Changes of heterogeneous cell populations in the Ishikawa cell line during long-term culture: Proposal for an in vitro clonal evolution model of tumor cells

Abstract

Genomic changes in tumor cell lines can occur during culture, leading to differences between cell lines carrying the same name. In this study, genome profiles between low and high passages were investigated in the Ishikawa 3-H-12 cell line (JCRB1505). Cells contained between 43 and 46 chromosomes and the modal number changed from 46 to 45 during culture. Cytogenetic analysis revealed that a translocation t(9;14), observed in all metaphases, is a robust marker for this cell line. Single-nucleotide polymorphism microarrays showed a heterogeneous copy number in the early passages and distinct profiles at late passages. These results demonstrate that cell culture can lead to elimination of ancestral clones by sequential selection, resulting in extensive replacement with a novel clone. Our observations on Ishikawa cells in vitro are different from the in vivo heterogeneity in which ancestral clones are often retained during tumor evolution and suggest a model for in vitro clonal evolution.

Clonal evolution through genetic bottlenecks and telomere attrition: Potential threats to in vitro data reproducibility

“…Recent reports based on high‐resolution copy number profiling have demonstrated that clones dominating in early cultures of cancer cell lines frequently disappear, to be replaced by related, but distinct clones with partly different genotypes . This is sometimes accompanied by an increased growth rate and a loss of clonal heterogeneity, indicating that a selection of more over less proliferative clones takes place under the nutrient rich conditions of culture (examples are depicted in Figure A‐C).…”

“…These alterations occur even under standardized, unchanged culture conditions. Notably, most studies penetrating the issue in depth have shown that the altered genetic profiles result not as much from an accumulation of mutations in vitro as from changes in the clonal composition of cultured cells …”

“…This is sometimes accompanied by an increased growth rate and a loss of clonal heterogeneity, indicating that a selection of more over less proliferative clones takes place under the nutrient rich conditions of culture (examples are depicted in Figure A‐C). Considering this propensity for clonal evolution of cancer cell lines over time in vitro, it is not surprising that different sublines grown from the same early cultures frequently have evolved partly different genomic profiles . Hence, genetic differences are frequently found by analysis of sister cell lines from different repositories, and in cells from the same line but showing different degrees of mesenchymal versus epithelial differentiation .…”

Incorrect strain information for mouse cell lines: sequential influence of misidentification on sublines

“…However, the differences are not significant to characterize each cell line because genetic components between cell lines carrying the same name can be changed during cell culture (Kasai et al 2016). This can be found in the human STR database, showing that all STR loci are not always identical between the same cell lines registered at different cell banks.…”

Fetal bovine serum (FBS): Past – present – future

“…The worst-case scenario is that bottlenecking selection procedures for the effects of newly purchased FBS batches on the different cell types are visible or measurable only in the rarest cases. Elimination of ancestral clones by sequential selection, possibly by unsuitable FBS charges on sophisticated cell culture, could result in replacement by novel clones that are genetically still identical but equipped with modified features (Kasai et al, 2016). A recent comparison of experimental methods for reproducible pharmacogenomic profiling of cancer cell line panels highlighted evidence that even the amount of FBS in growth media could have an impact (Haverty et al, 2016).…”