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. 2018 Oct;9(10):1312-1322.
doi: 10.1111/1759-7714.12845. Epub 2018 Aug 27.

Microarray expression profile of long non-coding RNAs in human lung adenocarcinoma

Zhiyi Yang  1 , Hongli Li  2 , Zhaoyan Wang  1 , Yuling Yang  1 , Jie Niu  3 , Yuanyuan Liu  3 , Zhiliang Sun  4 , Chonggao Yin  3
Affiliations

Microarray expression profile of long non-coding RNAs in human lung adenocarcinoma

Zhiyi Yang et al. Thorac Cancer. 2018 Oct.

Abstract

Background: Long non-coding RNAs (lncRNAs) participate in many biological dynamics and play significant roles in gene regulation. LncRNA expression is altered in many cancers; however, the expressions and functions of lncRNA genes in lung adenocarcinoma (LAD) remain unknown.

Methods: LncRNA and messenger RNA (mRNA) expression in LAD without lymphatic metastasis versus paired adjacent non-tumor (ANT) lung tissues and LAD with versus without lymphatic metastasis were analyzed using Human LncRNA Arraystar V3.0. The expression levels of four downregulated and four upregulated lncRNAs were verified using quantitative real-time PCR in cells and tissue specimens.

Results: In this study, 949 lncRNAs and 681 mRNAs had differential expression in LAD without lymphatic metastasis compared to ANT lung tissues, while 2740 lncRNAs and 1714 mRNAs were differentially expressed in LAD with lymphatic metastasis compared to LAD without lymphatic metastasis. The expression patterns of selected lncRNAs (LINC00113, AC005009.1, ARHGAP22-IT1, AC009411.1, SRGAP3-AS2, EGFEM1P, FAM66E, and HLA-F-AS1) were consistent with microarray data. Differentially expressed mRNA genes were enriched in crucial Gene Ontology terms and pathways.

Conclusion: Our results revealed differentially expressed lncRNAs in LAD, suggesting lncRNAs may be potential indicators for LAD diagnosis and therapy.

Keywords: Gene ontology; long non-coding RNA; lung adenocarcinoma; lymphatic metastasis; microarray.

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Figures

Figure 1
Figure 1
Long non‐coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles. (a) Hierarchical clustering of lncRNA profiles in lung adenocarcinoma (LAD) without lymphatic metastasis (group‐Exp1) compared to adjacent non‐tumor (ANT) lung tissues (group‐ctrl), and (b) in LAD with lymphatic metastasis (group‐Exp2) versus LAD without lymphatic metastasis (group‐Exp1). (c) Hierarchical clustering of mRNA profiles in group‐Exp1 compared to group‐ctrl, and (d) in group‐Exp2 versus group‐Exp1. The expression level increases from green to red (≥ 2‐fold, P < 0.05).
Figure 2
Figure 2
Long non‐coding RNA (lncRNA) and messenger RNA (mRNA) differential expression characteristics. A scatter plot shows the differences between (a) lncRNA and (b) mRNA expression in lung adenocarcinoma (LAD) without lymphatic metastasis (group‐Exp1) versus adjacent non‐tumor (ANT) lung tissues (group‐ctrl). A scatter plot of the differences in (c) lncRNA and (d) mRNA expression in LAD with lymphatic metastasis (group‐Exp2) versus LAD without lymphatic metastasis (group‐Exp1). The relative expression level increases from blue to red (≥ 2‐fold, P < 0.05).
Figure 3
Figure 3
Validation of differentially expressed long non‐coding RNA (lncRNA) genes. (a) Comparison of lncRNA gene expression using microarray and quantitative real‐time PCR (qRT‐PCR) (log2 scaled) (formula image) Microarray and (formula image) qRT‐PCR. (b) Expression of upregulated genes in referred cell lines by qRT‐PCR (formula image) LINC00113, (formula image) AC005009.1, (formula image) ARHGAP22‐IT1, and (formula image) AC009411.1. (c) Expression of downregulated genes in referred cell lines by qRT‐PCR (formula image) SRGAP3‐AS2, (formula image) EGFEM1P, (formula image) FAM66E and (formula image) HLA‐F‐AS1. (Triplicate assays were performed; P < 0.05).
Figure 4
Figure 4
The enrichment Gene Ontology (GO) terms of differentially expressed messenger RNA (mRNA) genes in lung adenocarcinoma (LAD) without lymphatic metastasis compared to adjacent non‐tumor (ANT) lung tissues. Biological process (BP), cellular component (CC) and molecular function (MF) of (a) upregulated and (b) downregulated mRNAs (P < 0.05).
Figure 5
Figure 5
The enrichment Gene Ontology (GO) terms of differentially expressed (DE) messenger RNA (mRNA) genes in lung adenocarcinoma (LAD) with and without lymphatic metastasis. Biological process (BP), cellular component (CC), and molecular function (MF) of (a) upregulated and (b) downregulated mRNAs (P < 0.05).
Figure 6
Figure 6
Kyoto Encyclopedia of Genes and Genomes pathway analysis. Significant enrichment pathways of differentially expressed (DE) (a) upregulated and (b) downregulated mRNAs in lung adenocarcinoma (LAD) without lymphatic metastasis compared to adjacent non‐tumor (ANT) lung tissues. Significant enrichment pathways of DE (c) upregulated and (d) downregulated mRNAs in LAD with and without lymphatic metastasis (P < 0.05).
See this image and copyright information in PMC

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