Proteomic profiling of mucosal and submucosal colonic tissues yields protein signatures that differentiate the inflammatory colitides

Abstract

BACKGROUND Differentiating ulcerative colitis (UC) from Crohn's colitis (CC) can be difficult and may lead to inaccurate diagnoses in up to 30 percent of inflammatory bowel disease (IBD) patients. Much of the diagnostic uncertainty arises from the overlap of clinical and histologic features. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) permits a histology-directed cellular protein analysis of tissues. As a pilot study, we evaluated the ability of histology-directed MALDI-MS to determine the proteomic patterns for potential differences between CC and UC specimens. METHODS Mucosal and submucosal layers of CC and UC colon resection samples were analyzed after histologic assessment. To determine whether MALDI-MS would distinguish inflammation, the uninflamed [n=21] vs. inflamed submucosa [n=22] were compared in UC and the uninflamed [n=17] vs. inflamed submucosa [n=20] in CC. To determine whether there were proteomic differences between the colitides, the uninflamed UC submucosa [n=21] was compared vs. the uninflamed CC submucosa [n=17], the inflamed UC submucosa [n=22] was compared vs. the inflamed CC submucosa [n=20], and inflamed UC mucosa vs. inflamed CC mucosa. Pair-wise statistics comparisons of the subsets were performed. RESULTS Pair-wise comparative analyses of the clinical groups allowed indentifying subsets of features important for classification. Comparison of inflamed vs. uninflamed CC submucosa showed two significant peaks: m/z 6445 (p=0.0003) and 12692 (p=0.003). In the case of inflamed vs. uninflamed UC submucosa, several significant differentiating peaks were found, but classification was worse. Comparisons of the proteomic spectra of inflamed submucosa between UC and CC identified two discrete significant peaks: m/z 8773 (p=0.006) and 9245 (p=0.0009). Comparisons of the proteomic spectra of uninflamed submucosa between UC and CC identified three discrete significant peaks: m/z 2778 (p=0.005), 9232 (p=0.005), and 9519 (p=0.005). No significantly different features were found between UC and CC inflamed mucosa. CONCLUSION MALDI-MS was able to distinguish CC and UC specimens while profiling the colonic submucosa. Further analyses and protein identification of the differential protein peaks may aid in accurately diagnosing IBD and developing appropriate personalized therapies.

Quantitative Proteomics of Gut-Derived Th1 and Th1/Th17 Clones Reveal the Presence of CD28+ NKG2D- Th1 Cytotoxic CD4+ T cells

“…A few proteomics studies using biopsies and PBMCs from Crohn's disease patients have been published (42)(43)(44). The heterogeneity of these samples makes it impossible to characterize the individual T cells.…”

Current application of proteomics in biomarker discovery for inflammatory bowel disease

“…Similarly, Han et al [34] identified a large number of differentially expressed proteins (37 relevant for CD, 27 for UC and 11 associated with general IBD) that were seen as candidate biomarkers. M'koma and colleagues conducted two studies that identified spec tral peaks representing unknown protein profiles and reported being able to accurately distinguish between the UC and CD using an algorithm [35,36] . These tissue findings however are likely to require validation in plas 30 February 15, 2016|Volume 7|Issue 1| WJGP|www.wjgnet.com…”

“…Normal colon: 3 M'koma et al [35] Colon samples CD: 27 Histology directed MALDI-TOF 5 m:z peaks were identified and cross-validated for the differentiation of UC and CD UC: 24 Seeley et al [36] Colon samples CD: 26 Histology directed MALDI-TOF Using a support vector machine and 25 m:z peaks, UC and CD cases were predicted in 93.3% and 60.4% respectively. A lower spectral accuracy cut-off increased sensitivity UC: 36…”

Systems biology in inflammatory bowel diseases

“…A wide selection of proteomic approaches has been applied to characterize IBD pathogenesis by investigating the dynamic nature of the proteome 41 , including surface-enhanced laser desorption ionization (SELDI) or matrix-assisted laser desorption (MALDI)-time of flight (TOF) mass spectrometry (MS) and liquid chromatography (LC/MS) combined with two-dimensional gel electrophoresis. Such proteomic studies have been performed for IBD using epithelial cell lines [42][43][44] , epithelial cells from colonic biopsies [45][46][47] and serum samples [48][49][50][51] . Currently, the greatest interest in proteomic applications lays in identifying biomarkers in biofluids (such as serum and urine) or tissue samples (such as colonic biopsies) 41 that are specific for UC and CD diseases and correlate with disease activity and other clinicopathological parameters.…”