Microarray-based differential expression profiling of long noncoding RNAs and messenger RNAs in formalin-fixed paraffin-embedded human papillary thyroid carcinoma samples

Hui-Xian Yan, Jin Du, Jing Fu, Wei Huang, Li-Meng Jia, Pang Ping, Ling Zhao, Ye-Qiong Song, Xiao-Meng Jia, Jing-Tao Dou, Yi-Ming Mu, Fu-Lin Wang, Wen Tian, Zhao-Hui Lyu


Background: Long noncoding RNAs (lncRNAs) can regulate the expression of genes at almost every level. The altered expression of lncRNAs was observed in many kinds of cancers. Until recently, few studies have focused on the function of lncRNAs in the context of papillary thyroid carcinoma (PTC).
Methods: In the current study, we collected seven PTC and nodular goiter tissue samples and explored mRNA and lncRNA expression patterns in these samples by microarray.
Results: We observed aberrant expression of 94 lncRNAs and 99 mRNAs in the seven PTC samples as compared to the nodular goiter tissue [fold change (FC) ≥2.0; P<0.01]. To confirm these microarray results, quantitative polymerase chain reaction (q-PCR) was performed to assess the expression of three randomly selected differentially expressed mRNAs and lncRNAs, confirming our microarray findings significantly. We then performed gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses to systematically characterize the twelve significantly differential genes. A co-expression analysis revealed that the lncRNAs n382996, n342483, and n409114 were closely related to the regulation of MT1G, MT1H, and MT1F. Conclusions: In the present study a string of novel lncRNAs associated with PTC were identified. Further study of these lncRNAs should be performed to identify novel target molecules which may improve diagnosis and treatment of PTC.