Genomic instability in EBV-transformed lymphoblastoid cell lines

Abstract

Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) promise to address the challenge posed by the limited availability of primary cells needed as a source of genomic DNA for genetic studies. However, the genetic stability of LCLs following prolonged culture has never been rigorously investigated. The impact of genomic aberration on the biological experiments such as gene expression and miRNA expression level has not been explored. Purposes of current study are to investigate whether genetic instability of LCLs might cause the accumulation of genetic modifications following their long-term subculture and to examine a correlation between genomic aberration and expression level in genes and miRNAs. To accomplish our goals, we isolated genomic DNA from human peripheral blood mononuclear cells and LCLs collected from 20 individuals and genotyped the DNA samples using the Affymetrix Gene Chip Human mapping 500K array set and Illumina HumanExome BeadChip array. Genotype concordance measurements between two sources of DNA from the same individual indicated that genotypic discordance is negligible in early-passage LCLs (<20 passages) but substantial in late-passage LCLs (>50 passages). Analysis of concordance on a chromosome-by chromosome basis identified genomic regions with a high frequency of genotypic errors resulting from the loss of heterozygosity observed in late-passage LCLs. Discovered genomic aberrations were of 90 regions of copy number variations (CNVs) observed in late-passage LCLs. In addition, integrated analysis revealed genomic aberration changed expression levels in genes and miRNAs.Our findings suggest that, although LCLs harvested during early stages of propagation are a reliable source of genomic DNA for genetic studies, investigations that involve genotyping of the entire genome should not use DNA from late-passage LCLs.