ELUCIDATING MECHANISMS OF SALL4 REACTIVATION IN HEPATOCELLULAR CARCINOMA

Abstract

Pseudogenes, non-coding homologs of protein-coding genes, were once considered non-functional evolutionary relics. However, certain pseudogene expression profiles have recently been described to associate with patient prognoses and cancer subtypes. Despite their clinical importance, only a handful of >12,000 pseudogenes in humans have been characterized in cancers to date. Here, we describe a previously unrecognized role for pseudogenes as potent epigenetic regulators that can demethylate and activate oncogenes. We focused on SALL4, a known oncogene in hepatocellular carcinoma (HCC) with 8 pseudogenes. Using a locus-specific demethylating technology, we identified the critical CpG region for SALL4 expression. We showed that SALL4 pseudogene 5 hypomethylates this region through interaction with DNMT1, resulting in SALL4 upregulation. In addition, we show that SALL4 pseudogenes could also regulate SALL4 expression by acting as competing endogenous RNAs (ceRNAs). Intriguingly, pseudogene 5 is significantly upregulated in a hepatitis B virus model prior to SALL4 induction, and both are increased in HBV-HCC patients. Our results suggest that pseudogene-mediated demethylation represents a novel mechanism of oncogene activation in cancer.