Investigating the mechanisms through which colorectal cancer liver metastases impede the local and systemic anti-tumour response
Primary Supervisor: Professor David Withers
Second supervisors: Dr Eileen Parkes, Professor Tim Elliott
Project Overview
Metastatic disease remains the fundamental challenge for treating cancer patients. Liver metastases present a particular issue for treatment, mediating both local and systemic suppression of anti-tumour immunity in the face of clinically approved immunotherapies. How this is mediated remains incompletely understood and multiple mechanisms featuring an array of cell types have been proposed. This project is focused on better understanding the suppressive mechanisms that develop within colorectal cancer (CRC) liver metastases with the aim of pinpointing the pathways to target to improve the anti-tumour response. The research will utilise cutting-edge in vivo models alongside cross-comparisons with patient samples to enable detailed mechanistic insight while probing patient relevance. We aim to unpick how and why the anti-tumour CD8 T cell response is impeded, leveraging an array of genetically-engineered mouse models (GEMMs) to better understand immune cell function and behaviour.
To study the composition of CRC liver metastases, implantation of mouse tumour-derived organoids (e.g. ‘AKPT’) into the colon will be used, supporting natural metastasis to the liver. Here, analysis using scRNA-seq combined with TCR-seq will enable unbiased assessment of immune composition (contrasting the primary tumour and liver metastases) as well as tracking of T cell clonality across both sites. Flow cytometry and immunofluorescence analyses (e.g. CellDIVE) will then be used to validate transcriptomic expression and interrogate cellular interactions predicted through extensive bioinformatics analyses. Additional models of liver metastases (intrasplenic injection or direct injection into the liver) will be utilised in the different GEMMs to test mechanisms, alongside blocking or depleting antibodies to establish cause and effect. Photolabeling of liver tumours, now established in the lab will be employed to capture temporal changes within developing liver metastases.
Collectively this research will provide new insight into why anti-tumour immunity is impeded in CRC liver metastases and clarify potential therapeutic targets.
Training Opportunities
This project will provide extensive further training in bioinformatics, largely focused on an array of scRNA-seq analyses additionally incorporating TCR-sequencing, supported by post-doctoral researchers within Withers Lab, the Centre for Immuno-Oncology and external collaborators. Key initial scRNA-seq experiments are scheduled for summer 2025 and will be performed before the start of this project. Training in the quantitation of spatial analyses (multiplex immunofluorescence) will also be developed to support transcriptomic characterisations and enumerate cellular interactions, utilising local collaborations and the growing spatial analysis platforms in Oxford. To complement the bioinformatics training, the project will also look to develop core cancer immunology expertise. This will include protein and cell level analyses (e.g. flow cytometry, ex vivo functional assays). Training will also be provided in the development and use of in vivo cancer models, including cell line and organoid culture, mouse handling, cell injection, monitoring tumour growth, tissue isolation and cell preps.
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