Single-cell CRISPR Screens Enabling Drug Discovery

Posted on 22nd June 2023

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Providing data that serves as a reliable starting point for drug discovery, Myllia Biotechnology leverages CRISPR screening in combination with single-cell sequencing to identify novel drug targets and increase understanding of the unknown mechanisms and actions of drugs. As a result of its accomplishments, the company has been awarded Most Innovative BioTech Company in the GHP Global Excellence Awards 2023. Here, we dive deeper into the fascinating work the company does.

Combining CRISPR screening with single-cell sequencing, Myllia Biotechnology uses two transformative technologies to facilitate genetic screening for complex phenotypes. Using the CRISPR workflow, the company maps the impact of genetic perturbations on the global transcriptome at single-cell resolution. Through this, it effectively establishes a paradigm for the next generation of CRISPR screens.

Myllia is a technology company that utilises a cutting-edge discovery engine. At the centre of its approach is the genome-scissor, CRISPR/Cas9, which can knock-out and activate genes. CRISPR has lots of potential to be used in cell and gene therapies, however Myllia focuses on using it to perturb cells. It does not merely perturb one cell at a time, instead it performs experiments in which many, if not all, of the genes are perturbed. This enables the company to identify cause-effect relationships between the genetic perturbation and the recorded phenotype, which is fundamentally more powerful than the correlative relationships discovered when using an observational approach.

CRISPR screening has revolutionised the unbiased annotation of gene function. However, most screens so far have been confined to simplistic read-outs, usually life or death of the target cells. By combining CRISPR perturbation with single-cell sequencing, researchers can assess much more complex phenotypes, broadening the scope of CRISPR screens.

The CROP-seq (“CRISPR droplet sequencing”) technology measures the individual transcriptome responses to CRISPR perturbation. It serves as a synthesis of two widely popular screening paradigms, offering both the flexibility of arrayed CRISPR screens and the scale of pooled CRISPR screens. The CROP-seq involves infecting cells with a library of lentiviral guide RNA (gRNA) in a pooled fashion, ensuring high throughput, then encapsulating them individually in liquid droplets with barcoded beads. Within the droplet, RNA isolation and reverse transcription occur, warranting compartmentalisation. As gRNA identities are also read, each single-cell transcriptome is linked to one gRNA.

Myllia’s approach has a range of applications. For example, its unique technology supports the identification of the critical genes and pathways that drive certain disease states or impact the disease phenotype. This is useful because, for a successful drug screen, it is critical that the disease model used is suitable, meaning the model must be functionally validated to assess whether its drivers and endpoints appropriately reflect the disease.

As well as this, Myllia’s technology is useful for learning about the unknown mechanisms of the actions of drugs. An important aspect of drug discovery and development is understanding how drugs act in the complex environment of a cell. Using single-cell CRISPR screening, more can be understood about the transcriptomic changes associated with drug action, as well as which genes affect the drug profile. This provides unique insights into drug mechanisms and actions and uncovers genes that modify drug responses, paving the way for combination therapy.

Furthermore, with Phenotypic Drug Discovery (PDD) receiving increased attention due to its uses in identifying drugs without prior knowledge of the specific drug target’s identity based on cellular read-outs, Myllia has developed a unique CROP-seq screening platform which can help decipher the molecular targets of drug candidates. This platform will allow PDD projects to progress to the next level.

Myllia uses its CROP-seq technology, developed by Co-Founder Christoph Bock, to perturb cells with CRISPR and profile transcriptional outcomes by RNA sequencing at single-cell resolution. Importantly, the company’s technology is applicable across a wide range of cell types, including primary cells.

Primary human T cells are currently of great interest in the scientific community in relation to the discovery of novel targets in immuno-oncology and cancer immunotherapy. To facilitate this discovery, Myllia has built a workflow that allows for functional genomic screens in CD4+ T cells from peripheral blood. Upon activation, naïve CD4+ cells proliferate and differentiate into specific T helper cell subsets like Th1, Th2, or Th17.

For the last two years, Myllia has worked to expand its platform into this therapeutic area. As a result, it is able to use primary human T cells for functional genomic screens. The T cells are extracted from healthy donors or patients, then Cas9 is introduced alongside a guide RNA library targeting multiple genes. The T cells are then activated in media conditions that bias the cells towards certain T cell subsets. The lineage commitment and activation state of the T cells are read out using single-cell RNA sequencing. Using CRISPR/Cas9 perturbation, Myllia is able to assess the impact of single gene perturbations on the specific T cell phenotype. Finally, the use of CRISPR screens in T cells could help optimise CAR-T cell potency by identifying novel T cell-intrinsic factors involved in activation, exhaustion, and survival mechanisms.

In the future, Myllia has two major goals. Currently, screens are limited in terms of the scale at which they are applied. As a result, CROP-seq screens have been considered a valuable tool for target validation, where a limited set of candidate genes are perturbed. Beyond this, Myllia wants to extend this offering and carry out CROP-seq screens at genome-scale, perturbing all 20,000 human genes at once. This will enable the company to provide comprehensive and unbiased analysis and position CROP-seq as a tool for drug target discovery.

Secondly, Myllia plans to extend its screening platform beyond primary human T cells to other immune cell types such as macrophages, natural killer cells, B lymphocytes, and many more. This will allow users to address questions that extend far beyond the immunology of T lymphocytes, therefore covering innate and adaptive immunity.

As a result of its ground-breaking work in relation to CRISPR screening and drug discovery, Myllia Biotechnology has been awarded Most Innovative BioTech Company, Austria, in the GHP Global Excellence Awards 2023. We congratulate the company on this admirable achievement. With big plans for the future, there is no doubt that Myllia will continue to innovate and succeed in its fundamental industry.

For business enquiries, contact Tilmann Burckstummer from Myllia Biotechnology on their website – www.myllia.com