Identifying a Wnt pathway inhibitor for stem cell maintenance in IBD

Lead Research Organisation: University of Nottingham
Department Name: School of Medicine

Abstract

Inflammatory bowel disease (IBD) represents a major healthcare burden which affects approximately 5 million people worldwide. Ulcerative colitis (UC) is one of the main forms of IBD which affects the colon (large bowel). The colon becomes inflamed with ulcers on the inner lining of the bowel which leads to acute and severe abdominal pain, persistent diarrhoea, nausea, fatigue, and fever. In severe cases an urgent operation may be necessary. This is a chronic (long lasting) condition but when the treatment is effective there will be periods when a patient will be symptom free. Unfortunately, less than half of UC patients do not show response to current therapies. Additionally, UC patients exposed to chronic inflammation have a 1 in 3 lifetime risk of colorectal cancer. So, there is an urgent need of more successful treatments to improve patient's quality of life and outcome.

In IBD patients the inflamed intestinal tissue fails to repair because chronic inflammation reduces the intestinal stem cell population which is responsible for tissue reparation. My lab has found a protein responsible to modulate the number of cells that are responsible to replace damage cells during chronic inflammation. In our project, we aim to discover novel effective approaches for treating IBD patients by inactivating this protein. First, we will study its mechanism of action and second, we will test blocking antibodies (i.e. inactivation of this protein). This will let us know if we can improve tissue regeneration and in consequence, decrease inflammation. We will use UC human samples from patients and healthy volunteers that will be cultured in an in vitro innovative 3D organoid model that will help us to understand the mechanism driving the disease forward and how to improve tissue repair. Our findings will be translated into improved treatments and will help improve IBD patient's health.

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Technical Summary

Inflammatory bowel disease (IBD) represents a major healthcare burden which affects approximately 5 million people worldwide. Ulcerative colitis (UC) is one of the main forms of IBD which affect the colon and rectum. UC involves several aberrations as defects in epithelial barrier function, overactivated host defence pathways, atypical immune regulation, and failing tissue repair. Unfortunately, less than half of UC patients do not show response to current therapies (e.g. anti-TNF agents). Additionally, UC patients exposed to chronic inflammation and in consequence to active tissue regeneration have a 1 in 3 lifetime risk of colorectal cancer. So, there is an urgent need of more successful treatments.

In IBD the inflamed intestinal tissue fails to repair because chronic inflammation reduces the intestinal stem cell population which is responsible for tissue reparation. Intestinal stem cells modulated by Wnt pathway are capable of self-renew as well as produce more specialized progenies to replace damaged cells. We have found that a novel Wnt inhibitor which is upregulated in intestinal inflammation, decreases stem cell activity and in consequence impairs tissue regeneration. These findings were confirmed by using mouse models and murine 3D-organoids.

In this project, we aim to discover new mechanisms to re-activate stem cells by blocking this protein function. We will study its mechanism of action; we will find the unknown receptor and we will test blocking antibodies. Our findings will characterize the mechanism of inhibition in attenuating the inflammatory response by using an innovative human UC enteroid model derived from patient's samples and healthy volunteers. Despite ongoing efforts in mouse models, clinical paradigms in IBD are still imprecise and human 3D organoids will help to understand basic mechanisms driving the disease forward and test treatment's efficiency. In conclusion, we aim to discover a novel therapeutic approach for UC patients.

Publications

10 25 50
 
Description Academy Industry Engagement Award
Amount £19,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2023 
End 05/2024
 
Description EPSRC-iCASE studentship
Amount £75,000 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2021 
End 09/2025
 
Description MRC-iCASE studentship
Amount £75,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 10/2026
 
Description UNICAS
Amount £5,000 (GBP)
Organisation University of Nottingham 
Sector Academic/University
Country United Kingdom
Start 02/2024 
End 08/2024
 
Title 3D IBD patient-derived organoids 
Description In vitro model to culture IBD patient-derived organoids 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2023 
Provided To Others? No  
Impact To gain into mechanisms of IBD 
 
Title Hydrogel to culture 3D organoids 
Description We have substituted Matrigel as it is low reproducible in culture with Hydrogel to culture 3D organoids 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? No  
Impact It is closed to publication as a method to culture organoids. We have applied to a NC3R grant, as helps to reduce animal experimentation. Also applied to pre-clinical research. 
 
Title 3D patient-derived organoids biobank (IBD and CRC) 
Description We have collected around 50 biopsies from the QMC Nottingham Hospital from colorectal cancer and inflammation bowel disease patients. We isolated crypts and established the 3D organoids. This is now our biobank that is used for our research. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? No  
Impact This will be published and available in the future to other researchers interested on the topic. An MTA would need to be signed beforehand. 
 
Title IBD plexus analysis to generate our own dataset 
Description IBD plexus was granted access to my team. It comprises more than 1,400 IBD patient's data (RNAseq and proteomics from tissue, blood, stool and plasma). We have analysed the data and by using bioinformatics performed a comprehensive study. We are preparing a manuscript. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? No  
Impact It will be published in a peer-reviewed journal. The impact is clear as this huge amount of data has been analysed to show how prediction can be done to help improve current treatments and outcomes. 
URL https://www.crohnscolitisfoundation.org/research/plexus
 
Title Machine learning used in RNAseq gene signature 
Description In collaboration with J. Biasetti from AZ we have used machine learning to identify how IBD patients respond to treatment. 
Type Of Material Computer model/algorithm 
Year Produced 2024 
Provided To Others? No  
Impact It will be available upon publication and machine learning methodology applied to medicine is a tool that we want to spread to other researchers to advance in this type of research. 
 
Title Mathematical model in collaboration with AstraZeneca 
Description We have collaborated with AZ to create a model to predict IBD drug response of patients by using patient-derived organoids. We have at the same time done a regression model to recreate stem cells dynamics compared to inflammation score. 
Type Of Material Computer model/algorithm 
Year Produced 2023 
Provided To Others? No  
Impact It will be available upon publication and will help to understand IBD mechanisms. 
 
Title RNAseq of patient-derived organoids 
Description We have generated a dataset by RNAseq analyses from patient-derived organoids of IBD samples and healthy individuals. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? No  
Impact This dataset will be available to other researchers upon publication. It will help to understand the mechanism behind IBD and we hope improve patient's outcome. 
 
Description 3D patient-derived organoids biobank 
Organisation Swiss Federal Institute of Technology in Lausanne (EPFL)
Country Switzerland 
Sector Public 
PI Contribution We have new experimental data using intestinal patient-derived organoids
Collaborator Contribution The biobank collected in the last years.
Impact No impact yet.
Start Year 2023
 
Description AstraZeneca - UoN 
Organisation AstraZeneca
Country United Kingdom 
Sector Private 
PI Contribution Our collaborative project combines clinical support (QMC Nottingham Hospital), 3D patient-derived intestinal organoids (PDOs) (SoM, UoN) models and mathematical approaches (AZ). Our team will identify gene signatures and key pathways in IBD which will be validated using PDOs. We will also study the response of PDOs to common IBD medications that will enable us to translate the effects of drugs on PDOs into predictions of treatment response, safety and efficacy in patients. The collaboration brings together expertise in clinical settings, organoid technology, genomics, and mathematical modelling to advance our understanding of IBD.
Collaborator Contribution Using a systems biology approach in collaboration with the mathematical group of Dr Pin and Dr Gall (Systems Medicine, AstraZeneca UK), we are working to identify the signalling pathways in the stem cell niche that govern cellular remodelling in IBD. The project aids in the development of fully mechanistic mathematical model of IBD (expanding on existing mathematical models of the intestinal epithelium).
Impact We have been awarded 20K - MRC Industry Academy Engagement Award
Start Year 2023
 
Description AstraZeneca Monolayers and toxins 
Organisation AstraZeneca
Country United Kingdom 
Sector Private 
PI Contribution We have optimized a monolayer enteroid technology to test toxins and drugs. We have set up in vivo imaging by microscopy.
Collaborator Contribution The partners have contributed with materials as the toxins and drugs.
Impact contribution of 6K
Start Year 2024
 
Description IBD plexus US charity Crohnscolitisfoundation.org 
Organisation Crohn's & Colitis Foundation
Country United States 
Sector Charity/Non Profit 
PI Contribution We have analysed data from IBD plexus https://www.crohnscolitisfoundation.org/research/plexus/what-is-ibd-plexus
Collaborator Contribution They have collected data from IBD patients, RNAseq, proteomics and clinical data
Impact No impact yet.
Start Year 2023
 
Description International outreach activity- Malaysia 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I participated in outreach activities in Malaysia in two universities. The attendance was about 50 general public and I communicated the activities done in my laboratory and team.
Year(s) Of Engagement Activity 2024
 
Description Open days School of Medicine- UoN 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Undergraduate students
Results and Impact During the open days at the University of Nottingham, I had the opportunity to present the work of my lab to undergraduates and families that were interested in the Cancer Sciences degree.
Year(s) Of Engagement Activity 2023