Quantitative proteomics of coeliac gut during 14-day gluten challenge: low-level baseline inflammation despite clinical and histological normality predicts subsequent response

Objective To shed light on gut mucosa processes provoked by gluten exposure in coeliac disease, we performed a quantitative proteomic analysis of duodenal tissue from well-treated coeliac patients before and after gluten challenge. Design We extracted and digested proteins from formalin-fixed paraffin-embedded tissue of 19 coeliac disease patients who had been challenged orally with gluten for 14 days. Protein identification and quantification was done by label-free quantitative mass spectrometry-based proteomics from total tissue and from laser capture microdissected epithelial cell layer. Proteomics data were compared with clinical, serological and histological data. Results At baseline, all patients were in clinical and mucosal remission (Marsh 0-1) except one (Marsh 3). After challenge, five patients reached Marsh 3 scores. Proteome analysis categorised these five and additionally two patients as responders. Already at baseline, responder patients differed from the remaining patients in their gut tissue protein composition with altered levels of inflammatory and enterocyte function proteins – the same proteins that changed upon gluten challenge. Patients classified as responders from the proteomic analysis also differed from the remaining patients at baseline, with mild crypt hyperplasia and a slight increase in blood inflammatory parameters and gluten specific CD4+ T-cell frequencies. Conclusion Despite clinical and histological remission, coeliac disease patients that develop a mucosal response after 14-day gluten challenge have already at baseline altered protein compositions of their gut tissue with signs of ongoing inflammation. Thus, apparently well-treated coeliac disease is frequently not fully quiescent with presence of low-grade anti-gluten immunity in gut mucosa.