title: MS-HRM assay identifies high levels of epigenetic heterogeneity in human immortalized cell lines.
abstract: Immortalized cell lines are widely used in genetic and epigenetic studies, from exploration of basic molecular pathways to evaluation of disease-specific cellular properties. They are also used in biotechnology, e.g., in drug toxicity tests and vaccine production. Cellular and genetic uniformity is the main feature of immortalized cell lines and it has been particularly advantageous in functional genomic research, which has in recent years been expanded to include epigenetic mechanisms of gene expression regulation. Using the MS-HRM technique, we demonstrated heterogeneity in locus-specific methylation patterns in different cell cultures of four human cell lines: HEK293, HEK293T, LCL and DU145. Our results show that some human immortalized cell lines consist of cells that differ in the methylation status of specific loci, i.e., that they are epigenetically heterogeneous. We show that even two cultures of the same cell line obtained from different laboratories can differ in the methylation status of the specific loci. The results indicated that epigenetic uniformity of the cell lines cannot be assumed in experiments which utilize cell cultures and that the methylation status of the specific loci in the immortalized cell lines should be re-characterized and carefully profiled before epigenetic studies are performed.
authors: Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, 17177 Stockholm, Sweden.
authors: Milica
authors: M
authors: Putnik
authors: Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, 17177 Stockholm, Sweden.
authors: Tomasz K
authors: TK
authors: Wojdacz
authors: Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, 17177 Stockholm, Sweden.
authors: Angeliki
authors: A
authors: Pournara
authors: Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, 17177 Stockholm, Sweden.
authors: Marie
authors: M
authors: Vahter
authors: Institute of Environmental Medicine, Unit of Metals and Health, Karolinska Institutet, Nobels väg 13, 17177 Stockholm, Sweden. Electronic address: annika.wallberg@ki.se.
authors: Annika E
authors: AE
authors: Wallberg
mesh_terms: D000123:Acetyltransferases / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D019175:DNA Methylation; D015254:DNA Modification Methylases / Q000235:genetics / Q000378:metabolism; D045643:DNA Repair Enzymes / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D015870:Gene Expression; D056426:Genetic Loci; D014644:Genetic Variation; D057809:HEK293 Cells; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D055751:SOXC Transcription Factors / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D044366:Transition Temperature; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: C484731:HOXC11 protein, human; D018398:Homeodomain Proteins; C097473:SOX11 protein, human; D055751:SOXC Transcription Factors; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; D015254:DNA Modification Methylases; C515491:MGMT protein, human; D000123:Acetyltransferases; C111246:HTATIP2 protein, human; D045643:DNA Repair Enzymes
keywords: DNA methylation; Gene expression; HEK293; MS-HRM; SOX11