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Novel diagnostic and therapeutic approach to inflammatory bowel disease based on functional characterization of patients: the CrUCCial index

Periodic Reporting for period 3 - CrUCCial (Novel diagnostic and therapeutic approach to inflammatory bowel disease based on functional characterization of patients: the CrUCCial index)

Reporting period: 2019-09-01 to 2021-02-28

Crohn’s disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel diseases (IBD) that mostly affect young adults, and that are characterized by a decreased quality of life due to symptoms of bloody diarrhea, urgency to attend the bathroom, abdominal cramps, perianal pain and incontinence and systemic symptoms of weight loss. IBD is a global healthcare problem with a substantial financial burden for patients but also for the health care system, and if treated suboptimal, characterized by a poor prognosis. The current hypothesis regarding etiology is that the disease results from a faulty immune recognition, tolerance and defense against the commensal microbiota and dietary antigens present in Westernized diets and this in a genetically susceptible host. This multifactorial etiology and heterogenous character of the disease require a personalized approach. An approach that starts at diagnosis, has the potential to aid in prognosis but should also apply to management. This last aspect has certainly not been the case in IBD where merely the end result being a state of chronic inflammation, is tackled. We hypothesize that a functional characterization of patients for the major identified pathways implicated in disease pathogenesis will improve patient management in many aspects. This type of screening (both genetic, transcriptional, functional and on microbiome level) could not only enable predictions of an individual’s disease course or capacity to metabolize therapeutic agents, it will ideally lead to a highly optimized personal regime to manage IBD, maximizing treatment response while avoiding unwanted adverse effects.
In the first part of the project, we successfully constructed a genetic risk score and a microbial dysbiosis score. Furthermore, we have also generated all necessary data to construct an inflammatory (transcriptomic and proteomic) score on a large number of patients.
For the functional readouts, we developed and validated a patient-derived ex-vivo intestinal epithelial cell culture system which can be used to study functional pathways and we have shown that patients with more endoplasmic reticulum (ER) stress and autophagy risk alleles have augmented epithelial ER stress responses. The primary intestinal epithelial model was further optimized in Transwell inserts in order to evaluate the barrier function. Additionally, we also generated functional readouts of intestinal permeability (using Lactulose/Mannitol and Ussing chambers). The latter techniques however proof to be challenging to transfer on a large scale basis to daily practice – instead genetics and RNA sequencing on blood and biopsies may generate (indirectly) the same information and - with translation to clinical practice in mind – we decided to replace the Ussing and urine sugar tests by RNA sequencing techniques on blood and biopsies. These techniques have been optimized in our laboratory.
Currently, we are developing and optimizing bioinformatic tools in order to integrate all the above-mentioned components into the CrUCCial index. This index will then reflect the proportional contributions of the different mechanisms in a given patient. We have optimized the methods to integrate so far 5 different individual components including proteomics, mucosal and blood transcriptomics and a patient’s genetic risk score.
In the second half of the project, we will prospectively include IBD patients in whom all the different components of the CrUCCial index will be characterized. Finally, the generated CrUCCial index will be tested for its ability to predict clinical outcomes and disease progression.