Keeping genetics straight in cancer cells

Agilent CGH platform helps assure quality of cancer cell lines

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SANTA CLARA, Calif.—It’s not news that some popular cell lines simply are not stable—that is, as cultures are propagated in labs, changes occur in biological properties and genetic makeup. Researchers at Agilent Technologies and several academic institutions have highlighted the scope of the problem—and have offered a suggestion for making things better—through the use of comparative genomic hybridization (CGH) technology.
The findings and suggestions are covered in a paper, “Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function,” published July 26 in Scientific Reports. In the work leading up to that paper, scientists using Agilent’s CGH technology showed that cancer cell lines, which are broadly used in all aspects of biomedical research, may have vast differences in their genetic makeup, even when grown in the same batch.
Despite the use of standard precautions and quality assurance methods to control such changes and validate authenticity of the cell lines, traditional measures may not be sufficient, the researchers say, noting in the paper, “Since much of what we know about the molecular mechanisms of cancer is derived from these cell lines, and they are broadly used for drug development and regulatory testing, this represents a key concern for putting such investigations on a sound footing.”
The findings come out of the efforts of a consortium of scientists from Agilent, Brown University, Georgetown University, Hamner Institutes for Health Sciences and Johns Hopkins Bloomberg School of Public Health, who have engaged in a multiyear study that aims to develop a new generation of assays for testing environmental toxicity. The study, known as the Human Toxome Project, combines multiple ‘omics technologies and bioinformatics.
The scientists, led by Dr. Thomas Hartung of Johns Hopkins, selected the well-established breast cancer cell line MCF-7, known to be prone to spontaneous rearrangements, as their model system. As noted in the paper, “the human breast adenocarcinoma cell line MCF-7 (Michigan Cancer Foundation-7) has served for over 40 years as a standard model for in-vitro cancer research as well as estrogen and progesterone receptor science and is one of the key cancer cell lines used as a model for investigation of processes that impact patient care.”
In an effort to establish reproducibility, they conducted cell culture work in two independent sites using identical laboratory protocols. They obtained the MCF-7 cells from the same cell bank and lot numbers, meaning they were grown in the same batch. Cells were validated using standard methods at the cell bank and at the project sites. However, despite extensive efforts to synchronize their protocols, the scientists were unable to obtain comparable results at the two sites.
They accumulated cytological, transcript profiling and phenotypic evidence that the cells were actually different. Of particular importance, they found that the cells demonstrated vastly different responses to induction by the natural human hormone estrogen—one of the two cell lines was hypersensitive to estrogen, the other was not.
Using CGH technology from Agilent, the scientists confirmed that the two cell lines had vast differences in their genetic makeup, in some cases as large as entire human chromosomes, writing, “We demonstrate by various techniques that there can be marked cellular and phenotypic heterogeneity in a single batch of cells from a cell bank that are invisible with the usual STR cell authentication protocols, and that this heterogeneity has serious consequences for reproducibility and primary outcomes of experiments.”
As a result, the scientists have recommended that cell culture banks use advanced genomic technologies, such as array CGH, to ensure the consistency of the cells they provide to the research community. For this project alone, the team estimated the additional costs of the unplanned experiments and delays to the project totaled around $1 million.
“Agilent’s array CGH platform is a leading technology used in hundreds of genomic and cytogenetic laboratories worldwide,” said Herman Verrelst, an Agilent vice president and general manager of the company’s Genomics Solutions Division and Clinical Applications Division. “We are pleased to see this example of using our technology to increase reproducibility of cell culture research. It is striking that a simple array CGH experiment, which would have cost less than $1,000 at a commercial service provider, could have prevented $1 million in lost research funding and several years of delay.”

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