How To Select Cancer Cell Lines For Your Experiments?

Before choosing cancer cell lines for your experiments, it’s essential to evaluate a few critical factors. Selecting the right cell line impacts the reliability and relevance of your results. Here are five key questions to consider to ensure that your chosen cancer cell line is credible, contamination-free, biologically appropriate, genetically stable, and suitable for your specific experimental requirements.

Here is a list of a few questions that you must ask before selecting cancer cell lines for your experiments:

1. Is it a credible cell line?

It is of utmost importance that you ask the question of whether a certain line is what it is claimed. You would be shocked to know that there are over 500 cell lines that have been masked and misidentified in the Register of Misidentified Cell Lines (v13 April, 2024). You sure can obtain cell lines from third-party cell banks like Kosheeka and NCCS. Even when you obtain these cell lines it is best to have them annually assessed using STR profiling.

If you start an experiment with a commercial cell line like BCC1/KMC, it could be you are actually not working with them. The only real way for you to make sure that you actually pick up cell lines that you need is to always go for a certificate of authentication and do STR profiling. STR profiling might be a long process, but doing it is necessary to ensure that you have an authentic biological model that works as it is intended.

2. Is it free of contamination?

Yes, even if you get an authentic line, it is necessary to ensure you have contaminant free cell lines. A simple bacterial infection can put added stress on these cell lines that will make their biology change. Now, if you get an infection that alters the biology, your experiments will change. That's because the microorganisms are so small and don't look like other bacteria (they don't have a solid wall, instead they have a plasma-like shape).

Reliable cell providers will provide cell stocks confirmed to be mycoplasma-free. When the contamination status of a cell stock is uncertain, it is advisable to cultivate it in a quarantine setting and confirm its "clean" status before transferring it to public circulation. This approach minimizes the chance of mycoplasma contaminating a whole cell culture laboratory.

3. What is the passage number of cells?

For in vitro cultures you will notice that their is genetic instability, and cancer cell lines start to accumulate these genetical errors. Even a recent study from Domcke et al., found "pronounced differences in molecular profiles between commonly used ovarian cancer cell lines.This is likely attributable to the age and resultant prolonged culture of particular lines, resulting in their divergence from the original malignancies.

To mitigate this, it is advisable to sustain cell stocks at the lowest passage feasible and to routinely (every 2-3 months) start cell culture with a new vial. Temporal alterations in cell lines may, in some instances, be visibly discernible; for instance, prolonged culture of U87 cells might result in a diminished monolayer and the formation of spheroids from the flask surface.

4. Does it show the right biology?

Your choice of cell line will almost definitely be determined by the question or problem you're attempting to address. If you're studying a certain disease condition, the closer the cell line resembles that sickness, the better.

Even across illness kinds, careful selection is essential. For example, if you're studying breast cancer, you might be interested in only triple negative breast cancer, or you might want to look at a variety of subtypes. Your research objectives will guide your choices.

If you are studying a disease, the Cancer Cell Line Encyclopaedia (CCLE) is a fantastic resource for identifying a cell line that expresses a specific biomarker or has a specific genetic abnormality. The CCLE offers public access to genomic data, analysis, and visualization for about 1000 cell lines, allowing you to not only choose an appropriate cell line but also place any results you generate within the context of the CCLE's enormous data set. 

If your focus is on basic biology rather than disease biology, you will frequently come across a model line from which a body of work has been created. By taking this same approach, discoveries can be placed in the context of existing scientific knowledge.

This method of selection, however, produces a self-perpetuating bias toward published cell lines, which may not have been chosen because they are the best suitable. Unsurprisingly, the age of a cell line can influence how frequently it appears in the literature, as with the first immortalized cell line, HeLa cells, which have been widely employed (their simplicity of cultivation no doubt contributing to their popularity).

The best method is to identify numerous cell lines and show results over a panel. This not only increases confidence in the results, but it also eliminates the idea that they are simply a quirk of a specific line.

5. Is it suitable for your experiment?

The selection of a cell line for any experiment necessitates a balance between identifying the most physiologically relevant model and opting for a cell line that is manageable for experimentation.

Cultural conditions, growth rate, transfectability, morphology, subcellular structure (for microscopy), and cost significantly influence the studies conducted and their probable success.

Induced pluripotent stem cells (iPSCs) may provide a more "normal" model compared to cancer cell lines; however, the demanding cell culture protocols and related expenses may render these lines unsuitable for certain laboratories.

The objective is to identify the optimal compromise—a cell line that has comparable biological characteristics, facilitates rigorous and efficient scientific inquiry, and withstands validation in external laboratories.

Detailed culture conditions and growth rates are provided by Kosheeka for numerous widely used cell lines.