title: Cell culture-induced aberrant methylation of the imprinted IG DMR in human lymphoblastoid cell lines.
abstract: 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.affiliation: Department of Human Genetics, McGill University, Montreal, QC, Canada.
authors.forename: Aabida
authors.initials: A
authors.lastname: Saferali
authors.forename: Elin
authors.initials: E
authors.lastname: Grundberg
authors.forename: Soizik
authors.initials: S
authors.lastname: Berlivet
authors.forename: Hugues
authors.initials: H
authors.lastname: Beauchemin
authors.forename: Lisanne
authors.initials: L
authors.lastname: Morcos
authors.forename: Constantin
authors.initials: C
authors.lastname: Polychronakos
authors.forename: Tomi
authors.initials: T
authors.lastname: Pastinen
authors.forename: Jinko
authors.initials: J
authors.lastname: Graham
authors.forename: Brad
authors.initials: B
authors.lastname: McNeney
authors.forename: Anna K
authors.initials: AK
authors.lastname: Naumova
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D018929:Cell Culture Techniques / Q000379:methods*; D002460:Cell Line; D002883:Chromosomes, Human, Pair 14; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D020868:Gene Silencing; D014644:Genetic Variation; D018392:Genomic Imprinting; D006801:Humans; D008214:Lymphocytes / Q000166:cytology*; D008875:Middle Aged