Integrative genomics analysis of hub genes and their relationship with prognosis and signaling pathways in esophageal squamous cell carcinoma

Analysis of Key Pathways, Genes and Immune Cell Infiltration in Metastatic Esophageal Squamous Cell Carcinoma Based on Bioinformatics

10.21203/rs.3.rs-938022/v1 ◽

2021 ◽

Author(s):

Zhangjiao Wang ◽

Yong Shen ◽

Qingxia Xu

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Tumor Markers ◽

Squamous Cell ◽

Protein Interaction ◽

Signal Pathway ◽

Hub Genes ◽

Immune Infiltration ◽

Geo Database

Abstract Objective: To seek potential metastatic tumor markers in esophageal squamous cell carcinoma (ESCC) by bioinformatics. Methods: Four datasets (GSE70409, GSE26886, GSE161533, GSE17351) were downloaded from GEO database, and the differential expression of mRNA was screened by Limma software package. Gene ontology function and kyoto encyclopedia of genes and genomes pathway enrichment analysis were performed using the database for annotation; Protein–protein interaction network of these DEGs was constructed based on STRING database; then, the hub gene were identified by six algorithms of Cytoscape software. Using GEPIA2 database and OncoLnc database to analyze the survival of hub genes. Immune infiltration was analyzed by TIMER2 database and CIBERSORT deconvolution method. Results: A total of 244 differentially expressed genes(DEGs)were screened from 4 data sets of GEO database, including 164 up-regulated genes and 80 down-regulated genes, which were mainly enriched at extracellular region and extracellular space, and involved in biological processes such as cell adhesion and proteolysis related to tumor invasion and metastasis. KEGG results showed that DEGs were mainly enriched in PI3K-Akt signal pathway and extracellular matrix (ECM) receptor interaction signal pathway. Through the protein interaction analysis of DEGs, we found that three hub genes (CXCL8, MMP9 and MMP13) were highly expressed in ESCC. However, the GEPIA2 database shows that only CXCL8 is associated with the overall survival of ESCC patients. The results of immune infiltration showed that macrophages and resting dendritic cells increased significantly, while mast cells and monocytes decreased significantly. Conclusion: Three hub genes and immune infiltrating cells may play an important role in ESCC, and are expected to become potential tumor markers of ESCC and be used in the diagnosis and treatment of ESCC.

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Signaling pathways and their potential therapeutic utility in esophageal squamous cell carcinoma

Clinical & Translational Oncology ◽

10.1007/s12094-021-02763-x ◽

2022 ◽

Author(s):

L. K. Kadian ◽

M. Arora ◽

C. P. Prasad ◽

R. Pramanik ◽

S. S. Chauhan

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Signaling Pathways ◽

Squamous Cell ◽

Therapeutic Utility

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Sa1145 NOVEL LNCRNA HERES REGULATES WNT SIGNALING PATHWAYS VIA INTERACTION WITH EZH2 IN ESOPHAGEAL SQUAMOUS CELL CARCINOMA.

Gastroenterology ◽

10.1016/s0016-5085(20)31418-9 ◽

2020 ◽

Vol 158 (6) ◽

pp. S-290

Author(s):

Bo-Hyun You ◽

Jung-Ho Yoon ◽

Hoin Kang ◽

Eun Kyung Lee ◽

Jin-Wu Nam ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Wnt Signaling ◽

Cell Carcinoma ◽

Signaling Pathways ◽

Squamous Cell

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Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma

BMC Genomics ◽

10.1186/s12864-015-1919-0 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 12

Author(s):

Nan Hu ◽

Chaoyu Wang ◽

Robert J. Clifford ◽

Howard H. Yang ◽

Hua Su ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Micro Rna ◽

Integrative Genomics

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Screening and identification of significant genes in esophageal squamous cell carcinoma by bioinformatical analysis

10.21203/rs.3.rs-16607/v1 ◽

2020 ◽

Author(s):

Weirui Ren ◽

Chuang Zhang ◽

Lei Pan ◽

Weijing Wang ◽

Wenjuan Zhao ◽

...

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Disease Free Survival ◽

Hub Genes ◽

Incidence And Mortality ◽

Bioinformatical Analysis

Abstract Background: Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers with notably high incidence and mortality rates. However, the molecular mechanism underlying ESCC pathogenesis and prognosis is very complicated. The main objective of our investigation has been to obtain some knowledge of significant genes with poor outcome and their underlying mechanisms.Methods: Gene expression profiles of GSE26886, GSE23400, GSE20347 and GSE17351 were available from GEO database. The differentially expressed genes (DEGs) were identified, and function enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using STRING and Cytoscape software.Results: A total of 105 DEGs were identified between normal esophagus and ESCC bioinformatical analysis samples. Functional annotations of the common DEGs indicate that extracellular matrix (ECM) remodeling plays a key role in tumor formation and progression.18 hub genes were identified and disease free survival analysis showed that CDKN3, RAD51AP1, KIF4A may be involved in poor prognosis in ESCC patients.Conclusions: DEGs and hub genes identified in the present study help us understand the molecular mechanisms underlying the carcinogenesis and progression of ESCC, and provide candidate targets for diagnosis and treatment of ESCC.

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Identification of Key Modules and Hub Genes Involved in Esophageal Squamous Cell Carcinoma Tumorigenesis Using WCGNA

Cancer Control ◽

10.1177/1073274820978817 ◽

2020 ◽

Vol 27 (1) ◽

pp. 107327482097881

Author(s):

Nanzheng Chen ◽

Guangjian Zhang ◽

Junke Fu ◽

Qifei Wu

Keyword(s):

Squamous Cell Carcinoma ◽

Esophageal Squamous Cell Carcinoma ◽

Cell Carcinoma ◽

Squamous Cell ◽

Mapk Signaling ◽

Clinical Samples ◽

Cancer Type ◽

Hub Genes ◽

Gene Modules ◽

Mechanistic Basis

Introduction: The mechanistic basis for the development of esophageal squamous cell carcinoma (ESCC) remains poorly understood. The goal of the present study was thus to characterize mRNA and long noncoding RNA (lncRNA) expression profiles associated with ESCC in order to identify key hub genes associated with the pathogenesis of this cancer. Materials and Methods: The GSE26866 and GSE45670 datasets from the Gene Expression Omnibus (GEO) database were used to conduct a weighted gene co-expression network analysis (WGCNA), after which Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Cytoscape was additionally used to construct lncRNA-mRNA networks, after which hub genes were identified and validated through the assessment of TCGA datasets and clinical samples. Results: Two gene modules were found to be closely linked to ESCC tumorigenesis. These genes were enriched in cell cycle, MAPK signaling, JAK-STAT signaling, pyrimidine metabolism, arachidonic acid metabolism, and P53 signaling pathway activity, all of which are directly linked with the development of cancer. In total, we identified and validated 9 hub genes associated with ESCC (DDX18, DNMT1, NCAPG, WDHD1, PRR11, VOPP1, ZKSCAN5, LC35C2, and PHACTR2). Conclusion: In summary, we identified key gene modules and hub genes associated with ESCC development, and we constructed a lncRNA-mRNA network pertaining to this cancer type. These results provide a foundation for future research regarding the mechanistic basis of ESCC.

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