Study Reveals Scope of Genomic Variation Within Cancer Cell Lines

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Tumor cell lines derived from single cells and curated at different reference labs have quietly evolved in vitro, accumulating distinct genomic aberrations.
Tumor cell lines derived from single cells and curated at different reference labs have quietly evolved in vitro, accumulating distinct genomic aberrations.

In vitro evolution of cancer cell lines probably helps to explain failures to replicate preclinical research findings, according to a study published in Nature.Study authors from Broad Institute of Harvard and Massachusetts Institute of Technology (MIT) in Cambridge and the Dana-Farber Cancer Institute, Harvard Medical School, Brigham and Women's Hospital, and Massachusetts General Hospital in Boston conducted extensive genomic analyses of 106 human cell lines available from 2 laboratories — Broad Institute's Cancer Cell Line Encyclopedia (CCLE) and Sanger Institute's Genomics of Drug Sensitivity in Cancer (GDSC) collections.1

A median of 19% of mutations found in a cell line from one of the labs were not identified in the same line obtained from the other lab, the authors found, though they did not include “silent” mutations that have no discernable impact on cell phenotype. More than a quarter of genes with copy number alterations were found only in the cell lines from one lab.1

The scope and magnitude of the differences surprised Chetan Bettegowda, MD, PhD, associate professor of neurosurgery and director of the Meningioma Center and associate professor of neurosurgery at Johns Hopkins Medicine in Baltimore, Maryland, who was not involved in the study. 

“It's really an extraordinary piece of research,” Dr Bettegowda said. “For the first time, in great depth, they showed exactly how heterogeneous and variable these cell lines really are. It was striking to see how rapidly these lines evolve and that even ‘identical' cell lines are so varied.”

The findings have “potentially far-reaching implications” for preclinical cancer research, Dr Bettegowda said.

The team's barcoding experiments showed that cell line evolution “occurs as a result of positive clonal selection that is highly sensitive to culture conditions,” reported senior study author Todd Golub, MD, chief scientific officer and cancer program director at Broad Institute, where he is also a founding member. Dr Golub is also an oncologist at Dana-Farber.

The team also examined 27 strains of MCF-7, a commonly studied estrogen receptor (ER)-positive breast cancer cell line, and discovered those strains had undergone “rapid genetic diversification.”When these strains were exposed to 321 anticancer drugs, responses varied dramatically, with three-quarters of drugs that had strong anticancer effects on some strains proving to be “completely inactive” in other strains.1

The team found similar diversity among strains of 13 other cell lines, they reported. 

“Notably, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation,” Dr Golub and colleagues reported.1

“[T]he investigators have convincingly documented substantial cellular evolution: They have demonstrated that cells with the same name can be highly variable simply as a result of a different laboratory history,” said C. Glenn Begley, MBBS, PhD, FAHMS, CEO of BioCurate Pty Ltd., in Victoria, Australia, who was not a part of the study but has written on reproducibility. 

Scientists have known for years that cancer cell lines can evolve under different in vitro conditions, but the magnitude of the resulting changes within cell lines has not been systematically quantified.

“The variation demonstrated here, simply as a result of cell culture in the laboratory, is striking,” Dr Begley said. 

The findings might explain some of the variation in experimental results between, and even within, laboratories, but Dr Begley cautioned that other factors likely explain more failures to replicate preclinical findings than in vitro evolution, including researchers failing to repeat experiments and, “most importantly, failing to perform experiments in a blinded fashion,” Dr Begley explained.2

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