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 Construction and Validation of an Immune-Related Gene Prognostic Index for Esophageal Squamous Cell Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Qinghua Ji ◽  
Yingying Cai ◽  
Sachin Mulmi Shrestha ◽  
Duo Shen ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Prognostic Index ◽  
Enrichment Analysis ◽  
Response To Therapy ◽  
Gene Set Enrichment Analysis ◽  
Related Gene ◽  
Immune Related Gene

Immune checkpoint inhibitor (ICI) therapy may benefit patients with advanced esophageal squamous cell carcinoma (ESCC); however, novel biomarkers are needed to help predict the response of patients to treatment. Differentially expressed immune-related genes within The Cancer Genome Atlas ESCC dataset were selected using the weighted gene coexpression network and lasso Cox regression analyses. Based on these data, an immune-related gene prognostic index (IRGPI) was constructed. The molecular characteristics of the different IRGPI subgroups were assessed using mutation information and gene set enrichment analysis. Differences in immune cell infiltration and the response to ICI therapy and other drugs were also analyzed. Additionally, tumor and adjacent control tissues were collected from six patients with ESCC and the expression of these genes was verified using real-time quantitative polymerase chain reaction. IRGPI was designed based on CLDN1, HCAR3, FNBP1L, and BRCA2, the expression of which was confirmed in ESCC samples. The prognosis of patients in the high-IRGPI group was poor, as verified using publicly available expression data. KMT2D mutations were more common in the high-IRGPI group. Enrichment analysis revealed an active immune response, and immune infiltration assessment showed that the high-IRGPI group had an increased infiltration degree of CD8 T cells, which contributed to the improved response to ICI treatment. Collectively, these data demonstrate that IRGPI is a robust biomarker for predicting the prognosis and response to therapy of patients with ESCC.

scholarly journals Autophagy-Related Three-Gene Prognostic Signature for Predicting Survival in Esophageal Squamous Cell Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Heyang Cui ◽  
Yongjia Weng ◽  
Ning Ding ◽  
Chen Cheng ◽  
Longlong Wang ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Prognostic Model ◽  
Cox Regression ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Discovery Cohort ◽  
Cox Regression Analysis

Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive malignant tumors in China, and its prognosis remains poor. Autophagy is an evolutionarily conserved catabolic process involved in the occurrence and development of ESCC. In this study, we described the expression profile of autophagy-related genes (ARGs) in ESCC and developed a prognostic prediction model for ESCC patients based on the expression pattern of ARGs. We used four ESCC cohorts, GSE53624 (119 samples) set as the discovery cohort, The Cancer Genome Atlas (TCGA) ESCC set (95 samples) as the validation cohort, 155 ESCC cohort, and Oncomine cohort were used to screen and verify differentially expressed ARGs. We identified 34 differentially expressed genes out of 222 ARGs. In the discovery cohort, we divided ESCC patients into three groups that showed significant differences in prognosis. Then, we analyzed the prognosis of 34 differentially expressed ARGs. Three genes [poly (ADP-ribose) polymerase 1 (PARP1), integrin alpha-6 (ITGA6), and Fas-associated death domain (FADD)] were ultimately obtained through random forest feature selection and were constructed as an ARG-related prognostic model. This model was further validated in TCGA ESCC set. Cox regression analysis confirmed that the three-gene signature was an independent prognostic factor for ESCC patients. This signature effectively stratified patients in both discovery and validation cohorts by overall survival (P = 5.162E-8 and P = 0.052, respectively). We also constructed a clinical nomogram with a concordance index of 0.713 to predict the survival possibility of ESCC patients by integrating clinical characteristics and the ARG signature. The calibration curves substantiated fine concordance between nomogram prediction and actual observation. In conclusion, we constructed a new ARG-related prognostic model, which shows the potential to improve the ability of individualized prognosis prediction 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 Human sperm-associated antigen 4 as a potential prognostic biomarker of lung squamous cell carcinoma

2021 ◽  
Vol 49 (7) ◽  
pp. 030006052110328
Author(s):  
Yongheng Wang ◽  
Yao Tang ◽  
Jianhui Li ◽  
Danfang Wang ◽  
Wenhan Li
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Malignant Tumors ◽  
Lung Squamous Cell Carcinoma ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Risk Scores ◽  
Tissue Samples

Objective Lung cancer (LC) is one of the most prevalent malignant tumors worldwide. As a subtype of LC, lung squamous cell carcinoma (LUSC) has a 5-year survival rate of less than 15%. In this study, we aimed to evaluate the prognostic value of a glycolysis-related gene signature in LUSC patients. Methods We obtained RNA-Seq data from The Cancer Genome Atlas (TCGA) database. Prognosis-related genes were screened out by Gene Set Enrichment Analysis (GSEA) and Cox proportional regression models. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to verify the mRNA expression levels in relevant tissues. Results We found that sperm-associated antigen 4 (SPAG4) overexpression was an independent risk factor for overall survival (OS) in LUSC. Patients with high-risk scores had higher mortality rates than those with low-risk scores. Moreover, by using RT-qPCR, we validated that SPAG4 mRNA was overexpressed in LUSC tissue samples compared with their paired para-cancerous histological normal tissues. Conclusions Analysis of aberrantly overexpressed SPAG4 may provide a further useful approach to complement existing methods and predict prognosis in LUSC patients.

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 MEOX2 Serves as a Novel Biomarker Associated with Macrophage Infiltration in Esophageal Squamous Cell Carcinoma

2021 ◽  
Author(s):  
zhen wang ◽  
han yang ◽  
rusi zhang ◽  
bin luo ◽  
bingchen xu ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Digestive System ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Macrophage Infiltration ◽  
High Morbidity

Abstract BackgroundEsophageal squamous cell carcinoma (ESCC) is a kind of digestive system malignant tumor with high morbidity and mortality worldwide. With the rise of immunotherapy applied in cancer treatment, immune-related mechanisms in ESCC and other digestive system carcinomas are in urgent need of being detected.MethodsIn our study, single-sample gene set enrichment analysis (ssGSEA) was performed at first to analyze the expression profile downloaded from NCBI Gene Expression Omnibus (GEO) database. Then via a series of bioinformatic analyses, including Mann-Whitney test, weighted gene co-expression network analysis (WGCNA), functional enrichment analysis and differentially expressed genes (DEGs) analysis, we identified targeting immunocyte and related genes. Finally, we validated the results in TIMER database.ResultsOur analyses showed that macrophage infiltrating level is obviously higher in advanced stages in ESCC compared with other types of immunocytes. MEOX2 was detected as a biomarker correlated with macrophage infiltration in ESCC and other types of digestive system carcinomas. And MEOX2 expression was strongly associated with mRNA expression of colony-stimulating factor 1 (CSF-1) and CSF-1 receptor (CSF-1R) in these kinds of carcinomas. ConclusionWe speculated that MEOX2 could facilitate macrophage infiltration via CSF-1/CSF-1R signaling in ESCC and other kinds of digestive system carcinomas, which might serve as a novel target in prospective tumor immunotherapy.

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