Benefits of cell panel and functional genomic screens in drug discovery

Choosing the right cell-based screen from the plethora of options available can quickly become a complicated decision process. Here, we review two of the major options: cell panel and functional genomic screening.

Cell panel screening provides drug response data across panels of genomically diverse cell lines from different tissue types. These screens can provide evidence of drug resistance and sensitivity, aid selection of efficacious drugs for treatment of a specific disease, stratify patients for clinical trials, re-purpose drugs with clinically acceptable profiles and provide data to inform mechanism of action (MoA) studies. Functional Genomic Screening (FGS), where RNAi or CRISPR is used to modify gene expression, can also address many similar questions to cell panel screens, but from a genetic point of view. In addition, FGS can be used to find and validate novel drug targets, identify the genetic basis of drug resistance or sensitivity, and identify genetic dependencies (often referred to as synthetic lethality).

Which screen do I need?

Simply put, it’s a numbers game (Figure 1). If, for example, your aim is to examine cellular responses to 100s of therapeutic agents, then cell panel screening is a good place to start. Whereas if you’re interested in finding 10s to 100s of genetic targets that influence the response to a handful of drugs, then FGS is the best choice.

You can use cell panel screens to analyse the sensitivity of characterized cell lines to a therapeutic candidate. In addition, you can find therapeutic targets and obtain MoA data by seeing whether your potential therapeutic of interest has similar response profiles to agents with well-defined MoA. But, if your new drug of interest has a novel function or is a novel biologic, then this route is unlikely to be that informative, owing to a dearth of similarly acting agents. If the agent's MoA is not fully understood or an assay isn’t possible in arrayed format, then this is where FGS comes into its own, as it can be used to identify genetic targets for most novel therapeutic agents.

Similarly, FGS can be employed to identify gene interactions and biological pathways that are necessary for a potential therapeutic synergy or to help elucidate the MoA. Modification of gene expression, whether through RNAi, CRISPR knockout, or the parallel approaches of CRISPR activation (CRISPRa) and CRISPR inhibition (CRISPRi) result in critical biologic information as to what specific gene interactions are occurring to drive therapeutic efficacy and biological activity. Further, owing to biological differences between knocking out or modifying gene expression and subsequent protein product, FGS can reveal the requirements of clinical synergies that are critical to understanding potential treatment outcomes and targeting proper patient populations. Often, investigators who run cell panel screens are also interested in analyzing a wide range of therapeutics that could be synergistic with their new drug or biologic of interest. Indeed, synergistic drug interactions identified in cell panel screens have translated to the clinic.

Cell Panel Screens vs Functional Genomic Screens 

Figure 1. Similarities and differences between FGS and cell panel screening

And what if I need to find new targets?

CRISPR screens are now widely used to understand the MoA of a new drug or to identify resistance or sensitivity mechanisms, which can also be a means to identify potential new drug combinations. However, one of the real strengths of a CRISPR screen is in finding new drug targets. CRISPR knockout (CRISPRko) screens were adopted early on to help with this process in cancer research, but CRISPRi and CRISPRa are now also being embraced. CRISPRi reduces but does not ablate gene expression, whereas CRISPRa increases gene expression. When used in combination — CRISPRko combined with CRISPRi, or CRISPRi combined with CRISPRa — these screens produce robust data sets that validate the targets identified in each individual screen and can reduce both time and money when searching for new drug targets.

Working in tandem

So, should cell panel screens and FGS be used only in isolation? No, because these two approaches can be powerful when used in tandem. For example, cell panel screens are the basis of phenotypic drug screens, where the impact of the drugs is measured through changes in a specific cell phenotype, confirming whether the drug kills a cell. Often, in these types of cell panel screens, the drug target and MoA are not known, and this is where FGS can rapidly assist for the reasons discussed above.

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