Genome-wide analysis of long noncoding RNA expression profile in papillary thyroid carcinoma

• We investigated the lncRNA and mRNA expression in PTC using microarray and qRT-PCR.
• Thousands of lncRNAs and mRNAs were significantly differentially expressed in PTC.
• Enriched GO terms and pathways among differentially expressed mRNAs were identified.
• Potential target genes of lncRNAs were predicted and functions were analyzed.
• Many lncRNAs may participate in biological pathways related to pathogenesis of PTC.

Long noncoding RNAs (lncRNAs) have been proved to play important roles in cancer biology. To understand their expression profile and potential functions in papillary thyroid carcinoma (PTC), we investigated the lncRNA and mRNA expression in PTC and paired adjacent noncancerous thyroid tissue using microarray. Quantitative real time polymerase chain reaction (qRT-PCR) was used to validate 10 differentially expressed lncRNAs. Gene ontology (GO) analysis and pathway analysis were also used to investigate the gene function. Potential target genes of lncRNAs were predicted according to two independent algorithms. The microarray revealed thousands of significantly differentially expressed lncRNAs and mRNAs in PTC relative to noncancerous thyroid tissue. The results of qRT-PCR were consistent with those of the microarray, in that all 10 lncRNAs were differentially expressed with the same trend (up- or down-regulated) (P < 0.05). Significantly enriched GO terms and pathways among differentially expressed mRNAs were identified. Many of these pathways were linked to cancer, such as “p53 signaling pathway” (associated with 25 genes), “pathways in cancer” (associated with 75 genes), “MAPK signaling pathway” (associated with 50 genes) and “PPAR signaling pathway” (associated with 16 genes). 1805 dysregulated lncRNAs were found to have cis or trans target genes. 463 of the cis target genes were found to be differentially expressed and might be regulated by lncRNAs in the tumorigenesis of PTC. Our study provides a genome-wide screening and analysis of lncRNA expression profile in PTC for the first time and lays the foundation for further investigation of lncRNAs related to PTC.