CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

Christopher J Kemp,James M Moore,Russell Moser,Brady Bernard,Matt Teater,Leslie E Smith,Natalia A Rabaia,Kay E Gurley,Justin Guinney,Stephanie E Busch,Rita Shaknovich,Victor V Lobanenkov,Denny Liggitt,Ilya Shmulevich,Ari Melnick,Galina N Filippova

doi:10.1016/j.celrep.2014.04.004

Abstract

Epigenetic alterations, particularly in DNA methylation, are ubiquitous in cancer, yet the molecular origins and the consequences of these alterations are poorly understood. CTCF, a DNA-binding protein that regulates higher-order chromatin organization, is frequently altered by hemizygous deletion or mutation in human cancer. To date, a causal role for CTCF in cancer has not been established. Here, we show that Ctcf hemizygous knockout mice are markedly susceptible to spontaneous, radiation-, and chemically induced cancer in a broad range of tissues. Ctcf(+/-) tumors are characterized by increased aggressiveness, including invasion, metastatic dissemination, and mixed epithelial/mesenchymal differentiation. Molecular analysis of Ctcf(+/-) tumors indicates that Ctcf is haploinsufficient for tumor suppression. Tissues with hemizygous loss of CTCF exhibit increased variability in CpG methylation genome wide. These findings establish CTCF as a prominent tumor-suppressor gene and point to CTCF-mediated epigenetic stability as a major barrier to neoplastic progression.

Highlights

CTCF (CCCTC-binding factor) is a highly conserved 11 Zn finger DNA binding protein that utilizes different combinations of its Zn fingers to bind a large number of highly divergent target sequences throughout the genome (Kim et al, 2007; Nakahashi et al, 2013)
The DNA binding protein CTCF regulates a diverse array of epigenetic processes and is frequently altered by hemizygous deletion or mutation in human cancer
Ctcf+/− tumors are characterized by increased aggressiveness including invasion, metastatic dissemination, and mixed epithelial/mesenchymal differentiation

Summary

Introduction

CTCF (CCCTC-binding factor) is a highly conserved 11 Zn finger DNA binding protein that utilizes different combinations of its Zn fingers to bind a large number of highly divergent target sequences throughout the genome (Kim et al, 2007; Nakahashi et al, 2013). Numerous epigenetic phenomena regulated by CTCF include X chromosome inactivation, imprinting, noncoding transcription, and RNA processing (Filippova, 2008; Ong and Corces, 2014). CTCF binds to target DNA sequences in a DNA methylation-dependent manner and regulates spreading of DNA methylation (Mukhopadhyay et al, 2004; Wang et al, 2012; Zampieri et al, 2012). As CTCF maps to 16q22.1, we hypothesized that it might be a haploinsufficient tumor suppressor gene in which inactivation of just one allele would increase cancer risk (Payne and Kemp, 2005). To directly address this possibility, we examined the tumor predisposition of Ctcf hemizygous knockout mice

Results

Discussion

Conclusion