Identification and functional analysis of long non-coding rnas in hepatocellular carcinoma

Résumé

Hepatocellular carcinoma (HCC) is a disease associated with high morbidity and mortality for which there is currently no curative treatment and molecular targeting remains ineffective. To search for new therapeutic targets, we have evaluated the coding and non-coding transcriptomes of all RNA-Seq data from the TCGA and GTEx projects. The analyses of tumor-deregulated gene expression indicated that coding genes have high tumor promiscuity. Non-coding genes, on the contrary, showed higher specificity and their expression was altered in a more tumor-specific manner, predictive of a therapeutic target with fewer secondary effects. In HCC, we found 1128 deregulated lncRNAs of which 138 were specific of HCC. Functional predictions indicate a positive relationship of deregulated lncRNAs with cell proliferation while the immune response is negatively associated. Ten Non-coding RNAs Induced in Cancer with Oncogenic Features (NICOs) were selected and their expression was validated in HCC cell lines and patient samples. Most tumor samples showed high expression levels of these lncRNAs when compared to paired peritumoral samples. When expression of NICOs was inhibited with antisense drugs in HCC cells, a drastic stall in proliferation was observed. After performing proteomic analyses, lncRNA candidate NICO7 was found to bind DNAPKcs and Ku80, effectors of the non-homologous end-joining (NHEJ) pathway of the DNA damage response. We tested this interaction with recombinant Ku70/80 and found that some motifs within NICO7 bind exceptionally well to Ku, similar to the binding of dsDNA. Since the expression of NICO7 is highly specific for HCC cell lines and the initial NHEJ can progress normally, NICO7 does not appear to play a fundamental role in the NHEJ canonical machinery but rather in its processivity and fidelity. We propose that when NICO7 is absent, defective NHEJ could result in replicative stress and the accumulation of damage at longer times after a DNA-damaging insult or ongoing replication. Therefore, NICO7 could be rather an advantageous malignant adaptation of liver cancer cells that could be partially involved in HCC`s radioresistance. This is suggested by the additive effect of DNA-PKcs inhibition and NICO7 depletion on HCC cell death. We believe this trait could be exploited in alternative therapeutic approaches against HCC.