The WD and linker domains of ATG16L1 required for non-canonical autophagy limit lethal influenza A virus infection at epithelial surfaces
Posted on: 9 March 2020
Preprint posted on 15 January 2020
Loss of non-canonical autophagy in mice increases sensitivity to influenza A virus infection by disrupting defences at the lung epithelial barrier, but not in phagocytic leukocytes.
Selected by Kirsty HooperCategories: cell biology, immunology, microbiology
Background
Autophagy is a well-characterised pathway, in which intracellular components sequestered in a double membrane autophagosome are degraded upon fusion with a lysosome (Dikic et al., 2018). The degraded subunits can then be recycled by the cell to promote survival and maintain homeostasis (Dikic et al., 2018). Non-canonical autophagy, however, is the recruitment of the autophagy protein LC3, among other components of the autophagy machinery, to single membrane compartments to help facilitate degradation of engulfed material taken up via phagocytosis, endocytosis or micropinocytosis (Upadhyay et al., 2019). This pathway is independent of upstream autophagy regulators and has been linked to innate immune defences (Upadhyay et al., 2019), cancer (Cunha et al., 2018) and Alzeimer’s disease (Heckmann et al., 2019). Among the pathogens known to induce non-canonical autophagy is influenza A virus (IAV) (Fletcher et al., 2018). To date, however, most studies investigating non-canonical autophagy in innate immune defence have been limited to in vitro models. There are existing mouse models that can be used to study non-canonical autophagy, such as the Rubicon-/- mouse (Martinez et al., 2015). Although these mice display loss of non-canonical autophagy, Rubicon also has distinct functions in the immune system that are separate from non-canonical autophagy (Yang et al., 2012).
Experimental model
ATG16L1 is a key protein in both canonical and non-canonical autophagy that facilitates LC3 lipidation to membranes (Dikic et al., 2018). This study used a mouse model with a truncation in ATG16L1 to remove the C-terminal WD and linker domains (δWD [ATG16L1δWD/δWD]), which enabled them to dissect these pathways by specifically disrupting the non-canonical pathway (Rai et al., 2019). The authors validated the mouse model by showing that cells from δWD mice were proficient in canonical autophagy but defective in non-canonical autophagy.
Key Findings
Systemic loss of non-canonical autophagy increases sensitivity to IAV in mice
Upon infection with a low pathogenicity strain of IAV, δWD mice had increased mortality compared to control mice, along with more severe weight loss, increased lung viral titres and evidence of fulminant viral pneumonia.
Non-canonical autophagy controls lung inflammation after IAV infection
δWD mice also displayed prolonged increases in pro-inflammatory cytokine expression (IL-1β, TNF-α and CCL2) and increased neutrophil and macrophage/monocyte infiltration post-IAV infection, compared with control mice. Previous studies have identified plasmacytoid dendritic cells (pDCs) as key mediators of cytokine storms (Davidson et al., 2014). Depletion of pDCs in δWD mice decreased morbidity in response to IAV infection, suggesting that exacerbated cytokine responses via pDCs led to the increased severity of infection in δWD mice.
Interestingly, there was no increase in IL-1β secretion, or frequencies of T cells, B cells and macrophages upon LPS treatment in δWD mice compared to littermate controls. This suggests that there was no alteration of inflammatory threshold or immune homeostasis in δWD mice, despite the amplified responses to IAV infection.
Non-canonical autophagy limits IAV infection independently of phagocytic cells
The authors determined that the high sensitivity to IAV infection seen in δWD mice was not due to defects in myeloid cells. Bone marrow chimeras of δWD mice with WT leukocytes had the same phenotype as δWD mice, and furthermore, LysMcre generated mice, with truncated ATG16L1 protein only present in myeloid cells had the same phenotype as control mice.
The activity of non-canonical autophagy in epithelial cells during IAV infection was then tested ex vivo, in precision cut lung slices and MEFs from δWD mice. This demonstrated that in the absence of phagocytic cells the exaggerated inflammatory responses and increased viral load in δWD mice persisted.
Why did I choose this paper?
Non-canonical autophagy is a rapidly emerging field implicated in a growing number of pathogenicities. As highlighted by the authors, however, the study of this pathway in vivo has been limited. The creation of the δWD mouse that specifically dissects canonical and non-canonical autophagy with minimal off-target effects can allow great advancements in this field. By characterising this pathway in vivo, the authors can define its systemic role in response to infection with IAV. This can pave the way for the characterisation of non-canonical autophagy in many more infection models and disease settings, and help delineate its molecular mechanisms.
Questions to the author/future directions?
- As stated by the authors, there are many studies showing the importance of non-canonical autophagy in innate immune responses in macrophages and dendritic cells. Would the authors predict that there would be a response more dependent on myeloid cells in this in vivo model when using an alternative pathogen that has more of a tropism for phagocytes, such as Aspergillus fumigatus or Listeria monocytogenes?
- In cell culture it was shown that IAV stimulated non-canonical autophagy via a mechanism involving the viral protein M2 (Fletcher et al., 2018). Would the authors expect this mechanism to be more preferential in epithelial cells? And could this mechanism be delineated further using this mouse model?
References
Cunha, L.D. et al. LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance. Cell. 4;175(2):429-441.e16. doi:10.1016/j.cell.2018.08.061 (2018)
Davidson, S. et al. Pathogenic potential of interferon alphabeta in acute influenza infection. Nat Commun 5, 3864, doi:10.1038/ncomms4864 (2014).
Dikic, I. and Elazar, Z. Mechanism and medical implications of mammalian autophagy. Nat Rev Mol Cell Biol. 19:349–364. (2018)
Fletcher, K. et al. The WD40 domain of ATG16L1 is required for its noncanonical role in lipidation of LC3 at single membranes. EMBO J. 37, doi:10.15252/embj.201797840 (2018).
Heckmann, B.L., et al. LC3-Associated Endocytosis Facilitates β-Amyloid Clearance and Mitigates Neurodegeneration in Murine Alzheimer’s Disease. Cell. 25;178(3):536-551.e14. doi:10.1016/j.cell.2019.05.056. (2019)
Martinez, J. et al. Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Nat Cell Biol 17, 893-906, doi:10.1038/ncb3192 (2015).
Rai, S. et al. The ATG5-binding and coiled coil domains of ATG16L1 maintain autophagy and tissue homeostasis in mice independently of the WD domain required for LC3-associated phagocytosis. Autophagy 15, 599-612, doi:10.1080/15548627.2018.1534507 (2019).
Upadhyay, S. and Philips, J.A. LC3-associated phagocytosis: host defense and microbial response. Curr Opin Immunol. 60:81-90. doi:10.1016/j.coi.2019.04.012 (2019)
Yang, C. S. et al. The autophagy regulator Rubicon is a feedback inhibitor of CARD9-mediated host innate immunity. Cell Host Microbe 11, 277-289, doi:10.1016/j.chom.2012.01.019 (2012).
doi: https://doi.org/10.1242/prelights.17439
Read preprintSign up to customise the site to your preferences and to receive alerts
Register hereAlso in the cell biology category:
Golgi compaction facilitates microtubule nucleation to drive adult vertebrate peripheral neuron regeneration
Vibha SINGH
Non-disruptive inducible labeling of ER-membrane contact sites using the Lamin B Receptor
Jonathan Townson
HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos
Anchel De Jaime Soguero
Also in the immunology category:
Global coordination of protrusive forces in migrating immune cells
yohalie kalukula
Integrin conformation-dependent neutrophil slowing obstructs the capillaries of the pre-metastatic lung in a model of breast cancer
Simon Cleary
Functional Diversity of Memory CD8 T Cells is Spatiotemporally Imprinted
Marina Schernthanner
Also in the microbiology category:
Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA
Leeba Ann Chacko
The bat Influenza A virus subtype H18N11 induces nanoscale MHCII clustering upon host cell attachment
Mitchell Sarmie, Mohammed A. Jalloh
Characterization of natural product inhibitors of quorum sensing in Pseudomonas aeruginosa reveals competitive inhibition of RhlR by ortho-vanillin
UofA IMB565 et al.
preListscell biology category:
in theBSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
List by | Reinier Prosee |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
List by | Alex Eve, Katherine Brown |
preLights peer support – preprints of interest
This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.
List by | preLights peer support |
The Society for Developmental Biology 82nd Annual Meeting
This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.
List by | Joyce Yu, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
List by | Alex Eve |
Journal of Cell Science meeting ‘Imaging Cell Dynamics’
This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.
List by | Helen Zenner |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
List by | Sergio Menchero et al. |
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
List by | Nadja Hümpfer et al. |
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
List by | Osvaldo Contreras |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
List by | Alex Eve |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
List by | Ana Dorrego-Rivas |
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
List by | Ana Dorrego-Rivas |
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
List by | Dey Lab, Samantha Seah |
1
Cell Polarity
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
List by | Maiko Kitaoka et al. |
3D Gastruloids
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.
List by | Paul Gerald L. Sanchez and Stefano Vianello |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
List by | Hiral Shah |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
List by | Madhuja Samaddar et al. |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
List by | Dey Lab |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
List by | Sandra Malmgren Hill |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
List by | Rob Hynds |
Cellular metabolism
A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.
List by | Pablo Ranea Robles |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
List by | Dey Lab |
MitoList
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
List by | Sandra Franco Iborra |
Biophysical Society Annual Meeting 2019
Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA
List by | Joseph Jose Thottacherry |
ASCB/EMBO Annual Meeting 2018
This list relates to preprints that were discussed at the recent ASCB conference.
List by | Dey Lab, Amanda Haage |
Also in the immunology category:
Journal of Cell Science meeting ‘Imaging Cell Dynamics’
This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.
List by | Helen Zenner |
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
List by | Osvaldo Contreras |
Single Cell Biology 2020
A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.
List by | Alex Eve |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
List by | Sandra Malmgren Hill |
Antimicrobials: Discovery, clinical use, and development of resistance
Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.
List by | Zhang-He Goh |
Zebrafish immunology
A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.
List by | Shikha Nayar |
Also in the microbiology category:
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
List by | Dey Lab, Samantha Seah |
1
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
List by | Hiral Shah |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
List by | Dey Lab |
Antimicrobials: Discovery, clinical use, and development of resistance
Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.
List by | Zhang-He Goh |