Servizio Comunitario di Informazione in materia di Ricerca e Sviluppo - CORDIS

Periodic Report Summary 1 - FXR-IBD (Industry-Academia exchange to further FXR-based therapeutic intervention and non-invasive diagnosis in Inflammatory Bowel Disease)

See Attachment to Periodic Report Year 2 FXR-IBD for a more detailed summary.

Project objectives FXR-IBD
Inflammatory Bowel Disease (IBD) covers a group of disorders that are characterized by chronic intestinal inflammation. Complications can be severe and in rare cases, IBD might even lead to mortality. IBD affects approximately 0.2% of the human population with a higher prevalence in Europe. The main types of IBD are Crohn’s Disease (CD) and Ulcerative Colitis (UC). IBD appears to result from a deregulated mucosal immune system combined with a compromised intestinal epithelial barrier function in genetically predisposed individuals.
Current treatment options of patients with IBD are mainly aimed at suppressing the immune response, i.e. treatment of the symptoms rather than targeting the root cause of the affliction. However, although reasonably effective, treatment failures and significant side effects such as bone demineralization, growth retardation, diabetes, and hypertension often occur. This clearly stresses the need for novel treatment options in the treatment of IBD.
Another problem is that no specific, non-invasive test exists to monitor IBD disease activity. Currently, patients have to undergo endoscopy, which is a burden for the patient, but may also present complications, such as bleedings and infections.
The above illustrates that there is an urgent need for further multi-disciplinary research, in order to develop novel and improved IBD diagnostic and treatment options.
The present training project proposal brings together skills, experiences and (fundamental, translational, and commercial) knowledge both from industry and academia, in the context of an innovative research project on novel diagnostic and therapeutic approaches for IBD and provides further education and training to a large group of researchers. In this study we aim to:
1. Develop a novel treatment for IBD, using the recently described anti-inflammatory effects of the bile acid sensor Farnesoid X receptor (FXR). We aim to develop agonists capable of selectively activating the FXR as potential pharmaceutical compounds.
2. Develop a non-invasive diagnostic tool using well-defined changes in the gut microbiome of people affected with IBD as a marker to diagnose and monitor disease progression or remission in stool samples.

The project is divided into 6 Work Packages (WP). Below, we give the most important results sofar:
Work Package 1. Project Management.
- kick-off meeting (M.1.1) in Utrecht, Netherlands (29th of January 2014)
- 25-26th of September 2014: consortium meeting at Enterome (Paris), managerial and scientific progress.
- 26th of September 2014: FXR-IBD organized open symposium on Microbiota in Inflammatory Bowel Disease: innovation in diagnostic and therapeutic tools',
- May 2015, consortium meeting Perugia, Italy, scientific progress. Discussions with Dr. Luciano Adorini (Intercept Pharma) and Dr. Antonio Moschetta (Associated Professor University Bari), to to explore common interests.
- Nov 2015, Utrecht, The Netherlands, Midterm Review Meeting.

Work Package 2. Investigate the molecular mechanisms of FXR-anti-inflammatory actions.
To investigate the molecular mechanisms of FXR anti-inflammatory action, we set out to confirm first that the inhibition of inflammation is caused by FXR activation in the epithelial cells of the gut, the enterocytes. To our surprise, mice that lack expression of FXR specifically in the enterocytes, still showed protection against chemically-induced colitis, indicating that the enterocytes do not play a role in FXR-mediated inhibition of colitis symptoms. This observation is very important to understand the mechanisms of FXR anti-inflammatory function, but it means that we will have to take a step back and investigate which organ or cell type is important for the protection against intestinal inflammation. We have recently generated a liver-specific FXR knock-out mouse and first data indicate that the liver-specific knockout is not protecting against colitis symptoms, indicating that FXR in the liver is important for the protection against inflammation in the intestine. Currently, we are further analysing these animal experiments. Once we understand which organ/cell type expressing FXR is mediating the anti-inflammatory function (D.2.2), can we begin to investigate the molecular mechanisms, as was initially written in Annex 1.

Work Package 3. Development of a non-invasive tool to assay disease remission.
This WP focuses on the development of a non-invasive tool to assess disease remission. Using alterations in number and type of bacteria residing in the stool samples of patients, Enterome aims to develop a microbiome fingerprint using whole genome metagenomics profiling on stool samples. This fingerprint will be translated into a non-invasive diagnostic tool. We had a setback for this WP, because after careful analysis, we established that the already available stool samples in the UMCU cohort (D.3.1) could not be used, since no preservative was added upon harvesting. We therefore amended the METC protocol for harvesting stool samples according to Enterome’s standards necessary for metagenomics analysis. This delayed us in generating the bacterial DNA biocollection (D.3.1). In the meantime, Enterome moved forward with the analysis of its internal study named “CrohnOmeter”, into which they recruited 99 patients with a total of 950 samples collected by Q4 2014. Analysis of 439 samples and subgroups has been performed and led to the identification of two patentable discoveries, the first one (dep. 19/09/2014) was on a gene named CDENT29 which was assembled when Enterome created a gene specific catalogue for Crohn Disease and the second patent is a novel marker of disease activity.
To date, UMCU has collected around 100 new stool samples from Crohn Disease patients that were biobanked by Enterome and will be used to validate the findings in a separate cohort (D.3.1 and D.3.2).

Work Package 4. Development of anti-inflammatory ligands.
To screen for selective FXR ligands (D.4.3), biological screens that differentiate between FXR metabolic and anti-inflammatory actions are necessary (D.4.1 and D.4.2). These screens will be used to perform reiterating rounds of computational studies and screening in order to select the most optimal compounds. The project partners will rank the identified compounds and with the best performing compounds proceed in WP5 to test their ability to inhibit intestinal inflammation in vivo.
Since we have developed and validate a high-throughput reporter assay (D.4.1 and M.4.2, see below), it is not necessary anymore to develop an inflammation specific FXR AlphaScreen cofactor interaction assay (D.4.1.and T.4.1).
An automated high-throughput reporter-based screen has been set-up (D.4.2) and used for compound screening. A small library of 1200 compounds of FDA-approved drugs was tested to validate the robustness of the screening method and it revealed one compound, Mometasone furoate, that reduced anti-inflammatory activity via FXR with no or limited effects on the metabolic function of FXR. With these results, for the first time it has been shown that separation of metabolic and anti-inflammatory functions of FXR in vitro is possible. Computational studies were performed to investigate the interaction of Mometasone with the FXR ligand binding domain, revealing 3 putative binding modes. Mometasone-bound FXR inhibited NF-κB subunit p65 recruitment to DNA of pro-inflammatory genes CXCL2 and IL8 and since Mometasone induced transactivation of metabolism associated genes such as SHP and IBABP was minimal this illustrates the possibility of developing anti-inflammatory selective compounds (D.4.3.). TES Pharma and UMCU have published a joint manuscript regarding these findings (see under WP6, Manuscript).
In addition, using the same screening method, UMCU has screened a library of novel compounds generated by TES Pharma for their ability to separate FXR functions, and also here we have found some interesting compounds that are currently tested in additional assays (D.4.4). These interesting compounds are bile acid derivatives characterized by an extended side chain that binds the non-canonical FXR S2 accessory ligand pocket, whereas the main scaffold binds the canonical S1 ligand pocket.

Work Package 5. In vivo validation.
In this work package, animal studies will be conducted with novel FXR agonists to investigate whether intestinal inflammation symptoms are decreased and whether they indeed act only on inflammation and not on metabolic actions of FXR. So far, we have tested one new compound in a dose finding study in vivo. 0, 10, 30 and 50 ug/kg of the compound was given for 7 days per oral gavage to mice (n=5 per group). We have established that this compound is very potent and highly selective for FXR, and we are currently following up by testing this compound in models of liver disease (not as part of the FXR-IBD consortium). Unfortunately, this compound is not suitable as an FXR-selective compound to decrease the inflammatory response, as it affects both metabolic and anti-inflammatory functions of FXR. Nevertheless, we show that our collaboration enables us to validate new compounds quickly in vivo. In the near future, we will screen a selection of diverse FXR ligands (e.g. E-Guggulsterone) described in literature to profile their differential effects in vivo in mice and investigate their potential to selectively induce FXR anti-inflammatory effects.

Work Package 6. Dissemination of results.
As part of the dissemination of knowledge and results, the following activities have been performed:
- We have generated a public website ( (D.6.2)
- We have organized an open symposium on 'Microbiota in inflammatory Bowel Disease: innovation in diagnostic and therapeutical tools'(25-26th September, Paris) (D.6.3).
- We are developing ideas to enlarge our collaboration and are evaluating to attract new possible parties (Intercept Pharma, Antonio Moschetta (Univ. Bari) with whom we want to develop future ideas for grant applications.
- Saskia van Mil has presented work of the FXR-IBD consortium at a symposium organized by the Center for Molecular Medicine of the UMC Utrecht: 'Bile acids have the gall to act as hormones'. CMM symposium (D.6.4), September 2015
- We have circulated a press release regarding the kick off meeting FXR-IBD (link to pdf) (D.6.4).
- Interview with Saskia van Mil in International Innovation on her research topic selective FXR ligands (link to pdf) (D.6.4).
- Results from this project were presented at different national and international conferences (see attachment for details).
- Results were published in 4 high impact publications (see attachment for details)

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Life Sciences