Abstract :
[en] Hepatocellular carcinoma (HCC), the main form of primary liver cancer, is the second leading cause of cancer-related deaths worldwide after lung cancer. Multiple aetiologies have been associated with the development of HCC, which arises in most cases in the context of a chronically inflamed liver. HCC is in fact an inflammation-driven cancer, with the TNF and IL6 families of cytokines playing key roles in maintaining a chronic inflammatory state, promoting hepatocarcinogenesis. IL6 signals mainly through the JAK1/STAT3 signal transduction pathway and is known to play key roles in liver physiology and disease.
In the interest of identifying novel players and downstream effectors of the IL6/JAK1/STAT3 signalling pathway that may contribute to the signal transduction of IL6 in liver-derived cells, we have been investigating the expression of long non-coding RNAs (lncRNAs) in response to treatment with the designer cytokine Hyper-IL6. Indeed, lncRNAs have recently emerged as a key layer of biological regulation and have been shown to be differentially expressed in cancer, including HCC. Upon analysis of time series transcriptomics data, we have identified hundreds of lncRNAs to be differentially expressed in HepG2, HuH7, and Hep3B hepatoma cells upon cytokine stimulation; 26 of which are common to the three cell lines tested. qPCR validation experiments have been performed for several lncRNAs, such as for the liver-specific lncRNA linc-ELL2. By functionally characterising identified clusters of IL6-regulated coding and non-coding genes in hepatoma cells, we propose, based on a guilt-by-association hypothesis, novel functions for previously poorly characterized lncRNAs and pseudogenes such as AL391422.4 or TUBA5P. Several lncRNA genes seem to be co-regulated with a protein-coding gene localized in their vicinity. For example, Hyper-IL-6 increases the mRNA and protein levels of XBP1, a well-known regulator of the unfolded protein response. At the same time, the expression of lncRNA AF086143 increases, which is expressed from the same gene locus in a bidirectional way. The targeted as well as a genome-wide analysis of lncRNA/mRNA gene pairs indicates a possible cis-regulatory role of lncRNAs with regards to their antisense and bidirectional protein coding counterparts.
Taken together, these results provide a comprehensive characterisation of the lncRNA and pseudogene repertoire of IL6-regulated genes in hepatoma cells. Our results emphasize lncRNAs as crucial components of the gene regulatory networks affected by cytokine signalling pathways.
