What is your professional and academic background that has led to you becoming a Team Leader at PhoreMost?
My scientific background is in cancer biology and biochemistry, with a Bachelor’s degree and Masters from the University of Cambridge. During my Masters, I completed a research project in Professor Gerard Evan’s Lab at the Department of Biochemistry, characterising a novel Myc driven metastatic hepatocellular carcinoma mouse model. I then completed my PhD at the Cancer Research UK Cambridge Institute under the supervision of Professor Shankar Balasubramanian, where I explored genetic interactions, setting up pooled shRNA screening to explore genetic dependencies on small molecules that bind G-quadruplexes, a secondary structure upregulated in cancers and other aging related diseases.
My PhD introduced me to the world of functional genomics and next generation sequencing, although my knowledge was mainly based on genetic perturbation approaches such as CRISPR and RNAi, and it was here that I learned of PhoreMost. Although PhoreMost’s work was technically similar to the research I was conducting, it had massively different conceptual applications. I was excited about the technology and translatable therapeutic application and so joined the Target Discovery team at PhoreMost in 2018.
In Target Discovery, we apply our proprietary PROTEINi lentiviral libraries to different therapeutic models to identify new druggable binding sites. My role is a diverse one, encompassing line management and project management, covering both internal programmes and collaborations with pharma partners. I like the variability my role provides – every day is different, and additionally allows me to interact with all members of the Target Discovery team. I am constantly amazed and in awe of the creativity and passion of Target Discovery members, and am a firm believer that people and culture are the key to success.
What significant milestones have your team achieved so far, and what do you see as your next important developments?
One of our most significant milestone relates to the library evolution of the SITESEEKER platform. When I joined PhoreMost, our libraries elucidated a lower hit validation rate, as expected with any new technology. Over the past few years, we have optimised our libraries to improve hit rates and data quality to develop our current library: the Hyper Diversity (HyperDiv) Library. I am excited to see future iterations and the success it will undoubtably provide.
Additionally, we have reached significant milestones in many of our Target Discovery alliances. Partners come to us with difficult questions and searching for targets, and as a team we translate that into something screenable. I have been very proud of the approach my team has taken to tackle these challenges to support our partners’ drug discovery programmes.
Our next milestones will see further developments in the refining and optimisation of our PROTEINi libraries and expansion of our Target Discovery alliances, as well as continuing to deploy the SITESEEKER platform for the rational discovery of molecular glues.
You recently attended CRISPR and Beyond: Perturbations at Scale to Understand Genomics (Cambridge, 22-24 Apr), can you tell us more about the event?
This year’s CRISPR and Beyond meeting highlighted recent advances in genetic screening enabled by emerging technologies and models including computational approaches and designing DNA for function, with discussions focused on recent developments in precision genome editing.
I have attended this conference several times over the last few years, and I enjoy going for two reasons: firstly, because PhoreMost’s SITESEEKER technology uses pooled screening, although using PROTEINi rather than CRISPR, and it is interesting to learn how other researchers are conducting their screening projects, and explore how our PROTEINi technology could be applicable. Secondly, is to understand how we can improve our target ID tools, using genetic perturbation, among other techniques. For this, it is fascinating to see how the perturbation field has developed in a relatively small timeframe.
As part of the conference, myself and a colleague presented a poster titled ‘SITESEEKER and CRISPR: Multiplexed perturbation tools to advance novel drug target discovery’. Here we explain how perturbation and SITESEEKER approaches go hand-in-hand as uniquely complementary methods for Target Discovery, the former highlighting the genes and pathways involved, and the latter identifying the exact target binding site and most important biochemical properties.
To advance this approach, we have recently developed combinatorial tools to massively streamline the workflow. ComboPROTEINi® uses a paired expression of the DNA-encoded PROTEINi® sequence and sgRNA element in a combinatorial pool of thousands of multiplexed guides and mini-protein sequences. This enables large scale validation of PROTEINi® phenotypes and functional genomic identification of the cognate target within the same pooled screen format.
What were your key learnings from the conference, and how do these relate PhoreMost’s work in Target Discovery?
Many of the discussions at the conference were highly relevant to the work we do at PhoreMost, but a few of the most exciting topics included:
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Development of innovative CRISPR design and analysis tools – There have been several bioinformatic advancements in the analysis of pooled CRISPR screens, which, as the tools become publicly available, I am excited to incorporate into our analysis pipeline. In addition, novel tools are available for screen design. One practical example referred to genome-wide CRISPR screening, an approach we sometimes use in-house to identify the mechanism of action for our bioactive mini-proteins. In practical terms, this can be labour intensive and low-throughput to explore > 20,000 genes. Therefore we often explore a specific subset of genes to make the CRISPR experiment smaller, in turn biasing our Target ID approach. One talk focussed on treating pathways as nodes, therefore hypothesising that genome-wide information can be achieved by hitting 200 key genes. This is really exciting and I’m keen to see how this research progresses further.
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Advancements in Target “prioritisation tools” – This included an updated version of The Cancer Dependency Map (DepMap), an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines, and the initiation of DepSHOCK , whereby both CRISPR and RNAseq data for cancer cell lines are being combined to provide a more holistic understanding of the drivers and dependency behind these diseases. As part of this, a second-generation cancer dependency maps reveals 370 priority oncology drug targets, a useful reference and benchmark for our own drug discovery programmes.
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Multiplexed screening methods – Recently, many pooled CRISPR screens incorporate secondary readouts, such as PerturbSeq, where single cell RNAseq is combined with genetic perturbation screens to couple the transcriptional profile to the perturbation and PERISCOPE, image based pool screening, enhancing phenotype/genotype linkage.
These innovative developments are all food for thought as we think about the next generation of SITESEEKER, and I look forward to seeing how we can incorporate new technologies into our platform to support us in unlocking the next generation of medicines.
