Leukocyte DNA as surrogate for the evaluation of imprinted Loci methylation in mammary tissue DNA.

Osman El-Maarri,Ludovic Barault,Holly R Harris,Craig D Shriver,Allyson L Valente,Karin B Michels,Rachel E Ellsworth

doi:10.1371/journal.pone.0055896

Abstract

There is growing interest in identifying surrogate tissues to identify epimutations in cancer patients since primary target tissues are often difficult to obtain. Methylation patterns at imprinted loci are established during gametogenesis and post fertilization and their alterations have been associated with elevated risk of cancer. Methylation at several imprinted differentially methylated regions (GRB10 ICR, H19 ICR, KvDMR, SNRPN/SNURF ICR, IGF2 DMR0, and IGF2 DMR2) were analyzed in DNA from leukocytes and mammary tissue (normal, benign diseases, or malignant tumors) from 87 women with and without breast cancer (average age of cancer patients: 53; range: 31–77). Correlations between genomic variants and DNA methylation at the studied loci could not be assessed, making it impossible to exclude such effects. Methylation levels observed in leukocyte and mammary tissue DNA were close to the 50% expected for monoallellic methylation. While no correlation was observed between leukocyte and mammary tissue DNA methylation for most of the analyzed imprinted genes, Spearman's correlations were statistically significant for IGF2 DMR0 and IGF2 DMR2, although absolute methylation levels differed. Leukocyte DNA methylation levels of selected imprinted genes may therefore serve as surrogate markers of DNA methylation in cancer tissue.

Highlights

The epigenetic code allows cell function and phenotype to vary without alteration of the DNA sequence
No significant correlation was observed between the levels of DNA methylation at the analyzed loci in mammary tissue and peripheral blood in women with benign disease, but significant correlations were identified in cancer patients for IGF2 DMR0 and IGF2 DMR2
This observation suggests that individual CpG dinucleotides do not adequately describe methylation at a gene locus and highlights the need for techniques other than those based upon the use of restriction enzymes or single nucleotide extension in order for more than one CpG site to be analyzed per locus

Summary

Introduction

The epigenetic code allows cell function and phenotype to vary without alteration of the DNA sequence. Imprinted genes are monoallelically expressed according to their parental origin [1], and many of them are candidates for oncogenes or tumor suppressor genes [2]. Their expression is largely controlled by specific DNA regions defined by distinct methylation patterns. These regions are called imprinting control regions (ICRs) if established in the germline, or somatic differentially methylated regions (sDMRs) if established postfertilization [3]. Altered methylation of DMRs has been found in cancer cell lines and various primary tumor tissues [7,8,9], and might precede carcinogenesis

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Conclusion