Centre for Inflammation Research

February 2021 - Gut Research Unit (GRU)

We are interested in understanding how the normal human gut works and the processes that lead to diseases such as Crohn’s and Ulcerative colitis.

Our vision and network

We are a ‘MELTING POT’ of researchers - immunologists, chemists, biologists, clinical trialists, clinicians and data scientists - with a shared vision to translate science to medicine.

We work closely with the Edinburgh IBD Science network, including clinical colleagues at the Western General Hospital and scientists at the Institute for Genetics and Cancer and Roslin Institute. We collaborate across Scotland with the Universities of Glasgow, Dundee and Napier.

Follow Edinburgh IBD Science on Twitter


A list of researchers in GRU and their research themes. Equivalent text is provided under 'Our Key Research'


Our key research

Our highly collaborative and integrated scientific work has a strong focus on direct studies on human gut and immune cells kindly provided by our research participants; and new complementary experimental models such as organoids (‘miniguts on a dish’).

Current research projects

GI-DAMPs – We are investigating how molecules released from the damaged gut lining (DAMPs) can trigger and maintain inflammation in IBD. We are finding ways to block these signals as potential new treatments in IBD (Gwo-tzer Ho).

IBD-IMAGE – We are designing new biomarker tests that can provide results instantly in the clinic, by emitting a fluorescent signal if certain signs of inflammation are present in IBD (Marc Vendrell). 

Monocyte-macrophage function in IBD - We are investigating how the macrophage population in gut can either worsen inflammation or begin the process of healing in Crohn’s disease. Macrophages are a type of immune cell. We are using a technique called single-cell RNA sequencing to study how these macrophage populations change when Crohn’s disease is diagnosed, initially treated and ultimately healed over time. This will allow us to identify new drug targets or cell-based treatments in Crohn’s disease. (Calum Bain, Gareth Jones and Thomas Fenton).

Anti-microbial peptide, LL-37 and T-cell function - We are investigating how a natural anti-microbial peptide LL-37 produced by our gut directs the migration of inflammatory T-cells to the gut lining in Crohn’s disease (Emily Findlay).

Prostaglandin E2 and its receptor EP4 in Crohn’s disease - We are investigating how the production of prostaglandins can change how the immune cells function in Crohn’s disease. Prostaglandins are molecules that can both protect the gut lining and bring about inflammation. Of interest, PTGER4 gene that encodes the EP4 receptor is one of the strongest genetic factors in Crohn’s disease (Chengcan Yao).

How the apthous ulcer forms in Crohn’s disease - We are using a new microsurgery technique in human gut to study a special immune cells, located within the lymphoid follicles in Crohn’s disease. As inflammation usually starts as ulcers over these lymphoid follicles, this allows us to understand how inflammation begins in Crohn’s disease and potentially find ways to stop this from happening (Thomas Fenton).

Targeting the neutrophils in IBD - We are finding new ways to reduce the damaging potential of the neutrophils (the ‘first responders’ of inflammation) in order to accelerate the healing process of the gut in IBD (Adriano Rossi and Gwo-tzer Ho).

Mitochondria and IBD – Mitochondria produce energy in the cell. They are also important in the health of our gut barrier function and can determine whether immune cells behave in a pro- or anti-inflammatory manner. Several lines of research are ongoing (Gwo-tzer Ho).

Gut microbiome and mucosal healing in IBD – Working with collaborators in Roslin Institute (Mick Watson) and Universities of Glasgow and Dundee (Konstantinos Gerasimidis and Craig Mowat), we are developing a new area of research to understand how the gut microbiome contributes to the healing of the gut lining in IBD.

Clinical trials

In the GRU, we have successfully taken basic science discoveries  made in 2014-2018 to Phase 2b human clinical trials in IBD (2021-2024) in line with our 'Science-to-Medicine' vision.

MARVEL - In the MARVEL Phase 2b clinical trial, we investigate if MitoQ (mitochondrial-targeted anti-oxidant) helps in treating patients with ulcerative colitis (UC). The MiniMARVEL trial looks at use of the same treatment in children with UC. Together, they form the first ‘all-ages’ IBD clinical trial, recruiting adults and children simultaneously. These multi-centre studies are set to open across UK in 2021.

Find out more on the MARVEL website

MUSIC -  In the MUSIC IBD Study, we are investigating how DAMPs or ‘danger signals’ can be used as a biomarker test for patients with Crohn's disease or Ulcerative colitis. This prospective longitudinal cohort study will study all established biomarkers in IBD patients, as well as experimental markers. Samples will be donated when the patients are diagnosed and when they receive medical treatments. Uniquely, we will study the usefulness of this scientific information in relation to how the gut lining heals in IBD. The MUSIC IBD Study is set to open in Edinburgh, Glasgow and Dundee in 2021.

Find out more on the MUSIC website


Pathology images of the gut wall


Who we work with

Our funders and research partners help to make our research possible, supporting staff and students at the cutting edge of gut repair science and medicine.


Crohn's and Colitis UK (CCUK) are the UK's leading charity for Crohn's and Colitis, funding research and providing information for patients, friends and family, medical practitioners and employers about these conditions.

European Research Council (ERC)  encourages the highest quality research in Europe through competitive funding and to support investigator-driven frontier research across all fields, on the basis of scientific excellence.

Helmsley Charitable Trust aspires to improve lives by supporting exceptional efforts around the world in health and select place-based initiatives. 

Guts UK is the only UK charity funding research into the digestive system from top to tail; the gut, liver and pancreas.

The Jon Moulton Charity Trust seeks to fund non-commercial clinical trials with the aim to make clinical advances and promote the relief of suffering.

Medical Research Council (MRC) seeks to encourage and support research to improve human health, produce skilled researchers, advance and disseminate knowledge and technology to improve the quality of life and economic competitiveness of the UK, and promote dialogue with the public about medical research.

Wellcome supports science to solve the urgent health challenges facing everyone.

The Edinburgh IBD Unit

The Edinburgh IBD Unit is based at the Western General Hospital, comprising Professor Charlie Lees, Shahida Din MD (Gastroenterologist), Ian Arnott MD (Gastroenterologist) and Audrey Kuchnowski (Lead Clinical Research Nurse). 

Involving patients and the public

Communicating with our patients and members of the public is a key part of our research process. We work closely with patient-centred charities and have an active Patient and Public Involvement (PPI) group led by Kris McGuire and Jon Rysdale.

The following animation, developed in collaboration with Edinburgh-based science animation company Cloud Chamber Studios, describes our work and how you can get involved.

Video: Healing the damaged gut
The Gut Research Unit at the Centre for Inflammation Research, University of Edinburgh, shares some of its work on healing the damaged gut in inflammatory bowel diseases (IBD) such as Crohn's disease and ulcerative colitis. Narrated by Dr Kris McGuire, a patient representative with the group.


CCUK's Patient Involvement Day in October 2020 was run virtually for the first time. Postdoctoral researcher Milly McAllister presented a virtual poster about her work on IBD biomarkers - specifically short protein strands produced by mitochondria, called 'mitochondrial formylated peptides' - which can be seen below.

Video: PPI Day 2020 Virtual Poster
Milly McAllister's virtual poster at the Crohn's and Colitis UK (CCUK) Patient Involvement Day 2020.


Our IRR Discovery Series video describes Thomas Fenton's work on isolated lymphoid follicles and how he discovered the micro-surgery technique used in the lab today.

Video: IRR Discovery Series: Dr Thomas Fenton
Dr Thomas Fenton, Visiting Scientist at the Centre for Inflammation Research, discusses a method he has developed which will give researchers a new way to analyse the intestinal immune system.


Our Let's Talk About Health lecture, delivered by Principal Investigator Gwo-tzer Ho, PhD student Emily Thompson and IBD patient Kris McGuire, talks about current work, what it's like to be in the lab day to day, and the importance of clinical trials from a patient perspective.

Video: Healing the damaged gut in inflammatory bowel diseases
A recording of the Let's Talk About Health public lecture given on 19 February 2020, talking about the perspectives of a medical researcher, IBD patient and PhD student on current IBD research at the Centre for Inflammation Research.


If you would like to get involved with our patient and public involvement groups as someone who lives with or alongside Crohn's and colitis, or is simply interested in research and clinical trials, do get in touch.

Contact CIR's Public Engagement & Communications Officer


Scottish Gut Seminar Series

Join our highly interactive online seminar with international and national experts dicussing the latest advances in science. Organised by Emily Findlay, Calum Bain and Gwo-tzer Ho. Runs from 1-2pm.

24 January 2021 - Professor Neil Mabbott (Roslin Institute).

9 February 2021 - Dr Kendle Maslowski (University of Birmingham)

9 March 2021 - Professor Balfour Sartor (University of North Carolina)

TBC May 2021 - Professor Alison Simmons (University of Oxford)

Updates and seminar details are posted via the @Edin_IBDScience Twitter feed.


News section

Herald article March 2021 - New genetic clues to Crohn's disease unravelled in Edinburgh hotspot

Herald article March 2021 - Crohn's disease ordeal for Edinburgh student who 'thought it was food poisoning'



We are currently recruiting students via the Medical Sciences and Translational Research with Engagement for Impact programme.

Rapid Next-Generation Metagenomic Sequencing of circulating blood DNA to identify pathogenic triggering factors in Crohn’s disease


We are also recruiting PhD students via the Precision Medicine programme. Application deadlines were on 7 January 2021.

Stratifying Intestinal Epithelial Cell Responses in Inflammmatory Bowel Disease Patients - Professor Kevin Maloy, Dr Gwo-tzer Ho 

The Oral-Gut Microbiome Axis in Crohn’s disease and Ulcerative Colitis - Dr Gwo-tzer Ho, Professor Mick Watson, Dr David Wilson 


Key publications

Resolution of Inflammation and Gut Repair in IBD: Translational Steps Towards Complete Mucosal Healing - G-T. Ho et al., Inflammatory Bowel Diseases 2020 - https://doi.org/10.1093/ibd/izaa045

Barrier-tissue macrophages: functional adaptation to environmental challenges - A.M. Mowat et al., Nature Medicine 2017 - https://doi.org/10.1038/nm.4430

Prostaglandin E2 constrains systemic inflammation through an innate lymphoid cell–IL-22 axis - R. Duffin et al., Science 2016 - https://doi.org/10.1126/science.aad9903

Biomarkers in Search of Precision Medicine in IBD - R. Boyapati et al., The American Journal of Gastroenterology 2016 - https://doi.org/10.1038/ajg.2016.441  


Want to help?

If you're passionate about healing the damaged gut, you can support our research by making a philanthropic donation. 

Get in touch with the Fundraise Your Way team