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Research Paper

Cell culture-induced aberrant methylation of the imprinted IG DMR in human lymphoblastoid cell lines

Aabida Saferali, Elin Grundberg, Soizik Berlivet, Hugues Beauchemin, Lisanne Morcos, Constantin Polychronakos, Tomi Pastinen, Jinko Graham, Brad McNeney and Anna K. Naumova

DNA methylation patterns are often poorly conserved through cell culturing. To determine the effect of cell immortalization and culture on DNA methylation profiles, we analyzed methylation in the differentially methylated regions (DMR) of five imprinted domains: the intergenic (IG) DMR on chromosome 14q32; potassium voltage-gated channel, KQT-like subfamily, member 1, (KCNQ1); small nuclear ribonucleoprotein polypeptide N (SNRPN), mesoderm specific transcript homolog (MEST); and H19 in lymphoblastoid cell lines (LCLs). In the IG DMR we found an aberrant methylation pattern that was consistent through all the cell lines tested, and significantly different from that of noncultured peripheral blood cells. Using a generalized linear mixed model to compare methylation profiles, we show that recently derived LCLs significantly differ from the CEPH LCLs. This implies a gradual cell-culture related deterioration of DNA methylation in the IG DMR with at least two steps that may be identified: loss of methylation at CG sites 1 and 8; and loss of allelic differences in DNA methylation. The IG DMR methylation profile also confirms the high level of clonality of the CEPH LCLs. We conclude that non-transformed primary cells may be less susceptible to epigenetic anomalies and therefore may provide a more accurate reflection of gene expression in vivo.

Authors

Aabida Saferali

McGill University

Elin Grundberg

McGill University; Genome Quebec Innovation Centre

Soizik Berlivet

McGill University

Hugues Beauchemin

McGill University

Lisanne Morcos

McGill University; Genome Quebec Innovation Centre

Constantin Polychronakos

McGill University; Genome Quebec Innovation Centre; Research Institute of the McGill University Health Centre

Tomi Pastinen

McGill University; Genome Quebec Innovation Centre

Jinko Graham

Simon Fraser University

Brad McNeney

Simon Fraser University

Anna K. Naumova Corresponding author: anna.naumova@muhc.mcgill.ca

McGill University; Research Institute of the McGill University Health Centre