Results demonstrating an abnormality on a newly acquired cell line are often met with astonishment by our clients working in RUO. Too often we hear that if the line showed genomic stability at the beginning of the workflow, it was expected to stay stable for a while.
In our experience, it rarely does. Still, we regularly meet research scientists experiencing this issue and coming to us when their cells display unusual behavior such as differentiation issues or accelerated proliferation.
These are the precautionary steps you could put in place to avoid this situation:
1. Don’t rely on G-Banding karyotyping alone
In the situations we described above, more often than not, the cell line in question was only tested with G-Banding karyotyping. Although G-Banding karyotyping is a robust and exhaustive technique to check the cell’s genome, it does not present sufficient resolution to detect the most common abnormalities found in hPSCs. Dr. Said Assou and Prof. John de Vos have explained the importance of using more resolutive detection methods to exhaustively capture CNVs (Copy Number Variations) that constitute the main source of chromosomal abnormalities in hPSCs (Assou et al., 2020). Case in point: the 20q amplicon that accounts for 1⁄4 of recurrent abnormalities in hPSCs worldwide (Assou et al., 2020; Avery et al., 2013; Halliwell et al., 2020). It is not detected by G-Banding alone. This is what our client Kurt Jacobs, Research Scientist at DiNAQOR, experienced. According to Kurt, “The iCS-digital™ PSC covers a wide range of mutations in a simple test. It helps us strengthen our quality control at various stages of our workflow. For instance, it picked up the 20q amplicon that was present in some of our hiPSC lines.”
This is also what our client Sandra Segeletz, Head of innovation at denovoMATRIX experienced firsthand: “Before using the iCS-digital™ tests, we only had G-Banding karyotypes in place in our workflow for our pluripotent stem cell (PSC) and mesenchymal stem cell (MSC) quality control. However, genetic changes can be subtle and not always detected by karyotyping alone. Therefore digital PCR has the extra sensitivity we require for better detection. We use both now to deliver the peace of mind our clients need,” added Sandra.
We are not suggesting that you leave G-Banding out of your testing strategy completely. It will provide you with an exhaustive structural and numerical variant analysis.
However, if you want to achieve complete peace of mind when acquiring a new cell line and avoid putting effort into an abnormal cell line from the start, we recommend associating G-Banding with a more resolutive test, such as iCS-digital™ PSC (see our Duo iCS-Karyo solution that combines both tests).
2. Find a cost-effective genomic testing solution to enable regular in-process testing
Several research papers have documented the propensity of hPSCs to develop genomic abnormalities during their time in culture. Dr. Assou and his team found that a genetically normal hPSC line can acquire harmful CNVs in just five passages (Assou et al., 2020). This was also previously observed by other research scientists looking at PSCs (McIntire et al., 2020; Pamies et al., 2017).
In the case of a newly acquired line, you can therefore start off with a stable line and see abnormalities develop after the first 5 passages.
The recommended guidelines are to test regularly every 5 to 10 passages to decrease your chances of seeing abnormalities appear and overtake your cell culture with damaging consequences. This also applies to a newly acquired cell line.
In practice, this can be challenging for teams working in RUO, as they often don’t have the required budget for regular genomic controls or quality controls in general. The fact that their final product does not come in direct contact with the patient does not help in claiming more budget for it either.
However, solutions such as iCS-digital™ PSC are perfectly suited for the RUO environment. Sandra Segeletz, Head of innovation at denovoMATRIX, shares her experience: “I would recommend the iCS-digital™ tests to anyone looking for a good genomic assessment with minimal effort. They are an easy entry into quality control for anyone with a limited budget.”
Fast and cost effective, this digital PCR-based solution makes it possible to check more than 90% of the most common abnormalities found in hPSC in record-breaking time. Just send DNA or cell pellets to us and you get straightforward results within 2 to 3 days, and all at a fraction of the cost of a G-Banding karyotype…