drugs for the therapy of ACC. Briefly, CENPF and related genes might be served as a novel prognostic biomarker or latent therapeutic target for ACC patients.

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GPX8 is transcriptionally regulated by FOXC1 and promotes the growth of gastric cancer cells through activating the Wnt signaling pathway

Cancer Cell International ◽

10.1186/s12935-020-01692-z ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Hong Chen ◽

Lu Xu ◽

Zhi-li Shan ◽

Shu Chen ◽

Hao Hu

Keyword(s):

Gastric Cancer ◽

Transcription Factor ◽

Western Blot ◽

Wnt Signaling ◽

Cancer Cells ◽

Signaling Pathway ◽

Wnt Signaling Pathway ◽

Migration And Invasion ◽

Gastric Cancer Cells ◽

Cancer Tissues

Abstract Background Glutathione Peroxidase 8 (GPX8) as a member of the glutathione peroxidase (GPx) family plays an important role in anti-oxidation. Besides, dysregulation of GPX8 has been found in gastric cancer, but its detailed molecular mechanism in gastric cancer has not been reported. Methods Our study detected the expression of GPX8 in gastric cancer tissues and cell lines using immunohistochemistry (IHC), western blot and qRT-PCR, and determined the effect of GPX8 on gastric cancer cells using CCK-8, colony formation, transwell migration and invasion assays. Besides, the effect of GPX8 on the Wnt signaling pathway was determined by western blot. Furthermore, the transcription factor of GPX8 was identified by bioinformatics methods, dual luciferase reporter and chromatin immunoprecipitation (CHIP) assays. In addition, the effect of GPX8 on tumor formation was measured by IHC and western blot. Results The over-expression of GPX8 was observed in gastric cancer tissues and cells, which facilitated the proliferation, migration and invasion of gastric cancer cells as well as the tumor growth. GPX8 knockdown effectively inhibited the growth of gastric cancer cells and tumors. Moreover, GPX8 could activate the Wnt signaling pathway to promote the cellular proliferation, migration and invasion through. Furthermore, FOXC1 was identified as a transcription factor of GPX8 and mediated GPX8 expression to affect cell development processes. Conclusions These findings contribute to understanding the molecular mechanism of GPX8 in gastric cancer. Additionally, GPX8 can be a potential biomarker for gastric cancer therapy.

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MicroRNA-19b-3p suppresses gastric cancer development by negatively regulating neuropilin-1

Cancer Cell International ◽

10.1186/s12935-020-01257-0 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Yingfeng Wei ◽

Sheng Guo ◽

Jianhua Tang ◽

Jianjun Wen ◽

Huifen Wang ◽

...

Keyword(s):

Gastric Cancer ◽

Cell Growth ◽

Western Blot ◽

Bioinformatics Analysis ◽

Luciferase Reporter ◽

Migration And Invasion ◽

Functional Assay ◽

Mrna Levels ◽

Neuropilin 1

Abstract Background Gastric cancer (GC) remains one of the most common digestive malignancies worldwide and ranked third causes of cancer-related death. Mounting evidence has revealed that miRNAs exert critical regulatory roles in GC development. Methods Immunohistochemistry (IHC) and western blot assay were performed to determine the protein expression levels of neuropilin-1 (NRP1) and mRNA levels were confirmed by quantitative RT-PCR (qRT-PCR) in GC tissues. Kaplan–Meier analysis was performed to evaluate the prognostic value of NRP1 in GC. Knockdown of NRP1 was conducted to analyse its function in vitro and vivo. Luciferase reporter assay, western blot and qRT-qPCR were employed to identify the miRNAs which directly targeted NRP1. Furthermore, Bioinformatics analysis and experimental verification were used to explore the potential molecular mechanism and signalling pathway. Results In the current study, we revealed that NRP1 was highly expressed in GC tumor tissues and was associated with poor prognosis in GC patients. NRP1 knockdown inhibited GC cell growth, migration and invasion in vitro, while suppressed GC xenograft tumor development in vivo. Bioinformatics analysis predicted that miR-19b-3p down-regulated NRP1 expression by targeting its 3′-UTR. Functional assay demonstrated that miR-19b-3p inhibited GC cell growth, migration and invasion via negatively regulating NRP1. Overexpression NRP1 partially reversed the regulatory effect of miR-19b-3p. Moreover, we showed that miR-19b-3p/NRP1 axis regulated the epithelial-to-mesenchymal transition and focal adhesion in GC, which might contribute the GC development and progression. Conclusions Taken together, our findings suggest a regulatory network of miR-19b-3p/NRP1 in GC development. The miR-19b-3p/NRP1 axis might be further explored as a potential diagnostic and therapeutic target in GC.

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A Network Pharmacology Approach to Uncover the Mechanisms of Shen-Qi-Di-Huang Decoction against Diabetic Nephropathy

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2018/7043402 ◽

2018 ◽

Vol 2018 ◽

pp. 1-14 ◽

Cited By ~ 9

Author(s):

Sha Di ◽

Lin Han ◽

Qing Wang ◽

Xinkui Liu ◽

Yingying Yang ◽

...

Keyword(s):

Diabetic Nephropathy ◽

Signaling Pathway ◽

Molecular Mechanisms ◽

Interaction Network ◽

Enrichment Analysis ◽

Network Pharmacology ◽

Pathway Enrichment Analysis ◽

Protein Protein Interaction ◽

Regulation Of Blood Pressure ◽

Protein Protein Interaction Network

Shen-Qi-Di-Huang decoction (SQDHD), a well-known herbal formula from China, has been widely used in the treatment of diabetic nephropathy (DN). However, the pharmacological mechanisms of SQDHD have not been entirely elucidated. At first, we conducted a comprehensive literature search to identify the active constituents of SQDHD, determined their corresponding targets, and obtained known DN targets from several databases. A protein-protein interaction network was then built to explore the complex relations between SQDHD targets and those known to treat DN. Following the topological feature screening of each node in the network, 400 major targets of SQDHD were obtained. The pathway enrichment analysis results acquired from DAVID showed that the significant bioprocesses and pathways include oxidative stress, response to glucose, regulation of blood pressure, regulation of cell proliferation, cytokine-mediated signaling pathway, and the apoptotic signaling pathway. More interestingly, five key targets of SQDHD, named AKT1, AR, CTNNB1, EGFR, and ESR1, were significant in the regulation of the above bioprocesses and pathways. This study partially verified and predicted the pharmacological and molecular mechanisms of SQDHD on DN from a holistic perspective. This has laid the foundation for further experimental research and has expanded the rational application of SQDHD in clinical practice.

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AKNA Is a Potential Prognostic Biomarker in Gastric Cancer and Function as a Tumor Suppressor by Modulating EMT-Related Pathways

BioMed Research International ◽

10.1155/2020/6726759 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Gang Wang ◽

Dan Sun ◽

Wenhui Li ◽

Yan Xin

Keyword(s):

Gastric Cancer ◽

Cell Adhesion ◽

Tumor Suppressor ◽

Western Blot ◽

Signaling Pathway ◽

Gene Set Enrichment Analysis ◽

Mesenchymal Transition ◽

Qrt Pcr ◽

Potential Biomarker ◽

Cell To Cell Adhesion

The AT-hook transcription factor, AKNA, is a nuclear protein that affects a few physiological and pathological processes including cancer. Here, we investigated the role of AKNA in gastric cancer (GC). By using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot assays, AKNA was found deregulated in both GC cell lines and 32 paired GC tissues. Subsequently, Kaplan-Meier analysis and clinicopathological analysis were conducted using both 32 GC cases’ data above and RNA-Seq data of AKNA in 354 GC patients and the corresponding clinical-pathological data obtained from The Cancer Genome Atlas (TCGA), and AKNA expression was found closely related to location, metastasis, and TNM staging of GC. Then, the potential molecular mechanisms of AKNA in GC were explored by gene set enrichment analysis (GSEA), qRT-PCR, and Western blot assays. AKNA was found to be a hub gene related to homotypic cell to cell adhesion, regulation of cell to cell adhesion, leukocyte cell to cell adhesion, and regulation of T cell proliferation in GC. GO analysis revealed that AKNA involved in the regulation of epithelial-mesenchymal transition (EMT)-related pathways including chemokine signaling pathway, cytokine to cytokine receptor interaction, cell adhesion molecules, and jak-stat signaling pathway in GC. To explore the regulation of AKNA expression, Targetscan and TargetMiner were used to predict the possible miRNA which targeted AKNA and found the expression of AKNA was negatively correlated to miR-762 which could be sponged by circTRNC18. In conclusion, AKNA could function as a tumor suppressor by modulating EMT-related pathways in GC. The expression of AKNA might be regulated by circTRNC18/miR-762 axis. AKNA could serve as a potential biomarker and an effective target for GC diagnosis and therapy.

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