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P204. Inflammatory joint- and bowel diseases - a clinical proteomics study seeking to identify the underlying biological triggers

T. Bennike1, T. Gelsing Carlsen1, L. Sennels1, K.B. Lauridsen1, H. Glerup2, O.K. Bonderup2, T.J. Ellingsen2, L. Vogel3, V. Andersen4, S. Birkelund1, A. Stensballe1, 1Aalborg University, Department of Health Science and Technology, Aalborg East, Denmark, 2Regional Hospital Silkeborg, Diagnostic Center, Section of Gastroenterology, Silkeborg, Denmark, 3Copenhagen University, Department of Molecular and Cellular Medicine, Copenhagen, Denmark, 4University of Southern Denmark, Institute for Regional Health Research, Odense, Denmark


In this project, we attempt to gain a deeper understanding of the underlying biological triggers of the autoimmune diseases and develop diagnostic tools for clinical use, by using inflammatory joint- and bowel diseases as a model system. In developing inflammatory bowel disease (IBD), the intestinal flora is a central factor, and discontinuation of the normal fecal stream will attenuate the inflammation in IBD. In addition to IBD, emerging evidence suggests the involvement of the intestinal microflora in other diseases, including rheumatoid arthritis (RA). The etiologies of the IBDs and RA remain unclear, but involve a complex interplay between genetic and environmental factors. Proteomics provide a powerful technique for identifying disease specific protein profiles. The detection is carried out on the protein level where the complexity of the proteome is highest. Therefore, we decided to investigate the proteins found in intestinal biopsy samples from RA and ulcerative colitis (UC) patients, and compare these to healthy controls. Given the recent development within the field of high-throughput protein identification using mass spectrometry (MS), which now allows for identifying and quantifying several thousand proteins in a single analysis, such analysis are likely to identify previously unknown dissimilarities (biomarkers). The identification of proteins and protein modifications (PTMs) associated to specific disease pathways will increase our knowledge of the inflammatory diseases. Such biomarkers can function as targets for novel diagnostic and therapeutic agents. Moreover, the biomarkers could aid physicians predict disease courses and in this way, identify patients in need of intensive treatment.


Intestinal biopsies from 10 UC, 10 RA and 10 healthy control subjects were extracted using colonscopy, from healthy looking tissue. The samples were processed and analysed using label-free bottom-up proteomics on a state-of-the art proteomics platform.


Methods for identifying and quantifying proteins in intestinal tissue have been optimized in collaboration with the proteomics core facility Steen and Steen lab at Children's Hospital Boston USA, Harvard medical school. Data from more than 500 hours of MS analysis time is under analysis, and a comparative analysis of protein profiles and PTMs in IBD and RA will be presented.

Figure: A major increase is encountered in the proteome complexity, from genes to transcripts and finally to the mature proteins.


The results will form basis for developing novel antibodies or protein arrays for diagnostic purposes, with focus on applicability for diagnostics and commercialization.