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

Abstract 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.