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Identification of promoters and enhancers specific for inflammatory bowel disease and its subtypes

Periodic Reporting for period 1 - IPEIBD (Identification of promoters and enhancers specific for inflammatory bowel disease and its subtypes)

Reporting period: 2015-06-01 to 2017-05-31

Inflammatory bowel disease (IBD) is a frequent chronic intestinal disorder, with two main types: Crohn’s disease (CD) and ulcerative colitis (UC). The incidence and prevalence of IBD is highest in Europe and North America (incidence up to 24 per 100,000 person-years) and affecting up to 0.5% in the Western world. IBD is not well-understood on a molecular level, and the distinction between CD and UC is critical for prescribing correct medication and especially surgery, yet the diagnosis is challenging. As the disease is chronic, patients typically require life-long treatment, often with very expensive biological drugs, which are not always effective. As diagnoses determines treatment, molecular methods for diagnosis complementing current state of the art methods would therefore be highly beneficial, but this requires comprehensive molecular screening of many subjects.

We identified a set of biomarkers (promoters and enhancers) that could predict IBD diagnosis (Crohn’s disease, ulcerative colitis or control) with an accuracy of 85%, using targeted microfluidics qPCR, where the prediction method was trained on one group of patients and evaluated in an independent group. This shows the potential for qPCR-based diagnostics methods for IBD, complementing current histology-based approaches. More generally, our results constitute a foundation for understanding the molecular pathology and genetics of IBD.
In this project, we have analyzed a unique emerging dataset of controlled gut biopsies taken from a large number of both UC, CD and healthy individuals (109 total) subjected to a unique RNA sequencing technology – CAGE – that can identify novel gene isoforms, transcribed enhancers and non-coding RNAs. The precise locations and activity of promoters and enhancers across the large patient population enabled us to train a classification method to predict the diagnosis of the subjects (healthy, Crohn’s disease or ulcerative colitis). This allowed us to identify a set of biomarkers, mentioned above, that have potential for use in the clinic for more accurate diagnosis of the disease.
This biomarker set is potentially applicable in the clinic as a way of increasing the accuracy of diagnosis and thus enable accurate medication – a cornerstone of precision medicine. It has commercial value for a wider use and we are in the process of looking for interested parties. A patent has been submitted for this set and it has commercial value for a wider use.