Accelerating Science: How to cure the incurable with cell and gene therapy

Editorial Article: Explore the role of CRISPR gene editing in target validation

Learn how researchers are using innovative gene editing techniques to uncover new drug targets

27 Nov 2023

Panos Zalmas
Dr. Panos Zalmas, Head of the Open Targets Validation Lab, Wellcome Sanger Institute

Target validation is a crucial step in pre-clinical drug discovery workflows that builds confidence on the identification of a genetic target as relevant to a disease. With recent advancements, CRISPR serves as a particularly powerful tool for this process, as it enables researchers to accurately modify genes and determine their function in a variety of experimental systems. 

One scientist leveraging CRISPR gene editing in this way is Dr. Panos Zalmas, Head of the Open Targets Validation Lab based at the Wellcome Sanger Institute, whose work focuses on discovering and validating new putative disease targets for the development of safe and effective medicines.

In this SelectScience® interview, we speak with Zalmas to learn how he is working to improve the rate of target adoption into drug discovery pipelines across therapy areas such as oncology, neurodegeneration, and immunology and inflammation. Here, Zalmas explains the importance of gene editing in his target validation workflows and highlights how CRISPR technologies in particular are key to the success of drug discovery.

Identifying drug targets at the Open Targets Validation Lab

Target validation is a crucial step in the lab’s drug target discovery process, as it generates an independent source of experimental evidence that builds on the probability that a gene discovered through a target ID effort, is relevant to the disease phenotype of interest.

Although a combination of approaches, including RNAi techniques and the use of drug modalities, can be employed to confirm target functions, these can be limited by their transient and incomplete responses in cells. Alternatively, gene editing technologies, such as CRISPR, that confer a permanent edit to the genome can increase phenotypic penetrance and extend the resolution and assay window, facilitating the characterization of important gene functions.

“We think of target validation as the sum of multiple lines of evidence,” explains Zalmas. “CRISPR technologies are invaluable in this setting, in particular due to their offer of orthogonality, which increases our confidence in the impact of target perturbation to disease biology.”

The team performs gene editing target validation experiments at scale, across many disease models and phenotypes. This high-throughput, systematic approach accelerates the interrogation of multiple targets in context to other targets, enables assessment of reproducibility and specificity, and delivers both validation and invalidation success rates to inform future efforts.

Beyond interrogating target performance, Zalmas and his colleagues have leveraged this gene editing technology to modify cell models in order to recapitulate human disease-relevant phenotypes, as well as incorporating reporter and sensor constructs to detect signals that are otherwise difficult to capture with current technologies. This enables the creation of more disease-accurate and enabling experimental systems which, combined with precise CRISPR screening, has the power to identify 'the right targets in the right context'. “Our approach enables us to comprehensively assess the ‘target-cell-phenotype’ connection and develop effective therapeutic hypotheses,” shares Zalmas.

Accelerating the development of drugs with CRISPR technology

There is excitement in the field for the continued advancement of genetic modulation technologies in terms of both their specificity and efficiency, as well as their compatibility with large-scale experimentation. Zalmas is particularly interested to see not only technological improvements and expansion of these modalities, but also improvements in their effective delivery to diverse tissues and cell states, with matched progress in the development of robust assays that measure gene function. These advances are expected to enhance the precision and power of functional genomics workflows, thereby increasing confidence in the function of genes and their products.

“The ability to edit multiple gene targets simultaneously is becoming increasingly achievable at scale,” says Zalmas. “As many genes function within larger biological networks, co-modulating multiple targets is key to exploring gene pathway function and better understanding their biological relevance in disease. In addition, the integration of CRISPR gene editing with single-cell technologies and high-content phenotyping is significantly advancing our understanding of gene function in the global cellular context.”

Other CRISPR modalities, such as CRISPRi and CRISPRa, provide important capabilities, enabling, for example, the investigation of bi-directional gene dosage effects and often better recapitulate target engagement by drugs. These approaches are expected to yield valuable insights into targets that were previously difficult to investigate. Technologies that enable site-specific modifications, such as base and prime editing, further the ability to understand gene function at the amino acid and nucleotide level and enable the investigation of non-coding genomic regions, chromatin regulatory elements, and RNA. This improves our ability to model and broadly understand human genetic variation.

Zalmas strongly encourages researchers to use gene editing in their drug discovery process, as the plethora of current and emerging technologies are extremely transformative. “Choosing the right tool is essential to harness the true potential of these technologies,” states Zalmas. “My advice is to always start with a specific hypothesis in mind, even if the experiment is exploratory. Spend some time understanding the strengths and limitations of each technology, considering their compatibility with the model system that is appropriate for each study. As with all experiments, the use of multiple negative and positive controls that define the potential of each experimental system is essential in correctly interpreting the outcomes of gene editing. Lastly, particular attention should be given to gene editing technologies that induce a double-strand break. This is a really impactful event for a cell and often leads to unwanted responses that are not immediately obvious or easily detected and hide real phenotypes”.

  

Looking for expert support to improve your gene editing workflow?

With a comprehensive portfolio of predesigned and custom CRISPR sgRNAs, Cas9 proteins, donor DNA kits, and easy-to-use software - such as the Invitrogen™ TrueDesign™ Genome Editor – Thermo Fisher Scientific is well positioned to support researchers with every step in the genome editing workflow. Discover how Thermo Fisher Scientific is helping to enable CRISPR gene editing research, explore the below expert interviews:

  • Dr. Yu Holly Chen, assistant professor at the University of Alabama at Birmingham, and Dr. Rinki Ratnapriya, assistant professor at the Baylor College of Medicine, explore the development of sequencing-based genome-wide methods to advance our knowledge of age-related macular degeneration disease mechanisms. 
  • Dr. Krishanu Saha, associate professor of biomedical engineering at the University of Wisconsin-Madison, highlights the potential of CRISPR to improve CAR T-cell efficacy for solid tumor treatment. 
  • Dr. Sergio Casas-Tintó, head of the Drosophila Models of Human Disease Unit at the Institute for Rare Diseases Research of ISCIII, shares how combining CRISPR gene editing with alternative animal models is uncovering the genes responsible for rare and ultra-rare diseases.