CpG Site-Specific Methylation-Modulated Divergent Expression of Transcript Variants Facilitates Nongenetic Intratumor Heterogeneity in Human Hepatocellular Carcinoma.

Background: Hepatocellular carcinoma (HCC) is one of the most lethal human tumors with extensive intratumor heterogeneity (ITH). Serine protease 3 (PRSS3) is an indispensable member of the trypsin family and has been implicated in the pathogenesis of several malignancies, including HCC. However, the paradoxical effects of on carcinogenesis due to an unclear molecular basis impede the utilization of its biomarker potential. We hereby explored the contribution of transcripts to tumor functional heterogeneity by systematically dissecting the expression of four known splice variants of () and their functional relevance to HCC.

Methods: The expression and DNA methylation of transcripts and their associated clinical relevance in HCC were analyzed using several publicly available datasets and validated using qPCR-based assays. Functional experiments were performed in gain- and loss-of-function cell models, in which transcript constructs were separately transfected after deleting expression by CRISPR/Cas9 editing.

Results: was aberrantly differentially expressed toward bipolarity from very low ( ) to very high ( ) expression across HCC cell lines and tissues. This was attributable to the disruption of , in which and/or were dominant transcripts leading to expression, whereas and were rarely or minimally expressed. The expression of or was inversely associated with site-specific CpG methylation at the promoter region that distinguished HCC cells and tissues phenotypically between hypermethylated low-expression (m ) and hypomethylated high-expression (um ) groups. displayed distinct functions from oncogenic to tumor-suppressive , or in HCC cells. Clinically, aberrant expression of was translated into divergent relevance in patients with HCC, in which significant epigenetic downregulation of was seen in early HCC and was associated with favorable patient outcome.

Conclusions: These results provide the first evidence for the transcriptional and functional characterization of transcripts in HCC. Aberrant expression of divergent disrupted by site-specific CpG methylation may integrate the effects of oncogenic and tumor-suppressive , resulting in the molecular diversity and functional plasticity of in HCC. Dysregulated expression of by site-specific CpG methylation may have potential diagnostic value for patients with early HCC.