The HNF1α-regulated lncRNA HNF1A-AS1 reverses the malignancy of hepatocellular carcinoma by enhancing the phosphatase activity of SHP-1

Background: Our previous study has demonstrated that hepatocyte nuclear factor 1 alpha (HNF1 alpha) exerts potent therapeutic effects on hepatocellular carcinoma (HCC). However, the molecular mechanisms by which HNF1 alpha reverses HCC malignancy need to be further elucidated. Methods: lncRNA microarray was performed to identify the long noncoding RNAs (lncRNAs) regulated by HNF1 alpha. Chromatin immunoprecipitation and luciferase reporter assays were applied to clarify the mechanism of the transcriptional regulation of HNF1 alpha to HNF1A antisense RNA 1 (HNF1A-AS1). The effect of HNF1A-AS1 on HCC malignancy was evaluated in vitro and in vivo. RNA pulldown, RNA-binding protein immunoprecipitation and the Bio-Layer Interferometry assay were used to validate the interaction of HNF1A-AS1 and Src homology region 2 domain-containing phosphatase 1 (SHP-1). Results: HNF1 alpha regulated the expression of a subset of lncRNAs in HCC cells. Among these lncRNAs, the expression levels of HNF1A-AS1 were notably correlated with HNF1 alpha levels in HCC cells and human HCC tissues. HNF1 alpha activated the transcription of HNF1A-AS1 by directly binding to its promoter region. HNF1A-AS1 inhibited the growth and the metastasis of HCC cells in vitro and in vivo. Moreover, knockdown of HNF1A-AS1 reversed the suppressive effects of HNF1 alpha on the migration and invasion of HCC cells. Importantly, HNF1A-AS1 directly bound to the C-terminal of SHP-1 with a high binding affinity (KD = 59.57 +/- 14.29 nM) and increased the phosphatase activity of SHP-1. Inhibition of SHP-1 enzymatic activity substantially reversed the HNF1 alpha- or HNF1A-AS1-induced reduction on the metastatic property of HCC cells. Conclusions: Our data revealed that HNF1A-AS1 is a direct transactivation target of HNF1a in HCC cells and involved in the anti-HCC effect of HNF1 alpha. HNF1A-AS1 functions as phosphatase activator through the direct interaction with SHP-1. These findings suggest that regulation of the HNF1 alpha/HNF1A-AS1/SHP-1 axis may have beneficial effects in the treatment of HCC.