Abstract 2027: MECP2 is a frequently amplified oncogene with an unusual epigenetic mechanism of action
Authors: Neupane Manish , Clark Allison P. , Birkbak Nicolai J. , Eklund Aron , Schumacher Steven E. , Beroukhim Rameen , Szallasi Zoltan , Vidal Marc , Hill David E. , Silver Daniel P. 
Published: August 2015

Introduction: We demonstrate that MECP2 is an oncogene, characterize the extent of MECP2 involvement in human cancers, and explore its mechanism of action.

Experimental Procedures: To identify new oncogenes that drive cancer development, we conducted an unbiased genome-scale screen for genes that can substitute for activated RAS in oncogenic transformation and explored one screen hit in detail.

Results: One of the new potential oncogenes identified in this screen, Methyl CpG Binding Protein 2 (MECP2), has no previously described role in malignancy and is amplified across 18% of all human cancers in the TCGA collection. MECP2 is an X-linked gene known to bind methylated cytosines, and can act as a transcriptional repressor in this context. Recent studies show that it also acts as a transcriptional activator, likely through binding to another epigenetic modification of DNA, 5-hydroxymethylcytosine (5hmC).

MECP2 was as potent as activated RAS in conferring anchorage independent growth upon primary human mammary epithelial cells (HMECs) previously transduced with the SV40 early region and hTERT (N−RAS HMECs). MECP2 partially rescued the growth inhibition of RAS-addicted human cancer cell lines after the shRNA-mediated suppression of RAS. MECP2 expresses two spliced isoforms; experiments showed the short isoform activated the MAPK pathway, while both isoforms activated the PI3K pathway. Neither isoform alone conferred growth of N−RAS HMECs as xenografts in nude mice; however, both isoforms together allowed tumor growth. The cancer-promoting activities of MECP2 absolutely required its DNA-binding activity. A mutant allele of MECP2, R133C, is known to have defective 5hmC binding but largely preserved 5-methylcytosine binding; interestingly, this mutation was 10% as active as wt MECP2 in conferring anchorage independent growth. We searched for genes whose expression is modulated by MECP2 that might be important for transformation; the kinase PAK3 was found to be required for the ability of MECP2 to confer anchorage independent growth, and was itself able to confer anchorage independent growth upon N−RAS HMECs.

A number of human cancer cell lines have amplified, overexpressed MECP2 and showed significant growth inhibition after shRNA-mediated downregulation of MECP2 (MECP2 addiction). N−RAS HMECs transformed with MECP2 were an order of magnitude more sensitive to the DNA methylation inhibitor 5-azacytidine than isogenic cells transformed by activated RAS, or isogenic cells without an additional transforming gene.

Conclusion: MECP2 is a commonly amplified and overexpressed oncogene whose two splicing isoforms together recapitulate the major oncogenic activities of activated RAS. Because MECP2 requires DNA binding to methylated or hydroxymethylated cytosines for its tumor-promoting activities, DNA methylation inhibition with FDA-approved drugs may be therapeutic for tumors overexpressing MECP2.

Citation Format: Manish Neupane, Allison P. Clark, Nicolai J. Birkbak, Aron Eklund, Steven E. Schumacher, Rameen Beroukhim, Zoltan Szallasi, Marc Vidal, David E. Hill, Daniel P. Silver. MECP2 is a frequently amplified oncogene with an unusual epigenetic mechanism of action. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2027. doi:10.1158/1538-7445.AM2015-2027