Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database

Abstract Background Esophageal squamous cell carcinoma (ESCC) is the most common histological type of esophageal cancer in the world with high incidence rate and poor prognosis. Infiltrated immune and stromal cells are vital components of tumor microenvironment (TME) and have a significant impact on...

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Autores principales:	Danlei Song, Yongjian Wei, Yuping Hu, Xia Chen, Ya Zheng, Min Liu, Yuping Wang, Yongning Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Springer 2021
Materias:	Esophageal squamous cell carcinoma Tumor microenvironment Weighted gene co-expression network analysis Competing endogenous RNA network Prognosis Relative abundance of tumor infiltrating immune cells Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
Acceso en línea:	https://doaj.org/article/e0a5c9a90fba406184f94a9552d77005
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spelling	oai:doaj.org-article:e0a5c9a90fba406184f94a9552d770052021-11-08T11:19:22ZIdentification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database10.1007/s12672-021-00442-52730-6011https://doaj.org/article/e0a5c9a90fba406184f94a9552d770052021-11-01T00:00:00Zhttps://doi.org/10.1007/s12672-021-00442-5https://doaj.org/toc/2730-6011Abstract Background Esophageal squamous cell carcinoma (ESCC) is the most common histological type of esophageal cancer in the world with high incidence rate and poor prognosis. Infiltrated immune and stromal cells are vital components of tumor microenvironment (TME) and have a significant impact on the progression of ESCC. The competitive endogenous RNA (ceRNA) hypothesis has been proved important in the molecular biological mechanisms of tumor development. However, there are few studies on the relationship between ceRNA and ESCC TME. Methods The proportion of tumor-infiltrating immune cells and the amount of stromal and immune cells in ESCC cases were calculated from The Cancer Genome Atlas database using the CIBERSORT and ESTIMATE calculation methods. After stratified identification of differentially expressed genes, WGCNA and miRNA prediction system were applied to construct ceRNA network. Finally, PPI network and survival analysis were selected to discriminate prognostic signature. And the results were verified in two independent groups from Gene Expression Omnibus and Lanzhou, China. Results We found that high Stromal and ESTIMATE scores were significantly associated with poor overall survival. Three TME-related key prognostic genes were screened, namely, LCP2, CD86, SLA. And the expression of them was significantly correlated with infiltrated immunocytes. It is also found that ESTIMATE Score and the expression of CD86 were both related to TNM system of ESCC. Conclusions We identified three novel TME-related prognostic markers and their lncRNA-miRNA-mRNA pathway in ESCC patients, which may provide new strategies for the targeted therapy.Danlei SongYongjian WeiYuping HuXia ChenYa ZhengMin LiuYuping WangYongning ZhouSpringerarticleEsophageal squamous cell carcinomaTumor microenvironmentWeighted gene co-expression network analysisCompeting endogenous RNA networkPrognosisRelative abundance of tumor infiltrating immune cellsNeoplasms. Tumors. Oncology. Including cancer and carcinogensRC254-282ENDiscover Oncology, Vol 12, Iss 1, Pp 1-22 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Esophageal squamous cell carcinoma Tumor microenvironment Weighted gene co-expression network analysis Competing endogenous RNA network Prognosis Relative abundance of tumor infiltrating immune cells Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282
spellingShingle	Esophageal squamous cell carcinoma Tumor microenvironment Weighted gene co-expression network analysis Competing endogenous RNA network Prognosis Relative abundance of tumor infiltrating immune cells Neoplasms. Tumors. Oncology. Including cancer and carcinogens RC254-282 Danlei Song Yongjian Wei Yuping Hu Xia Chen Ya Zheng Min Liu Yuping Wang Yongning Zhou Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database
description	Abstract Background Esophageal squamous cell carcinoma (ESCC) is the most common histological type of esophageal cancer in the world with high incidence rate and poor prognosis. Infiltrated immune and stromal cells are vital components of tumor microenvironment (TME) and have a significant impact on the progression of ESCC. The competitive endogenous RNA (ceRNA) hypothesis has been proved important in the molecular biological mechanisms of tumor development. However, there are few studies on the relationship between ceRNA and ESCC TME. Methods The proportion of tumor-infiltrating immune cells and the amount of stromal and immune cells in ESCC cases were calculated from The Cancer Genome Atlas database using the CIBERSORT and ESTIMATE calculation methods. After stratified identification of differentially expressed genes, WGCNA and miRNA prediction system were applied to construct ceRNA network. Finally, PPI network and survival analysis were selected to discriminate prognostic signature. And the results were verified in two independent groups from Gene Expression Omnibus and Lanzhou, China. Results We found that high Stromal and ESTIMATE scores were significantly associated with poor overall survival. Three TME-related key prognostic genes were screened, namely, LCP2, CD86, SLA. And the expression of them was significantly correlated with infiltrated immunocytes. It is also found that ESTIMATE Score and the expression of CD86 were both related to TNM system of ESCC. Conclusions We identified three novel TME-related prognostic markers and their lncRNA-miRNA-mRNA pathway in ESCC patients, which may provide new strategies for the targeted therapy.
format	article
author	Danlei Song Yongjian Wei Yuping Hu Xia Chen Ya Zheng Min Liu Yuping Wang Yongning Zhou
author_facet	Danlei Song Yongjian Wei Yuping Hu Xia Chen Ya Zheng Min Liu Yuping Wang Yongning Zhou
author_sort	Danlei Song
title	Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database
title_short	Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database
title_full	Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database
title_fullStr	Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database
title_full_unstemmed	Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database
title_sort	identification of prognostic biomarkers associated with tumor microenvironment in cerna network for esophageal squamous cell carcinoma: a bioinformatics study based on tcga database
publisher	Springer
publishDate	2021
url	https://doaj.org/article/e0a5c9a90fba406184f94a9552d77005
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Identification of prognostic biomarkers associated with tumor microenvironment in ceRNA network for esophageal squamous cell carcinoma: a bioinformatics study based on TCGA database

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