Stress-induced lncRNA LAS3 fosters fitness of cancer cells by regulating SART3-mediated spliceosome recycling

Long non-coding RNAs (lncRNAs) represent a novel class of anti-cancer therapeutic targets. Hypoxia-induced lncRNAs are associated with the aggressive tumor phenotypes and might serve as putative drug targets. Here, we unraveled lncRNAs whose expression is upregulated in hypoxic breast tumors. One of the hypoxia-induced lncRNA, LAS3 (LncRNA Associated to SART3), is commonly upregulated not only in all breast cancer subtypes, but also in several types of epithelial cancers. LAS3 expression is driven by the stress-induced JNK/c-JUN pathway, which is frequently activated in human cancer. By pull down of LAS3 coupled to mass spectrometry-based proteomics, we identified SART3, a component of the splicing machinery, as a LAS3-interacting partner. In a second proteomics experiment, pull down of SART3-containing complexes from MCF10A cells treated with either scramble, or LAS3-specific GapmeRs showed that LAS3 regulates splicing efficiency by triggering SART3 dissociation from the U4/U6 snRNP during the recycling phase of the spliceosome cycle. Finally, differential shotgun analysis of MDA-MB-231/tet-shLAS3 cells allowed us to quantify expression of 2,940 proteins. Here, genes with significant intron retention showed decreased protein expression levels, indicating that widespread LAS3-mediated intron retention disrupts open reading frame integrity leading to stochastic decrease of protein expression and decreased fitness of cancer cells. Together, our data show that LAS3 is essential for growth of LAS3-positive triple negative breast tumors and indicate that LAS3 inhibition might be a suitable therapeutic approach for breast cancer treatment.