Integrative analysis of Paneth cell proteomic data from intestinal organoids reveals functional processes affected in Crohn's disease due to autophagy impairment

Crohn9s disease (CD) is associated with Paneth cell dysfunctions such as altered antimicrobial secretion that is dependent on autophagy which recycles cellular components. Patients carrying the CD risk allele in ATG16L1 - an important component of the autophagy machinery - have Paneth cell abnormalities, as reproduced in Atg16l1-deficient mouse models. However, the direct effect of Atg16l1-deficiency and autophagy-impairment in Paneth cells has not been analyzed. To investigate this, we generated a mouse model lacking Atg16l1 specifically in intestinal epithelial cells (Atg16l1ΔIEC) making these cells impaired in autophagy. Using a 3D intestinal organoid culture model that we enriched for Paneth cells, we compared the proteomic profiles of organoids derived from the wild-type (WT) and Atg16l1ΔIEC mice. We used an integrated computational approach combining protein-protein interaction networks, autophagy targeted proteins and functional information to identify the mechanistic link between autophagy-impairment and disrupted cellular processes. Of the 284 altered proteins, 198 (70%) were more abundant in autophagy-impaired organoids compared to WT organoids indicating a reduced protein degradation. Interestingly, the 284 differentially abundant proteins comprised 116 proteins (41%), which are potentially targeted by selective autophagy proteins such as p62, LC3 and ATG16l1. Our integrative analysis revealed autophagy-mediated mechanisms which degrade essential proteins belonging to key Paneth cell functions such as exocytosis, apoptosis and DNA damage repair. We performed validation experiments focusing on Paneth cell-derived lysozyme to confirm our inferred observation of down-regulated exocytosis. Our observations could explain how protein level alterations in CD as a result of autophagy impairment could affect Paneth cell functions.