TK6 genome profile compared with WIL2-NS: Reference data to improve the reproducibility of genotoxicity studies

Abstract The TK6 cell line has been widely used for genotoxicity screening by taking advantage of the TK1 mutations. A number of publications have employed TK6 as a tool for the assay; however, its characterization is limited. Because genomes of cell lines are often changed during cell culture, differences in TK6 genomes could be observed between laboratories, which would cause potential problems with reproducibility using TK6. In this study, TK6(IVGT) (JCRB1435), registered with the JCRB Cell Bank as the standard for TK6, has been characterized by karyotyping, SNP microarray and targeted sequencing, and were then compared to WIL2-NS (JCRB9063), a subline derived from a common ancestor with TK6. Changes at the chromosome level were quantitatively assessed by the microarray data, which were shown by DNA sizes and Scales of Genomic Alterations (SGA). An extinct common ancestral cell line, WI-L2 originated from hereditary spherocytosis, has been extrapolated from analysis of genomic signatures shared between TK6 and WIL2-NS, revealing a point mutation in SPTA1, related to the disease. DNA size is calculated to be 102.6%, 103.1% and 103.9% for WI-L2, TK6(IVGT) and WIL2-NS respectively, with the reference values of a normal diploid genome, and each genome shows SGA of 2.8%, 4.5% and 4.2% respectively. Differences between TK6(IVGT) and WIL2-NS are due to regions and sizes of gains, implying that genomes of both cells tend to increase their DNA size independently. Our data provide fundamental genomic features of TK6 and serve as a reference profile of the standardized TK6 cell line, which leads to an increase in robustness of assays using the TK6 cells.