bims-auttor 2021-02-21 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2021–02–21
23 papers selected by
Viktor Korolchuk, Newcastle University

Regulation of Autophagy Enzymes by Nutrient Signaling.
Bulk autophagy induction and life extension is achieved when iron is the only limited nutrient in Saccharomyces cerevisiae.
RNF167 activates mTORC1 and promotes tumorigenesis by targeting CASTOR1 for ubiquitination and degradation.
Enterovirus 71 induces autophagy in mice via mTOR inhibition and ERK pathway activation.
Identification of Novel Lipid Droplet Factors that Regulate Lipophagy and Cholesterol Efflux in Macrophage Foam Cells.
Crosstalk between exosomes and autophagy: A review of molecular mechanisms and therapies.
Assessing Autophagy in Microglia: A Two-Step Model to Determine Autophagosome Formation, Degradation, and Net Turnover.
Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids.
Causes and consequences of DNA damage-induced autophagy.
Enhanced Autophagy in GAB1-Deficient Vascular Endothelial Cells Is Responsible for Atherosclerosis Progression.
Targeting PRAS40: a novel therapeutic strategy for human diseases.
The functions of autophagy at the tumour-immune interface.
Regulation and metabolic functions of mTORC1 and mTORC2.
Non-canonical autophagy functions of ATG16L1 in epithelial cells limit lethal infection by influenza A virus.
Resveratrol promotes lysosomal function via ER calcium-dependent TFEB activation to ameliorate lipid accumulation.
Advanced single-cell pooled CRISPR screening identifies C19orf53 required for cell proliferation based on mTORC1 regulators.
The ATG4 protease integrates redox and stress signals to regulate autophagy.
Suppression of optineurin impairs the progression of hepatocellular carcinoma through regulating mitophagy.
Taurine ameliorates axonal damage in sciatic nerve of diabetic rats and high glucose exposed DRG neuron by PI3K/Akt/mTOR-dependent pathway.
Autophagy in liver diseases.
THOC4 regulates energy homeostasis by stabilizing TFEB mRNA during prolonged starvation.
PFKP facilitates Atg4B phosphorylation during amino acid deprivation-induced autophagy.
An autophagy-related protein Becn2 regulates cocaine reward behaviors in the dopaminergic system.

Trends Biochem Sci. 2021 Feb 13. pii: S0968-0004(21)00020-7. [Epub ahead of print]

Regulation of Autophagy Enzymes by Nutrient Signaling.

Karyn E King, Truc T Losier, Ryan C Russell.

  Autophagy is the primary catabolic program of the cell that promotes survival in response to metabolic stress. It is tightly regulated by a suite of kinases responsive to nutrient status, including mammalian target of rapamycin complex 1 (mTORC1), AMP-activated protein kinase (AMPK), protein kinase C-α (PKCα), MAPK-activated protein kinases 2/3 (MAPKAPK2/3), Rho kinase 1 (ROCK1), c-Jun N-terminal kinase 1 (JNK), and Casein kinase 2 (CSNK2). Here, we highlight recently uncovered mechanisms linking amino acid, glucose, and oxygen levels to autophagy regulation through mTORC1 and AMPK. In addition, we describe new pathways governing the autophagic machinery, including the Unc-51-like (ULK1), vacuolar protein sorting 34 (VPS34), and autophagy related 16 like 1 (ATG16L1) enzyme complexes. Novel downstream targets of ULK1 protein kinase are also discussed, such as the ATG16L1 subunit of the microtubule-associated protein 1 light chain 3 (LC3)-lipidating enzyme and the ATG14 subunit of the VPS34 complex. Collectively, we describe the complexities of the autophagy pathway and its role in maintaining cellular nutrient homeostasis during times of starvation.

Keywords:  AMPK; ATG complexes; amino acids; glucose; mTORC1; oxygen

DOI:  https://doi.org/10.1016/j.tibs.2021.01.006
Biochem J. 2021 Jan 28. pii: BCJ20200849. [Epub ahead of print]

Bulk autophagy induction and life extension is achieved when iron is the only limited nutrient in Saccharomyces cerevisiae.

Sandra Montella-Manuel, Nuria Pujol-Carrion, Mónica A Mechoud, Maria Angeles de la Torre-Ruiz.

  We have investigated the effects that iron limitation provokes in Saccharomyces cerevisiae exponential cultures. We have demonstrated that one primary response is the induction of bulk autophagy mediated by TORC1. Coherently, Atg13 became dephosphorylated whereas Atg1 appeared phosphorylated. The signal of iron deprivation requires Tor2/Ypk1 activity and the inactivation of Tor1 leading to Atg13 dephosphorylation, thus triggering the autophagy process. Iron replenishment in its turn, reduces autophagy flux through the AMPK Snf1 and the subsequent activity of the iron responsive transcription factor, Aft1. This signalling converges in Atg13 phosphorylation mediated by Tor1. Iron limitation promotes accumulation of trehalose and the increase in stress resistance leading to a quiescent state in cells. All these effects contribute to the extension of the chronological life, in a manner totally dependent on autophagy activation.

Keywords:  Iron metabolism; SNF1/AMPK; TOR2/YPK1; TORC1; autophagy; cell signalling

DOI:  https://doi.org/10.1042/BCJ20200849
Nat Commun. 2021 02 16. 12(1): 1055

RNF167 activates mTORC1 and promotes tumorigenesis by targeting CASTOR1 for ubiquitination and degradation.

Tingting Li, Xian Wang, Enguo Ju, Suzane Ramos da Silva, Luping Chen, Xinquan Zhang, Shan Wei, Shou-Jiang Gao.

mTORC1, a central controller of cell proliferation in response to growth factors and nutrients, is dysregulated in cancer. Whereas arginine activates mTORC1, it is overridden by high expression of cytosolic arginine sensor for mTORC1 subunit 1 (CASTOR1). Because cancer cells often encounter low levels of nutrients, an alternative mechanism might exist to regulate CASTOR1 expression. Here we show K29-linked polyubiquitination and degradation of CASTOR1 by E3 ubiquitin ligase RNF167. Furthermore, AKT phosphorylates CASTOR1 at S14, significantly increasing its binding to RNF167, and hence its ubiquitination and degradation, while simultaneously decreasing its affinity to MIOS, leading to mTORC1 activation. Therefore, AKT activates mTORC1 through both TSC2- and CASTOR1-dependent pathways. Several cell types with high CASTOR1 expression are insensitive to arginine regulation. Significantly, AKT and RNF167-mediated CASTOR1 degradation activates mTORC1 independent of arginine and promotes breast cancer progression. These results illustrate a mTORC1 regulating mechanism and identify RNF167 as a therapeutic target for mTORC1-dysregulated diseases.

DOI: https://doi.org/10.1038/s41467-021-21206-3
Life Sci. 2021 Feb 11. pii: S0024-3205(21)00173-9. [Epub ahead of print]271 119188

Enterovirus 71 induces autophagy in mice via mTOR inhibition and ERK pathway activation.

Baixin Wang, Yuanzhi Zhu, Lei Liu, Binshan Wang, Mei Chen, Jingtao Wang, Limin Yang, JiGuang Liu.

   AIMS: Enterovirus 71 (EV71) is one of the main viruses that cause hand-foot-mouth disease; however, its pathogenic mechanism remains unclear. This study characterized the relationship between EV71 infection and autophagy in vivo and explored the molecular mechanism underlying EV71-induced autophagy.
MATERIALS AND METHODS: A mouse model of EV71 infection was prepared by intraperitoneally injecting one-day-old BALB/c suckling mice with 30 μL/g of EV71 virus stock solution for 3 days. The behavior, fur condition, weight, and mice mortality were monitored, and disease scores were calculated. The pathological damage to the brain, lung, and muscle tissues after the viral infection was assessed by hematoxylin and eosin staining. Western blot and immunofluorescence analyses were used to detect the expression levels of viral protein 1, Beclin-1, microtubule-associated protein light chain 3B, mammalian target of rapamycin (mTOR), phosphorylated (p)-mTOR, extracellular signal-regulated protein kinase (ERK) 1/2, and p-ERK.
KEY FINDINGS: EV71 infection can trigger autophagy in the brains, lungs, and muscles of infected mice. The autophagy response triggered by EV71 is achieved by the simultaneous mTOR inhibition and the ERK pathway activation. Blocking the mTOR pathway may aggravate autophagy, whereas ERK inhibition alleviates autophagy but cannot completely prevent it.
SIGNIFICANCE: EV71 infection can induce autophagy in mice, involving mTOR and ERK signaling pathways. These two signaling pathways are independent and do not interfere with each other.

Keywords:  Autophagy; Enterovirus 71; Extracellular signal-regulated kinase; Hand-foot-mouth disease; Mammalian target of rapamycin

DOI:  https://doi.org/10.1016/j.lfs.2021.119188
Autophagy. 2021 Feb 16.

Identification of Novel Lipid Droplet Factors that Regulate Lipophagy and Cholesterol Efflux in Macrophage Foam Cells.

Sabrina Robichaud, Garrett Fairman, Viyashini Vijithakumar, Esther Mak, David P Cook, Alexander R Pelletier, Sylvain Huard, Barbara C Vanderhyden, Daniel Figeys, Mathieu Lavallée-Adam, Kristin Baetz, Mireille Ouimet.

  Macrophage autophagy is a highly anti-atherogenic process that promotes the catabolism of cytosolic lipid droplets (LDs) to maintain cellular lipid homeostasis. Selective autophagy relies on tags such as ubiquitin and a set of selectivity factors including selective autophagy receptors (SARs) to label specific cargo for degradation. Originally described in yeast cells, 'lipophagy' refers to the degradation of LDs by autophagy. Yet, how LDs are targeted for autophagy is poorly defined. Here, we employed mass spectrometry to identify lipophagy factors within the macrophage foam cell LD proteome. In addition to structural proteins (e.g., PLIN2), metabolic enzymes (e.g., ACSL) and neutral lipases (e.g., PNPLA2), we found the association of proteins related to the ubiquitination machinery (e.g., AUP1) and autophagy (e.g., HMGB, YWHA/14-3-3 proteins). The functional role of candidate lipophagy factors (a total of 91) was tested using a custom siRNA array combined with high-content cholesterol efflux assays. We observed that knocking down several of these genes, including Hmgb1, Hmgb2, Hspa5, and Scarb2, significantly reduced cholesterol efflux, and SARs SQSTM1/p62, NBR1 and OPTN localized to LDs, suggesting a role for these in lipophagy. Using yeast lipophagy assays, we established a genetic requirement for several candidate lipophagy factors in lipophagy, including HSPA5, UBE2G2 and AUP1. Our study is the first to systematically identify several LD-associated proteins of the lipophagy machinery, a finding with important biological and therapeutic implications. Targeting these to selectively enhance lipophagy to promote cholesterol efflux in foam cells may represent a novel strategy to treat atherosclerosis.

Keywords:  Autophagy; cholesterol efflux; lipid droplet; lipolysis; lipophagy; macrophage foam cell

DOI:  https://doi.org/10.1080/15548627.2021.1886839
J Cell Mol Med. 2021 Jan 27.

Crosstalk between exosomes and autophagy: A review of molecular mechanisms and therapies.

Huifang Xing, Jin Tan, Yuyang Miao, Yingmei Lv, Qiang Zhang.

  Exosomes are extracellular vesicles that primarily exist in bodily fluids such as blood. Autophagy is an intracellular degradation process, which, along with exosomes, can significantly influence human health and has therefore attracted considerable attention in recent years. Exosomes have been shown to regulate the intracellular autophagic process, which, in turn, affects the circulating exosomes. However, crosstalk between exosomal and autophagic pathways is highly complex, depends primarily on the environment, and varies greatly in different diseases. In addition, studies have demonstrated that exosomes, from specific cell, can mitigate several diseases by regulating autophagy, which can also affect the excessive release of some harmful exosomes. This phenomenon lays a theoretical foundation for the improvement of many diseases. Herein, we review the mechanisms and clinical significance of the association and regulation of exosomes and autophagy, in order to provide a new perspective for the prevention and treatment of associated diseases.

Keywords:  autophagy; exosomes; mesenchymal stem cells; miRNA; molecular mechanisms; therapies

DOI:  https://doi.org/10.1111/jcmm.16276
Front Immunol. 2020 ;11 620602

Assessing Autophagy in Microglia: A Two-Step Model to Determine Autophagosome Formation, Degradation, and Net Turnover.

Ainhoa Plaza-Zabala, Virginia Sierra-Torre, Amanda Sierra.

  Autophagy is a complex process that encompasses the enclosure of cytoplasmic debris or dysfunctional organelles in membranous vesicles, the autophagosomes, for their elimination in the lysosomes. Autophagy is increasingly recognized as a critical process in macrophages, including microglia, as it finely regulates innate immune functions such as inflammation. A gold-standard method to assess its induction is the analysis of the autophagic flux using as a surrogate the expression of the microtubule-associated light chain protein 3 conjugated to phosphatidylethanolamine (LC3-II) by Western blot, in the presence of lysosomal inhibitors. Therefore, the current definition of autophagy flux actually puts the focus on the degradation stage of autophagy. In contrast, the most important autophagy controlling genes that have been identified in the last few years in fact target early stages of autophagosome formation. From a biological standpoint is therefore conceivable that autophagosome formation and degradation are independently regulated and we argue that both stages need to be systematically analyzed. Here, we propose a simple two-step model to understand changes in autophagosome formation and degradation using data from conventional LC3-II Western blot, and test it using two models of autophagy modulation in cultured microglia: rapamycin and the ULK1/2 inhibitor, MRT68921. Our two-step model will help to unravel the effect of genetic, pharmacological, and environmental manipulations on both formation and degradation of autophagosomes, contributing to dissect out the role of autophagy in physiology and pathology in microglia as well as other cell types.

Keywords:  LC3; autophagosome; autophagy; degradation; formation; microglia

DOI:  https://doi.org/10.3389/fimmu.2020.620602
Proc Natl Acad Sci U S A. 2021 Feb 23. pii: e2014941118. [Epub ahead of print]118(8):

Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids.

Gabriel Talaia, Joseph Amick, Shawn M Ferguson.

  PQLC2, a lysosomal cationic amino acid transporter, also serves as a sensor that responds to scarcity of its substrates by recruiting a protein complex composed of C9orf72, SMCR8, and WDR41 to the surface of lysosomes. This protein complex controls multiple aspects of lysosome function. Although it is known that this response to changes in cationic amino acid availability depends on an interaction between PQLC2 and WDR41, the underlying mechanism for the regulated interaction is not known. In this study, we present evidence that the WDR41-PQLC2 interaction is mediated by a short peptide motif in a flexible loop that extends from the WDR41 β-propeller and inserts into a cavity presented by the inward-facing conformation of PQLC2. The data support a transceptor model wherein conformational changes in PQLC2 related to substrate transport regulate the availability of the WDR41-binding site on PQLC2 and mediate recruitment of the WDR41-SMCR8-C9orf72 complex to the surface of lysosomes.

Keywords:  C9orf72; PQLC2; lysosome; transceptor; transporter

DOI:  https://doi.org/10.1073/pnas.2014941118
Matrix Biol. 2021 Feb 15. pii: S0945-053X(21)00027-5. [Epub ahead of print]

Causes and consequences of DNA damage-induced autophagy.

Thomas Juretschke, Petra Beli.

  Autophagy is a quality control pathway that maintains cellular homeostasis by recycling surplus and dysregulated cell organelles. Identification of selective autophagy receptors demonstrated the existence of pathways that selectively degrade organelles, protein aggregates or pathogens. Interestingly, different types of DNA damage can induce autophagy and autophagy-deficiency leads to genomic instability. Recent studies provided first insights into the pathways that connect autophagy with the DNA damage response. However, the physiological role of autophagy and the identity of its targets after DNA damage remain enigmatic. In this review, we summarize recent literature on the targets of autophagy and mechanisms that lead to its activation after DNA damage, and discuss potential consequences of DNA damage-induced autophagy.

Keywords:  DNA damage response (DDR); DNA repair; autophagy; genomic stability; selective autophagy

DOI:  https://doi.org/10.1016/j.matbio.2021.02.004
Front Physiol. 2020 ;11 559396

Enhanced Autophagy in GAB1-Deficient Vascular Endothelial Cells Is Responsible for Atherosclerosis Progression.

Xin Qian, Han Wang, Yuli Wang, Jiaquan Chen, Xiangjiang Guo, Haoyu Deng.

  Autophagy is a host machinery that controls cellular health. Dysfunction of autophagy is responsible for the pathogenesis of many human diseases that include atherosclerosis obliterans (ASO). Physiologically, host autophagy removes aging organelles and delays the formation of atherosclerotic plaque. However, in ischemia event, dysregulated autophagy can be induced to trigger autosis, leading to an inevitable cellular death. Grb2-associated binder 1 (GAB1) is a docking/scaffolding adaptor protein that regulates many cell processes including autophagy. Our study first reported that the protein expression of GAB1 significantly decreased in ASO. Mechanically, our results showed that inhibition of Akt (protein kinase B), the upstream of mTOR (mechanistic target of rapamycin), significantly enhanced autophagy by demonstrating the downregulation of p62/Sequestosome 1 expression and the upregulation of the ratio of LC3II/LC3I. Conversely, we found that the inhibition of ERK1/2 (extracellular signal-regulated kinases1/2), p38, and JNK (c-Jun N-terminal kinase) signaling pathway, respectively, significantly inhibited autophagy by demonstrating the upregulation of p62 expression and the downregulation of the ratio of LC3II/LC3I. Further, we demonstrated that knockdown of GAB1 significantly increased autophagy in HUVECs (human umbilical vein endothelial cells) via activation of MAPK (mitogen-activated protein kinase) pathways that include ERK1/2, p38, and JNK. Moreover, we found that knockdown of GAB1 profoundly inhibited HUVEC proliferation, migration, and tube formation. Taken together, this study first suggests that GAB1 is a key regulator of autophagy in HUVECs. Targeting GAB1 may serve as a potential strategy for the atherosclerosis treatment.

Keywords:  Gab1; atherosclerosis; autophagy; endothelia cell; peripheral artery disease (PAD)

DOI:  https://doi.org/10.3389/fphys.2020.559396
J Drug Target. 2021 Jan 28. 1-44

Targeting PRAS40: a novel therapeutic strategy for human diseases.

Qun Zhou, Shengsong Tang, Xianhui Zhang, Linxi Chen.

  Proline-rich Akt substrate of 40 kD (PRAS40) is not only the substrate of protein kinase B (PKB/Akt), but also the binding protein of 14-3-3 protein. PRAS40 is expressed in a variety of tissues in vivo and has multiple phosphorylation sites, which its activity is closely related to phosphorylation. Studies have shown that PRAS40 is involved in regulating cell growth, cell apoptosis, oxidative stress, autophagy and angiogenesis, as well as various of signaling pathways such as mammalian target of mammalian target rapamycin (mTOR), protein kinase B (Akt), nuclear factor kappa-B(NF-κB), proto-oncogene serine/threonine-protein kinase PIM-1(PIM1) and pyruvate kinase M2 (PKM2). The interactive roles between PRAS40 and these signal proteins were analyzed by bioinformatics in this paper. Moreover, it is of great necessity for analyze the important roles of PRAS40 in some human diseases including cardiovascular disease, ischemia-reperfusion injury, neurodegenerative disease, cancer, diabetes and other metabolic diseases. Finally, the effects of miRNA on the regulation of PRAS40 function and the occurrence and development of PRAS40-related diseases are also discussed. Overall, PRAS40 is expected to be a drug target and provide a new treatment strategy for human diseases.

Keywords:  Cancer; PIM1; PKM2; PRAS40; ischemia-reperfusion injury

DOI:  https://doi.org/10.1080/1061186X.2021.1882470
J Cell Mol Med. 2021 Feb 18.

The functions of autophagy at the tumour-immune interface.

Xiaobo Luo, Yan Qiu, Palani Dinesh, Wang Gong, Lu Jiang, Xiaodong Feng, Jing Li, Yuchen Jiang, Yu L Lei, Qianming Chen.

  Autophagy is frequently induced in the hypoxic tumour microenvironment. Accumulating evidence reveals important functions of autophagy at the tumour-immune interface. Herein, we propose an update on the roles of autophagy in modulating tumour immunity. Autophagy promotes adaptive resistance of established tumours to the cytotoxic effects of natural killer cells (NKs), macrophages and effector T cells. Increased autophagic flux in tumours dampen their immunogenicity and inhibits the expansion of cytotoxic T lymphocytes (CTLs) by suppressing the activation of STING type I interferon signalling (IFN-I) innate immune sensing pathway. Autophagy in suppressive tumour-infiltrating immune subsets maintains their survival through metabolic remodelling. On the other hand, autophagy is involved in the antigen processing and presentation process, which is essential for anti-tumour immune responses. Genetic deletion of autophagy induces spontaneous tumours in some models. Thus, the role of autophagy is context-dependent. In summary, our review has revealed the dichotomous roles of autophagy in modulating tumour immunity. Broad targeting of autophagy may not yield maximal benefits. The characterization of specific genes regulating tumour immunogenicity and innovation in targeted delivery of autophagy inhibitors into certain tumours are among the most urgent tasks to sensitize cold cancers to immunotherapy.

Keywords:  autophagy; immune cell; tumour cell; tumour immunity

DOI:  https://doi.org/10.1111/jcmm.16331
Physiol Rev. 2021 Feb 18.

Regulation and metabolic functions of mTORC1 and mTORC2.

Angelia Szwed, Eugene Kim, Estela Jacinto.

  Cells metabolize nutrients for biosynthetic and bioenergetic needs to fuel growth and proliferation. The uptake of nutrients from the environment and their intracellular metabolism is a highly controlled process that involves crosstalk between growth signaling and metabolic pathways. Despite constant fluctuations in nutrient availability and environmental signals, normal cells restore metabolic homeostasis to maintain cellular functions and prevent disease. A central signaling molecule that integrates growth with metabolism is the mechanistic target of rapamycin (mTOR). mTOR is a protein kinase that responds to levels of nutrients and growth signals. mTOR forms two protein complexes, mTORC1, which is sensitive to rapamycin and mTORC2, which is not directly inhibited by this drug. Rapamycin has facilitated the discovery of the various functions of mTORC1 in metabolism. Genetic models that disrupt either mTORC1 or mTORC2 have expanded our knowledge on their cellular, tissue as well as systemic functions in metabolism. Nevertheless, our knowledge on the regulation and functions of mTORC2, particularly in metabolism, has lagged behind. Since mTOR is an important target for cancer, aging and other metabolism-related pathologies, understanding the distinct and overlapping regulation and functions of the two mTOR complexes is vital for the development of more effective therapeutic strategies. This review will discuss the key discoveries and recent findings on the regulation and metabolic functions of the mTOR complexes. We highlight findings from cancer models, but also discuss other examples of the mTOR-mediated metabolic reprogramming occurring in stem and immune cells, type 2 diabetes/obesity, neurodegenerative disorders and aging.

Keywords:  cancer metabolism; mTOR; mTORC; metabolic reprogramming; metabolism

DOI:  https://doi.org/10.1152/physrev.00026.2020
EMBO J. 2021 Feb 15. e105543

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

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

  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.

Keywords:  ATG16L1 WD Domain; cytokine storm; influenza; intrinsic defence; non-canonical autophagy

DOI:  https://doi.org/10.15252/embj.2020105543
Biochem J. 2021 Feb 19. pii: BCJ20200676. [Epub ahead of print]

Resveratrol promotes lysosomal function via ER calcium-dependent TFEB activation to ameliorate lipid accumulation.

Rong Shao, Jiahui Shi, Kaili Du, Na Wang, Weijie Cai, Siyu Liu, Zongxian Ding, Yihan Wang, Dan Li.

  Abnormal lipid accumulation is associated to the development of metabolic diseases such as hepatic steatosis and lipid storage diseases. Pharmacological agents that can attenuate lipid accumulation therefore have therapeutic potentials for these diseases. Resveratrol (RSV), a natural active substance found in fruits and nuts, has been reported to effectively reduce the intracellular lipid accumulation, but the underlying mechanisms of RSV remain elusive. Here, we show that RSV triggers an endoplasmic reticulum (ER)- Ca2+ signaling that activates transcriptional factor EB (TFEB), a master transcriptional regulator of autophagic and lysosomal biogenesis. Moreover, RSV activates protein phosphatase 2A (PP2A), which binds and dephosphorylates TFEB, promoting its nuclear translocation and the expression of TFEB target genes required for autophagosome and lysosomal biogenesis. Notably, genetic inhibition of TFEB significantly ameliorates RSV-mediated lipid clearance. Taken together, these data link RSV-induced ER calcium signaling, PP2A and TFEB activation to promote autophagy and lysosomal function, by which RSV may trigger a cellular self-defense mechanism that effectively mitigate lipid accumulation commonly associated with many metabolic diseases.

Keywords:  Lysosome; PP2A; Resveratrol; TFEB

DOI:  https://doi.org/10.1042/BCJ20200676
Cell Biol Toxicol. 2021 Feb 13.

Advanced single-cell pooled CRISPR screening identifies C19orf53 required for cell proliferation based on mTORC1 regulators.

Yulong Tang, Simeng Liao, Guang Liu, Xia Xiong, Hongnan Liu, Fengna Li, Zhiliang Tan, Xiangfeng Kong, Yulong Yin, Bie Tan.

  Multiplexed single-cell CRISPR screening has accelerated the systematic dissection of biological discoveries; however, the efficiency of CRISPR-based gene knockout has inherent limitations. Here, we present DoNick-seq, an advanced method for facilitating gene knockout and reducing off-target activity. We re-engineered two popular plasmid constructs suitable for use in pooled CRISPR screening of the single-cell transcriptome. We then used DoNick-seq to probe mTORC1 regulators and obtain genomic perturbation and transcriptome profiles from the same cell. Thus, DoNick-seq enabled us to simultaneously evaluate multiple gene interactions and the effect of amino acid depletion. By analyzing more than 20,000 cells from two cell lines, DoNick-seq efficiently identified gene targets, cell numbers, and cellular profiles. Our data also revealed the characteristics of mTORC1 negative and positive regulators, thereby shedding new insights into the mechanisms regulating cell growth and inhibition. We demonstrate that mTORC1 hyperactivation exhausts cellular free amino acids via increased proliferation ability. Furthermore, DoNick-seq identified the gene C19orf53, which mediates excessive cell proliferation, resulting in metabolic imbalance, and greatly enhances oxidative stress in response to toxins. Thus, our findings suggest that DoNick-seq facilitates high-throughput functional dissection of complex cellular responses at the single-cell level and increases the accuracy of CRISPR single-cell transcriptomics.

Keywords:  Amino acid sensing pathway; CRISPR-Cas9; Cell proliferation; Single-cell transcriptome; mTORC1 regulators

DOI:  https://doi.org/10.1007/s10565-021-09586-0
J Exp Bot. 2021 Feb 15. pii: erab063. [Epub ahead of print]

The ATG4 protease integrates redox and stress signals to regulate autophagy.

María Esther Pérez-Pérez, Stéphane D Lemaire, José Luis Crespo.

  Autophagy is a highly conserved degradative pathway that ensures cellular homeostasis through the removal of damaged or useless intracellular components including proteins, membranes or even entire organelles. A main hallmark of autophagy is the biogenesis of autophagosomes, double membrane vesicles that engulf and transport to the vacuole the material to be degraded and recycled. The formation of autophagosomes responds to integrated signals produced as consequence of metabolic reactions or different types of stress and is mediated by the coordinated action of core autophagy-related (ATG) proteins. ATG4 is a key Cys-protease with a dual function in both ATG8 lipidation and free ATG8 recycling whose balance is crucial for proper biogenesis of the autophagosome. ATG4 is conserved in the green lineage and its regulation by different post-translational modifications has been reported in the model systems Chlamydomonas reinhardtii and Arabidopsis thaliana. In this review, we discuss the major role of ATG4 in the integration of stress and redox signals that regulate autophagy in algae and plants.

Keywords:  ATG4; Chlamydomonas; ROS; autophagy; microalga; plant; protease; redox regulation; stress

DOI:  https://doi.org/10.1093/jxb/erab063
Cancer Med. 2021 Feb 18.

Suppression of optineurin impairs the progression of hepatocellular carcinoma through regulating mitophagy.

Shoichi Inokuchi, Tomoharu Yoshizumi, Takeo Toshima, Shinji Itoh, Kyohei Yugawa, Noboru Harada, Hiroyuki Mori, Takasuke Fukuhara, Yoshiharu Matsuura, Masaki Mori.

  Autophagy removes damaged organelles to inhibit malignant transformation during tumor initiation. Once a cancer matures, it uses the autophagic pathway as an energy source. Optineurin (OPTN) is an autophagy adaptor protein that recruits microtubule-associated protein 1 light chain 3, an autophagosome marker, to the autophagosome. Despite studies of the relation between cancer progression and autophagy adaptor proteins, there are no reports to our knowledge of a correlation between hepatocellular carcinoma (HCC) and OPTN. We aimed here to investigate the effects of OPTN expression on HCC progression through autophagy. Immunohistochemistry was used to measure the OPTN expression in the tissues of 141 Japanese patients with HCC. The effects of OPTN expression on HCC progression and mitophagy were assessed using an OPTN knockout (KO) cell line in vitro. We used this KO cell line to establish and exploit a mouse model of HCC to determine the effects of OPTN expression on tumor progression. Immunohistochemical analysis showed that patients with elevated expression of OPTN experienced shorter overall survival (OS) and recurrence-free survival (RFS). OPTN KO cells proliferated relatively slower versus wild-type (WT) cells in vitro. Western blot analysis showed that mitophagy was suppressed in OPTN KO cells, and ATP synthesis and beta-oxidation were reduced. The mouse model of HCC showed that OPTN KO cells formed smaller tumors versus WT cells less 10 weeks after implantation. Overall, the present findings suggest that OPTN is a key mediator of mitophagy that contributes to HCC progression through mitochondrial energy production.

Keywords:  adaptor protein; autophagy; beta-oxidation; liver; mitochondria

DOI:  https://doi.org/10.1002/cam4.3519
Amino Acids. 2021 Feb 18.

Taurine ameliorates axonal damage in sciatic nerve of diabetic rats and high glucose exposed DRG neuron by PI3K/Akt/mTOR-dependent pathway.

Mengren Zhang, Xiaoxia Shi, Mengxin Luo, Qi Lan, Hayan Ullah, Cong Zhang, Shuangyue Li, Xiaochi Chen, Yachen Wang, Fengyuan Piao.

  Diabetic peripheral neuropathy (DPN) is a common complication of diabetes and axonopathy is its main pathological feature. Previous studies suggested an advantage of taurine against diabetes. However, there are few reports which study the effect of taurine against axonopathy. In this study, we confirmed that taurine significantly decreased blood glucose level, mitigated insulin resistance and improved dysfunctional nerve conduction in diabetic rats. Taurine corrected damaged axonal morphology of sciatic nerve in diabetic rats and induced axon outgrowth of Dorsal root ganglion (DRG) neurons exposed to high glucose. Taurine up-regulated phosphorylation levels of PI3K, Akt, and mTOR in sciatic nerve of diabetic rats and DRG neurons exposed to high glucose. However, Akt and mTOR inhibitors (MK-2206 and Rapamycin) blocked the effect of taurine on improving axonal damage. These results indicate that taurine ameliorates axonal damage in sciatic nerve of diabetic rats by activating PI3K/Akt/mTOR signal pathway. Our findings provide taurine as a potential candidate for axonopathy and a new evidence for elucidating protective mechanism of taurine on DPN.

Keywords:  Axonal repair; Diabetic peripheral neuropathy; PI3K/Akt/mTOR pathway; Taurine

DOI:  https://doi.org/10.1007/s00726-021-02957-1
World J Hepatol. 2021 Jan 27. 13(1): 6-65

Autophagy in liver diseases.

Elias Kouroumalis, Argryro Voumvouraki, Aikaterini Augoustaki, Dimitrios N Samonakis.

  Autophagy is the liver cell energy recycling system regulating a variety of homeostatic mechanisms. Damaged organelles, lipids and proteins are degraded in the lysosomes and their elements are re-used by the cell. Investigations on autophagy have led to the award of two Nobel Prizes and a health of important reports. In this review we describe the fundamental functions of autophagy in the liver including new data on the regulation of autophagy. Moreover we emphasize the fact that autophagy acts like a two edge sword in many occasions with the most prominent paradigm being its involvement in the initiation and progress of hepatocellular carcinoma. We also focused to the implication of autophagy and its specialized forms of lipophagy and mitophagy in the pathogenesis of various liver diseases. We analyzed autophagy not only in well studied diseases, like alcoholic and nonalcoholic fatty liver and liver fibrosis but also in viral hepatitis, biliary diseases, autoimmune hepatitis and rare diseases including inherited metabolic diseases and also acetaminophene hepatotoxicity. We also stressed the different consequences that activation or impairment of autophagy may have in hepatocytes as opposed to Kupffer cells, sinusoidal endothelial cells or hepatic stellate cells. Finally, we analyzed the limited clinical data compared to the extensive experimental evidence and the possible future therapeutic interventions based on autophagy manipulation.

Keywords:  Autophagy; Fatty liver disease; Fibrosis; Lipophagy; Liver sinusoidal cells; Mitophagy

DOI:  https://doi.org/10.4254/wjh.v13.i1.6
J Cell Sci. 2021 Feb 15. pii: jcs.248203. [Epub ahead of print]

THOC4 regulates energy homeostasis by stabilizing TFEB mRNA during prolonged starvation.

Toshiharu Fujita, Sayaka Kubo, Tatsuya Shioda, Ayaka Tokumura, Satoshi Minami, Megumi Tsuchiya, Yoshitaka Isaka, Hidesato Ogawa, Maho Hamasaki, Li Yu, Tamotsu Yoshimori, Shuhei Nakamura.

  TFEB, a bHLH transcription factor, is a master regulator of autophagy, lysosome biogenesis, and lipid catabolism. Compared to the post-translational regulation, the regulation of TFEB mRNA stability remains relatively uncharacterized. In this study, we identified the mRNA-binding protein THOC4 as a novel regulator of TFEB. In mammalian cells, siRNA-mediated knockdown of THOC4 decreased the level of TFEB protein to a greater extent than other bHLH transcription factors. THOC4 bound to TFEB mRNA and stabilized it after transcription through maintaining polyA length. We further found that this mode of regulation was conserved in C. elegans and was essential for TFEB mediated lipid break-down which becomes overrepresented during prolonged starvation. Taken together our study reveals the presence of an additional layer of TFEB regulation by THOC4 and provide novel insights into the function TFEB mediating autophagy and lipid metabolism.

Keywords:  : TFEB; Autophagy; Lipid catabolism; MRNA stability; THOC4

DOI:  https://doi.org/10.1242/jcs.248203
Cell Signal. 2021 Feb 16. pii: S0898-6568(21)00044-9. [Epub ahead of print] 109956

PFKP facilitates Atg4B phosphorylation during amino acid deprivation-induced autophagy.

Xiuzhi Li, Lingling Sun, Guokai Yan, Xianghua Yan.

  Atg4B facilitates autophagy by promoting autophagosome maturation through the reversible lipidation and delipidation of LC3. Recent reports have shown that phosphorylation of Atg4B regulates its activity and LC3 processing, leading to modulate autophagy activity. However, the mechanism about how Atg4B phosphorylation is regulated by amino acid deprivation is unclear. Here, we combined the tandem affinity purification with mass spectrometry (MS) to identify the Atg4B-interacting proteins including its well-known partner gamma-aminobutyric acid receptor-associated protein (GABARAP, a homolog of LC3) and phosphofructokinase 1 platelet isoform (PFKP). Further immunoprecipitation assays showed that amino acid deprivation strengthened the interaction between Atg4B and PFKP. By genetic depletion of PFKP using CRISPR/Cas9, we uncovered that PFKP KO reduced degradation of LC3-II and p62 due to a partial block in autophagic flux. MS analysis of Flag-tagged Atg4B identified phosphorylation of Atg4B serine 34 residue (S34) and PFKP serine 386 residue (S386) under amino acid deprivation condition. In vitro kinase assay validated that PFKP functioning as a protein kinase phosphorylated Atg4B at S34. This phosphorylation could enhance Atg4B activity and p62 degradation. In addition, PFKP S386 phosphorylation abundance correlates with Atg4B S34 phosphorylation abundance and autophagy in HEK293T cells. In brief, our findings described that PFKP, a rate-limiting enzyme in the glycolytic pathway, functions as a protein kinase for Atg4B to regulate Atg4B activity and autophagy under amino acid deprivation condition.

Keywords:  Amino acid deprivation; Atg4B; Autophagy; PFKP; Phosphorylation

DOI:  https://doi.org/10.1016/j.cellsig.2021.109956
Sci Adv. 2021 Feb;pii: eabc8310. [Epub ahead of print]7(8):

An autophagy-related protein Becn2 regulates cocaine reward behaviors in the dopaminergic system.

Yoon-Jin Kim, Qingyao Kong, Soh Yamamoto, Kenta Kuramoto, Mei Huang, Nan Wang, Jung Hwa Hong, Tong Xiao, Beth Levine, Xianxiu Qiu, Yanxiang Zhao, Richard J Miller, Hongxin Dong, Herbert Y Meltzer, Ming Xu, Congcong He.

Drug abuse is a foremost public health problem. Cocaine is a widely abused drug worldwide that produces various reward-related behaviors. The mechanisms that underlie cocaine-induced disorders are unresolved, and effective treatments are lacking. Here, we found that an autophagy-related protein Becn2 is a previously unidentified regulator of cocaine reward behaviors. Becn2 deletion protects mice from cocaine-stimulated locomotion and reward behaviors, as well as cocaine-induced dopamine accumulation and signaling, by increasing presynaptic dopamine receptor 2 (D2R) autoreceptors in dopamine neurons. Becn2 regulates D2R endolysosomal trafficking, degradation, and cocaine-induced behaviors via interacting with a D2R-bound adaptor GASP1. Inactivating Becn2 by upstream autophagy inhibitors stabilizes striatal presynaptic D2R, reduces dopamine release and signaling, and prevents cocaine reward in normal mice. Thus, the autophagy protein Becn2 is essential for cocaine psychomotor stimulation and reward through regulating dopamine neurotransmission, and targeting Becn2 by autophagy inhibitors is a potential strategy to prevent cocaine-induced behaviors.

DOI: https://doi.org/10.1126/sciadv.abc8310