Cell lines, as the key elements of cancer research, which is usually collected from the tumor samples of patient and cultured in the laboratory, and can be grown indefinitely in vitro, therefore, that will be applied in everything from basic genetic research to drug discovery. Scientists believed that cell lines will remain genetically consistent even though individual cell lines continue to grow and divide, but in a new study, researchers from American Broad Researcher, Dana-Farber Cancer Institute, Harvard Medical School, Massachusetts General Hospital, Brigham and Women’s Hospital and Howard Hughes Medical Institute found that cell lines can actually evolve in a way that dramatically changes their response to drugs. The continued evolution of cell line in cell lines (which may be triggered by the laboratory conditions in which they grow) may be helpful to explain why different studies using the same cell line often produce conflicting results. Related study result is published in the journal of Nature.
These findings suggest that scientists need to be extra careful to ensure that cell line-based cancer models accurately reflect the tumor they are studying. The researchers also released an online tool – Cell STRAINER – to help scientists benchmark their models.
Golub, the communication author of this paper and founding member of the Broward Fellows, said that ‘The information conveyed by this study does not mean that models based on cell lines and cell cultures are not good. In contrast, we should understand the model and its nature and limitations. In addition to the factors we usually consider, a certain degree of genetic and genomic characterization is required. It is not a good choice to skim this detailed representation’
Evolution in Laboratory Culture Dishes
It has long been recognized that cell lines can not fully mimic the tumors of their origin. Nonetheless, they are still considered representative and stable enough to provide an accurate understanding of cancer biology and drug response. In fact, every cancer treatment available nowadays is tested at some points with these laboratory models. However, it is often difficult for scientists to replicate research results from cell lines. In addition, there is no systematic efforts have been made currently to measure how and what degree the cells in cancer cell lines change genetically over time, and whether these changes affect the drug response.
Uri Ben-David, the first author of the paper and a postdoctoral researcher at Golub Labs, said, ‘You can find many examples in the literature that indicate inconsistencies in drug sensitivity data in cell line experiments. We expect to find out signs of evolution and establish a correlation between changes in cell lines and these inconsistencies.’
While re-analyzing 106 cell lines from two large collections- the Broad-Novartis Cancer Cell Line Encyclopedia (CCLE) and the Sanger Institute’s Genomics of Drug Sensitivity in Cancer). At first, they speculated that these cell lines would evolve, but the high levels of variation being found, such as they found that 19% of genetic mutations exist only in one of the collections.
Afterward, the researchers performed an in-depth molecular analysis of 27 cell lines and 23 cell lines from two widely used cell lines – Estrogen receptor positive breast cancer cell line MCF-7 and lung cancer cell line A549. The analysis includes whole-genome DNA sequencing, targeted DNA sequencing of nearly 450 genes that are frequently mutated in cancer, bulk RNA sequencing, and single-cell RNA sequencing. Each cell line represents a population of cells from a cell line with different histories, such as different types of laboratory procedures, different lengths of in vitro culture, and different original origins.
These data reveal astonishing genomic differences between different cell lines, ranging from single-base-pair mutations to large-scale changes in genomic structure (eg, loss of entire chromosome arms) to major changes in gene expression, all of which indicate that these cell lines are not stable or as imaginative, furthermore, these genetic and expression differences also affect the growth rate, cell size, shape and other traits of these cell lines. The researchers expanded their findings by targeted sequencing of 11 other cancer cell lines that represent multiple tumor types, such as prostate, colon, liver, and skin cancer. In all cases, they found extensive genetic variation in these cancer cell lines.
The researchers found that even changing the type of nutrient medium in a cultured cell line by experimenting under different laboratory conditions allows certain cells in one cell line to have growth advantages over other cells, therefore, allowing genetically distinct cell populations to evolve. They also found that the isolated progeny of individual cells were able to spontaneously acquire new mutations via extracting individual cells and culturing them in vitro, suggesting that a new genetically diverse population of cells may originate from a single isolated cell in a cell line.
Cell line Variation Affects Drug Sensitivity
The researchers tested the response of 27 MCF-7 cell lines to 321 drugs in order to figure out how these genetic changes might affect drug response. In fact, the ability of any given drug to slow the growth of cells in a cell line or kill cells in a cell line is associated with the genetic characteristics of the cell line and the gene expression of the drug.
These findings complemented another study previously led by Ben-David, Beroukhim, and Golub, which used a patient-derived xenograft (PDX) model, of which the model is produced by implanting tumor cells of cancer patients into mice. In 2017, they reported in the journal of Nature Genetics that human cancer cells in the PDX model have lost the unique genetic characteristics observed in patients over time and acquired new features not observed in humans that are associated with changes in drug sensitivity of these models.
Change of Ideas and New Opportunities
In summary, these findings emphasize the necessity for scientists to understand the extent to which the cells they use are genetically different from their parental cell lines, allowing accurate comparisons between different experiments.
To this end, these researchers have developed and will release an online tool – Cell STRAINER – to help them estimate the genetic differences between the cell lines they use and the reference cell line samples in the Brod-Novo Cancer Cell Encyclopedia. The researchers also pointed out that the evolutionary capabilities of these cell lines may actually provide an opportunity to study various aspects of cancer biology and tumor evolution.
Golub said, ‘Based on the same general genetic background of these cell lines, it will be available to test the same compounds on both cell lines and apply their characteristics to study the action mechanism of the compound, or the effect of differences in gene expression on sensitivity, even you can study tumor heterogeneity and selective stress leading to cell line evolution.’