Genome-wide analyses of long noncoding RNA expression profiles in lung adenocarcinoma.

Abstract

LncRNAs have emerged as a novel class of critical regulators of cancer. We aimed to construct a landscape of lncRNAs and their potential target genes in lung adenocarcinoma. Genome-wide expression of lncRNAs and mRNAs was determined using microarray. qRT-PCR was performed to validate the expression of the selected lncRNAs in a cohort of 42 tumor tissues and adjacent normal tissues. R and Bioconductor were used for data analysis. A total of 3045 lncRNAs were differentially expressed between the paired tumor and normal tissues (1048 up and 1997 down). Meanwhile, our data showed that the expression NONHSAT077036 was associated with N classification and clinical stage. Further, we analyzed the potential co-regulatory relationship between the lncRNAs and their potential target genes using the 'cis' and 'trans' models. In the 25 related transcription factors (TFs), our analysis of The Cancer Genome Atlas database (TCGA) found that patients with lower expression of POU2F2 and higher expression of TRIM28 had a shorter overall survival time. The POU2F2 and TRIM28 co-expressed lncRNA landscape characterized here may shed light into normal biology and lung adenocarcinoma pathogenesis, and be valuable for discovery of biomarkers.

• Authors: Zhenzi Peng, Jun Wang, Bin Shan, Fulai Yuan, Bin Li, Yeping Dong, Wei Peng, Wenwen Shi, Yuanda Cheng, Yang Gao, Chunfang Zhang, Chaojun Duan
• Journal: Scientific reports (Sci Rep) Vol. 7 Issue 1 Pg. 15331 (11 10 2017) ISSN: 2045-2322 [Electronic] England
• PMID: 29127420 (Publication Type: Clinical Trial, Journal Article, Multicenter Study, Research Support, Non-U.S. Gov't)

Chemical References

• Biomarkers, Tumor
• RNA, Long Noncoding

Topics

• Adenocarcinoma of Lung (genetics, metabolism)
• Adult
• Biomarkers, Tumor (biosynthesis, genetics)
• Databases, Nucleic Acid
• Female
• Gene Expression Profiling
• Gene Expression Regulation, Neoplastic
• Gene Regulatory Networks
• Genome-Wide Association Study
• Humans
• Lung Neoplasms (genetics, metabolism)
• Male
• RNA, Long Noncoding (biosynthesis, genetics)