Characterization of the small intestinal lesion in celiac disease by label-free quantitative mass spectrometry

Abstract Global characterization of tissue proteomes from small amounts of biopsy material has become feasible due to advances in mass spectrometry and bioinformatics tools. In celiac disease (CD), dietary gluten induces an immune response which is accompanied by pronounced remodeling of the small intestine. Removal of gluten from the diet abrogates the immune response and the tissue architecture normalizes. In this study differences in global protein expression of small intestinal biopsies from CD patients were quantified by analyzing formalin-fixed, paraffin-embedded material using liquid-chromatography mass spectrometry and label-free protein quantitation. Protein expression was compared in biopsies collected from the same patients before and after one year treatment with gluten-free diet (n=10) or before and after three-day gluten provocation (n=4). Differential expression of proteins in particular from mature enterocytes, neutrophils, and plasma cells could distinguish untreated from treated CD mucosa, and immunoglobulin variable region IGHV5-51 expression was found to serve as a CD-specific marker of ongoing immune activation. In patients that had undergone gluten challenge coordinated up-regulation of wound response proteins including the CD autoantigen transglutaminase 2 was observed. Our study provides a global and unbiased assessment of antigen-driven changes in protein expression in the celiac intestinal mucosa.