Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response.

Abstract

Defective autophagy is strongly associated with chronic inflammation. Loss-of-function of the core autophagy gene <i>Atg16l1</i> increases risk for Crohn's disease in part by enhancing innate immunity through myeloid cells such as macrophages. However, autophagy is also recognized as a mechanism for clearance of certain intracellular pathogens. These divergent observations prompted a re-evaluation of ATG16L1 in innate antimicrobial immunity. In this study, we found that loss of <i>Atg16l1</i> in myeloid cells enhanced the killing of virulent <i>Shigella flexneri (S.flexneri)</i>, a clinically relevant enteric bacterium that resides within the cytosol by escaping from membrane-bound compartments. Quantitative multiplexed proteomics of murine bone marrow-derived macrophages revealed that ATG16L1 deficiency significantly upregulated proteins involved in the glutathione-mediated antioxidant response to compensate for elevated oxidative stress, which simultaneously promoted <i>S.flexneri</i> killing. Consistent with this, myeloid-specific deletion of <i>Atg16l1</i> in mice accelerated bacterial clearance in <i>vitro</i> and <i>in vivo</i>. Pharmacological induction of oxidative stress through suppression of cysteine import enhanced microbial clearance by macrophages. Conversely, antioxidant treatment of macrophages permitted <i>S.flexneri</i> proliferation. These findings demonstrate that control of oxidative stress by ATG16L1 and autophagy regulates antimicrobial immunity against intracellular pathogens.