Identification of specific modules and hub genes associated with the progression of gastric cancer

2019 ◽  
Vol 40 (10) ◽  
pp. 1269-1277 ◽  
Author(s):  
Congcong Gong ◽  
Yang Hu ◽  
Mao Zhou ◽  
Maojin Yao ◽  
Zhengxiang Ning ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cell Adhesion ◽  
Cancer Progression ◽  
Messenger Rna ◽  
Large Scale ◽  
Early Stage ◽  
Expression Profiles ◽  
High Morbidity ◽  
Hub Genes ◽  
Micro Rnas

Abstract Gastric cancer (GC) has high morbidity and mortality rates worldwide. Abundant literature has reported several individual genes and their related pathways intimately involved in tumor progression. However, little is known about GC progression at the gene network level. Therefore, understanding the underlying mechanisms of pathological transition from early stage to late stage is urgently needed. This study aims to identify potential vital genes and modules involved in the progression of GC. To understand the gene regulatory network of GC progression, we analyzed micro RNAs and messenger RNA s expression profiles by using a couple of bioinformatics tools. miR-205 was identified by differentially expressed analysis and was further confirmed through using multiple kernel learning-based Kronecker regularized least squares. Using weighted gene co-expression network analysis, the gastric cancer progression-related module, which has the highest correlation value with cancer progression, was obtained. Kyoto Encyclopedia of Genes and Genomes pathways and biological processes of the GCPR module genes were related to cell adhesion. Meanwhile, large-scale genes of GCPR module were found to be targeted by miR-205, including two hub genes SORBS1 and LPAR1. In brief, through multiple analytical methods, we found that miR-205 and the GCPR module play critical roles in GC progression. In addition, miR-205 might maintain cell adhesion by regulating SORBS1 and LPAR1. To screen the potential drug candidates, the gene expression profile of the GCPR module was mapped connectivity map (Cmap), and the mTOR inhibitor (Sirolimus) was found to be the most promising candidate. We further confirmed that Sirolimus can suppress cell proliferation of GC cell in vitro.

scholarly journals Identification of Gastric Cancer-Related Circular RNA through Microarray Analysis and Bioinformatics Analysis

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Wei Gu ◽  
Ying Sun ◽  
Xiong Zheng ◽  
Jin Ma ◽  
Xiao-Ying Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Microarray Analysis ◽  
Cancer Progression ◽  
Pathway Analysis ◽  
Bioinformatics Analysis ◽  
Malignant Tumors ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Target Mrnas

Gastric cancer is one of the common malignant tumors worldwide. Increasing studies have indicated that circular RNAs (circRNAs) play critical roles in the cancer progression and have shown great potential as useful markers and therapeutic targets. However, the precise mechanism and functions of most circRNAs are still unknown in gastric cancer. In the present study, we performed a microarray analysis to detect circRNA expression changes between tumor samples and adjacent nontumor samples. The miRNA expression profiles were obtained from the National Center of Biotechnology Information Gene Expression Omnibus (GEO). The differentially expressed circRNAs and miRNAs were identified through fold change filtering. The interactions between circRNAs and miRNAs were predicted by Arraystar’s home-made miRNA target prediction software. After circRNA-related miRNAs and dysregulated miRNAs were intersected, 23 miRNAs were selected. The target mRNAs of miRNAs were predicted by TarBase v7.0. Gene ontology (GO) enrichment analysis and pathway analysis were performed using standard enrichment computational methods for the target mRNAs. The results of pathway analysis showed that p53 signaling pathway and hippo signal pathway were significantly enriched and CCND2 was a cross-talk gene associated with them. Finally, a circRNA-miRNA-mRNA regulation network was constructed based on the gene expression profiles and bioinformatics analysis results to identify hub genes and hsa_circRNA_101504 played a central role in the network.

scholarly journals CircPTK2 Suppresses the Progression of Gastric Cancer by Targeting the MiR-196a-3p/AATK Axis

2021 ◽  
Vol 11 ◽  
Author(s):  
Ling Gao ◽  
Tingting Xia ◽  
Mingde Qin ◽  
Xiaofeng Xue ◽  
Linhua Jiang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cancer Cells ◽  
Cancer Progression ◽  
Luciferase Reporter ◽  
Migration And Invasion ◽  
Circular Rnas ◽  
High Morbidity ◽  
Gastric Cancer Cells ◽  
Mirna Sponges ◽  
Gastric Cancer Cell Proliferation

BackgroundGastric cancer is a type of malignant tumor with high morbidity and mortality. It has been shown that circular RNAs (circRNAs) exert critical roles in gastric cancer progression via working as microRNA (miRNA) sponges to regulate gene expression. However, the role and potential molecular mechanism of circRNAs in gastric cancer remain largely unknown.MethodsCircPTK2 (hsa_circ_0005273) was identified by bioinformatics analysis and validated by RT-qPCR assay. Bioinformatics prediction, dual-luciferase reporter, and RNA pull-down assays were used to determine the interaction between circPTK2, miR-196a-3p, and apoptosis-associated tyrosine kinase 1 (AATK).ResultsThe level of circPTK2 was markedly downregulated in gastric cancer tissues and gastric cancer cells. Upregulation of circPTK2 significantly suppressed the proliferation, migration, and invasion of gastric cancer cells, while circPTK2 knockdown exhibited opposite effects. Mechanically, circPTK2 could competitively bind to miR-196a-3p and prevent miR-196a-3p to reduce the expression of AATK. In addition, overexpression of circPTK2 inhibited tumorigenesis in a xenograft mouse model of gastric cancer.ConclusionCollectively, circPTK2 functions as a tumor suppressor to suppress gastric cancer cell proliferation, migration, and invasion through regulating the miR-196a-3p/AATK axis, suggesting that circPTK2 may serve as a novel therapeutic target for gastric cancer.

scholarly journals A Tumor Progression Related 7-Gene Signature Indicates Prognosis and Tumor Immune Characteristics of Gastric Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Fen Liu ◽  
Zongcheng Yang ◽  
Lixin Zheng ◽  
Wei Shao ◽  
Xiujie Cui ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
High Risk ◽  
Cancer Progression ◽  
Risk Score ◽  
Risk Model ◽  
Cox Regression ◽  
Hub Genes ◽  
Cox Regression Analysis ◽  
High Risk Patients ◽  
Risk Patients

BackgroundGastric cancer is a common gastrointestinal malignancy. Since it is often diagnosed in the advanced stage, its mortality rate is high. Traditional therapies (such as continuous chemotherapy) are not satisfactory for advanced gastric cancer, but immunotherapy has shown great therapeutic potential. Gastric cancer has high molecular and phenotypic heterogeneity. New strategies for accurate prognostic evaluation and patient selection for immunotherapy are urgently needed.MethodsWeighted gene coexpression network analysis (WGCNA) was used to identify hub genes related to gastric cancer progression. Based on the hub genes, the samples were divided into two subtypes by consensus clustering analysis. After obtaining the differentially expressed genes between the subtypes, a gastric cancer risk model was constructed through univariate Cox regression, least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analysis. The differences in prognosis, clinical features, tumor microenvironment (TME) components and immune characteristics were compared between subtypes and risk groups, and the connectivity map (CMap) database was applied to identify potential treatments for high-risk patients.ResultsWGCNA and screening revealed nine hub genes closely related to gastric cancer progression. Unsupervised clustering according to hub gene expression grouped gastric cancer patients into two subtypes related to disease progression, and these patients showed significant differences in prognoses, TME immune and stromal scores, and suppressive immune checkpoint expression. Based on the different expression patterns between the subtypes, we constructed a gastric cancer risk model and divided patients into a high-risk group and a low-risk group based on the risk score. High-risk patients had a poorer prognosis, higher TME immune/stromal scores, higher inhibitory immune checkpoint expression, and more immune characteristics suitable for immunotherapy. Multivariate Cox regression analysis including the age, stage and risk score indicated that the risk score can be used as an independent prognostic factor for gastric cancer. On the basis of the risk score, we constructed a nomogram that relatively accurately predicts gastric cancer patient prognoses and screened potential drugs for high-risk patients.ConclusionsOur results suggest that the 7-gene signature related to tumor progression could predict the clinical prognosis and tumor immune characteristics of gastric cancer.

Predicting functional circular RNA-based competitive endogenous RNA network in gastric carcinoma using novel bioinformatics analysis

2021 ◽  
pp. 153537022110487
Author(s):  
Zirui Zhu ◽  
Rui Huang ◽  
Baojun Huang
Keyword(s):  
Messenger Rna ◽  
Expression Profiles ◽  
Clinical Stage ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Rank Aggregation ◽  
Circular Rnas ◽  
Pathway Enrichment Analysis ◽  
Hub Genes ◽  
Competitive Endogenous Rna

Gastric cancer (GC) remains one of the most prevalent types of malignancies worldwide, and also one of the most reported lethal tumor-related diseases. Circular RNAs (circRNAs) have been certified to be trapped in multiple aspects of GC pathogenesis. Yet, the mechanism of this regulation is mostly undefined. This research is designed to discover the vital circRNA-microRNA (miRNA)-messenger RNA (mRNA) regulatory network in GC. Expression profiles with diverse levels including circRNAs, miRNAs, and mRNAs were all determined using microarray public datasets from Gene Expression Ominous (GEO). The differential circRNAs expressions were recognized against the published robust rank aggregation algorithm. Besides, a circRNA-based competitive endogenous RNA (ceRNA) interaction network was visualized via Cytoscape software (version 3.8.0). Functional and pathway enrichment analysis associated with differentially expressed targeted mRNAs were conducted using Cytoscape and an online bioinformatics database. Furthermore, an interconnected protein–protein interaction association network which consisted of 51 mRNAs was predicted, and hub genes were screened using STRING and CytoHubba. Then, several hub genes were chosen to explore their expression associated with survival rate and clinical stage in GEPIA and Kaplan-Meier Plotter databases. Finally, a carefully designed circRNA-related ceRNA regulatory subnetwork including four circRNAs, six miRNAs, and eight key hub genes was structured using the online bioinformatics tool.

scholarly journals Identification of key biomarkers associated with development and prognosis in patients with ovarian carcinoma: evidence from bioinformatic analysis

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Jiayu Shen ◽  
Shuqian Yu ◽  
Xiwen Sun ◽  
Meichen Yin ◽  
Jing Fei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Adhesion ◽  
Adhesion Molecules ◽  
Transforming Growth Factor Beta ◽  
Cell Adhesion Molecules ◽  
Cellular Response ◽  
Transforming Growth Factor ◽  
Expression Profiles ◽  
Regulation Of Transcription ◽  
Hub Genes

Abstract Background Ovarian cancer (OC) is the deadliest cause in the gynecological malignancies. Most OC patients are diagnosed in advanced stages with less than 40% of women cured. However, the possible mechanism underlying tumorigenesis and candidate biomarkers remain to be further elucidated. Results Gene expression profiles of GSE18520, GSE54388, and GSE27651 were available from Gene Expression Omnibus (GEO) database with a total of 91 OC samples and 22 normal ovarian (OV) tissues. Three hundred forty-nine differentially expressed genes (DEGs) were screened between OC tissues and OV tissues via GEO2R and online Venn software, followed by KEGG pathway and gene ontology (GO) enrichment analysis. The enriched functions and pathways of these DEGs contain male gonad development, cellular response to transforming growth factor beta stimulus, positive regulation of transcription from RNA polymerase II promoter, calcium independent cell-cell adhesion via plasma membrane cell adhesion molecules, extracellular matrix organization, pathways in cancer, cell cycle, cell adhesion molecules, PI3K-AKT signaling pathway, and progesterone mediated oocyte maturation. The protein-protein network (PPI) was established and module analysis was carried out using STRING and Cytoscape. Next, with PPI network analyzed by four topological methods in Cytohubba plugin of Cytoscape, 6 overlapping genes (DTL, DLGAP5, KIF15, NUSAP1, RRM2, and TOP2A) were eventually selected. GEPIA and Oncomine were implemented for validating the gene expression and all the six hub genes were highly expressed in OC specimens compared to normal OV tissues. Furthermore, 5 of 6 genes except for DTL were associated with worse prognosis using Kaplan Meier-plotter online tool and 3 of 6 genes were significantly related to clinical stages, including RRM2, DTL, and KIF15. Additionally, cBioPortal showed that TOP2A and RRM2 were the targets of cancer drugs in patients with OC, indicating the other four genes may also be potential drug targets. Conclusion Six hub genes (DTL, DLGAP5, KIF15, NUSAP1, RRM2, and TOP2A) present promising predictive value for the development and prognosis of OC and may be used as candidate targets for diagnosis and treatment of OC.

Proteomic analysis of extracellular vesicles from medullospheres reveals a role for iron in the cancer progression of medulloblastoma

2019 ◽  
pp. 1-12
Author(s):  
Maja Larsen ◽  
Matthias Kuhlmann Kuhlmann ◽  
Michael Hvam ◽  
Kenneth Howard
Keyword(s):  
Cell Lines ◽  
Cancer Progression ◽  
Early Stage ◽  
Cell Communication ◽  
Treatment Strategies ◽  
Iron Chelators ◽  
High Morbidity ◽  
New Treatment ◽  
Stem Cell Populations

Background: Medulloblastoma (MB) is the most common malignant childhood brain tumor with the propensity todisseminate at an early stage, and is associated with high morbidity. New treatment strategies are needed toimprove cure rates and to reduce life-long cognitive and functional deficits associated with current therapies.Extracellular Vesicles (EVs) are important players in cell-to-cell communication in health and diseases. A clearerunderstanding of cell-to-cell communication in tumors can be achieved by studying EV secretion inmedullospheres. This can reveal subtle modifications induced by the passage from adherent to non-adherentgrowth, as spheres may account for the adaptation of tumor cells to the mutated environment.Methods: Formation of medullospheres from MB cell lines stabilized in adherent conditions was obtained throughculture conditioning based on low attachment flasks and specialized medium. EVs collected by ultracentrifugation,in adherent conditions and as spheres, were subjected to electron microscopy, NanoSight measurements andproteomics.Results: Interestingly, iron carrier proteins were only found in EVs shed by CSC-enriched tumor cell population ofspheres. We used iron chelators when culturing MB cell lines as spheres. Iron chelators induced a decrease innumber/size of spheres and in stem cell populations able to initiate in vitro spheres formation.Conclusions: This work suggests a not yet identified role of iron metabolism in MB progression and invasion andopens the possibility to use chelators as adjuvants in anti-tumoral chemotherapy.

Long-term prognosis of patients with gastric cancer in stage UICC I without lymph-node involvement.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e15068-e15068
Author(s):  
Christoph Treese ◽  
Pedro Sanchez ◽  
Ioannis Anagnostopoulos ◽  
Peter M. Schlag ◽  
Michael Kruschewski ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Risk Factor ◽  
Lymph Node ◽  
Early Stage ◽  
Expression Profiles ◽  
Lymph Node Involvement ◽  
Term Survival ◽  
Immunohistochemical Markers ◽  
Node Involvement

e15068 Background: Despite radical oncologic resection with extended lymph node removal, patients with adenocarcinoma of the gastro-esophageal junction or stomach in UICC stage I show only a 5-year survival of 60-80% (Hölscher et al, 2009; Siewert et al. 1998). The aim of this retrospective study was to analyze the long-term survival of caucasian patients with early stage gastric cancer as for this population exist only sparse data. Patients with lymph-node involvement were not included as this parameter is a well-known negative prognostic marker. Methods: Tissue specimens and clinical data from patients with gastric cancer treated in the years 1993 to 2010 at the Charité, Berlin were collected retrospectively. Patients with stage T1 and T2 pN0M0 gastric cancer treated only by surgery including D1- and D2-lymphnode dissection were included in this study. Patients without relapse were followed-up for a minimum period of 24 months. Results: 97 patients (w = 36, m = 61, age 29-90 years) with a follow-up time from 6 to 208 months were identified. The 5-year survival was 94.85% (for details, see Table). Conclusions: The present data indicate a much better prognosis (5-year survival of 95%) of UICC I patients than previously described (60-80%). In harmony with other studies, our data demonstrate that R1, L1 or V1 resection seem to be a risk factor for recurrence whereas signet-ring differentiation was not found as a risk factor in our patient cohort. Ongoing work involves a broad panel of immunohistochemical markers to select prognostic expression profiles which help to identify patients with early gastric cancer at higher risk. This study was supported by the Berliner Krebsgesellschaft, grant DAFF201101. [Table: see text]

scholarly journals Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

2020 ◽  
Author(s):  
Xige He ◽  
Rihan Wu ◽  
Yueying Yun ◽  
Xia Qin ◽  
Lu Chen ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Messenger Rna ◽  
Noncoding Rna ◽  
Target Genes ◽  
Early Stage ◽  
Expression Profiles ◽  
Theoretical Data ◽  
Differentially Expressed ◽  
Growth Stages ◽  
Complex Biological Process

Abstract Background: Sunite sheep are a fat-tailed sheep species with a low percentage of intramuscular fat and good quality lean meat, and their tail fat can be used as a source of dietary fat by humans. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6 months, 18 months, and 30 months.Results: A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep (false discovery rate < 0.05, |Fold Change| ≥ 2). Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found that fat-related DEGs were mainly expressed at 6 months of age, and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their trans-regulators (53 mRNAs at most). Further, we obtained several fat-related differentially-expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Conclusions: Finally, we conclude that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process, and our findings will provide some basic theoretical data for future studies on tail fat development of fat-tailed sheep.

scholarly journals Qiguiyin Decoction Improves Multidrug-Resistant Pseudomonas aeruginosa Infection in Rats by Regulating Inflammatory Cytokines and the TLR4/MyD88/NF-κB Signaling Pathway

2022 ◽  
Vol 2022 ◽  
pp. 1-11
Author(s):  
Guochao Chen ◽  
Wanqiao Zhang ◽  
Lingbo Kong ◽  
Chengxiang Wang ◽  
Xiaojing Lai ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Signaling Pathway ◽  
Inflammatory Cytokines ◽  
Bacterial Infections ◽  
Early Stage ◽  
Expression Profiles ◽  
Multidrug Resistant ◽  
Antibody Array ◽  
High Morbidity ◽  
High Detection Rate

Pseudomonas aeruginosa (PA), a Gram-negative bacterium, has a high detection rate in hospital-acquired infections. Recently, the frequent appearance of multidrug-resistant (MDR) PA strain with high morbidity and mortality rates has aggravated the difficulty in treating infectious diseases. Due to its multiple resistance mechanisms, the commonly used antibiotics have gradually become less effective. Qiguiyin decoction (QGYD) is a clinically experienced prescription of Chinese herbal medicine, and its combined application with antibiotics has been confirmed to be effective in the clinical treatment of MDR PA infection, which could be a promising strategy for the treatment of drug-resistant bacterial infections. However, the mechanism of QGYD restoring antibiotics susceptibility to MDR PA remains unclear. In the present study, we investigated the effects of QGYD and levofloxacin (LEV) singly or in combination on MDR PA-induced pneumonia rat models. Further analysis was carried out in the serum differential expression profiles of inflammatory cytokines by cytokine antibody array. Besides, the lung TLR4/MyD88/NF-κB signaling pathway was detected by RT-qPCR. Our results showed that based on the treatment of MDR PA-infected rat model with LEV, the combination of QGYD improved the general state and immune organ index. Furthermore, it moderately increased the expressions of proinflammatory cytokines including IL-1β, IL-6, and TNF-α in the early stage of infection and decreased their release rapidly in the later stage, while regulated the same phase change of anti-inflammatory cytokine IL-10. In addition, the adhesion molecule ICAM-1 was significantly downregulated after QGYD combined with LEV treatment. Moreover, the mRNA expressions of TLR4, MyD88, NF-κB, and ICAM-1 were significantly downregulated. These results indicated that the mechanism of QGYD restoring LEV susceptibility to MDR PA was related to its regulation of inflammatory cytokines and the TLR4/MyD88/NF-κB signaling pathway, which provides theoretical support for the clinical application of QGYD combined with LEV therapy to MDR PA infection.

scholarly journals Bioinformatics Analysis for Identifying Micro-RNAs, Long Noncoding RNAs, Transcription Factors, Immune Genes Regulatory Networks, and Potential Therapeutic Agents for Diabetic Cardiomyopathy Using an Integrated Bioinformatics Analysis

2021 ◽  
Author(s):  
Jiefang Zhou ◽  
Xiaowei Ji ◽  
Xiuwei Shen ◽  
Kefeng Yan ◽  
Peng Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Diabetic Cardiomyopathy ◽  
Bioinformatics Analysis ◽  
Expression Profiles ◽  
Therapeutic Agents ◽  
Hub Genes ◽  
Ppi Networks ◽  
Micro Rnas ◽  
Rna Interaction

Abstract Objectives We identified functional genes and studied the underlying molecular mechanisms of diabetic cardiomyopathy (DCM) using bioinformatics tools. Methods Original gene expression profiles were obtained from the GSE21610 and GSE112556 datasets. We used GEO2R to screen the differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on DEGs. Protein–protein interaction (PPI) networks of DEGs were constructed using STRING and hub genes of signaling pathways were identified using Cytoscape. Aberrant hub gene expression was verified using The Cancer Genome Atlas dataset. Connectivity Map was used to predict the drugs that could treat DCM. Results The DEGs in DCM were mainly enriched in the nuclei and cytoplasm and involved in DCM- and chemokine-related signaling pathways. In the PPI network, 32 nodes were chosen as hub nodes and an RNA interaction network was constructed with 517 interactions. The expression of key genes (JPIK3R1, CCR9, XIST, WDFY3.AS2, hsa-miR-144-5p, and hsa-miR-146b-5p) was significantly different between DCM and normal tissues. Danazol, ikarugamycin, and semustine were identified as therapeutic agents against DCM using CMAP. Conclusion The identified hub genes could be associated with DCM pathogenesis and the above drugs could be used for treating DCM.

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