WIME: WNT-mediated immune evasion in intestinal homeostasis, regeneration and cancer
Lead Research Organisation:
The Francis Crick Institute
Department Name: Research
Abstract
WNT signalling plays a critical role in normal in WNT signalling plays a critical role in normal intestinal homeostasis, regeneration and tumorigenesis. WNT is required for intestinal stem cell maintenance and injury-induced regeneration, while aberrant WNT activation causes cancer. Specifically, APC-truncating mutation are detected in ~80% of colorectal cancer (CRC), leading to hyperactivation of WNT signalling. Despite decades of research, targeting WNT signalling remains challenging due to on-target toxicity in stem cell compartments. Targeting WNT in CRC remains an unmet need. Immune checkpoint inhibition (ICI) shows remarkable responses in solid cancers such as melanoma. However, the majority of CRC patients with high WNT signature do not respond to current ICI strategies. Genomic analysis of the clinical data shows that the "T cell-inflamed" phenotype and WNT-low signature are the two strongest predictors of ICI response in multiple cancer types, suggesting a link between the two. Understanding the underlying biological processes appears fundamental to the development of immunotherapies and will benefit a large proportion of patients with WNT-activated tumour.
Our preliminary data show that WNT activation causes cytotoxic T cell (CTL) exclusion not only in CRC, but also in normal WNT-high intestinal crypts and in WNT-dependent irradiation-induced regeneration, suggesting that the role of WNT signalling in subverting immune responses is a physiological mechanism, highjacked by cancers. We propose a unique approach to study the mechanisms underlying WNT activation and the associated immunosuppression in normal intestine, regeneration and cancer. These insights will guide the development of tumour-specific therapies to sensitise ICI response in WNT-activated CRCs and other cancers with minimal toxicity. Our extensive expertise in WNT signalling, intestinal stem cell, CRC and organoid research will place us in a unique position to study WNT-mediated immune evasion.
Our preliminary data show that WNT activation causes cytotoxic T cell (CTL) exclusion not only in CRC, but also in normal WNT-high intestinal crypts and in WNT-dependent irradiation-induced regeneration, suggesting that the role of WNT signalling in subverting immune responses is a physiological mechanism, highjacked by cancers. We propose a unique approach to study the mechanisms underlying WNT activation and the associated immunosuppression in normal intestine, regeneration and cancer. These insights will guide the development of tumour-specific therapies to sensitise ICI response in WNT-activated CRCs and other cancers with minimal toxicity. Our extensive expertise in WNT signalling, intestinal stem cell, CRC and organoid research will place us in a unique position to study WNT-mediated immune evasion.
People |
ORCID iD |
| Vivian Li (Principal Investigator) |
Publications
Gerli MFM
(2024)
Single-cell guided prenatal derivation of primary fetal epithelial organoids from human amniotic and tracheal fluids.
in Nature medicine
Meran L
(2023)
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds.
in Nature protocols
Novellasdemunt L
(2023)
USP7 inactivation suppresses APC-mutant intestinal hyperproliferation and tumor development.
in Stem cell reports
Vande Voorde J
(2023)
Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target.
in Nature metabolism
| Description | We have established a new CRISPR genome targeting technology using organoids which allows us to screen for potential targets involved in immunotherapy resistance in colorectal cancer. |
| Exploitation Route | This technology is potentially applicable to many other researchers working on organoids. |
| Sectors | Education Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | The outcome of this funding is to find new drug targets that can sensitise immunotherapy treatment in WNT-high colorectal cancer. We have generated CRISPR screening which has generated a number of interesting targets. This is still ongoing, but once validated, it may present a game changing drug for cancer patients who previously do not respond to immunotherapy treatment. |
| First Year Of Impact | 2025 |
| Sector | Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal Economic |
| Description | AstraZeneca/Crick Alliance Award |
| Amount | £200,814 (GBP) |
| Funding ID | PRJ_20943 |
| Organisation | AstraZeneca |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2025 |
| End | 12/2027 |
| Description | Establishing antigen removal in vivo CRISPR screens for novel tumour immunotherapy targets |
| Amount | £73,970 (GBP) |
| Funding ID | PRJ_20600 |
| Organisation | Francis Crick Institute |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 12/2024 |
| Title | Antigen removal in vivo CRISPR screens |
| Description | Our lab has developed a series of new mouse CRC model systems that resemble human CRC in many important ways and are a substantial improvement on current preclinical systems. We will use these exciting CRC models to map tumour-intrinsic immune evasion pathways, utilising a newly developed in vivo CRISPR approach. Importantly, this project will bring this exciting screening technology to the Crick. The screening method we will use has been invented and highly optimised by the Manguso Lab, who are a world leader in developing CRISPR technologies to identify new immunotherapy targets. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | This is still ongoing project. We will conduct a sub-genome screen in our AKPT CRC cell lines, using 10,000 sgRNAs. This will be the first time an in vivo CRISPR immune evasion screen will ever have been conducted with tumour cells that model human CRC in immunocompetent mice. The sub-genome screen will enable us to bring this exciting discovery platform to the Crick and establish the workflow at reasonable scale. |
| Title | CRISPR screen |
| Description | We have established whole genome and targeted CRISPR screening in CRC organoids in vitro as well as tumour development in vivo. This has generated valuable dataset to short list candidates that can sensitise immune checkpoint blockade. We can apply this technique to screen for other drug resistant targets such as for chemotherapy resistance. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | CRISPR targeting in organoids is challenging due to the 3D culture condition. We have optimised effective targeting in organoids, which can benefit anyone working on organoid research. |
| Title | Crispr/Cas9 |
| Description | Crispr/Cas9 is the state-of-the-art genome editing technique to mutate genomic DNA endogenously. We have incorporated this technique to our organoid culture that we can genetically modified intestinal epithelium in organoids and study the functional role in vitro. We can also use the Crispr system to knockout genes in cell lines, which offers a clean and effective way to study functional role in vitro as compare to the conventional siRNA/shRNA method. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2013 |
| Provided To Others? | Yes |
| Impact | Our Crispr/Cas9-coupled organoid screening represents a powerful tool to functionally shortlist our candidates by loss-of-function experiments. This can largely reduce the number of usage of animals, which support the 3R policy. |
| Title | Intestinal tissue engineering |
| Description | We engineered intestinal construct by co-culturing various cell types, including intesitnal epithelial organoids, fibroblasts, smooth muscle cells, endothelial cells and neural crest cells on the dellularised intestinal scaffold. We also optimised a simpler 3D model by co-culturing all cells in a collagen-based gel. |
| Type Of Material | Model of mechanisms or symptoms - human |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The idea is to reconstruct a structural and functional competent intestine using patient-derived tissues for autologous transplantation to treat intestinal failure patients. |
| Title | Organoid culture |
| Description | We have established the in vitro culture of intestinal organoids derived from both mouse and human. These organoids, also called "mini-guts", grow 3-dimensionally in matrigel in a defined condition to form intestinal crypt-villus budding structure encompassing all cellular lineages. |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2009 |
| Provided To Others? | Yes |
| Impact | This is a fantastic system to study functional role of the candidate genes/pathways in the intestine in vitro. We can also use the system for genetic modification, drug screening and tissue engineering etc. We are keen to promote our genome editing screening approach in organoids in vitro to perform high-throughput functional screening to minimise the use of animals. |
| Title | Transgenic mice |
| Description | We have a collection of mouse strains to study functional roles of candidate genes/pathway in vivo in the intestine. We are also generating new conditional knockout mice to analyse the effect of gene deletion in the gut on stem cell and cancer transformation. |
| Type Of Material | Model of mechanisms or symptoms - mammalian in vivo |
| Year Produced | 2013 |
| Provided To Others? | Yes |
| Impact | Animal studies are essential to provide relevant physiologically readout of genetic alterations and to confirm the functional data obtained in vitro work. |
| Description | Antigen removal in vivo CRISPR screening |
| Organisation | Broad Institute |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Robert Manguso from the Broad Institute has pioneered the antigen removal approach to perform in vivo CRISPR screen. This is particularly useful for our project to study anti-PD1 resistance in colorectal cancer. We contribute the experimental design, including syngeneic CRC models, immunotherapy treatment and tumour collection and analysis. |
| Collaborator Contribution | The Broad Institute and Robert Manguso's lab provide technical support for the antigen removal CRISPR screening library and technology. |
| Impact | My postdoc Colin has travelled to Robert Manguso's lab in 2023 for 2 months to learn the antigen removal CRISPR screening technology. |
| Start Year | 2023 |
| Description | Crick/AstraZeneca Alliance |
| Organisation | AstraZeneca |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We collaborate with AstraZeneca to explore the transcriptional changes of Wnt/beta-catenin pathway during colorectal cancer progression, with the aim to find new tumour-specific targets for drug development. We contribute our expertise in organoids, colorectal cancer, transcriptomics, CRISPR targeting and in vivo functional validation in mice. |
| Collaborator Contribution | AZ will contribute their expertise in proteomics and transcriptional analysis to this project. They fund a postdoc for 2 years. |
| Impact | Received a 2 year postdoc to work on this project. |
| Start Year | 2025 |
| Description | Intestinal tissue engineering |
| Organisation | University College London |
| Department | NIHR Biomedical Research Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have established the in vitro intestinal organoids culture system of both mouse and human in NIMR. We plan to make use of the organoid stem cell culture to repopulate the decellularised intestinal scaffold generated by my collaborator. We will have to optimise the whole culture and seeding protocol. We will first perform the experiment in mouse and rat, and will finally proceed to human tissues. |
| Collaborator Contribution | My collaborator works on the decellularisation protocol to obtain accellular intestinal scaffold obtained from human donor. They can also maintain the scaffold in the bioreactor and perform surgery to transplant the intestinal unit back to patients after the scaffold stem cell seeding. |
| Impact | The project has been recently started. We have successfully competed for a joint medical PhD student Laween Meran through the NIHR UCL BRCs / Francis Crick Institute Clinical Research Training Fellowships Scheme to work on this project. Laween has optimised the human decellularisation as well as human intestinal organoid culture protocol. Preliminary data suggests that organoid seeding in acellular scaffold allow intestinal epithelial cell propagation and differentiation. The collaboration is multi-disciplinary to combine basic stem cell research with the clinic. This is a translational regenerative medicine project aiming to improve health quality of intestinal failure patients. |
| Start Year | 2014 |