Many stem cell lines used for research and therapies carry large number of mutations, Cambridge researchers find – Cambridge Independent

The remarkable power of stem cells - which can be programmed to become almost any type of cell in the body - means they are key to many scientific studies.

Increasingly, they are also being used for new cell-based therapies to treat a range of diseases.

While originally we could only get stem cells from embryos, now we can derive them from a range of adult tissues, including skin or blood, using Nobel Prize-winning technology.

But Cambridge researchers have found DNA damage caused by factors such as ultraviolet radiation affected 72 per cent of the stem cell lines they studied that had been derived from human skin cells. This has important implications for research and medicine.

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

Induced pluripotent stem cells (iPSCs), as those derived from other cell types or tissues are known, hold huge potential for tackling diseases, including rare conditions.

It is even suggested that iPSCs programmed to grow into nerve cells could be used to replace those lost to neurodegeneration in diseases such as Parkinsons.

The new research, published in Nature Genetics, represents the largest genetic study to date of iPSCs to date.

Dr Foad Rouhani, who carried out the work while at the University of Cambridge and the Wellcome Sanger Institute, said: 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.

The most striking thing was that pairs of iPS cells would have a vastly different genetic landscape one line would have minimal damage and the other would have a level of mutations more commonly seen in tumours.

One possible reason for this could be that a cell on the surface of the skin is likely to have greater exposure to sunlight than a cell below the surface and therefore eventually may lead to iPS cells with greater levels of genomic damage.

[Read more: Evidence of new causes of cancer uncovered as genomic data of 12,000 NHS patients is studied by University of Cambridge researchers]

DNA comprises three billion pairs of nucleotides - molecules represented by the letters A, C, G and T.

Damage from sources such as ultraviolet radiation or smoking leads to mutations, meaning a letter C might change to T, for example.

Studying the mutational fingerprints on our DNA can reveal what is responsible for the damage.

An accumulation of mutations can have a profound effect on cell function and in some cases lead to tumours.

Using whole genome sequencing, the researchers inspected the entire DNA of stem cell lines from different sources, including the HipSci cohort at the Wellcome Sanger Institute.

They found blood-derived iPSCs - which are increasingly common, due to the ease with which blood can be taken - also carried mutations but at a lower level than skin-derived iPS cells, and they had no UV damage.

Some 26.9 per cent of them, however, carried mutations in a gene called BCOR, which is an important gene in blood cancers.

Next the researchers investigated whether these BCOR mutations had any functional impact.

They differentiated the iPSCs, turning them into neurons and tracking their progress along the way.

[Read more: 4m funding for Cambridge scientists under Cancer Grand Challenges initiative]

Dr Rouhani said: What we saw was that there were problems in generating neurons from iPSCs that have BCOR mutations they had a tendency to favour other cell types instead. This is a significant finding, particularly if one is intending to use those lines for neurological research.

Analysis of the blood samples showed the BCOR mutations were not present within the patient.

So it seemed that the process of culturing cells increased the frequency of the mutations, which could have implications for other researchers working with cells in culture.

Typically, scientists using cell lines will screen them at the chromosomal level checking, for example, that the requisite 23 pairs of chromosomes are present.

Such analysis would not pick up the potentially major problems that this new study has identified, however,

The researchers warn that without looking in detail at the genomes of these stem cells, researchers and clinicians would be unaware of the underlying damage in them.

The DNA damage that we saw was at a nucleotide level, explained Prof Nik-Zainal. If you think of the human genome as like a book, most researchers would check the number of chapters and be satisfied that there were none missing. But what we saw was that even with the correct number of chapters in place, lots of the words were garbled.

Using whole genome sequencing, however, would enable errors to be discovered 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, said Prof 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.

Dr Rouhani adds: In recent years we have been finding out more and more about how even our healthy cells carry many mutations and therefore it is not a realistic aim to produce stem cell lines with zero mutations.

The goal should be to know as much as possible about the nature and extent of the DNA damage to make informed choices about the ultimate use of these stem cell lines.

If a line is to be used for cell based therapies in patients for example, then we need to understand more about the implications of these mutations so that both clinicians and patients are better informed of the risks involved in the treatment.

The research was funded by Cancer Research UK, the Medical Research Council and Wellcome, and supported by NIHR Cambridge Biomedical Research Centre and the UK Regenerative Medicine Platform.

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Many stem cell lines used for research and therapies carry large number of mutations, Cambridge researchers find - Cambridge Independent