Investigating and defining ‘new biology’ and therapeutic targets in lung cancer via CRISPR-driven functional genomic screening

Each year in the UK ~47,000 people are diagnosed with lung cancer (2018 CRUK). In a large proportion of these patient tumours there is significant loss of expression of the tumour suppressor gene LIMD1. We can conservatively predict that at least 20,000 lung cancer patents each year will be deficient for LIMD1 expression. Unfortunately, there is of yet no specific targeted therapies for LIMD1-deficient cancers. To address this, we have performed a CRISPR-driven functional screen to identify novel targets/biology to treat these cancer sub-types. This PhD studentship will help us identify, validate and understand the most important targets in this exciting and first of its kind study.

To date there are no targeted therapies for LIMD1 deficient lung cancer. We have performed a comparative screen of an isogenic pair of lung adenocarcinoma cell lines which has identified differences in critical genes and pathways required for LIMD1 negative cancers to survive. This approach therefore has revealed potential new druggable targets relevant to LIMD1 negative lung cancers. The project will involve validation of these and determine the biology/mechanism of action.

Aims:
1. Validation screen. We will target the top 5% of depleted hits from CRISPR screen (up to a maximum of 94 hits) using a Dharmacon ‘Cherry pick’ siRNA screen. This will be performed in an additional panel of LIMD1+/+ and LIMD1-/- cell lines, including primary lung small airway epithelial control cells that have been extensively characterised and utilised in our group.
2. Secondary validation and In vivo validation. Top 5-10 hits from this screen will be taken forward to in vivo tumorgenicity biology
3. Analysis of gene expression. Concurrently to our in vitro and in vivo validation, we will utilise online portals with access to TCGA data, such as cbioportal, to identify any correlation between LIMD1 expression and gene expression of our identified hits. These will be cross compared with RNA-seq data we have already generated, in our isogenic lines used in the screen. And finally validated in IHC of human LIMD1 negative lung tissue, which we have access to through a recently awarded project application between Barts Cancer Institute and Barts health-NHS trust.
4. Characterising the mechanism of action for hit(s) will be a key goal of this work and studentship in the medium and long term. We will utilise our extensive experience in cellular and molecular biology to do so.

This is an exceptional opportunity for the successful candidate to learn cutting edge CRISPR-editing biology and functional screening from world leading researchers at the new CRUK-AstraZeneca Functional Genomic Centre based at Cambridge University. The training there will be second to none in this area of biology and preclinical research. This will be combined with further training in all aspects of in vitro and in vivo cancer cell and molecular biology at the CRUK- Barts Cancer Institute, a CRUK Centre of Excellence. Additional training in bioinformatics, IT, manuscript writing and presentation skills are also integral to this studentship and training program at CRUK – Barts Centre.