Variable characteristics overlooked in human K-562 leukemia cell lines with a common signature

Abstract

K-562 is a well-known in vitro cellular model that represents human leukemia cell lines. Although the K-562 cells have been extensively characterized, there are inconsistencies in the data across publications, showing the presence of multiple K-562 cell lines. This suggests that analyzing a single K-562 cell line is insufficient to provide reliable reference data. In this study, we compared three K-562 cell lines with different IDs (RCB0027, RCB1635, and RCB1897) to investigate the fundamental characteristics of K-562 cells. Amplifications of the BCR-ABL1 fusion gene and at 13q31 were detected in all three cell lines, whereas each genome exhibited distinctive features of sequence variants and loss of heterozygosity. This implies that each K-562 cell line can be characterized by common and unique features through a comparison of multiple K-562 cell lines. Variations in transcriptome profiles and hemoglobin synthesis were also observed among the three cell lines, indicating that they should be considered sublines that have diverged from the common ancestral K-562 despite no changes from the original cell name. This leads to unintentional differences in genotypes and/or phenotypes among cell lines that share the same name. These data show that characterizing a single K-562 cell line does not necessarily provide data that are applicable to other K-562 cells. In this context, it is essential to modify cell names in accordance with changes in characteristics during cell culture. Furthermore, our data could serve as a reference for evaluating other K-562 sublines, facilitating the discovery of new K-562 sublines with distinct characteristics. This approach results in the accumulation of K-562 sublines with diverged characteristics and expands the options available, which may help in selecting the most suitable K-562 subline for each experiment.

Keywords: Cell line authentication; Cell name; Cell subline; In vitro cellular model; Reference data.

Figure 1

Copy number profiles compared among three K-562 sublines based on DNA microarray analysis. The horizontal and vertical axes represent chromosomes and DNA copy numbers, respectively. The red bars above the chromosome numbers indicate the loss of heterozygosity, which is listed in Table S3. The regions of LOH commonly observed in the three sublines exceeds 900 Mb, with additional changes detected in each lineage. Amplifications in chromosomes 9, 13, and 22 (Fig. S4D–F), and deletions in chromosome 9 are identical across all three profiles (Fig. S4C). RCB0027 (A) exhibits complex rearrangements on chromosome 18, unlike the other two sublines (Fig. S4A). RCB1635 (B) can be characterized by having 2 or 3 mosaic copies of the X chromosome, which is different from RCB0027 that has two copies and RCB1897 that has only one copy. RCB1897 (C) exhibits a high level of LOH, spanning a total of 1193.7 Mb in total. Whole profiles, including allele differences based on SNP data, are presented in Fig. S3.

Figure 2

Distance matrix of three K-562 sublines and KU812. Based on transcriptome profiling, the maximal distance is denoted by a deep red color. The expression pattern indicates that RCB0027 and RCB1635 are in close proximity.

Figure 3

K-562 Fact Sheet, illustrating its fundamental cell data. The data consist of three parts: the clinical data, the establishment of the cell line, and current features. Differences between cellular characteristics at the establishment and the present are indicated in red. RCB0027 and RCB1635 exhibit loss of heterozygosity (LOH) in the HLA region. Additionally, RCB1635 harbors a cryptic gain in the MYC region, while RCB1897 is marked by extensive LOH. These alterations are identified based on shared characteristics. Relationships among the three sublines are shown in purple lines based on hierarchical clustering of these transcriptomic profiles. Three K-562 cell lines require unique ID numbers to distinguish them from each other and from other K-562 sublines.