Pluripotent Stem Cell Lines Retain Damaged DNA

Stem cells' programmability makes them essential to numerous neurological, immunological, and developmental studies. Though derived initially from embryos, stem cells are now typically gleaned from adult skin cells. These cells, called pluripotent stem cells (iPSCs), are currently used for research relating to organ development, cell-based therapies, and more.

However, researchers at the University of Cambridge and Wellcome Sanger Institute made some critical observations about abnormalities occurring in these specific cell lines. "We noticed that some of the iPS cells that we were generating looked really different from each other, even when they were derived from the same patient and derived in the same experiment," said lead author Dr. Foad Rouhani. 

To investigate these differences, the team utilized whole genome sequencing to analyze DNA from stem cell lines in different cohorts, including the HipSci cohort at the Wellcome Sanger Institute. Their findings revealed that as many as 72% of these lines showed significant UV damage.

Nucleotide bases — such as adenine (A), guanine (G), cytosine (C), and thymine (T) — compose the basic building blocks of DNA strands. The pairing of these bases is essential to correct translation into RNA and, ultimately, proteins. Once damage occurs to the base pairing of a strand, such as that found from ultraviolet radiation, profound effects can occur on cellular function, sometimes resulting in tumor formation.

"Almost three—quarters of the cell lines had UV damage," said Professor Serena Nik-Zinal from the Department of Medical Genetics at the University of Cambridge. "Some samples had an enormous amount of mutations – sometimes more than we find in tumors.  We were all hugely surprised to learn this, given that most of these lines were derived from skin biopsies of healthy people."

Due to the ease of use to obtain blood samples, the team turned their attention toward blood derived iPSCs, in addition to cell lines from skin. While the level of mutations was lower in these blood derived iPSCs compared to skin cells, a quarter of the observed population contained mutations for BCOR, an important gene in blood cancers.

To further investigate these BCOR mutations, the team differentiated the iPSCs and turned them into neurons while tracking their progress. "What we saw was that there were problems in generating neurons from iPSCs that have BCOR mutations — they had a tendency to favor other cell types instead," stated Dr. Rouhani. "This is a significant finding, particularly if one is intending to use those lines for neurological research."

When they examined the blood samples, they discovered that the BCOR mutations were not present in the patient. Instead, the process of culturing cells appears to increase the frequency of these mutations, which may have implications for other researchers working with cells in culture.

While scientists typically screen cell lines for any issues at the chromosomal level, this level of detail is not sufficient enough to identify the potentially major problems that this study identified. By looking at stem cell genomics in detail, researchers and clinicians can spot potentially dangerous cell lines before working with them, saving resources down the line. Professor Nik-Zainal says the primary way to mitigate this issue is by using whole genome sequencing to identify errors at the outset.

"The cost of whole genome sequencing has dropped dramatically in recent years to around £500 per sample, though it's the analysis and interpretation that's the hardest bit," commented Professor Nik-Zainal. "If a research question involves cell lines and cellular models, and particularly if we're going to introduce these lines back into patients, we may have to consider sequencing the genomes of these lines to understand what we are dealing with and get a sense of whether they are suitable for use."