ABSTRACT
PURPOSE: Laryngeal squamous-cell carcinoma (LSCC) is the second most common malignant tumor of head and neck squamous cell carcinoma. The study was aimed to identify key long non-coding RNAs (lncRNAs) biomarkers for LSCC. METHODS: Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between LSCC and adjacent tissues were obtained based on The Cancer Genome Atlas. DElncRNA-DEmRNAs co-expression and DElncRNA-nearby-target DEmRNA interaction networks were constructed. Receiver operating characteristic and survival analysis were performed. A published dataset were as used to validate the result of bioinformatics analysis. RESULTS: We obtained 1103 DEmRNAs and 306 DElncRNAs between LSCC and adjacent tissues. A total of 338 DElncRNA-DEmRNA co-expression pairs and 229 DElncRNA-nearby-target DEmRNA pairs were obtained. Ten DElncRNAs and six DEmRNAs has great diagnostic value for LSCC. HOXB9 has potential prognostic value for LSCC. The results of GSE84957 validation were generally consistent with our results. CONCLUSION: Our study provided clues for understanding the mechanism and developing potential biomarkers for LSCC.
Subject(s)
Gene Expression Regulation, Neoplastic , Laryngeal Neoplasms/genetics , RNA, Long Noncoding/genetics , RNA, Messenger/genetics , Squamous Cell Carcinoma of Head and Neck/genetics , Biomarkers, Tumor/genetics , Computational Biology , Databases, Factual , Gene Expression Profiling , Gene Regulatory Networks , Genome, Human , Humans , Laryngeal Neoplasms/mortality , Prognosis , Reproducibility of Results , Squamous Cell Carcinoma of Head and Neck/mortality , Squamous Cell Carcinoma of Head and Neck/pathologyABSTRACT
The aim of the present study was to investigate the key genes, miRNAs and pathways in hypopharyngeal squamous cell carcinoma (HPSCC) and to elucidate the mechanisms underlying HPSCC development. The gene and microRNA (miRNA) expression profiles of HPSCC tissues and adjacent normal tissues from three subjects were obtained. Differentially expressed genes (DEGs) and differentially expressed miRNAs were identified in HPSCC. Functional annotation and proteinprotein interaction (PPI) network were conducted to elucidate the biological functions of DEGs. A total of 160 DEGs (16 upregulated and 144 downregulated genes) and 79 differentially expressed miRNAs (48 upregulated and 31 downregulated miRNAs) were identified in HPSCC. The deregulated genes were significantly involved in spliceosome, cell cycle and RNA degradation. In the PPI network, Sphase kinase associated protein 1 (SKP1), nonPOU domain containing octamer binding (NONO) and zinc activated ion channel (ZACN) were identified as hub proteins. On the whole, the present study may help to gain a comprehensive understanding of tumorigenesis in HPSCC and provide valuable information for early diagnosis and drug design of HPSCC in future research.
Subject(s)
Carcinoma, Squamous Cell/genetics , Gene Expression/genetics , Hypopharyngeal Neoplasms/genetics , MicroRNAs/genetics , Carcinogenesis/genetics , Cell Cycle/genetics , Computational Biology/methods , Down-Regulation/genetics , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic/genetics , Gene Ontology , Head and Neck Neoplasms/genetics , Humans , Male , Middle Aged , Molecular Sequence Annotation/methods , Protein Interaction Maps/genetics , RNA Stability/genetics , Sequence Analysis, RNA/methods , Squamous Cell Carcinoma of Head and Neck , Up-Regulation/geneticsABSTRACT
The aim of the present study was to elaborate the underlying pathogenesis of laryngeal squamous cell carcinoma (LSCC). Micro (mi) RNA and messenger (m) RNA expression profiling of patients with LSCC were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed miRNAs (DEMIs) and differentially expressed mRNAs (DEMs) were identified in LSCC compared to normal control tissues. The DEMs targeted by DEMIs were identified and the negative correlation between DEMs and DEMIs was subjected to visualization. The potential functions of DEMs targeted by DEMIs were annotated in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 663 dysregulated DEMs (449 upregulated and 214 downregulated) and 33 DEMIs (24 upregulated and 8 downregulated) were identified in LSCC compared with normal controls. 502 negative correlations between DEMIs and DEMs were identified and subjected to construct interaction network. In the network, hsamiR486, 34c, 206 and 182 had the highest connectivity with DEMs, and respectively regulated 39, 33, 28 and 27 DEMs. DEMs targeted by DEMIs were significantly enriched in signal transduction, actin binding and extracellular region of GO terms and focal adhesion and extracellular matrixreceptor interaction of KEGG pathways. The present study may provide valuable information for understanding the potential oncogenesis mechanism in LSCC and provide the foundation work for diagnosis biomarkers and therapeutic targets for LSCC.
