Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility

et al. (2012) Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility. PLoS ONE 7(7): e41361. doi:10.1371/journal.pone.0041361 Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility Lovisa E. Reinius 0 Nathalie Acevedo 0 Maaike Joerink 0 Go ran Pershagen 0 Sven-Erik Dahle n 0 Dario Greco 0 Cilla So derha ll 0 Annika Scheynius 0 Juha Kere 0 Angela H. Ting, Cleveland Clinic Foundation, United States of America 0 1 Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden, 2 Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet, Stockholm, Sweden, 3 Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden, 4 Science for Life Laboratory, Stockholm, Sweden, 5 Department of Medical Genetics, University of Helsinki and Folkha lsan Institute of Genetics , Helsinki , Finland Methylation of cytosines at CpG sites is a common epigenetic DNA modification that can be measured by a large number of methods, now even in a genome-wide manner for hundreds of thousands of sites. The application of DNA methylation analysis is becoming widely popular in complex disorders, for example, to understand part of the ''missing heritability''. The DNA samples most readily available for methylation studies are derived from whole blood. However, blood consists of many functionally and developmentally distinct cell populations in varying proportions. We studied whether such variation might affect the interpretation of methylation studies based on whole blood DNA. We found in healthy male blood donors there is important variation in the methylation profiles of whole blood, mononuclear cells, granulocytes, and cells from seven selected purified lineages. CpG methylation between mononuclear cells and granulocytes differed for 22% of the 8252 probes covering the selected 343 genes implicated in immune-related disorders by genome-wide association studies, and at least one probe was differentially methylated for 85% of the genes, indicating that whole blood methylation results might be unintelligible. For individual genes, even if the overall methylation patterns might appear similar, a few CpG sites in the regulatory regions may have opposite methylation patterns (i.e., hypo/hyper) in the main blood cell types. We conclude that interpretation of whole blood methylation profiles should be performed with great caution and for any differences implicated in a disorder, the differences resulting from varying proportions of white blood cell types should be considered. - Funding: This study was supported by a grant from the Swedish Foundation for Strategic Research (RBc08-0027) and the Swedish Research Council. LER was supported by the Osher Initiative for Research on Severe Asthma at Karolinska Institutet, NA was supported by a PhD grant from Karolinska Institutet, and MJ was supported by a Marie Curie Intra-European Fellowship (PIEF-GA-2008-219680). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. DNA methylation is the covalent addition of a methyl group in the position 5 of a cytosine (C) when this nucleotide occurs next to a guanine (G) forming a CpG site. There are around 28 million CpG sites in the human genome. Depending on the chromosomal region, cell type, developmental stage, alleles and parent-of-origin, a CpG site can be methylated, unmethylated or hemi-methylated. DNA methylation is involved in regulation of transcriptional repression and gene silencing. Together with other epigenetic mechanisms, DNA methylation functions as a switch that turns relevant genes on and off, a mechanism that is crucial in development, differentiation and homeostasis [1]. Certain CpG sites are highly methylated in hematopoietic progenitors but become unmethylated during differentiation [2,3,4]. There is also a small number of genes that gain cell specific methylation when the embryonic stem (ES) cells differentiate into the three germ layers [5]. The search for those methylated and/or unmethylated CpG sites that may categorize tissues and cell populations have been under extensive research for more than two decades [6,7]. It is known that cell specific DNA methylation patterns convey cell memory, which is transmitted to the progeny by mitosis [8]. Therefore, every differentiated cell type has CpG sites that are specifically methylated or unmethylated for that specific lineage but not for others [2,9]. There is currently extensive research ongoing aiming at the identification of specific changes in DNA methylation that may contribute to human diseases. Alterations in DNA methylation have been shown to cause monogenic disease such as Rett syndrome [10], and mediate genomic instab (...truncated)