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KMID : 0381120170390030277
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Genes and Genomics
2017 Volume.39 No. 3 p.277 ~ p.284
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Transcriptome analysis of non-small cell lung cancer and genetically matched adjacent normal tissues identifies novel prognostic marker genes
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Bang Man-Seok
Kang Keun-Soo
Lee Jung-Ju
Lee Yea-Jin
Choi Jin-Eun
Ban Ju-Yeon
Oh Chung-Hun
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Abstract
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Lung cancer can be classified into two different types, non-small cell lung cancer (NSCLC) and small cell lung cancer. Up to 85% of lung cancer cases are NSCLC. To identify prognostic marker genes for NSCLC, we conducted 10 pairs of genetically matched transcriptome (NSCLC and adjacent normal tissues obtained from 10 patients) analysis using next-generation sequencing. Pathway analysis revealed that the genes associated with the cell cycle are highly upregulated in NSCLC. Integrative analysis of two independent NSCLC studies, 71 pairs (GSE40419) and 58 pairs (TCGA-LUAD), also confirmed that cell cycle?related genes are mostly upregulated in NSCLC. All three independent NSCLC transcriptomes concordantly identified 10 potential tumor-marker genes that are highly expressed as well as significantly altered in NSCLC. A quantitative real-time polymerase chain reaction experiment validated the altered expressions of the genes. Among them, downregulation of MFAP4 and AGER and upregulation of SPP1 genes in NSCLC compared to normal tissues were significantly associated with poor prognosis as evaluated by Kaplan?Meier survival and receiver operating characteristic analyses. A further analysis indicated that the expression ratio of MFAP4 and SPP1 or AGER and SPP1 can be used as potential prognostic marker genes for NSCLC.
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KEYWORD
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Non-small cell lung cancer, NSCLC, Lung cancer, RNA-seq, Tumor marker
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