Immunogenomics of oesophageal cancer to improve early detection

Oesophageal adenocarcinoma (OAC) is a deadly disease whose incidence has increased substantially in recent years. OAC is preceded by a pre-cancer condition named Barrett’s oesophagus (BO). However, not all BOs will transform into OAC and the transition from BO to OAC remains hard to predict.

This PhD project aims to study the transformational events triggering BO-OAC transition at the genomic, transcriptomic and microenvironmental levels. The student will be part of a team within a broad network of oesophageal cancer experts with access to one of the largest collections of BOs and OACs worldwide. This will allow comparison of genomic and transcriptomic alterations across hundreds of BO-OAC pairs. In parallel, the student will analyse high dimensional tissue images of the same samples to characterise the BO-OAC immune microenvironment at single cell resolution. Immunogenomic data will be eventually integrated and the knowledge gained from this study will underpin risk stratification biomarkers to be tested in future clinical trials.

The student will be based in the Ciccarelli lab at the Francis Crick Institute where they will gain expertise in computational genomics, systems biology and cancer immunology. They will also receive training in epidemiology through the second supervisor, Prof Peter Sasieni, a leading expert in cancer epidemiology. The student will have access to a vast range of cutting-edge computational facilities as well as training opportunities at King's and Crick.

Start date: February 2023

Open to Home students only (UK and EU pre settled status)

Representative publications:

·    Bortolomeazzi et al. A SIMPLI Single-cell Identification from MultiPlexed Images) approach for spatially resolved tissue phenotyping at single-cell resolution. Nature Comms (accepted; https://doi.org/10.1101/2021.04.01.437886)

·    Nulsen et al Pan-cancer detection of driver genes at the single-patient resolution (2021) Genome Medicine (https://doi.org/10.1186/s13073-021-00830-0)

·    Mourikis, T, et al Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma (2019) Nature Comms (https://doi.org/10.1038/s41467-019-10898-3)

Websites:

https://www.crick.ac.uk/research/labs/francesca-ciccarelli

https://www.kcl.ac.uk/people/peter-sasieni

https://www.crick.ac.uk/

Please visit the studentship webpage for details on how to apply.

Please note, you do not need to submit a project when applying for this post on the KCL website.