Edinburgh Cancer Research

Understanding the chromosome 11 CRC risk locus genes and the role they play in intestinal homeostasis

Dr S Farrington, Dr Seth Coffelt, Dr Farhat Din, Dr Vidya Rajasekaran-Sutherland

Susan Farrington Research Image

About the Project

The 11q23 locus, was identified by GWAS as a CRC risk locus (Tenesa*, Farrington* et al, 2008). The three genes within the locus – C11orf53, COLCA1 and COLCA2 – have also been shown to be eQTLs (expression quantitative trait loci) for regional SNPs in human colonic normal epithelium (Vaughan-Shaw et al, 2021).

The function of these genes and their possible role in CRC remains enigmatic although recent publications, have highlighted a role in tuft cell dynamics and interactions with POU2F3, designated a master regulator of tuft cells (Harris et al, 2022; Wu et al, 2022; Szczepanski et al, 2022). To address the role of the CRC risk loci genes at 11q23, we used CRISPR gene editing in mouse blastocysts to delete a large region encompassing all 3 genes, revealing an intestinal phenotype comprising altered mucus production, along with disordered DCLK1 and CLCA1 markers of Tuft and goblet cells respectively. Analysis of transcriptional dynamics of these models has indicated co-registration with analysis of human transcriptional data, both from in-house RNAseq data and publicly available scRNAseq studies (Harris et al, 2022). We have demonstrated altered intestinal homeostasis in these models and several specific phenotypes, including reduced survival, increased tumour progression and alteration of the enigmatic tuft cell, linking immune regulation and defense response.

This project will investigate these candidate CRC risk genes, to determine and understand their cellular role and how they are involved in cancer risk and progression, in particular the impact of these genes on transcriptional profile of intestinal cells using in-house and scRNAseq datasets available and the impact of this dysregulation on intestinal cell markers and tumourigenesis using in-house models to explore the possible mechanisms on CRC initiation and progression, including any microbiome alteration in these models.

We aim to explore and further interrogate the intestinal and immune related phenotypes in our in vivo and ex vivo model, facilitating the understanding of specific gene function and utilise the knowledge to explore CRC development/progression and survival, with concurrent translation back to our human clinical samples leading to improvement of prevention, screening, and CRC therapy.

The newly established links with POU2F3 also afford the opportunity to explore its role with the genes of interest and establish any co-dependency in intestinal tumourigenesis by isolating tuft cells and co-culturing with epithelial organoids (Glasgow lab), or indeed other cancer organoids where this locus is implicated (pancreatic and ovarian). Interrogation of datasets for co-registration of POU2F3 and our genes of interest and subsequent biochemical investigation will further understanding of these tuft cell markers in CRC.

Hence, they will receive expert training in phenotyping, genomic data generation and analysis (imaging, proteomics, transcriptomics, and their analysis, including the use of R and other bioinformatics approaches) and biochemical/phenotypical analyses. The model systems include mouse/organoid culture and are already generated/established (although novel co-culturing approaches will be explored), providing invaluable data including demonstrating altered intestinal homeostasis and links with a specific immune related intestinal cell type and the project will develop from these exciting observations and translate back into the clinical domain.

Application procedure

Up to 4 studentships are available to start in September 2023 for outstanding applicants with a stipend of £21,000 p/a. These 4 STUDENTSHIPS are funded by the CRUK Scotland Centre, a joint initiative between Edinburgh and Glasgow. Successful students for Edinburgh lead projects will be registered for their degree in Edinburgh and will undertake their project in Edinburgh. 

Candidates should hold at least an upper second-class degree in a relevant subject and comply with University of Edinburgh English language requirements.

For further information on how to apply, please visit: https://www.ed.ac.uk/cancer-centre/graduate-research-and-training/cancer-research-uk-phd-programme

Susan Farrington Research Group 

Farhat Din Research Group