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

• Published in: eLife Vol. 10
• Main Authors: Maculins, Timurs, Verschueren, Erik, Hinkle, Trent, Choi, Meena, Chang, Patrick, Chalouni, Cecile, Rao, Shilpa, Kwon, Youngsu, Lim, Junghyun, Katakam, Anand Kumar, Kunz, Ryan C, Erickson, Brian K, Huang, Ting, Tsai, Tsung-Heng, Vitek, Olga, Reichelt, Mike, Senbabaoglu, Yasin, Mckenzie, Brent, Rohde, John R, Dikic, Ivan, Kirkpatrick, Donald S, Murthy, Aditya
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 04.06.2021; eLife Sciences Publications, Ltd
• Subjects: Animals; Antimicrobial agents; Antioxidants; Apoptosis; Autophagy; Autophagy-Related Proteins - deficiency; Autophagy-Related Proteins - genetics; Bacteria; Bone marrow; Cell Biology; Cells, Cultured; Crohn's disease; Cytosol; Disease Models, Animal; Dysentery, Bacillary - immunology; Dysentery, Bacillary - metabolism; Dysentery, Bacillary - microbiology; Experiments; Glutathione; Host-Pathogen Interactions; Immunity, Innate; Immunology and Inflammation; Infections; Inflammation Mediators - metabolism; Inflammatory bowel disease; Innate immunity; Intracellular; Macrophages; Macrophages - immunology; Macrophages - metabolism; Macrophages - microbiology; mass spectrometry; Mice; Mice, Inbred C57BL; Mice, Knockout; Microbial Viability; Myeloid cells; oxidative damage; Oxidative Stress; Pathogens; Phagocytosis; Proteins; Proteome; Proteomics; Salmonella; shigella flexneri; Shigella flexneri - immunology; Shigella flexneri - metabolism; Shigella flexneri - pathogenicity; Spleen; Virulence; mouse; macrophages; autophagy; cell biology; proteomics; shigella flexneri; inflammation; mass spectrometry; oxidative damage; immunology
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.62320

Defective autophagy is strongly associated with chronic inflammation. Loss-of-function of the core autophagy gene Atg16l1 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 Atg16l1 in myeloid cells enhanced the killing of virulent Shigella flexneri (S.flexneri) , 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 S.flexneri killing. Consistent with this, myeloid-specific deletion of Atg16l1 in mice accelerated bacterial clearance in vitro and in vivo . Pharmacological induction of oxidative stress through suppression of cysteine import enhanced microbial clearance by macrophages. Conversely, antioxidant treatment of macrophages permitted S.flexneri proliferation. These findings demonstrate that control of oxidative stress by ATG16L1 and autophagy regulates antimicrobial immunity against intracellular pathogens.