Long non-coding RNAs are differentially expressed in hepatocellular carcinoma cell lines with different metastatic potential

We describe the lncRNA expression profiles of two HCC cell lines, one with high potential for metastasis to the lung (HCCLM3) and the other to lymph nodes (HCCLYM-H2). The HCCLM3(LM3) and HCCLM6 cell lines were derived from the same parental cell line MHCC-97H. LM3 metastasizes to the lung, while HCCLM6 can metastasize to multiple organs in a mouse model. By subcloning HCCLM6, we established the HCCLYM-H2(H2) cell line, which showed stable and high metastatic potential specific to the lymph nodes. In the present study, we compared the expression profiles of HCC cell lines with a similar genetic background but different potential for lung or lymph node metastasis. We found that expression signatures comprising lncRNAs and protein-coding mRNAs were significantly associated with organ-specific HCC metastasis. To further validate microarray data, we selected six lncRNAs (CR613944, BC058547, RP5-1014O16.1, NCRNA00173, lincRNA-CALCA, lincRNA-TSPAN8) and two mRNAs (TSPAN8, CALCB) in the two HCC cell lines using qRT-PCR. Data obtained from qRT-PCR and the microarray was consistent. Differentially expressed lncRNAs between high lymphatic metastatic potential HCC cell H2 and high lung metastatic potiential HCC cell LM3 were identified by microarray and validated using quantitative real-time polymerase chain reaction.