There is no cure for millions of patients worldwide suffering from Inflammatory Bowel Disease (IBD), new therapeutic strategies are thus sorely needed. Over the past years, we have revealed that the intestinal epithelium constitutively secretes active thrombin and elastase into the intestinal lumen. We found that physiological concentrations of thrombin had a proteolytic action on microbial biofilm matrices, preventing deleterious contact with the epithelium. Preliminary and unpublished results tend to support a similar role for epithelial elastase. In addition, we found that the activity of these epithelial proteases was upregulated in IBD patients and directly contributed to their pathophysiology. In this research program, our hypothesis is that the overproduction of epithelial proteases during IBD will cause proteolytic damage to the microbiota biofilm, which will then amplify the tissue damage. The requested funds will be devoted to testing this hypothesis over a 3-year period, using complementary in vitro, in vivo and ex vivo models, as well as state-of-the-art omics tools. We also propose to test strategies to restore the physiological concentration of epithelial proteases in the gut, in order to provide preclinical proof-of-concept data for new therapies for IBD patients.

Structural variants (SVs) are defined as genomic variations involving 50 nucleotides or more. They can take multiple forms, from simple deletions and insertions to complex rearrangements formed by multiple SV types like inversions, translocations and duplications. Most SVs are under-studied because of the technical challenges to identify them. Their impact is also more difficult to predict, as they often affect multiple functional elements or can trigger epigenetic changes. Although the sequencing of short DNA fragments of about 300 nucleotides (short read sequencing) is widely used today, it cannot identify many types of SVs. Long read sequencing, in contrast, can sequence longer DNA fragments (thousands of nucleotides) and detect SVs at much higher resolution, but remains costly. We have shown that short read sequencing data can be analyzed with pangenomes to accurately genotype SVs that had been discovered with long read sequencing. A pangenome represents multiple genomes and provides a framework to enhance a reference genome by integrating known variants. I propose to reanalyze sequencing data from large cohorts, like the UK Biobank, to test the association between SVs and disease traits in human. By including SVs in these genome-wide association studies, the aim is to identify novel disease genetic factors or identify the causal variant of known disease associations. The specialized computational genomics tools developed for this project will be combined with experimental assays to validate the findings. I propose to first validate this approach on hemochromatosis, a disease characterized by an excess of iron and with a known genetic risk factor but incomplete penetrance. With positive replication and experimental validation, this project would lay the groundwork for future studies on other diseases. The integration of variants that couldn't be studied before will help explain a fraction of the "missing heritability", observed for numerous traits.

Anemia, defined as a decreased quantity of circulating red blood cells, is a major source of morbidity and mortality affecting a-third of the worldwide population. As a functional component of erythrocytes hemoglobin, iron is essential for oxygen storage and transport. The liver-derived peptide hepcidin is the master regulator of iron homeostasis. During anemia, the erythroid hormone erythroferrone regulates hepcidin synthesis to ensure the proper supply of iron to the bone marrow for red blood cells synthesis. However, we provided evidence that another factor may exert a similar function. We identified a previously undescribed suppressor of hepcidin that is highly induced in the liver in response to hypoxia during the recovery from anemia and in thalassemic mice. We demonstrated that this hepatokine is a potent suppressor of hepcidin in vitro and in vivo. Our preliminary data further indicated that it acts by impairing the canonical BMP-SMAD signaling cascade that governs hepcidin regulation but the molecular mechanism is unknown. Our aims are to confirm the role this hepatokine in hepcidin regulation and iron metabolism, to identify its exact mechanism, to explore its involvement in human pathologies and to investigate the therapeutic potential of its manipulation in murine models of anemia. Successful completion of this project will open new areas of investigation and provide a better understanding of the pathophysiology of anemia and hypoxia and liver physiology. Ultimately, it will lead to the development of new therapeutic strategies for the treatment of various forms of anemias for which current treatments remain largely ineffective.

Intestinal epithelium is a single layer of cells exposed to external aggressive conditions, that is renewed every 4–5 days, that makes it one of the most sensitive part of human body. Its tissue homeostasis is highly sensitive to proliferation and cell migration; events occurring in a specific microenvironment: the intestinal crypt. However, mechanical interaction within this niche may be difficult to observe in vivo and mechanical properties of this model are poorly described. Recent developments in cell imaging and culture, with the creation of artificial tissue respecting natural architecture or organoids, have opened new access for the creation of epithelial tissues models that can easily be virtualized. We propose a combination of ‘computational models’, integrating the Finite Element Method Updated and Deep Learning, and organoids humanly designed ‘biological models’, to characterize colon epithelial structures, offering a promising avenue for fully automated diagnosis analysis.

Mycotoxins in the trichothecenes family are natural contaminants found in cereals. Resistant to heating, they contaminate the food chain and reach the consumer's plate. On the other hand, an increased number of Europeans harbor in their intestinal microbiota E. coli strains producing a genotoxin, colibactin, suspected of promoting colorectal cancer. We have recently demonstrated that the genotoxicity of colibactin is strongly exacerbated by the presence of a tricothecene in the diet. The objective of this project is to evaluate how this association could contribute to the development of neoplastic colorectal lesions. The project combines three research teams recognized internationally for their expertise on bacterial genotoxins, food mycotoxins, and the health effects of the microbiota. This project will appreciate for the first time the combined risk of a food contaminant and microbiota in colorectal cancer.