Non-canonical autophagy functions of ATG16L1 in epithelial cells limit lethal infection by influenza A virus.

Yingxue Wang,David Bitto,Ulrike Mayer,Angela Man,Alex Zhekova,Simon R Carding,Yohei Yamauchi,Penny P Powell,Janine L Coombes,Ralph A Tripp,Anja Kipar,Timothy Pearson,Matthew Jefferson,Thomas Wileman,Yongping Bao,Weijiao Zhang,James P Stewart,Parul Sharma,Ben Bone

doi:10.15252/embj.2020105543

Abstract

Influenza A virus (IAV) and SARS‐CoV‐2 (COVID‐19) cause pandemic infections where cytokine storm syndrome and lung inflammation lead to high mortality. Given the high social and economic cost of respiratory viruses, there is an urgent need to understand how the airways defend against virus infection. Here we use mice lacking the WD and linker domains of ATG16L1 to demonstrate that ATG16L1‐dependent targeting of LC3 to single‐membrane, non‐autophagosome compartments – referred to as non‐canonical autophagy – protects mice from lethal IAV infection. Mice with systemic loss of non‐canonical autophagy are exquisitely sensitive to low‐pathogenicity IAV where extensive viral replication throughout the lungs, coupled with cytokine amplification mediated by plasmacytoid dendritic cells, leads to fulminant pneumonia, lung inflammation and high mortality. IAV was controlled within epithelial barriers where non‐canonical autophagy reduced IAV fusion with endosomes and activation of interferon signalling. Conditional mouse models and ex vivo analysis showed that protection against IAV infection of lung was independent of phagocytes and other leucocytes. This establishes non‐canonical autophagy in airway epithelial cells as a novel innate defence that restricts IAV infection and lethal inflammation at respiratory surfaces.

Highlights

Influenza A virus (IAV) is a respiratory pathogen of major global public health concern (Yamayoshi & Kawaoka, 2019)
The graphs (Fig 1B) show that numbers of autophagosomes induced by Hanks balanced salt solution (HBSS) were the same in each cell type but Mouse embryonic fibroblasts (MEFs) from dWD were unable to recruit LC3 to large vacuoles when incubated with chloroquine or monensin
Quantification of Western blots (Fig 1D) showed that there was no significant difference between LC3II signals in control and dWD MEFs after starvation suggesting that autophagy was active in the two cell types

Summary

Introduction

Influenza A virus (IAV) is a respiratory pathogen of major global public health concern (Yamayoshi & Kawaoka, 2019). IAV infects airway and alveolar epithelium and damage results from a combination of the intrinsic pathogenicity of individual virus strains as well as the strength and timing of the host innate/inflammatory responses. Even though infection of the lower respiratory tract can result in inflammation, flooding of alveolar spaces, acute respiratory distress syndrome and respiratory failure, the factors that control IAV replication at epithelial surfaces and limit lethal lung inflammation remain largely unknown. Transport to lysosomes can be enhanced by non-canonical autophagy pathways which conjugate autophagy marker protein LC3 to endo-lysosome compartments to increase lysosome fusion.

Methods

Results

Conclusion