1. Exploring the long noncoding RNAs-based biomarkers and pathogenesis of malignant transformation from dysplasia to oral squamous cell carcinoma by bioinformatics method
- Author
-
Xuan Wang, Hongcheng Jia, and Zheng Sun
- Subjects
Cancer Research ,differentially expressed genes ,Epidemiology ,Pseudogene ,Datasets as Topic ,Biology ,medicine.disease_cause ,Malignant transformation ,03 medical and health sciences ,0302 clinical medicine ,dysplasia ,medicine ,Biomarkers, Tumor ,Humans ,Gene Regulatory Networks ,030212 general & internal medicine ,long noncoding RNA ,Gene ,Oligonucleotide Array Sequence Analysis ,Regulation of gene expression ,Microarray analysis techniques ,Squamous Cell Carcinoma of Head and Neck ,transformation ,Gene Expression Profiling ,Public Health, Environmental and Occupational Health ,Mouth Mucosa ,Computational Biology ,medicine.disease ,Gene expression profiling ,oral squamous cell carcinoma ,Gene Expression Regulation, Neoplastic ,stomatognathic diseases ,Cell Transformation, Neoplastic ,Oncology ,Dysplasia ,030220 oncology & carcinogenesis ,Cancer research ,Research Papers: Head & Neck Cancer ,biomarker ,Mouth Neoplasms ,RNA, Long Noncoding ,Carcinogenesis ,Signal Transduction - Abstract
Long noncoding RNAs (lncRNAs) play an important role in many biological processes and carcinogenesis. We aimed to explore lncRNA-based pathogenesis, diagnostic biomarkers, and predictive factors of malignant transformation from dysplasia to oral squamous cell carcinoma (OSCC). Microarray data of GSE30784 consisting of 167 OSCC, 17 dysplasia, and 45 normal oral tissues were downloaded from the GEO database. The differentially expressed genes (DEGs) and lncRNAs between the three samples were identified using R, followed by lncRNA-mRNA coexpression and coregulation network analysis for the prediction of lncRNA target genes. Gene Ontology and Kyoto encydopedia of gene and genomes pathway analysis were performed to further characterize potential interactions. A total of 4462 DEGs and 76 differentially expressed lncRNAs were screened between the three groups, and 200 DEGs and only double homeobox A pseudogene 10 (DUXAP10) were screened among the three groups. A total of 1662 interactions of 46 lncRNAs and their coexpressed target genes were predicted, and 38 pairs of lncRNA-lncRNA coregulated 843 target genes. The coregulated target genes significantly enriched in antigen adaptive immune response, activation of phagocytosis receptor signaling, mast granule NF-κB inflammation, etc. Overall, lncRNAs were differentially expressed in OSCC and dysplasia. The target genes might play an important role in the carcinogenesis and development of OSCC. These results improve our understanding regarding the lncRNA-based pathogenesis and identify some potential targets for early diagnosis of malignant transformation from dysplasia to OSCC.
- Published
- 2016