Long Noncoding RNA MEG3 Is an Epigenetic Determinant of Oncogenic Signaling in Functional Pancreatic Neuroendocrine Tumor Cells

ABSTRACT

The long noncoding RNA (lncRNA) MEG3 is significantly downregulated in pancreatic neuroendocrine tumors (PNETs). MEG3 loss corresponds with aberrant upregulation of the oncogenic hepatocyte growth factor (HGF) receptor c-MET in PNETs. Meg3 overexpression in a mouse insulin-secreting PNET cell line, MIN6, downregulates c-Met expression. However, the molecular mechanism by which MEG3 regulates c-MET is not known. Using chromatin isolation by RNA purification and sequencing (ChIRP-Seq), we identified Meg3 binding to unique genomic regions in and around the c-Met gene. In the absence of Meg3, these c-Met regions displayed distinctive enhancer-signature histone modifications. Furthermore, Meg3 relied on functional enhancer of zeste homolog 2 (EZH2), a component of polycomb repressive complex 2 (PRC2), to inhibit c-Met expression. Another mechanism of lncRNA-mediated regulation of gene expression utilized triplex-forming GA-GT rich sequences. Transfection of such motifs from Meg3 RNA, termed triplex-forming oligonucleotides (TFOs), in MIN6 cells suppressed c-Met expression and enhanced cell proliferation, perhaps by modulating other targets. This study comprehensively establishes epigenetic mechanisms underlying Meg3 control of c-Met and the oncogenic consequences of Meg3 loss or c-Met gain. These findings have clinical relevance for targeting c-MET in PNETs. There is also the potential for pancreatic islet β-cell expansion through c-MET regulation to ameliorate β-cell loss in diabetes.

KEYWORDS:

• epigenetic
• insulinoma
• Meg3
• pancreatic neuroendocrine tumors
• triplex-forming oligonucleotides
• c-MET

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at https://doi.org/10.1128/MCB.00278-17.

ACKNOWLEDGMENTS

We thank the NIDDK genomics core for processing the ChIRP-Seq samples and Susan Dombrowski of Genomatix Software, Inc., for bioinformatic analyses of ChIRP-Seq data.

This work was supported by the Intramural Program of the National Institute of Diabetes and Digestive and Kidney Diseases (Project ZIADK075035-07 and Project ZIADK075085-03, to S.K.A.).

We have no financial disclosures to make and declare no conflicts of interest.

S.I. and S.K.A. conceptualized, designed, and performed the experiments. S.D.M. and S.K.A. conceived of, designed, and performed the initial ChIRP-Seq experiments. S.I. and S.K.A. collected, analyzed, and interpreted the data. S.K.A. supervised the project and obtained project funding. S.I. and S.K.A. drafted and wrote the manuscript. All authors provided consent and approval for the final manuscript version submitted.