No abstract

A coding polymorphism (Thr300Ala) in the essential autophagy gene, autophagy related 16-like 1 (ATG16L1), confers increased risk for the development of Crohn disease, although the mechanisms by which single disease-associated polymorphisms contribute to pathogenesis have been difficult to dissect given that environmental factors likely influence disease initiation in these patients. Here we introduce a knock-in mouse model expressing the Atg16L1 T300A variant. Consistent with the human polymorphism, T300A knock-in mice do not develop spontaneous intestinal inflammation, but exhibit morphological defects in Paneth and goblet cells. Selective autophagy is reduced in multiple cell types from T300A knock-in mice compared with WT mice. The T300A polymorphism significantly increases caspase 3-and caspase 7-mediated cleavage of Atg16L1, resulting in lower levels of full-length Atg16Ll T300A protein. Moreover, Atg16L1 T300A is associated with decreased antibacterial autophagy and increased IL-1β production in primary cells and in vivo. Quantitative proteomics for protein interactors of ATG16L1 identified previously unknown nonoverlapping sets of proteins involved in ATG16L1-dependent antibacterial autophagy or IL-1β production. These findings demonstrate how the T300A polymorphism leads to cell typeand pathway-specific disruptions of selective autophagy and suggest a mechanism by which this polymorphism contributes to disease. H uman genetic studies offer an unbiased approach to identify genes and DNA variants underlying susceptibility to complex diseases. Although this approach has been successful at identifying more than 160 loci associated with Crohn disease (CD), a chronic inflammatory condition affecting the gastrointestinal tract (1, 2), ascribing function to specific risk variants has been difficult. Individuals who harbor a common threonine to alanine coding variant at position 300 in autophagy related 16-like 1 (ATG16L1) (T300A) are at increased risk of developing CD compared with individuals who possess a threonine at this position (T300T) (3, 4). The T300A variant lies within a structurally unclassified region of ATG16L1, making it challenging to identify the effect of this polymorphism.ATG16L1 is a component of the core autophagy machinery that plays a critical role in immunity and inflammation. Initial studies investigating ATG16L1 used hypomorphic Atg16L1 mouse models, which show Paneth cell abnormalities relevant to CD such as abnormal mitochondria, irregular patterns of granule morphology and lysozyme distribution, and increased expression of genes implicated in inflammation (5, 6). Although these studies have been useful in highlighting the important role of autophagy proteins in intestinal cells such as Paneth cells and goblet cells, the precise mechanisms by which ATG16L1 T300A influences pathogenesis remain unclear (7)(8)(9)(10).Previous studies have demonstrated that Atg16L1-deficient macrophages produce elevated levels of active caspase 1 and secrete higher levels of the cytokines IL-1β and IL-18 u...