Identifying Diagnostic Markers and Studying Etiologic Factors of Inflammatory Bowel Diseases Using a High‐Throughput Proteomic Approach

Abstract

The objectives of our study are to identify diagnostic markers for Inflammatory Bowel Diseases (IBDs), define the features of the proteome at different colonic locations and under different physiologic conditions, and investigate the host and microbial interactome at the mucosal interface. We collected bowel‐rinse samples from IBD patients and normal individuals, and analyzed each sample using high‐throughput surface enhanced laser desorption/ionization‐time of flight (SELDI‐TOF) mass spectrometry (MS). SELDI data preprocessing was done in CiphergenExpress®. The resulting spectra were further analyzed in R. Peaks were compared between groups to search for biomarker candidates, whereas the Permutation analysis was used to evaluate the featured differences between groups of samples. Hierarchical clustering heat maps were generated in Cluster3.0 and visualized in TreeView. We also used oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) to study the microbes in the bowel‐rinse samples. We have thus far identified several potential IBD biomarkers which are confirmed by western blotting. The heat‐map showed discriminative protein/peptide patterns in different locations of the colon, and between IBD patients and normal individuals. Preliminary OFRG study suggested that certain types of microorganism are highly associated with certain secreted protein/peptide in the colon.