TGFβ-induced long non-coding RNA LINC00313 activates Wnt signalling and promotes cholangiocarcinoma progression

Background: Cholangiocarcinoma (CCA) is a devastating liver cancer characterized by high aggressiveness and resistance to therapy, which results to poor prognosis. Long non-coding RNAs (lncRNAs) and signals imposed by oncogenic pathways, such as transforming growth factor β (TGFβ) frequently contribute to CCA development. Here, we explored novel effectors of TGFβ signalling in CCA. Methods: : We performed gene expression profiling to identify TGFβ-regulated genes in CCA cell lines. RNA-sequencing and ATAC-sequencing after LINC00313 gain-of-function were used to identify transcriptional targets of LINC00313 , in vitro . We evaluated the impact of LINC00313 on TCF/LEF signalling by luciferase assays. Mouse xenograft models were used to evaluate the effects of LINC00313 on CCA progression, in vivo . Integrative analysis revealed the clinical relevance of LINC00313 in CCA. We identified LINC00313 -interacting proteins by RNA-pull down, followed by mass spectrometry. Results: : LINC00313 was identified as a novel target of TGFβ signalling in CCA cells. TGFβ induced LINC00313 expression in a TβRI/Smad-dependent manner. LINC00313 regulated genes involved in Wnt signalling. LINC00313 gain-of-function increased TCF7 expression. Of note, LINC00313 enhanced TCF/LEF-dependent transcriptional responses, promoted colony-forming capacities of CCA cells in vitro and accelerated tumour growth in vivo . Genes associated with LINC00313 over-expression in CCA tumours were characterized by KRAS and TP53 mutations and reduced patient’s overall survival. Mechanistically, actin-like 6A (ACTL6A), a subunit of the SWI/SNF chromatin remodelling complex, interacted with LINC00313 and impacted on TCF7 and SULF2 transcription and TCF/LEF signalling output. Conclusions: : We propose a model whereby TGFβ induces LINC00313 in order to regulate expression of a subset of target genes, possibly in co-operation with SWI/SNF. By regulating key genes of the Wnt pathway, LINC00313 fine-tunes Wnt/TCF/LEF-dependent transcriptional responses and boosts cholangiocarcinogenesis.