Transcriptome analysis reveals the link between lncRNA-mRNA co-expression network and tumor immune microenvironment and overall survival in head and neck squamous cell carcinoma

• DOI: 10.1186/s12920-020-0707-0
• Publication Date: 2020-03-30T11:03:04Z
• Authors: Zhaoming Zhong; Min Hong; Xiao Chen; Yan Xi; Yuanyuan Xu; Deyu Kong; Jun Deng; Yun Li; Rui Hu; Chuanzheng Sun; Jin Liang
• Keywords: Male; 0301 basic medicine; QH426-470; HNSCC; 03 medical and health sciences; lncRNA; Genetics; Biomarkers, Tumor; Tumor Microenvironment; Humans; Gene Regulatory Networks; Internal medicine; Squamous Cell Carcinoma of Head and Neck; Computational Biology; Middle Aged; Prognosis; RC31-1245; 3. Good health; Immune; Gene Expression Regulation, Neoplastic; Survival Rate; MicroRNAs; Tumor microenvironment; Head and Neck Neoplasms; Female; RNA, Long Noncoding; Gene expression; Transcriptome; Research Article

Abstract Background As the sixth most common cancer worldwide, head and neck squamous cell carcinoma (HNSCC) develops visceral metastases during advanced stage of disease exhibits a low five-year survival rate. The importance tumor microenvironment (TME) in initiation metastasis is widely recognized. In addition, accumulating evidence indicates that long non-coding RNA (lncRNA) involved crosstalk between TME cells. However, lncRNA-associated regulators modulating HNSCC progression remain largely unknown. Methods publicly available transcriptome data matched clinical were collected from Cancer Genome Atlas (TCGA). Immune scores (ISs) stromal (SSs) calculated using ESTIMATE algorithm. Weighted gene co-expression network analysis (WGCNA) was conducted to determine co-expressed lncRNAs protein-coding mRNAs. Results showed high IS male patient subgroup exhibited improved survival. Additionally, we identified 169 825 mRNAs differentially expressed samples, with up-regulated displaying enrichment immune-related biological processes. Notably, lncRNA-mRNA module (i.e., purple module) strong correlation ISs. This contained 79 442 mRNAs, including 26 215 showing association expression Consistently, 207 group enriched signaling pathways. Based on bioinformatics analyses previous functional assays, certain (e.g., AL365361.1 PCED1B-AS1 ) likely contributed modification immune (TIME) patients, achieved by regulating transcription abundant genes CCR7 TLR8 ). Conclusions summary, ascertained displayed ISs good probability. We hundreds specific patterns this as well highly great potential for modulation TIME HNSCC. Our study provides link network, TIME, progression, highlights therapeutic targets disease.