title: Analysis of gene expression profiles of non-small cell lung cancer at different stages reveals significantly altered biological functions and candidate genes.
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.
authors.affiliation: Department of Cardiothoracic Surgery, Yancheng Hospital, Medical School of Southeast University, The Third People's Hospital, Yancheng, Jiangsu 224001, P.R. China.
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Cardiothoracic Surgery, Yancheng Hospital, Medical School of Southeast University, The Third People's Hospital, Yancheng, Jiangsu 224001, P.R. China.
authors.forename: Jianxiang
authors.initials: J
authors.lastname: Song
authors.affiliation: Department of Cardiothoracic Surgery, Yancheng Hospital, Medical School of Southeast University, The Third People's Hospital, Yancheng, Jiangsu 224001, P.R. China.
authors.forename: Zhengya
authors.initials: Z
authors.lastname: Gao
authors.affiliation: Department of Cardiothoracic Surgery, Yancheng Hospital, Medical School of Southeast University, The Third People's Hospital, Yancheng, Jiangsu 224001, P.R. China.
authors.forename: Xudong
authors.initials: X
authors.lastname: Huo
authors.affiliation: Department of Cardiothoracic Surgery, Yancheng Hospital, Medical School of Southeast University, The Third People's Hospital, Yancheng, Jiangsu 224001, P.R. China.
authors.forename: Yajun
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Cardiothoracic Surgery, Yancheng Hospital, Medical School of Southeast University, The Third People's Hospital, Yancheng, Jiangsu 224001, P.R. China.
authors.forename: Wencai
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Cardiothoracic Surgery, Yancheng Hospital, Medical School of Southeast University, The Third People's Hospital, Yancheng, Jiangsu 224001, P.R. China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Qi
authors.affiliation: Department of Cardiothoracic Surgery, The First Affiliated Hospital of Suzhou University, Suzhou, Jiangsu 215006, P.R. China.
authors.forename: Shiying
authors.initials: S
authors.lastname: Zheng
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000473:pathology; D002478:Cells, Cultured; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008168:Lung / Q000378:metabolism*; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D009367:Neoplasm Staging; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction
chemical_list: D014408:Biomarkers, Tumor; D012333:RNA, Messenger