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. 2019 Jun 30;39(6):641-649.
doi: 10.12122/j.issn.1673-4254.2019.06.03.

[Identification of differentially expressed genes between lung adenocarcinoma and squamous cell carcinoma using transcriber signature analysis]

[Article in Chinese]
Shuxian Peng  1 , Xun Li  2 , Qin Liu  2 , Yingheng Zhang  1 , Liming Zou  2 , Xiaoli Gong  2 , Miaomiao Wang  2 , Xiaodong Ma  2
Affiliations

[Identification of differentially expressed genes between lung adenocarcinoma and squamous cell carcinoma using transcriber signature analysis]

[Article in Chinese]
Shuxian Peng et al. Nan Fang Yi Ke Da Xue Xue Bao. .

Abstract
in English, Chinese

Objective: To analyze the differentially expressed genes (DEGs) between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) with bioinformatics analysis and search for potential biomarkers for clinical diagnosis of nonsmall cell lung cancer (NSCLC).

Methods: The gene expression profiling datasets of LUAD and LUSC were acquired. The transcriptome differences between LUAD and LUSC were identified using R language processing and t-test analysis. The differential expressions of the genes were shown by Venn diagram. The DEGs identified by GEO2R were analyzed with DAVID and Ingenuity Pathway Analysis (IPA) to identify the signaling pathways and biomarkers that could be used for differential diagnosis of LUAD and LUSC. The TCGA data and the biomarker expression data from clinical lung cancer samples were used to verify the differential expressions of the Osteoarthritis pathway and LXR/RXR between LUAD and LUSC. We further examined the differential expressions of miR-181 and its two target genes, WNT5A and MBD2, in 23 clinical specimens of lung squamous cell carcinoma and the paired adjacent tissues.

Results: GEO data analysis identified 851 DEGs (including 276 up-regulated and 575 down-regulated genes) in LUAD and 885 DEGs (including 406 up-regulated and 479 down-regulated genes) in LUSC. DAVID and IPA analysis revealed that leukocyte migration and inflammatory responses were more abundant in LUAD than in LUSC. Osteoarthritis pathway was inhibited in LUAD and activated in LUSC. IPA analysis showed that transcription factors (GATA4, RELA, YBX1, TP63 and MBD2), cytokines (WNT5A and IL1A) and microRNAs (miR-34a, miR-181b and miR-15a) differed significantly between LUAD and LUSC. miR-34a with IL-1A, miR-15a with YBX1, and miR-181b with WNT5A and MBD2 could serve as the paired microRNA and mRNA targets for differential diagnosis of NSCLC subtypes. Analysis of the clinical samples showed an increased expression of miR-181b-5p and the down-regulation of WNT5A, which could be used as molecular markers for the diagnosis of LUSC.

Conclusions: Through transcriptome analysis, we identified candidate genes, paired microRNAs and pathways for differentiating LUAD and LUSC, and they can provide novel differential diagnosis and therapeutic strategies for LUAD and LUSC.

目的: 对非小细胞肺癌两种亚型肺腺癌和肺鳞状细胞癌的基因差异表达进行生物信息学分析，寻找非小细胞肺癌潜在的生物学标志物运用于临床诊断，进而提高患者生存率。

方法: 获取肺腺癌和肺鳞状细胞癌的基因表达谱分析数据集，使用R语言处理，t检验分析鉴定肺腺癌和肺鳞状细胞癌之间的转录组差异，并通过维恩图显示所鉴定的基因差异表达。从GEO获得差异表达的基因，用DAVID及IPA进行分析，进一步确定潜在可用于鉴别肺腺癌和肺鳞状细胞癌的几种信号通路和生物标记。利用TCGA数据和临床肺癌样本中的生物标记表达，验证Osteoarthritis pathway和LXR/RXR分别在肺腺癌和肺鳞状细胞癌的基因差异表达；挑选miR-181b-5p及其靶基因WNT5A和MBD2进行验证，收集23例肺鳞癌患者的肺肿瘤组织（23例肿瘤组织，实验组）及其邻近肺组织（23例癌旁肺组织，对照组），检测miR-181b-5p和其靶基因WNT5A和MBD2的表达差异用于鉴别肺腺癌和肺鳞状细胞癌。

结果: GEO数据分析结果揭示肺腺癌和肺鳞状细胞癌的差异表达基因：肺腺癌中有851个DEGs（276个上调，575个下调），而肺鳞状细胞癌中有885个DEGs（406个上调，479个下调）。DAVID和IPA分析差异表达基因结果显示，白细胞迁移和炎症反应在肺腺癌中比肺鳞状细胞癌富集程度更高，Osteoarthritis pathway在肺腺癌中是抑制状态，而在肺鳞状细胞癌中显示是激活状态。IPA对重要转录因子、细胞因子和miRNA的分析结果显示肺腺癌和肺鳞状细胞癌之间的区别主要是：转录因子（GATA4，RELA，YBX1，TP63和MBD2）；细胞因子（WNT5A和IL-1A）和microRNA（miR-34a，miR-181b和miR-15a）。其中miR-34a和IL-1A、miR-15a和YBX1、miR-181b和WNT5A和MBD2可作为鉴别非小细胞肺癌亚型的成对microRNA和mRNA靶点。临床样本实验结果支持miR-181b-5p的表达上升和WNT5A的表达下调可视为诊断肺鳞状细胞癌的分子标记物。

结论: 通过对转录组数据分析，发现了肺腺癌和肺鳞状细胞癌的候选基因、成对的microRNA鉴别肺腺癌和肺鳞状细胞癌，为其鉴别诊断和治疗提供了新的思路。

Keywords: lung adenocarcinoma; lung squamous cell carcinoma; mRNA; microRNAs; transcriptome signature.

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Figures

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肺腺癌与肺鳞癌差异表达基因在不同数据库的鉴定 Identification of differentially expressed genes (DEGs) between lung adenocarcinoma and lung squamous cell carcinoma. A: Gene numbers of the 4 sets of gene expression microarray data; B: Venn diagram of 2 LUAD datasets of gene expression microarray data (GSE27262 and GSE19188); C: Venn diagram of 2 LUSC datasets of gene expression microarray data (GSE33479 and GSE19188).
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2
生物功能和IPA信号通路分析 Biological function and ingenuity pathway analysis. A: Biological functions in lung adenocarcinoma; B: Biological functions in lung squamous carcinoma; C: Canonical pathways in lung adenocarcinoma; D: Canonical pathways in lung squamous carcinoma.
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IPA分析肺腺癌和肺鳞癌中的差异表达转录因子和细胞因子 Transcription factor and cytokines analysis in LUAD and LUSC. Transcription factor of the differential expression genes signature in LUAD (A) and LUSC (B); Cytokines of the differential expression genes signature in LUAD (C) and LUSC (D); microRNAs associated with differential expression genes signature in LUAD (E) and LUSC (F).
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TCGA数据分析miR-181b-5p和靶基因WNT5A，MBD2在肺腺癌和肺鳞癌的表达 miR-181b-5p and expression of its target genes in clinical LUAD and LUSC patients from TCGA. The relative expression of miR-181b-5p (A), WNT5A (B) and MBD2 (C) in the tumors and its adjacent tissues of LUAD and LUSC patients from TCGA; D: Correlation analysis of miR-181b-5p vs WNT5A in LUAD and LUSC; E: Correlation analysis of miR-181b-5p vs MBD2 in LUAD and LUSC; F: Correlation analysis of WNT5A vs MBD2 in LUAD and LUSC; Spearman's rank correlation analysis was performed.
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临床肺鳞状细胞癌样本中miR-181b-5p和其靶基因的表达 miR-181b-5p and expression of its target genes in clinical squamous cell carcinoma patients. A: The relative expression of miR-181b-5p, WNT5A, and MBD2 in the tumors and its adjacent tissues of lung squamous cell carcinoma patients, **P < 0.01; B, C: Spearman's rank correlation analysis of the correlation between miR-181b-5p and WNT5A and between miR-181b-5p and MBD2 in lung squamous cell carcinoma.
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References

    1. Yang H, Linandy Y. Treatment of lung carcinosarcoma and other rare histologic subtypes of non-small cell lung cancer. Curr Treat Options Oncol. 2017;18(9):54–65. doi: 10.1007/s11864-017-0494-9. - DOI - PubMed
    1. Lim SL, Jia ZA, Lu YH, et al. Metabolic signatures of four major histological types of lung cancer cells. Metabolomics. 2018;14(9):118–27. doi: 10.1007/s11306-018-1417-x. - DOI - PubMed
    1. Ettinger DS, Akerley W, Borghaei H, et al. Non-small cell lung cancer, version 2.2013. J Natl Compr Canc Netw. 2013;11(6):645–53. doi: 10.6004/jnccn.2013.0084. - DOI - PubMed
    1. Bjorkqvist AM, Husgafvel-Pursiainen K, Anttila S, et al. DNA gains in 3q occur frequently in squamous cell carcinoma of the lung, but not in adenocarcinoma. Genes Chromosomes Cancer. 1998;22(1):79–82. - PubMed
    1. Cooper WA, Lam DC, O'toole SA, et al. Molecular biology of lung cancer. http://d.old.wanfangdata.com.cn/OAPaper/oai_doaj-articles_89f8e87237faaa.... J Thorac Dis. 2013;5(5):S479–90. - PMC - PubMed