bims-nocaut 2023-04-16 papers

Issue of 2023–04–16
five papers selected by
Quentin Frenger, University of Strasbourg

Int J Mol Sci. 2023 Apr 04. pii: 6716. [Epub ahead of print]24(7):

Transcriptomic Changes Predict Metabolic Alterations in LC3 Associated Phagocytosis in Aged Mice.

Anuradha Dhingra, John W Tobias, Nancy J Philp, Kathleen Boesze-Battaglia.

LC3b (Map1lc3b) plays an essential role in canonical autophagy and is one of several components of the autophagy machinery that mediates non-canonical autophagic functions. Phagosomes are often associated with lipidated LC3b to promote phagosome maturation in a process called LC3-associated phagocytosis (LAP). Specialized phagocytes, such as mammary epithelial cells, retinal pigment epithelial (RPE) cells, and sertoli cells, utilize LAP for optimal degradation of phagocytosed material, including debris. In the visual system, LAP is critical to maintain retinal function, lipid homeostasis, and neuroprotection. In a mouse model of retinal lipid steatosis-mice lacking LC3b (LC3b-/-), we observed increased lipid deposition, metabolic dysregulation, and enhanced inflammation. Herein, we present a non-biased approach to determine if loss of LAP mediated processes modulate the expression of various genes related to metabolic homeostasis, lipid handling, and inflammation. A comparison of the RPE transcriptome of WT and LC3b-/- mice revealed 1533 DEGs, with ~73% upregulated and 27% downregulated. Enriched gene ontology (GO) terms included inflammatory response (upregulated DEGs), fatty acid metabolism, and vascular transport (downregulated DEGs). Gene set enrichment analysis (GSEA) identified 34 pathways; 28 were upregulated (dominated by inflammation/related pathways) and 6 were downregulated (dominated by metabolic pathways). Analysis of additional gene families identified significant differences for genes in the solute carrier family, RPE signature genes, and genes with a potential role in age-related macular degeneration. These data indicate that loss of LC3b induces robust changes in the RPE transcriptome contributing to lipid dysregulation and metabolic imbalance, RPE atrophy, inflammation, and disease pathophysiology.

Keywords: LC3-associated phagocytosis (LAP); cholesterol metabolism; cholesterol trafficking; fatty acid metabolism; inflammation; monocarboxylate transporters; peroxisomes; retinal pigment epithelium (RPE); transcriptomics

DOI: https://doi.org/10.3390/ijms24076716

Dev Cell. 2023 Apr 10. pii: S1534-5807(23)00130-2. [Epub ahead of print]

ATG5 provides host protection acting as a switch in the atg8ylation cascade between autophagy and secretion.

Fulong Wang, Ryan Peters, Jingyue Jia, Michal Mudd, Michelle Salemi, Lee Allers, Ruheena Javed, Thabata L A Duque, Masroor A Paddar, Einar S Trosdal, Brett Phinney, Vojo Deretic.

ATG5 is a part of the E3 ligase directing lipidation of ATG8 proteins, a process central to membrane atg8ylation and canonical autophagy. Loss of Atg5 in myeloid cells causes early mortality in murine models of tuberculosis. This in vivo phenotype is specific to ATG5. Here, we show using human cell lines that absence of ATG5, but not of other ATGs directing canonical autophagy, promotes lysosomal exocytosis and secretion of extracellular vesicles and, in murine Atg5fl/fl LysM-Cre neutrophils, their excessive degranulation. This is due to lysosomal disrepair in ATG5 knockout cells and the sequestration by an alternative conjugation complex, ATG12-ATG3, of ESCRT protein ALIX, which acts in membrane repair and exosome secretion. These findings reveal a previously undescribed function of ATG5 in its host-protective role in murine experimental models of tuberculosis and emphasize the significance of the branching aspects of the atg8ylation conjugation cascade beyond the canonical autophagy.

Keywords: ATG5; ESCRT; SARS-CoV-2; atg8ylation; autophagy; coronavirus; exosomes; lysosome; neutrophils; tuberculosis

DOI: https://doi.org/10.1016/j.devcel.2023.03.014

Autophagy. 2023 Apr 13. 1-2

STING recruits WIPI2 for autophagosome formation.

Wei Wan, Wei Liu.

Induction of autophagy is a primordial function of the cGAS-STING pathway. However, the molecular mechanisms regulating autophagosome formation during STING-induced autophagy remain largely unknown. Recently, we reported that STING directly interacts with WIPI2 to recruit WIPI2 onto STING-positive vesicles for LC3 lipidation and autophagosome formation. We found that STING and PtdIns3P competitively bind to the FRRG motif of WIPI2, resulting in a mutual inhibition between STING-induced and PtdIns3P-dependent autophagy. We also showed that STING-WIPI2 interaction is necessary for cells to clear cytoplasmic DNA and attenuate activated cGAS-STING signaling. In summary, by identifying the interaction between STING and WIPI2, our study revealed a mechanism that allows STING to bypass the canonical upstream machinery to induce autophagosome formation.Abbreviations: ATG: autophagy-related; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; cGAMP: cyclic GMP-AMP; cGAS: cyclic GMP-AMP synthase; ER: endoplasmic reticulum; ERGIC: ER-Golgi intermediate compartment; IRF3: interferon regulatory factor 3; PtdIns3P: phosphatidylinositol-3-phosphate; SQSTM1: sequestosome 1; STING: stimulator of interferon genes; TBK1: TANK-binding kinase 1; ULK1: unc-51 like autophagy activating kinase 1; WIPI2: WD repeat domain, phosphoinositide interacting 2.

Keywords: Autophagosome; STING; WIPI2; autophagy; cGAS

DOI: https://doi.org/10.1080/15548627.2023.2202108

Autophagy Rep. 2023 ;pii: 2178996. [Epub ahead of print]2(1):

AUTOPHAGY IN THE EYE: FROM PHYSIOLOGY TO PATHOPHYSOLOGY.

Paloma B Liton, Kathleen Boesze-Battaglia, Michael E Boulton, Patricia Boya, Thomas A Ferguson, Ian G Ganley, Anu Kauppinnen, Gordon W Laurie, Noboru Mizushima, Hideaki Morishita, Rossella Russo, Jaya Sadda, Rajalekshmy Shyam, Debasish Sinha, Debra A Thompson, David N Zacks.

Autophagy is a catabolic self-degradative pathway that promotes the degradation and recycling of intracellular material through the lysosomal compartment. Although first believed to function in conditions of nutritional stress, autophagy is emerging as a critical cellular pathway, involved in a variety of physiological and pathophysiological processes. Autophagy dysregulation is associated with an increasing number of diseases, including ocular diseases. On one hand, mutations in autophagy-related genes have been linked to cataracts, glaucoma, and corneal dystrophy; on the other hand, alterations in autophagy and lysosomal pathways are a common finding in essentially all diseases of the eye. Moreover, LC3-associated phagocytosis, a form of non-canonical autophagy, is critical in promoting visual cycle function. This review collects the latest understanding of autophagy in the context of the eye. We will review and discuss the respective roles of autophagy in the physiology and/or pathophysiology of each of the ocular tissues, its diurnal/circadian variation, as well as its involvement in diseases of the eye.

Keywords: AMD; RGC; RPE; autophagy; cataracts; cornea; corneal dystrophy; dry eye; eye; eye diseases; glaucoma; lens; lysosomes; outflow pathway; photoreceptors; retina; retinal detachment; retinal epithelial cells; retinal ganglion cells; retinitis pigmentosa; trabecular meshwork; vision cycle

DOI: https://doi.org/10.1080/27694127.2023.2178996

Nat Microbiol. 2023 Apr 10.

Autophagy restricts Mycobacterium tuberculosis during acute infection in mice.

Guillaume R Golovkine, Allison W Roberts, Huntly M Morrison, Rafael Rivera-Lugo, Rita M McCall, Hannah Nilsson, Nicholas E Garelis, Teresa Repasy, Michael Cronce, Jonathan Budzik, Erik Van Dis, Lauren M Popov, Gabriel Mitchell, Reena Zalpuri, Danielle Jorgens, Jeffery S Cox.

Whether or not autophagy has a role in defence against Mycobacterium tuberculosis infection remains unresolved. Previously, conditional knockdown of the core autophagy component ATG5 in myeloid cells was reported to confer extreme susceptibility to M. tuberculosis in mice, whereas depletion of other autophagy factors had no effect on infection. We show that doubling cre gene dosage to more robustly deplete ATG16L1 or ATG7 resulted in increased M. tuberculosis growth and host susceptibility in mice, although ATG5-depleted mice are more sensitive than ATG16L1- or ATG7-depleted mice. We imaged individual macrophages infected with M. tuberculosis and identified a shift from apoptosis to rapid necrosis in autophagy-depleted cells. This effect was dependent on phagosome permeabilization by M. tuberculosis. We monitored infected cells by electron microscopy, showing that autophagy protects the host macrophage by partially reducing mycobacterial access to the cytosol. We conclude that autophagy has an important role in defence against M. tuberculosis in mammals.

DOI: https://doi.org/10.1038/s41564-023-01354-6