Histone Methyltransferase SETD3 Is Regulated by a Couple of microRNAs and Plays Opposing Roles in Proliferation and Metastasis of Hepatocellular Carcinoma

Background: Previous study reported that histone methyltransferase SETD3 is upregulated in tumor tissues of hepatocellular carcinoma (HCC) and is associated with the growth of HCC. However, the clinical significance and the effect of SETD3 on HCC metastasis remain unclear. Methods: The mRNA and protein expression levels of SETD3 were measured in 172 HCC patients using immunohistochemistry (IHC). In vitro and in vivo experiments were carried out to unveil the effect of SETD3 on HCC proliferation and metastasis. The RNA-seq, immunoprecipitation (IP), chromatin immunoprecipitation (ChIP), methylation specific PCR (MSP) and bacterial colonies sequencing were performed to investigate the mechanism of SETD3 in regulating the HCC metastasis. Finding: the protein level of SETD3 in HCC tissues was significantly higher than that in non-tumorous tissues, which was inconsistent with the mRNA level of SETD3. The high protein level of SETD3 in HCC tissues was significantly associated with male gender, poor pathological differentiation, liver cirrhosis and unfavorable prognosis of HCC patients. Subsequently, we demonstrated that SETD3 could be regulated at post-transcriptional step by a couple of miRNAs (miR-16, miR-195 and miR-497). Additionally, in vitro and in vivo studies revealed that SETD3 played opposing roles in proliferation and metastasis of HCC: promoting proliferation but inhibiting metastasis. Mechanistic experiments revealed that doublecortin-like kinase 1 (DCLK1) was a downstream target of SETD3, SETD3 could increase the DNA methylation level of DCLK1 promoter to inhibit the expression of DCLK1. Further study revealed that DCLK1/PI3K/MMP-2 was an important pathway that mediated the effect of SETD3 on HCC metastasis. Interpretation: This study revealed that SETD3 is associated with hepatocarcinogenesis and is a promising biomarker for predicting the prognosis of HCC patients after surgical resection. In addition, SETD3 plays inhibitory role on HCC metastasis partly through DCLK1/PI3K/MMP-2 pathway. Funding Statement: This study was supported by the Key Technology Research and Development Program of the Sichuan Province (2019YFS0208, 2017FZ0082, and 2015SZ0131), the grants of National Natural Science Foundation of China (No. 71673193), Chinese foundation for hepatitis prevention and control — TianQing liver disease research fund subject (TQGB20190202), the Natural Science Foundation for Young Scientists and the Science & Technology Planning Project of Gansu Province (18JR3RA058). Declaration of Interests: The authors declare that they have no conflict of interest. Ethics Approval Statement: The use of clinical specimen was approved by the Biomedical Ethics Committee of the West China Hospital, and written informed consent was obtained from each patient.