Analysis of long non-coding RNA expression profile in papillary thyroid carcinoma

Objective Long noncoding RNAs (lncRNAs) play an important role in cancer growth and development. Gene chip technology was used in this study to screen the differential expression lncRNA in papillary thyroid cancer. Targeted genes regulated by these lncRNA were predicted and analyzed. Methods Microarray was used in this study to investigate the lncRNA expression in three paired samples of papillary thyroid cancer (PTC) and paired adjacent noncancerous thyroid tissue. Gene function was evaluated by Gene Ontology (GO) and pathway analysis. Potential target genes of lncRNAs were also predicted. Results Compared with the adjacent noncancerous thyroid tissue, a total of 855 lncRNAs displayed differential expression in tumor tissues, including 195 up-regulated lncRNAs and 660 down-regulated lncRNAs (FC>2, P<0.05). 2 370 differently expressed mRNAs were found of which 801 were upregulated and 1 569 were downregulated (FC>2, P<0.05). Among them, the more differential expression lncRNAs were 23, while mRNA were 79 (FC>4). lncRNA-SLC34A2 with its related mRNA GRCh38 (NM_001177998) was the most dysregulated lncRNA and mRNA with a FC of 23.5. Significantly enriched GO terms and pathways among differentially expressed mRNAs were identified. Some were related to cancer, such as "Focal adhesion", "ECM-receptor interaction", "MAPK signaling pathway" and "PI3K/AKT signaling pathway". Forty-two pathways were significantly enriched among the differentially expressed transcripts showed by pathways analysis (P<0.05). Among them, 'Focal adhesion' (P=8.499×10^-7) was the most enriched pathway which was directly associated with 47 differential expressed genes. In all, 239 lncRNAs with its related mRNAs may be associated with cis-regulation. The relative positional relationship between the locus of lnRNAs and mRNAs were in different site of the gene. Conclusions Our study is the supplement to the related lncRNA profile of thyroid tumor. We found certain numbers of differentially expressed lncRNAs and predict its functional targeted genes and pathways. In the future, we will select greater numbers of samples to deepen the research into the lncRNA molecular mechanism and biochemical function, in order to provide a novel accurate method for the early diagnosis and therapy of thyroid cancer.