scholarly journals Identification of Differentially Expressed Genes and miRNAs Associated with Esophageal Squamous Cell Carcinoma by Integrated Analysis of Microarray Data

2020 ◽  
Vol 2020 ◽  
pp. 1-16
Author(s):  
Lemeng Zhang ◽  
Jianhua Chen ◽  
Tianli Cheng ◽  
Hua Yang ◽  
Changqie Pan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Survival Analysis ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Microarray Data ◽  
Regulatory Network ◽  
Differentially Expressed ◽  
Pathway Enrichment

To identify candidate key genes and miRNAs associated with esophageal squamous cell carcinoma (ESCC) development and prognosis, the gene expression profiles and miRNA microarray data including GSE20347, GSE38129, GSE23400, and GSE55856 were downloaded from the Gene Expression Omnibus (GEO) database. Clinical and survival data were retrieved from The Cancer Genome Atlas (TCGA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) was analyzed via DAVID, while the DEG-associated protein-protein interaction network (PPI) was constructed using the STRING database. Additionally, the miRNA target gene regulatory network and miRNA coregulatory network were constructed, using the Cytoscape software. Survival analysis and prognostic model construction were performed via the survival (version 2.42-6) and rbsurv R packages, respectively. The results showed a total of 2575, 2111, and 1205 DEGs, and 226 differentially expressed miRNAs (DEMs) were identified. Pathway enrichment analyses revealed that DEGs were mainly enriched in 36 pathways, such as the proteasome, p53, and beta-alanine metabolism pathways. Furthermore, 448 nodes and 1144 interactions were identified in the PPI network, with MYC having the highest random walk score. In addition, 7 DEMs in the microarray data, including miR-196a, miR-21, miR-205, miR-194, miR-103, miR-223, and miR-375, were found in the regulatory network. Moreover, several reported disease-related miRNAs, including miR-198a, miR-103, miR-223, miR-21, miR-194, and miR-375, were found to have common target genes with other DEMs. Survival analysis revealed that 85 DEMs were related to prognosis, among which hsa-miR-1248, hsa-miR-1291, hsa-miR-421, and hsa-miR-7-5p were used for a prognostic survival model. Taken together, this study revealed the important roles of DEGs and DEMs in ESCC development, as well as DEMs in the prognosis of ESCC. This will provide potential therapeutic targets and prognostic predictors for ESCC.

Integrated Bioinformatics Analysis of Differentially-Expressed Genes and Immune Cell Infiltration Characteristics in Esophageal Squamous Cell Carcinoma

2021 ◽  
Author(s):  
Zitong Feng ◽  
Jingge Qu ◽  
Xiao Liu ◽  
Jinghui Liang ◽  
Yongmeng Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Bioinformatics Analysis ◽  
Immune Cell ◽  
Cell Infiltration ◽  
Immune Cell Infiltration

Abstract Esophageal squamous cell carcinoma (ESCC) is a life-threatening thoracic tumor with a poor prognosis. Identifying the best-targeted therapy, appropriate biomarkers and individual treatment for patients with ESCC remains a significant challenge. The present study aimed to elucidate key candidate genes and immune cell infiltration characteristics in ESCC by integrated bioinformatics analysis. We downloaded nine gene expression datasets from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between ESCC tissues and normal tissues in each dataset were identified by the “limma” R package, and a total of 152 robust DEGs were identified by robust rank aggregation (RRA) algorithm. Functional enrichment analyses of the robust DEGs showed that these genes were significantly associated with extracellular matrix related process. Immune cell infiltration analysis was also conducted by CIBERSORT algorithm. We found that M0 and M1 macrophages were increased dramatically in ESCC while M2 macrophages decreased. Nine hub genes were picked out from a protein-protein interaction (PPI) network used by the CytoHubba plugin in Cytoscape. According to the receiver operating characteristic (ROC) curves and Kaplan-Meier survival analysis, the genes PLAU, SPP1 and VCAN had high diagnostic and prognostic values for ESCC patients. Based on univariate and multivariate regression analyses, seven genes (IL18, PLAU, ANO1, SLCO1B3, CST1, NELL2 and MAGEA11) from the robust DEGs were used to construct a good prognostic model. A nomogram that incorporates seven genes signature was established to develop a quantitative method for ESCC prognosis. Our results might provide aid for exploring potential therapeutic targets and prognosis evaluation in ESCC.

scholarly journals Analysis of Differentially Expressed Genes in a Chinese Cohort of Esophageal Squamous Cell Carcinoma

2020 ◽  
Vol 11 (13) ◽  
pp. 3783-3793 ◽  
Author(s):  
Gang Liu ◽  
Yuan Zhao ◽  
Huili Chen ◽  
Jinru Jia ◽  
Xiaomin Cheng ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Differentially Expressed ◽  
Chinese Cohort

scholarly journals Research and Clinical Significance of the Differentially Expressed Genes TP63 and LMO4 in Human Immunodeficiency Virus-Related Penile Squamous Cell Carcinoma

2021 ◽  
Vol 15 (2) ◽  
pp. 155798832110113
Author(s):  
Wenrui Xue ◽  
Xin Zheng ◽  
Xiaopeng Hu ◽  
Yu Zhang
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Differentially Expressed ◽  
Control Group ◽  
Go Enrichment ◽  
Differential Gene ◽  
Penile Squamous Cell Carcinoma

To study the differential gene expression and clinical significance in human immunodeficiency virus-infected individuals (HIVIIs) with penile squamous cell carcinoma. At our hospital from 2019 to 2020, we selected six samples of HIV-related penile squamous cell carcinoma for the experimental group and six samples of non-HIV-related penile squamous cell carcinoma for the control group. Transcriptome sequencing of sample mRNAs was performed by high-throughput sequencing. Differential gene expression analysis, differential Gene Ontology (GO) enrichment analysis and differential Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were carried out, and the reads per kilobase per million reads (RPKM) value was used as a measure of gene expression. A total of 2418 differentially expressed genes were obtained, of which 663 were upregulated and 1755 were downregulated (absolute value of logFC >1 and p value <.05). On the basis of the significance of the GO enrichment analysis, we found that the tumor protein p63 (TP63) gene was significantly upregulated and that the LIM domain only 4 (LMO4) gene was significantly downregulated in the experimental group compared with the control group. KEGG pathway analysis of the differentially expressed genes revealed that DNA replication was the most significant pathway associated with the upregulated genes and cell adhesion molecule (CAM) metabolism was the most significant pathway associated with the downregulated genes. The gene expression profiles of HIV-related penile squamous cell carcinoma and non-HIV-related penile squamous cell carcinoma are significantly different and involve significant GO enrichment and KEGG metabolic pathways, and this is very meaningful for the study of non-AIDS-defining cancers (NADCs). Differential expression of genes may be an important target for the prevention of penile squamous cell carcinoma in HIVIIs.

Comprehensive bioinformation analysis of methylated and differentially expressed genes in esophageal squamous cell carcinoma

2019 ◽  
Vol 15 (1) ◽  
pp. 88-100 ◽  
Author(s):  
Hao Peng ◽  
Shasha Wang ◽  
Lijuan Pang ◽  
Lan Yang ◽  
Yunzhao Chen ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Crucial Role ◽  
Differentially Expressed ◽  
Differentially Methylated Genes

Differentially methylated genes (DMGs) play a crucial role in the etiology and pathogenesis of esophageal squamous cell carcinoma (ESCC).

scholarly journals Identifying the p65-Dependent Effect of Sulforaphene on Esophageal Squamous Cell Carcinoma Progression via Bioinformatics Analysis

2020 ◽  
Vol 22 (1) ◽  
pp. 60
Author(s):  
Sichong Han ◽  
Zhe Wang ◽  
Jining Liu ◽  
Qipeng Yuan
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Squamous Cell ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Dependent Manner

Understanding the mechanism by which sulforaphene (SFE) affects esophageal squamous cell carcinoma (ESCC) contributes to the application of this isothiocyanate as a chemotherapeutic agent. Thus, we attempted to investigate SFE regulation of ESCC characteristics more deeply. We performed gene set enrichment analysis (GSEA) on microarray data of SFE-treated ESCC cells and found that differentially expressed genes are enriched in TNFα_Signaling_via_the_NFκB_Pathway. Coupled with the expression profile data from the GSE20347 and GSE75241 datasets, we narrowed the set to 8 genes, 4 of which (C-X-C motif chemokine ligand 10 (CXCL10), TNF alpha induced protein 3 (TNFAIP3), inhibin subunit beta A (INHBA), and plasminogen activator, urokinase (PLAU)) were verified as the targets of SFE. RNA-sequence (RNA-seq) data of 182 ESCC samples from The Cancer Genome Atlas (TCGA) were grouped into two phenotypes for GSEA according to the expression of CXCL10, TNFAIP3, INHBA, and PLAU. The enrichment results proved that they were all involved in the NFκB pathway. ChIP-seq analyses obtained from the Cistrome database indicated that NFκB-p65 is likely to control the transcription of CXCL10, TNFAIP3, INHBA, and PLAU, and considering TNFAIP3 and PLAU are the most significantly differentially expressed genes, we used chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) to verify the regulation of p65 on their expression. The results demonstrated that SFE suppresses ESCC progression by down-regulating TNFAIP3 and PLAU expression in a p65-dependent manner.

scholarly journals Systematic Identification of circRNA–miRNA–mRNA Regulatory Network in Esophageal Squamous Cell Carcinoma

2021 ◽  
Vol 12 ◽  
Author(s):  
Yi Shen ◽  
Yi Shao ◽  
Chen Niu ◽  
Xiaoli Ruan ◽  
Zhaoping Zang ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Regulatory Network ◽  
Regulatory Mechanism ◽  
Differentially Expressed ◽  
Healthy Controls ◽  
Hub Genes ◽  
A Genome

BackgroundCircular RNAs (circRNAs) are described as endogenous non-coding RNAs that have been reported to play important roles in the development and progression of cancers. This study aimed to reveal the circRNA-related regulatory mechanism in esophageal squamous cell carcinoma (ESCC).MethodsA genome-wide circRNA microarray assay was performed to profile the expression of circRNAs in the blood of preoperative ESCC patients and healthy controls. A systematic method of data mining was performed to identify the differentially expressed miRNAs (DEmiRs) and differentially expressed genes (DEGs) based on the metaMA and RankProd analysis. Bioinformatics analyses and multiple tools were employed to construct the potential circRNA–miRNA–mRNA regulatory network.ResultsThirty-three differentially expressed circRNAs were identified in the ESCC blood, including 31 downregulated and two upregulated circRNAs in the blood of ESCC patients compared with the healthy controls. Twenty-three DEmiRs and 2,220 DEGs were obtained by the integration of microarray datasets. An ESCC-associated circRNA–miRNA–mRNA network was constructed based on 31 circRNAs, 3 DEmiRs, and 190 DEGs. Enrichment analyses indicated that the DEGs were associated with a series of biological processes and cancer-related pathways. The protein–protein interaction (PPI) network was generated by the 190 DEGs, with 10 hub genes verified in the network. Subsequently, a sub-network was established for ESCC, which included 29 circRNAs, 2 miRNAs, and 10 hub genes.ConclusionOur study provided a novel clue to help understand the circRNA–miRNA–mRNA regulatory mechanism, highlighting the potential roles of circRNAs in the pathogenesis and development of ESCC.

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