Under the microscope: Leveraging CRISPR libraries for target discovery

How can CRISPR libraries be utilised in screening studies?

Arrayed CRISPR libraries are mostly used for functional genomics work, to identify new targets or to find targets that would, for example, stop the proliferation of cancer cells or ameliorate a disease phenotype in a neuronal disease model. Then, you can either design a CRISPR drug to target the particular gene that you have identified or you could investigate traditional small molecules to achieve the same goal. With pooled CRISPR libraries, a biological system is exposed to the pool of the entire genome. The cells that then show a particular phenotype of interest are fished out and sequenced to reveal which guide RNA targeted those cells. After this, targets can be identified.

What is the main benefit of using those CRISPR libraries?

The main benefit is clear when CRISPR libraries are compared to the more traditional siRNA approach for functional genomics. With CRISPR, genes are knocked out permanently, but siRNA is focused on functionality – or blocking functionality for 24 to 48 hours. After this, the siRNA will start degrading, whereas with CRISPR, you can look at the assay and biological effects longer term. A lot of customers that we work with utilise both approaches at the same time for drug discovery and target identification to compare results, as both permanent and temporary gene disruption have value.

What kind of CRISPR libraries does Thermo Fisher offer and what kind of features that are included with them?

We have two main CRISPR libraries. One is our LentiArray CRISPR library, which is an arrayed library where every well has an individual gene target with at least four different guide RNAs targeting each gene. For these, we have a whole genome library available to purchase, or sub-categories; for example, we have the ion channels collection, druggable genome collection and many others. We have about 17 smaller sub‑libraries available, to address the different areas of biology and drug discovery. We also have our LentiPool CRISPR library, which is a pooled library. For this, we either have a whole genome library or custom libraries available for whatever the customer requires.

What is the downstream value of leveraging these libraries for target identification?

The above CRISPR libraries have different approaches, but the value of both is that as a permanent knock-out, there is a solid manipulation of the gene. The outcome of this is that it is less likely to result in off‑target effects. From a downstream point of view, the secondary assay and follow-up is therefore easier.

How does Thermo Fisher support its clients who are using these CRISPR libraries?

At the basic level, we provide pre-made libraries that the customer can purchase and support for that library. We also provide support when making custom libraries by working with the customer to design their libraries of custom arrays. We can also run services with these libraries on behalf of the customer. If the customer does not have the resources, equipment or know‑how to run pooled or arrayed screens, then we have the capability to run it as a service within Thermo Fisher. Often, we end up providing our internal expertise when communicating with customers that purchase our libraries. Our approach is very collaborative, especially when it comes to service. Depending on what the customer requires, we can either provide a certain level of support or collaborate the whole way through a project.

Erik Willems, PhD

Erik is Senior Manager, Cell Biology R&D at Thermo Fisher Scientific. He was trained as a stem cell biologist in Brussels, Belgium where he obtained his PhD in 2007. He then developed expertise in the use of pluripotent stem cells in high-throughput screening assays for understanding the basic biology and disease of the developing heart at the Sanford Burnham Prebys Medical Discovery Institute in San Diego, California. Pursuing his passion for the development and application of biotechnology tools, Erik currently leads a team focused on customer driven projects and product applications at Thermo Fisher Scientific in Carlsbad, California. Ongoing projects involve the generation of cell models (cell engineering, reprogramming and stem cell differentiation) and tool production (genome editing and virus tools) as well as their implementation in drug discovery applications (assay development and screening) and cell therapy.