1. Analysis of gene expression profiles of non-small cell lung cancer at different stages reveals significantly altered biological functions and candidate genes
- Author
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Jin Wang, Yajun Zhang, Xudong Huo, Wencai Wang, Shiying Zheng, Jianxiang Song, Zhengya Gao, and Jianwei Qi
- Subjects
0301 basic medicine ,Cancer Research ,Candidate gene ,Lung Neoplasms ,Gene regulatory network ,Biology ,medicine.disease_cause ,Real-Time Polymerase Chain Reaction ,03 medical and health sciences ,0302 clinical medicine ,Carcinoma, Non-Small-Cell Lung ,Gene expression ,medicine ,Biomarkers, Tumor ,Humans ,Gene Regulatory Networks ,RNA, Messenger ,Gene ,Lung ,Cells, Cultured ,Neoplasm Staging ,Regulation of gene expression ,Microarray analysis techniques ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,General Medicine ,Cell biology ,Gene expression profiling ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,Carcinogenesis ,Signal Transduction - Abstract
We attempt to dissect the pathology of non-small cell lung cancer (NSCLC) patients at different stages and discover the novel candidate genes. Microarray data (GSE21933) were retrieved from the Gene Expression Omnibus database. The differential expression profiles of lung tumor tissues during different stages were analyzed. The significantly altered functions and pathways were assessed and the key nodes in a protein-protein interaction (PPI) network were screened out. Then, the coexpression gene pairs and tumor-related genes were assessed. RT-PCR analysis was performed to validate the candidate gene, natural killer-tumor recognition sequence (NKTR). The number of differentially expressed genes (DEGs) for stage IB, IIB, IIIA and IV tumors were 499, 602, 592 and 457, respectively. Most of the DEGs were NSCLC-related genes identified through literature research. A few genes were commonly downregulated in all the 4 stages of tumors, such as CNTN6 and LBX2. The DEGs in early‑stage tumors were closely related with the negative regulation of signal transduction, the apoptosis pathway and the p53 signaling pathway. DEGs in late-stage tumors were significantly enriched in transcription, response to organic substances and synapse regulation-related biological processes. A total of 16 genes (including NKTR) made up the significant coexpression network. NKTR was a key node in the PPI network and was significantly upregulated in lung cancer cells. The mechanism of NSCLC progression in different tumor stages may be different. NKTR may be the target candidate for NSCLC prevention and treatment.
- Published
- 2016