Custom cell lines: Factors to consider before you begin

The cost of working with suboptimal custom cell lines

More than $17 billion is wasted annually in the preclinical phase of pharmaceutical research on ineffective biological reagents, including cell line models ¹. This cost is due to failed experiments, having to purchase alternative reagents, pursuing false biomarkers and mistaken target identification due to inaccurate data and poorly validated models.

Working with a less-than-optimal cell line model may provide incomplete or inaccurate data, increasing the downstream risk to your project.

Removing this issue by ensuring that your custom cell line is fit-for-purpose and expertly designed and validated could help to accelerate your pipeline, improving research efficiency and helping to transition projects to the trials phase faster and more accurately. Consulting with custom cell line development experts prior to beginning your project can make sure the custom cell line you receive contains the right gene edits to progress your research.

Researching to rapid project timelines

While unnecessary reagent expenditure is important, the greatest unaccounted cost to life science research is the human capital expenditure. This includes the time spent researching, designing, executing, and analyzing experiments ².

The average researcher spends five months generating the gene-edited cell lines they need, and most repeat their experiments 3-4 times before they are successful ³.

To avoid unnecessary delays in your research, outsourcing reagent development to experts in custom cell line development can speed your timelines and help to get you to market faster. If you require a custom cell line, it is important to make sure that the custom cell line provider can work to your project timelines to prevent projects from being stalled and allowing you to hit your milestones.

A precise gene-edit in the right cell background

Your project will define the specific gene edit you need. A range of edits can be achieved with a number of different expression systems to help meet different project goals. These include:

• Knock-ins which may be either adding tags/reporter molecules to your gene of interest, such as fluorescence or luciferase, or the use of dual reporter systems combining both strategies.
• Knock-outs where one or multiple endogenous genes are removed.
• Gene activation where endogenous gene expression is activated or up-regulated.
• Gene repression where endogenous gene expression is repressed or down-regulated.
• Expression of exogenous genes, including in inducible systems.

While common cell line backgrounds, such as HEK293 and HeLa, are easier to transfect and so most often used for custom cell line development, cells such as primary cells, iPSCs, and immune and hematopoietic cell lineages, can be more difficult to work with. However, selecting the right cell background for your edit can make the difference between advancing your project or adding to  avoidable experimental expenditure.

For example, if you're interested in exploring axonal regeneration targets, then using a gene-edited cell line of non-neuronal origin may not help to answer your questions. It is crucial to know your target and understand what wild-type cell background would suit you best ⁴. Discussing this with your custom cell line service provider could help to navigate any downstream stumbling blocks in your plans.

Validated gene edits for reliable data outputs

Once a custom cell line has been established, adequate validation of the specific gene edits is essential to make sure your custom cell line is edited correctly and that the data you generate with that cell line is reliable and can be easily interpreted.

Multiple methods exist to validate gene-edited cell lines, from Sanger sequencing and exon gene sequencing to confirm your required edits at the genomic level, to western blotting for proteomic confirmation of your custom cell line edits.

If your custom cell line project requires more extensive downstream analysis or you want to use a tailored service, working with gene-editing experts that can support additional assays, such as gene copy number analysis, functional assays, and biomarker identification, can provide a complete data package to fast-track your research.

Downstream protection for your work

To keep your research on track and offer the broadest range of potential cell edits, your custom cell line development partner must operate under the correct licenses, with Broad Institute and Sigma-Aldrich CRISPR Use Licenses available. Regulatory approval can be simplified if your CRISPR-edited cell line is provided with FDA and IND compliant documentation.

Ensuring the security of supply for your custom cell line, with the option to store your edited cell line with the supplier, can help to mitigate potential downstream problems should anything happen to your cell stocks in your lab.

We have a depth of experience delivering the most challenging custom cell line edits across a range of cell types, offer tailored assay services and end-to-end consultation on all projects. Our robust processes and platform ensure rapid delivery, with standard custom cell line projects achieved in just 8-12 weeks.

For any further information please get in touch.

References

1. Freedman, L. P. et al. The Economics of Reproducibility in Preclinical Research. PLOS Biology 13(6) (2015).
2. BenchSci. Avoidable Experimental Expenditure. (2020)
3. Synthego CRISPR Benchmark Report: A look at what’s happening at the benchtop (2019)
4. SelectScience. Know your target: How to achieve research success with knockout models. (2020)