Cryoniss interviews Amanda Capes-Davis, Chair of ICLAC
Can you tell us a bit about yourself?
I am one of those people who enjoy both science and the arts (particularly history). I discovered cell culture in the 1990s while doing my PhD and found it the perfect mix of both – many cell lines are very old and they all have a story. Most scientists fall in love with a field of research; in my case, I fell in love with a technique.
How did you get into the field of cell banking, and become the Founding Manager of CellBank Australia?
Children’s Medical Research Institute (CMRI) was awarded funding in 2005 to set up a new cell bank in Sydney, Australia. It was difficult to access good quality cell lines at that time because it cost about a thousand dollars to ship them on dry ice from a cell bank in the US or Europe. I was working at CMRI and put my hand up to set up the new facility. Four of us did the work together, based on publications and other resources from scientists overseas who knew the ins and outs of cell banking – I was privileged to meet many of these experts later on, when I started working on misidentified cell lines.
You have authored several papers surrounding the challenges of mis-identified cell lines? Could you explain a bit about this field?
Every cell line can be traced back to a particular sample of tissue or body fluids. A misidentified cell line is one that no longer corresponds to the original sample. Misidentified cell lines became famous in the 1960s when a geneticist (Stanley Gartler) discovered that the panel of cell lines he ordered in for his work were all HeLa. This probably happened due to cross-contamination. HeLa grows quickly and recovers well at low numbers, so if you accidentally introduce a few HeLa cells into a different dish or plate, it takes over very quickly. The same is true for any other fast-growing cell line – which many common cell lines are. It’s why they are so popular.
How widespread is this problem, and what is the impact to data, publications, institutions, and company’s bottom lines?
Colleagues from the DSMZ in Germany have been compiling data on the incidence of misidentified cell lines and mycoplasma contamination (another bane of the cell culturist’s existence). They found that the risk of getting a misidentified cell line from a secondary source – that’s anyone except for the original lab or a cell bank – is one in six. The impact depends on how much you use the cell line before you test it and what its actual identity is. But overall, a misidentified cell line leads to wasted time and effort that can easily be avoided through authentication testing.
Cell line authentication services are widely available as off-the-shelf kits, and there are plenty of contract research organisations offering authentication assays. Are all assays created equally though?
Authentication testing has to be genotype-based, so you cannot use methods that are based on expression of tissue-specific markers or changes in appearance. Cells can change phenotype in culture, so those things can be misleading. Short tandem repeat (STR) and Single nucleotide polymorphism (SNP) loci are mostly used for authentication and can be very effective, provided you use sufficient loci to avoid random similarity. A core set of STR loci should be used for human cell lines, which was agreed as part of a Standard published by ANSI in 2012. That consensus is important because labs need to compare their results to pick up problems – a cell line may have become mixed up in another laboratory, so you would need to compare to their cell lines in order to pick up the problem.
If you were a researcher looking to qualify the genotype of their cell line, what would you consider?
STR genotyping is the recommended technique at present. Testing is mostly outsourced, but once you have a result, there are publicly available search engines that you can use to check for matches to other commonly used cell lines. People have been using STR loci for cell line authentication for about 20 years, so we have a large body of data for comparison (although never enough considering the vast number of cell lines out there).
SNP genotyping is increasingly used by large labs or facilities that do next-generation sequencing, since you can incorporate it into sequencing workflows. Unfortunately, we don’t have a consensus for what SNP loci should be used for comparison between laboratories. So it’s mostly used for in-house testing once you have done STR profiling and satisfied yourself that the material that originally entered your lab is authentic.
Tell me your story about how you came to Chair of the International Committee for Cell Line Authentication (ICLAC)?
I mentioned that there was a Standard published in 2012 on how to authenticate human cell lines using STR profiling. That effort brought together scientists from different organisations with expertise in authentication testing, and we wanted to continue working together in some way. Many of the original members are still involved along with other colleagues who heard about what we were doing later and offered to help. I put my hand up to chair the group initially, and so far, no-one has kicked me out!
Could you introduce ICLAC and its mission statement?
ICLAC’s primary aim is to make the research community more aware of the problem of misidentified cell lines and the need to perform authentication testing. We keep a register of known misidentified cell lines, based on publications and other data that come our way. The ICLAC Register is incorporated into other resources, particularly Cellosaurus (a fantastic cell line knowledge resource), where we have a close collaboration. We also try to help if people contact us with questions about authentication testing or results that are hard to interpret – most results are pretty straightforward, but some cell lines like to keep us on our toes!
Given the challenges you have outlined here, do you feel that the bioscience community is doing everything it should rectify the problem?
I have seen improvements over the last 15 years, but we have a long way to go before the problem is rectified. I suspect many scientists feel that misidentified cell lines aren’t likely to happen to them, because they are careful. But the way I see it, anyone can have a problem – even if you are normally very careful, you can still make mistakes now and again. So testing is essential for everyone who works with cell lines.
If not, why? What additional steps should we be doing as an industry?
According to the data I have seen, the majority of labs still don’t test their cell lines. Many of us involved in authentication testing feel that it needs to be mandatory – a lab should provide testing data as a condition of funding or publication. But that means journals and funders must agree to it. Alternatively, we need new test methods that can be integrated with experimental work so that cells are assessed as part of genomic analysis.
For those conscientious researchers out there, what advice would you give to them to give them greater assurance that they can trust their data?
ICLAC has some resources online for how to incorporate quality steps into everyday cell culture practice. Before you start work with a new cell line, look it up on Cellosaurus to find out more information and check that it is not known to be problematic. Obtain the cell line from a reliable source – preferably a repository or core facility that tests its cell lines – and use that initial sample to prepare a “cell bank” to freeze in liquid nitrogen. Test your cell bank for authenticity and other quality concerns such as mycoplasma. It takes time to go through that process, but once it’s done, you will have good quality material that you can keep coming back to in future. And if you are establishing cell lines yourself, always prepare DNA from the original sample that you can come back to as a reference for testing later on.
Alongside being a CellBank Australia Honorary Scientist, Chairing ICLAC, you have also established your own consultancy business for technical writing and education, Lint Free Logic. Could you tell us what inspired you to set up your own company, and how are you finding it?
At the time I set up Lint Free Logic, I needed to find a career that would give me flexible working hours. I have been working in this area for about 10 years and have written all kinds of content – most recently in a textbook, Freshney’s Culture of Animal Cells, that will be published next year. I love to write and teach, and hope to continue doing so, provided I keep getting enough work to pay the bills!
We are living in a particularly interesting time. Alongside a global pandemic, climate change and political unrest, scientific advancements are accelerating at a rate of knots, with the omics revolutions, gene editing and the application of artificial intelligence and machine learning to name but a few areas. What is your vision of the future? How do you think science will look in 20 years’ time?
Specialised cell culture techniques are becoming accessible to any lab that wishes to use them. To give you an example, people talk about 3D culture as “new” but it’s actually quite old – scientists were doing 3D culture in the early 1950s, and “organ culture” was pioneered even earlier in the 1920s. But it was done in only a few labs that specialised in those techniques. Procedures are becoming more standardised and streamlined, and suppliers are offering products that make the work faster and easier. I hope that in 20 years’ time labs will be using those specialised techniques for personalised therapy – growing cells from a patient and using them to make a diagnosis and select the best treatments. We are already seeing the field moving in that direction. But whatever happens, I think cell lines will still have a place in research labs.
What do you think will be the future of cell biology research? And are there any lessons of the past that we should be implementing now to ensure that the foundations of these new research areas are strong? And who should be implementing them?
The risk in making specialised techniques more accessible is that we don’t always have a good grasp of the basic concepts. People come to cell culture without understanding its limitations and quality concerns. The lesson that I would love to bring from the past is the need for cell culture training – we should be giving everyone who starts cell culture a foundation in how to do it well, teaching them the “why” as well as the “how”. I believe it should be formally taught as part of postgraduate study as well as in labs that do cell culture.
You have had such a varied and impactful career to date, what aspects have you enjoyed most, and what are you most proud of?
I really enjoyed working on a cell culture textbook – it is an opportunity to work out the basic principles that apply to everyday techniques, and I found some wonderful stories along the way. I am also very proud of the work that I and my colleagues have done to investigate dubious cell lines. The best outcome is when we find authentic material that allows an old cell line to be used more effectively. An example of that kind of work is included in the links below.
Finally, you clearly like to keep yourself very busy with work; however, how do you like to relax at the end of a busy day?
I enjoy making beaded jewellery and am learning how to draw (I am a fan of Zentangle, which involves drawing patterns and is very soothing after a busy day at work). And I am a mad reader – I read the outside of the cereal boxes if I don’t have a book to read at breakfast.
Many thanks Amanda for an engaging interview, and for the following useful links for our readers to access:
Links for further reading
“Authentication of M14 melanoma cell line proves misidentification of MDA-MB-435 breast cancer cell line” (detective story investigating two cell lines, published in the journal International Journal of Cancer)