Loss of Imprinting and Allelic Switching at the <em>DLK1-MEG3</em> Locus in Human Hepatocellular Carcinoma

<div><p>Deregulation of imprinted genes is an important molecular mechanism contributing to the development of cancer in humans. However, knowledge about imprinting defects in human hepatocellular carcinoma (HCC), the third leading cause of cancer mortality worldwide, is still limited. Therefore, a systematic meta-analysis of the expression of 223 imprinted loci in human HCC was initiated. This screen revealed that the <em>DLK1-MEG3</em> locus is frequently deregulated in HCC. Deregulation of <em>DLK1</em> and <em>MEG3</em> expression accompanied by extensive aberrations in DNA methylation could be confirmed experimentally in an independent series of human HCC (n = 40) in more than 80% of cases. Loss of methylation at the <em>DLK1-MEG3</em> locus correlates linearly with global loss of DNA methylation in HCC (r² = 0.63, p<0.0001). Inhibition of DNMT1 in HCC cells using siRNA led to a reduction in <em>MEG3-DMR</em> methylation and concomitant increase in <em>MEG3</em> RNA expression. Allele-specific expression analysis identified loss of imprinting in 10 out of 31 informative samples (32%), rendering it one of the most frequent molecular defects in human HCC. In 2 cases unequivocal gain of bi-allelic expression accompanied by substantial loss of methylation at the <em>IG-DMR</em> could be demonstrated. In 8 cases the tumour cells displayed allelic switching by mono-allelic expression of the normally imprinted allele. Allelic switching was accompanied by gains or losses of DNA methylation primarily at <em>IG-DMR1</em>. Analysis of 10 hepatocellular adenomas (HCA) and 5 cases of focal nodular hyperplasia (FNH) confirmed that this epigenetic instability is specifically associated with the process of malignant transformation and not linked to increased proliferation <em>per se</em>. This widespread imprint instability in human HCC has to be considered in order to minimize unwanted side-effects of therapeutic approaches targeting the DNA methylation machinery. It might also serve in the future as predictive biomarker and for monitoring response to epigenetic therapy.</p>