Bioinformatics analysis reveals the competing endogenous RNA (ceRNA) coexpression network in the tumor microenvironment and prognostic biomarkers in soft tissue sarcomas

ABSTRACT

Soft tissue sarcomas (STSs) are rare, heterogeneous mesenchymal neoplasias. Understanding the tumor microenvironment (TME) and identifying potential biomarkers for prognosis associated with the TME of STS might provide effective clues for immune therapy. We evaluated the immune scores and stromal scores of STS patients by using the RNA sequencing dataset from The Cancer Genome Atlas (TCGA) database and the ESTIMATE algorithm. Then, the differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified after comparing the high- and low-score groups. Next, we established a competing endogenous RNA (ceRNA) network and explored the prognostic values of biomarkers involved in the network with the help of bioinformatics analysis. High immune score was significantly associated with favorable overall survival in STS patients. A total of 328 DEGs, 18 DEMs and 67 DELs commonly regulated in the immune and stromal score groups were obtained. A ceRNA network and protein–protein interaction (PPI) network identified some hub nodes with considerable importance in the network. Kaplan–Meier survival analysis demonstrated that nine mRNAs, two miRNAs and three lncRNAs were closely associated with overall survival of STS patients. Gene set enrichment analysis (GSEA) suggested that these three lncRNAs were mainly involved in immune response-associated pathways in STS patients. Finally, the expression levels of five mRNAs (APOL1, EFEMP1, LYZ, RARRES1 and TNFAIP2) were verified, which were consistent with the results of the TCGA cohort. The results of our study confirmed the prognostic value of immune scores for STS patients. We also identified several TME-related biomarkers that might contribute to prognostic prediction and immune therapy.

Graphical Abstract

KEYWORDS:

• Soft tissue sarcomas
• tumor microenvironment
• estimate
• prognosis
• ceRNA

Highlights

Soft tissue sarcomas; tumor microenvironment; ESTIMATE; prognosis; ceRNA

Data Availability

The datasets of this article were generated from the TCGA and GEO database.

Disclosure statement

The authors declare that there was no potential conflict of interest.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Notes on contributors

Dandan Zou

Dandan Zou and Yang Wang: conception and design of the research. Meng Wang and Bo Zhao: acquisition of data and analysis and interpretation of data. Fei Hu, Yanguo Li and Bingming Zhang: statistical analysis. Dandan Zou and Yang Wang: drafting the manuscript. Yang Wang, Fei Hu, Yanguo Li and Bingming Zhang: revision of manuscript. All authors have read and approved the final manuscript.