bims-auttor 2021-11-07 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2021–11–07
forty papers selected by
Viktor Korolchuk, Newcastle University

A gene toolbox for monitoring autophagy transcription.
Targeting autophagy using small-molecule compounds to improve potential therapy of Parkinson's disease.
Hayatine inhibits amino acid-induced mTORC1 activation as a novel mTOR-Rag A/C interaction disruptor.
Identification of a novel compound that simultaneously impairs the ubiquitin-proteasome system and autophagy.
SHISA5/SCOTIN restrains spontaneous autophagy induction by blocking contact between the ERES and phagophores.
Regulation of mTORC1 by amino acids in mammalian cells: A general picture of recent advances.
PTEN-induced kinase 1 (PINK1) and Parkin: Unlocking a mitochondrial quality control pathway linked to Parkinson's disease.
Emerging roles of ATG7 in human health and disease.
Activation of Akt-mTORC1 signalling reverts cancer-dependent muscle wasting.
Ajugol enhances TFEB-mediated lysosome biogenesis and lipophagy to alleviate non-alcoholic fatty liver disease.
Endothelial cell autophagy keeps neutrophil trafficking under control.
Amino Acid Homeostasis in Mammalian Cells with a Focus on Amino Acid Transport.
Natural compounds in the regulation of proteostatic pathways: An invincible artillery against stress, ageing, and diseases.
Ubiquitination of G3BP1 mediates stress granule disassembly in a context-specific manner.
Mycobacterium bovis induces mitophagy to suppress host xenophagy for its intracellular survival.
Ubiquitination is essential for recovery of cellular activities after heat shock.
Targeting eIF4F translation complex sensitizes B-ALL cells to tyrosine kinase inhibition.
Disruption of morphogenic and growth pathways in lysosomal storage diseases.
The SQSTM1/p62 UBA domain regulates Ajuba localisation, degradation and NF-κB signalling function.
Salicylic acid and the viral virulence factor 2b regulate the divergent roles of autophagy during cucumber mosaic virus infection.
GNS561, a clinical-stage PPT1 inhibitor, is efficient against hepatocellular carcinoma via modulation of lysosomal functions.
Newcastle disease virus degrades SIRT3 via PINK1-PRKN-dependent mitophagy to reprogram energy metabolism in infected cells.
Alternative Mitophagy Protects the Heart Against Obesity-Associated Cardiomyopathy.
Role of autophagy in gastric carcinogenesis.
Autophagy in Viral Infection and Pathogenesis.
Constitutive activation of the PI3K-Akt-mTORC1 pathway sustains the m.3243 A > G mtDNA mutation.
FYVE2, a phosphatidylinositol 3-phosphate effector, interacts with the COPII machinery to control autophagosome formation in Arabidopsis.
Autophagy takes the STING out of DNA sensing.
CHMP2B regulates TDP-43 phosphorylation and cytotoxicity independent of autophagy via CK1.
Visualization of lipophagy using a supramolecular FRET pair.
TSC1 loss increases risk for tauopathy by inducing tau acetylation and preventing tau clearance via chaperone-mediated autophagy.
Autophagy Regulates the Survival of Hair Cells and Spiral Ganglion Neurons in Cases of Noise, Ototoxic Drug, and Age-Induced Sensorineural Hearing Loss.
Induction of osteoclast formation by LOX mutant (LOXG473A) through regulation of autophagy.
Hormetic effect of low doses of rapamycin triggers anti-aging cascades in WRL-68 cells by modulating an mTOR-mitochondria cross-talk.
Radiosensitizing pancreatic cancer via effective autophagy inhibition.
The Genetic Basis of Phenotypic Heterogeneity in the Neuronal Ceroid Lipofuscinoses.
Calcium/calmodulin-dependent protein kinase IV regulates vascular autophagy and insulin signaling through Akt/mTOR/CREB pathway in ob/ob mice.
FAIM regulates autophagy through glutaminolysis in lung adenocarcinoma.
Plasmacytoid dendritic cell activation is dependent on coordinated expression of distinct amino acid transporters.
Mice with disrupted mitochondria used to model Parkinson's disease.

Cell Death Dis. 2021 Nov 02. 12(11): 1044

A gene toolbox for monitoring autophagy transcription.

Matteo Bordi, Rossella De Cegli, Beatrice Testa, Ralph A Nixon, Andrea Ballabio, Francesco Cecconi.

Autophagy is a highly dynamic and multi-step process, regulated by many functional protein units. Here, we have built up a comprehensive and up-to-date annotated gene list for the autophagy pathway, by combining previously published gene lists and the most recent publications in the field. We identified 604 genes and created main categories: MTOR and upstream pathways, autophagy core, autophagy transcription factors, mitophagy, docking and fusion, lysosome and lysosome-related genes. We then classified such genes in sub-groups, based on their functions or on their sub-cellular localization. Moreover, we have curated two shorter sub-lists to predict the extent of autophagy activation and/or lysosomal biogenesis; we next validated the "induction list" by Real-time PCR in cell lines during fasting or MTOR inhibition, identifying ATG14, ATG7, NBR1, ULK1, ULK2, and WDR45, as minimal transcriptional targets. We also demonstrated that our list of autophagy genes can be particularly useful during an effective RNA-sequencing analysis. Thus, we propose our lists as a useful toolbox for performing an informative and functionally-prognostic gene scan of autophagy steps.

DOI: https://doi.org/10.1038/s41419-021-04121-9
Acta Pharm Sin B. 2021 Oct;11(10): 3015-3034

Targeting autophagy using small-molecule compounds to improve potential therapy of Parkinson's disease.

Kai Zhang, Shiou Zhu, Jiamei Li, Tingting Jiang, Lu Feng, Junping Pei, Guan Wang, Liang Ouyang, Bo Liu.

  Parkinson's disease (PD), known as one of the most universal neurodegenerative diseases, is a serious threat to the health of the elderly. The current treatment has been demonstrated to relieve symptoms, and the discovery of new small-molecule compounds has been regarded as a promising strategy. Of note, the homeostasis of the autolysosome pathway (ALP) is closely associated with PD, and impaired autophagy may cause the death of neurons and thereby accelerating the progress of PD. Thus, pharmacological targeting autophagy with small-molecule compounds has been drawn a rising attention so far. In this review, we focus on summarizing several autophagy-associated targets, such as AMPK, mTORC1, ULK1, IMPase, LRRK2, beclin-1, TFEB, GCase, ERRα, C-Abelson, and as well as their relevant small-molecule compounds in PD models, which will shed light on a clue on exploiting more potential targeted small-molecule drugs tracking PD treatment in the near future.

Keywords:  3-MA, 3-methyladenine; 5-HT2A, Serotonin 2A; 5-HT2C, serotonin 2C; A2A, adenosine 2A; AADC, aromatic amino acid decarboxylase; ALP, autophagy-lysosomal pathway; AMPK, 5ʹAMP-activated protein kinase; ATG, autophagy related protein; ATP13A2, ATPase cation transporting 13A2; ATTEC, autophagosome-tethering compound; AUC, the area under the curve; AUTAC, autophagy targeting chimera; Autophagy; BAF, bafilomycinA1; BBB, blood−brain barrier; CL, clearance rate; CMA, chaperone-mediated autophagy; CNS, central nervous system; COMT, catechol-O-methyltransferase; DA, dopamine; DAT, dopamine transporter; DJ-1, Parkinson protein 7; DR, dopamine receptor; ER, endoplasmic reticulum; ERRα, estrogen-related receptor alpha; F, oral bioavailability; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; GBA, glucocerebrosidase β acid; GWAS, genome-wide association study; HDAC6, histone deacetylase 6; HSC70, heat shock cognate 71 kDa protein; HSPA8, heat shock 70 kDa protein 8; IMPase, inositol monophosphatase; IPPase, inositol polyphosphate 1-phosphatase; KI, knockin; LAMP2A, lysosome-associated membrane protein 2 A; LC3, light chain 3; LIMP-2, lysosomal integrated membrane protein-2; LRRK2, leucine-rich repeat sequence kinase 2; LRS, leucyl-tRNA synthetase; LUHMES, lund human mesencephalic; Lamp2a, type 2A lysosomal-associated membrane protein; MAO-B, monoamine oxidase B; MPP+, 1-methyl-4-phenylpyridinium; MPTP, 1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine; MYCBP2, MYC-binding protein 2; NMDA, N-methyl-d-aspartic acid; ONRs, orphan nuclear receptors; PD therapy; PD, Parkinson's disease; PDE4, phosphodiesterase 4; PI3K, phosphatidylinositol 3-kinase; PI3P, phosphatidylinositol 3-phosphate; PINK1, PTEN-induced kinase 1; PLC, phospholipase C; PREP, prolyl oligopeptidase; Parkin, parkin RBR E3 ubiquitin−protein ligase; Parkinson's disease (PD); ROS, reactive oxygen species; SAR, structure–activity relationship; SAS, solvent accessible surface; SN, substantia nigra; SNCA, α-synuclein gene; SYT11, synaptotagmin 11; Small-molecule compound; TFEB, transcription factor EB; TSC2, tuberous sclerosis complex 2; Target; ULK1, UNC-51-like kinase 1; UPS, ubiquitin−proteasome system; mAChR, muscarinic acetylcholine receptor; mTOR, the mammalian target of rapamycin; α-syn, α-synuclein

DOI:  https://doi.org/10.1016/j.apsb.2021.02.016
Biochem Biophys Res Commun. 2021 Oct 21. pii: S0006-291X(21)01412-1. [Epub ahead of print]583 71-78

Hayatine inhibits amino acid-induced mTORC1 activation as a novel mTOR-Rag A/C interaction disruptor.

Meiling Lu, Lei Yu, Yanrong Yang, Jiali Zhu, Sujing Qiang, Xinbo Wang, Jia Wang, Xiao Tan, Weifeng Wang, Yue Zhang, Weichao Wang, Jian Xie, Xinyan Chen, Hongbing Wang, Xianghuan Cui, Xin Ge.

  Abnormal activation of the mechanistic target of rapamycin (mTOR) signaling is commonly observed in many cancers and attracts extensive attention as an oncology drug discovery target, which is encouraged by the success of rapamycin and its analogs (rapalogs) in treatment of mTORC1-hyperactive cancers in both pre-clinic models and clinical trials. However, rapamycin and existing rapalogs have typically short-lasting partial responses due to drug resistance, thereby triggering our interest to investigate a potential mTORC1 inhibitor that is mechanistically different from rapamycin. Here, we report that hayatine, a derivative from Cissampelos, can serve as a potential mTORC1 inhibitor selected from a natural compound library. The unique properties owned by hayatine such as downregulation of mTORC1 activities, induction of mTORC1's translocation to lysosomes followed by autophagy, and suppression on cancer cell growth, strongly emphasize its role as a potential mTORC1 inhibitor. Mechanistically, we found that hayatine disrupts the interaction between mTORC1 complex and its lysosomal adaptor RagA/C by binding to the hydrophobic loop of RagC, leading to mTORC1 inhibition that holds great promise to overcome rapamycin resistance. Taken together, our data shed light on an innovative strategy using structural interruption-based mTORC1 inhibitors for cancer treatment.

Keywords:  Hayatine; Rag A/C; Rapamycin; mTOR

DOI:  https://doi.org/10.1016/j.bbrc.2021.10.014
Autophagy. 2021 Nov 05. 1-17

Identification of a novel compound that simultaneously impairs the ubiquitin-proteasome system and autophagy.

Tatiana A Giovannucci, Florian A Salomons, Henriette Stoy, Laura K Herzog, Shanshan Xu, Weixing Qian, Lara G Merino, Maria E Gierisch, Martin Haraldsson, Alf H Lystad, Hanna Uvell, Anne Simonsen, Anna-Lena Gustavsson, Michaela Vallin, Nico P Dantuma.

  The ubiquitin-proteasome system (UPS) and macroautophagy/autophagy are the main proteolytic systems in eukaryotic cells for preserving protein homeostasis, i.e., proteostasis. By facilitating the timely destruction of aberrant proteins, these complementary pathways keep the intracellular environment free of inherently toxic protein aggregates. Chemical interference with the UPS or autophagy has emerged as a viable strategy for therapeutically targeting malignant cells which, owing to their hyperactive state, heavily rely on the sanitizing activity of these proteolytic systems. Here, we report on the discovery of CBK79, a novel compound that impairs both protein degradation by the UPS and autophagy. While CBK79 was identified in a high-content screen for drug-like molecules that inhibit the UPS, subsequent analysis revealed that this compound also compromises autophagic degradation of long-lived proteins. We show that CBK79 induces non-canonical lipidation of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 beta) that requires ATG16L1 but is independent of the ULK1 (unc-51 like autophagy activating kinase 1) and class III phosphatidylinositol 3-kinase (PtdIns3K) complexes. Thermal preconditioning of cells prevented CBK79-induced UPS impairment but failed to restore autophagy, indicating that activation of stress responses does not allow cells to bypass the inhibitory effect of CBK79 on autophagy. The identification of a small molecule that simultaneously impairs the two main proteolytic systems for protein quality control provides a starting point for the development of a novel class of proteostasis-targeting drugs.

Keywords:  Autophagy; compound screen; inhibitor; proteostasis; stress response; ubiquitin-proteasome system

DOI:  https://doi.org/10.1080/15548627.2021.1988359
Autophagy. 2021 Oct 31. 1-16

SHISA5/SCOTIN restrains spontaneous autophagy induction by blocking contact between the ERES and phagophores.

Jee-Eun Lee, Nari Kim, Minkyo Jung, Ji-Young Mun, Joo-Yeon Yoo.

  The phagophore expands into autophagosomes in close proximity to endoplasmic reticulum (ER) exit sites (ERESs). Here, we propose that a single-pass ER transmembrane protein, SHISA5/SCOTIN, acts as an autophagy suppressor under basal condition by blocking the contact between the phagophore and ERES. HeLa cells lacking SHISA5 displayed higher levels of macroautophagy/autophagy. The enhanced autophagy in SHISA5 KO cells requires class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1) activity and functional assembly of ERES, but not ULK1 activity. A proximity ligation assay (PLA) of SEC16A (Sec16 homolog A, endoplasmic reticulum export factor)-WIPI2 (WD repeat domain, phosphoinositide interacting 2) and SEC31A (Sec31 homolog A, COPII coat complex component)-MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 beta) demonstrated that contact between the ERES and phagophore increased in SHISA5 KO cells, and the cytosolic domain of SHISA5 was sufficient to rescue this phenotype. Close proximity between ERES and phagophore in SHISA5 KO cells was also visualized by performing an ultrastructure correlative image analysis of SEC31A associated with LC3-positive membranes. Furthermore, we observed that SHISA5 was located near ERES under basal conditions, but displaced away from ERES under autophagy-inducing conditions. These data suggest that SHISA5 functions to block spontaneous contact between ERES and phagophore, and the blockage effect of SHISA5 should be relieved for the proper induction of autophagy.

Keywords:  Constitutive autophagy; SHISA5/SCOTIN; endoplasmic reticulum exit sites; membrane contact; phagophore

DOI:  https://doi.org/10.1080/15548627.2021.1994297
Anim Nutr. 2021 Dec;7(4): 1009-1023

Regulation of mTORC1 by amino acids in mammalian cells: A general picture of recent advances.

Shizhe Zhang, Xueyan Lin, Qiuling Hou, Zhiyong Hu, Yun Wang, Zhonghua Wang.

  The mechanistic target of rapamycin complex 1 (mTORC1) integrates various types of signal inputs, such as energy, growth factors, and amino acids to regulate cell growth and proliferation mainly through the 2 direct downstream targets, eukaryotic translation initiation factor 4E-binding protein 1 (4EBP1) and ribosomal protein S6 kinase 1 (S6K1). Most of the signal arms upstream of mTORC1 including energy status, stress signals, and growth factors converge on the tuberous sclerosis complex (TSC) - Ras homologue enriched in brain (Rheb) axis. Amino acids, however, are distinct from other signals and modulate mTORC1 using a unique pathway. In recent years, the transmission mechanism of amino acid signals upstream of mTORC1 has been gradually elucidated, and some sensors or signal transmission pathways for individual amino acids have also been discovered. With the help of these findings, we propose a general picture of recent advances, which demonstrates that various amino acids from lysosomes, cytoplasm, and Golgi are sensed by their respective sensors. These signals converge on mTORC1 and form a huge and complicated signal network with multiple synergies, antagonisms, and feedback mechanisms.

Keywords:  Amino acids; Leucine; Mammal; Signaling pathway; mTORC1

DOI:  https://doi.org/10.1016/j.aninu.2021.05.003
Curr Opin Neurobiol. 2021 Oct 27. pii: S0959-4388(21)00106-9. [Epub ahead of print]72 111-119

PTEN-induced kinase 1 (PINK1) and Parkin: Unlocking a mitochondrial quality control pathway linked to Parkinson's disease.

Shalini Agarwal, Miratul M K Muqit.

Dissection of the function of two Parkinson's disease-linked genes encoding the protein kinase, PTEN-induced kinase 1 (PINK1) and ubiquitin E3 ligase, Parkin, has illuminated a highly conserved mitochondrial quality control pathway found in nearly every cell type including neurons. Mitochondrial damage-induced activation of PINK1 stimulates phosphorylation-dependent activation of Parkin and ubiquitin-dependent elimination of mitochondria by autophagy (mitophagy). Structural, cell biological and neuronal studies are unravelling the key steps of PINK1/Parkin-dependent mitophagy and uncovering new insights into how the pathway is regulated. The emerging role for aberrant immune activation as a driver of dopaminergic neuron degeneration after loss of PINK1 and Parkin poses new exciting questions on cell-autonomous and noncell-autonomous mechanisms of PINK1/Parkin signalling in vivo.

DOI: https://doi.org/10.1016/j.conb.2021.09.005
EMBO Mol Med. 2021 Nov 02. e14824

Emerging roles of ATG7 in human health and disease.

Jack J Collier, Fumi Suomi, Monika Oláhová, Thomas G McWilliams, Robert W Taylor.

  The cardinal stages of macroautophagy are driven by core autophagy-related (ATG) proteins, whose ablation largely abolishes intracellular turnover. Disrupting ATG genes is paradigmatic of studying autophagy deficiency, yet emerging data suggest that ATG proteins have extensive biological importance beyond autophagic elimination. An important example is ATG7, an essential autophagy effector enzyme that in concert with other ATG proteins, also regulates immunity, cell death and protein secretion, and independently regulates the cell cycle and apoptosis. Recently, a direct association between ATG7 dysfunction and disease was established in patients with biallelic ATG7 variants and childhood-onset neuropathology. Moreover, a prodigious body of evidence supports a role for ATG7 in protecting against complex disease states in model organisms, although how dysfunctional ATG7 contributes to manifestation of these diseases, including cancer, neurodegeneration and infection, in humans remains unclear. Here, we systematically review the biological functions of ATG7, discussing the impact of its impairment on signalling pathways and human pathology. Future studies illuminating the molecular relationship between ATG7 dysfunction and disease will expedite therapies for disorders involving ATG7 deficiency and/or impaired autophagy.

Keywords:  ATG7; autophagy; disease; neurodegeneration; therapeutics

DOI:  https://doi.org/10.15252/emmm.202114824
J Cachexia Sarcopenia Muscle. 2021 Nov 06.

Activation of Akt-mTORC1 signalling reverts cancer-dependent muscle wasting.

Alessia Geremia, Roberta Sartori, Martina Baraldo, Leonardo Nogara, Valeria Balmaceda, Georgia Ana Dumitras, Stefano Ciciliot, Marco Scalabrin, Hendrik Nolte, Bert Blaauw.

   BACKGROUND: Cancer-related muscle wasting occurs in most cancer patients. An important regulator of adult muscle mass and function is the Akt-mTORC1 pathway. While Akt-mTORC1 signalling is important for adult muscle homeostasis, it is also a major target of numerous cancer treatments. Which role Akt-mTORC1 signalling plays during cancer cachexia in muscle is currently not known. Here, we aimed to determine how activation or inactivation of the pathway affects skeletal muscle during cancer cachexia.
METHODS: We used inducible, muscle-specific Raptor ko (mTORC1) mice to determine the effect of reduced mTOR signalling during cancer cachexia. On the contrary, in order to understand if skeletal muscles maintain their anabolic capacity and if activation of Akt-mTORC1 signalling can reverse cancer cachexia, we generated mice in which we can inducibly activate Akt specifically in skeletal muscles.
RESULTS: We found that mTORC1 signalling is impaired during cancer cachexia, using the Lewis lung carcinoma and C26 colon cancer model, and is accompanied by a reduction in protein synthesis rates of 57% (P < 0.01). Further reduction of mTOR signalling, as seen in Raptor ko animals, leads to a 1.5-fold increase in autophagic flux (P > 0.001), but does not further increase muscle wasting. On the other hand, activation of Akt-mTORC1 signalling in already cachectic animals completely reverses the 15-20% loss in muscle mass and force (P < 0.001). Interestingly, Akt activation only in skeletal muscle completely normalizes the transcriptional deregulation observed in cachectic muscle, despite having no effect on tumour size or spleen mass. In addition to stimulating muscle growth, it is also sufficient to prevent the increase in protein degradation normally observed in muscles from tumour-bearing animals.
CONCLUSIONS: Here, we show that activation of Akt-mTORC1 signalling is sufficient to completely revert cancer-dependent muscle wasting. Intriguingly, these results show that skeletal muscle maintains its anabolic capacities also during cancer cachexia, possibly giving a rationale behind some of the beneficial effects observed in exercise in cancer patients.

Keywords:  Akt; Cancer cachexia; Muscle growth; Raptor; Skeletal muscle force; mTOR

DOI:  https://doi.org/10.1002/jcsm.12854
Pharmacol Res. 2021 Oct 31. pii: S1043-6618(21)00548-X. [Epub ahead of print] 105964

Ajugol enhances TFEB-mediated lysosome biogenesis and lipophagy to alleviate non-alcoholic fatty liver disease.

Heng Zhang, Junfeng Lu, Hao Liu, Lingling Guan, Shiqing Xu, Zai Wang, Yang Qiu, Honglin Liu, Liang Peng, Xiuli Men.

  Lipophagy is the autophagic degradation of lipid droplets. Dysregulated lipophagy has been implicated in the development of non-alcoholic fatty liver disease (NAFLD). Ajugol is an active alkaloid isolated from the root of Rehmannia glutinosa which is commonly used to treat various inflammatory and metabolic diseases. This study aimed to investigate the effect of ajugol on alleviating hepatic steatosis and sought to determine whether its potential mechanism via the key lysosome-mediated process of lipophagy. Our findings showed that ajugol significantly improved high-fat diet-induced hepatic steatosis in mice and inhibited palmitate-induced lipid accumulation in hepatocytes. Further analysis found that hepatic steatosis promoted the expression of LC3-II, an autophagosome marker, but led to autophagic flux blockade due to a lack of lysosomes. Ajugol also enhanced lysosomal biogenesis and promoted the fusion of autophagosome and lysosome to improve impaired autophagic flux and hepatosteatosis. Mechanistically, ajugol inactivated mammalian target of rapamycin and induced nuclear translocation of the transcription factor EB (TFEB), an essential regulator of lysosomal biogenesis. siRNA-mediated knockdown of TFEB significantly abrogated ajugol-induced lysosomal biogenesis as well as autophagosome-lysosome fusion and lipophagy. We conclude that lysosomal deficit is a critical mediator of hepatic steatosis, and ajugol may alleviate NAFLD via promoting the TFEB-mediated autophagy-lysosomal pathway and lipophagy.

Keywords:  Ajugol; Autophagic flux; BODIPY 493/503 (PubChem: CID: 134716599); Carboxymethylcellulose (CMC-Na) (PubChem CID: 24748); DMSO (PubChem CID: 679); Lipophagy; NAFLD; PVDF (PubChem CID: 3082294); Phenylmethylsulfonyl fluoride (PMSF) (PubChem CID: 4784); TFEB

DOI:  https://doi.org/10.1016/j.phrs.2021.105964
Autophagy. 2021 Oct 31. 1-3

Endothelial cell autophagy keeps neutrophil trafficking under control.

Natalia Reglero-Real, Lorena Pérez-Gutiérrez, Sussan Nourshargh.

  A defining feature of an inflammatory reaction is infiltration of neutrophils into tissues, a response that requires breaching of endothelial cells (ECs) that line the lumenal aspect of blood vessels. Dysregulated neutrophil trafficking is a hallmark of pathology, but details of the molecular mechanisms that terminate neutrophil breaching of venular walls remain unclear. In this work, we have identified EC autophagy as a negative regulator of neutrophil diapedesis in acute physiological inflammation. Specifically, in vivo, inflamed venular ECs upregulate autophagy, a response that is selectively localized to EC contacts and temporally aligned with the peak of neutrophil trafficking. Genetic ablation of EC autophagy leads to excessive neutrophil tissue infiltration in multiple inflammatory models and supports enhanced neutrophil transendothelial migration (TEM), while pharmacological induction of autophagy inhibits neutrophil migration. Mechanistically, autophagy machinery regulates the architecture of EC contacts and controls the reorganization and degradation of adhesion molecules, constituting a physiological brake on leukocyte trafficking.

Keywords:  ATG16L1; ATG5; endothelium; inflammation; junctions; neutrophils

DOI:  https://doi.org/10.1080/15548627.2021.1987675
J Nutr. 2021 Oct 27. pii: nxab342. [Epub ahead of print]

Amino Acid Homeostasis in Mammalian Cells with a Focus on Amino Acid Transport.

Stefan Bröer, Gregory Gauthier-Coles.

  Amino acid homeostasis is maintained by import, export, oxidation, and synthesis of nonessential amino acids, and by the synthesis and breakdown of protein. These processes work in conjunction with regulatory elements that sense amino acids or their metabolites. During and after nutrient intake, amino acid homeostasis is dominated by autoregulatory processes such as transport and oxidation of excess amino acids. Amino acid deprivation triggers processes such as autophagy and the execution of broader transcriptional programs to maintain plasma amino acid concentrations. Amino acid transport plays a crucial role in the absorption of amino acids in the intestine, the distribution of amino acids across cells and organs, the recycling of amino acids in the kidney, and the recycling of amino acids after protein breakdown.

Keywords:  ATF4; GCN2; autophagy; mTORC1; solute carrier; transceptor

DOI:  https://doi.org/10.1093/jn/nxab342
Acta Pharm Sin B. 2021 Oct;11(10): 2995-3014

Natural compounds in the regulation of proteostatic pathways: An invincible artillery against stress, ageing, and diseases.

Arun Upadhyay.

  Cells have different sets of molecules for performing an array of physiological functions. Nucleic acids have stored and carried the information throughout evolution, whereas proteins have been attributed to performing most of the cellular functions. To perform these functions, proteins need to have a unique conformation and a definite lifespan. These attributes are achieved by a highly coordinated protein quality control (PQC) system comprising chaperones to fold the proteins in a proper three-dimensional structure, ubiquitin-proteasome system for selective degradation of proteins, and autophagy for bulk clearance of cell debris. Many kinds of stresses and perturbations may lead to the weakening of these protective cellular machinery, leading to the unfolding and aggregation of cellular proteins and the occurrence of numerous pathological conditions. However, modulating the expression and functional efficiency of molecular chaperones, E3 ubiquitin ligases, and autophagic proteins may diminish cellular proteotoxic load and mitigate various pathological effects. Natural medicine and small molecule-based therapies have been well-documented for their effectiveness in modulating these pathways and reestablishing the lost proteostasis inside the cells to combat disease conditions. The present article summarizes various similar reports and highlights the importance of the molecules obtained from natural sources in disease therapeutics.

Keywords:  17-AAG, 17-allylamino-geldanamycin; APC, anaphase-promoting complex; Ageing; Autophagy; BAG, BCL2-associated athanogene; CAP, chaperone-assisted proteasomal degradation; CASA, chaperone-assisted selective autophagy; CHIP, carboxy-terminus of HSC70 interacting protein; CMA, chaperone-mediated autophagy; Cancer; Chaperones; DUBs, deubiquitinases; Drug discovery; EGCG, epigallocatechin-3-gallate; ESCRT, endosomal sorting complexes required for transport; HECT, homologous to the E6-AP carboxyl terminus; HSC70, heat shock cognate 70; HSF1, heat shock factor 1; HSP, heat shock protein; KFERQ, lysine-phenylalanine-glutamate-arginine-glutamine; LAMP2a, lysosome-associated membrane protein 2a; LC3, light chain 3; NBR1, next to BRCA1 gene 1; Natural molecules; Neurodegeneration; PQC, protein quality control; Proteinopathies; Proteostasis; RING, really interesting new gene; UPS, ubiquitin–proteasome system; Ub, ubiquitin; Ubiquitin proteasome system

DOI:  https://doi.org/10.1016/j.apsb.2021.01.006
Science. 2021 Jun 25. 372(6549): eabf6548

Ubiquitination of G3BP1 mediates stress granule disassembly in a context-specific manner.

Youngdae Gwon, Brian A Maxwell, Regina-Maria Kolaitis, Peipei Zhang, Hong Joo Kim, J Paul Taylor.

Tailoring stress responsesWhen faced with environmental stress, cells respond by shutting down cellular processes such as translation and nucleocytoplasmic transport. At the same time, cells preserve cytoplasmic messenger RNAs in structures known as stress granules, and many cellular proteins are modified by the covalent addition of ubiquitin, which has long been presumed to reflect degradation of stress-damaged proteins (see the Perspective by Dormann). Maxwell et al. show that cells generate distinct patterns of ubiquitination in response to different stressors. Rather than reflecting the degradation of stress-damaged proteins, this ubiquitination primes cells to dismantle stress granules and reinitiate normal cellular activities once the stress is removed. Gwon et al. show that persistent stress granules are degraded by autophagy, whereas short-lived granules undergo a process of disassembly that is autophagy independent. The mechanism of this disassembly depends on the initiating stress.Science, abc3593 and abf6548, this issue p. eabc3593 and p. eabf6548; see also abj2400, p. 1393.

DOI: https://doi.org/10.1126/science.abf6548
Autophagy. 2021 Oct 31. 1-15

Mycobacterium bovis induces mitophagy to suppress host xenophagy for its intracellular survival.

Yinjuan Song, Xin Ge, Yulan Chen, Tariq Hussain, Zhengmin Liang, Yuhui Dong, Yuanzhi Wang, Chengyuan Tang, Xiangmei Zhou.

  Mitophagy is a selective autophagy mechanism for eliminating damaged mitochondria and plays a crucial role in the immune evasion of some viruses and bacteria. Here, we report that Mycobacterium bovis (M. bovis) utilizes host mitophagy to suppress host xenophagy to enhance its intracellular survival. M. bovis is the causative agent of animal tuberculosis and human tuberculosis. In the current study, we show that M. bovis induces mitophagy in macrophages, and the induction of mitophagy is impaired by PINK1 knockdown, indicating the PINK1-PRKN/Parkin pathway is involved in the mitophagy induced by M. bovis. Moreover, the survival of M. bovis in macrophages and the lung bacterial burden of mice are restricted by the inhibition of mitophagy and are enhanced by the induction of mitophagy. Confocal microscopy analysis reveals that induction of mitophagy suppresses host xenophagy by competitive utilization of p-TBK1. Overall, our results suggest that induction of mitophagy enhances M. bovis growth while inhibition of mitophagy improves growth restriction. The findings provide a new insight for understanding the intracellular survival mechanism of M. bovis in the host.

Keywords:  Macrophage; Mycobacterium bovis; mitophagy; p-TBK1; xenophagy

DOI:  https://doi.org/10.1080/15548627.2021.1987671
Science. 2021 Jun 25. 372(6549): eabc3593

Ubiquitination is essential for recovery of cellular activities after heat shock.

Brian A Maxwell, Youngdae Gwon, Ashutosh Mishra, Junmin Peng, Haruko Nakamura, Ke Zhang, Hong Joo Kim, J Paul Taylor.

Tailoring stress responsesWhen faced with environmental stress, cells respond by shutting down cellular processes such as translation and nucleocytoplasmic transport. At the same time, cells preserve cytoplasmic messenger RNAs in structures known as stress granules, and many cellular proteins are modified by the covalent addition of ubiquitin, which has long been presumed to reflect degradation of stress-damaged proteins (see the Perspective by Dormann). Maxwell et al. show that cells generate distinct patterns of ubiquitination in response to different stressors. Rather than reflecting the degradation of stress-damaged proteins, this ubiquitination primes cells to dismantle stress granules and reinitiate normal cellular activities once the stress is removed. Gwon et al. show that persistent stress granules are degraded by autophagy, whereas short-lived granules undergo a process of disassembly that is autophagy independent. The mechanism of this disassembly depends on the initiating stress.Science, abc3593 and abf6548, this issue p. eabc3593 and p. eabf6548; see also abj2400, p. 1393.

DOI: https://doi.org/10.1126/science.abc3593
Sci Rep. 2021 Nov 04. 11(1): 21689

Targeting eIF4F translation complex sensitizes B-ALL cells to tyrosine kinase inhibition.

Thanh-Trang Vo, Lee-Or Herzog, Roberta Buono, Jong-Hoon Scott Lee, Sharmila Mallya, Madeleine R Duong, Joshua Thao, Moran Gotesman, David A Fruman.

The mechanistic target of rapamycin (mTOR) is a kinase whose activation is associated with poor prognosis in pre-B cell acute lymphoblastic leukemia (B-ALL). These and other findings have prompted diverse strategies for targeting mTOR signaling in B-ALL and other B-cell malignancies. In cellular models of Philadelphia Chromosome-positive (Ph+) B-ALL, mTOR kinase inhibitors (TOR-KIs) that inhibit both mTOR-complex-1 (mTORC1) and mTOR-complex-2 (mTORC2) enhance the cytotoxicity of tyrosine kinase inhibitors (TKIs) such as dasatinib. However, TOR-KIs have not shown substantial efficacy at tolerated doses in blood cancer clinical trials. Selective inhibition of mTORC1 or downstream effectors provides alternative strategies that may improve selectivity towards leukemia cells. Of particular interest is the eukaryotic initiation factor 4F (eIF4F) complex that mediates cap-dependent translation. Here we use novel chemical and genetic approaches to show that selective targeting of either mTORC1 kinase activity or components of the eIF4F complex sensitizes murine BCR-ABL-dependent pre-B leukemia cells to dasatinib. SBI-756, a small molecule inhibitor of eIF4F assembly, sensitizes human Ph+ and Ph-like B-ALL cells to dasatinib cytotoxicity without affecting survival of T lymphocytes or natural killer cells. These findings support the further evaluation of eIF4F-targeted molecules in combination therapies with TKIs in B-ALL and other blood cancers.

DOI: https://doi.org/10.1038/s41598-021-00950-y
WIREs Mech Dis. 2021 Sep;13(5): e1521

Disruption of morphogenic and growth pathways in lysosomal storage diseases.

Thiago Corrêa, Bruno C Feltes, Roberto Giugliani, Ursula Matte.

  The lysosome achieved a new protagonism that highlights its multiple cellular functions, such as in the catabolism of complex substrates, nutrient sensing, and signaling pathways implicated in cell metabolism and growth. Lysosomal storage diseases (LSDs) cause lysosomal accumulation of substrates and deficiency in trafficking of macromolecules. The substrate accumulation can impact one or several pathways which contribute to cell damage. Autophagy impairment and immune response are widely studied, but less attention is paid to morphogenic and growth pathways and its impact on the pathophysiology of LSDs. Hedgehog pathway is affected with abnormal expression and changes in distribution of protein levels, and a reduced number and length of primary cilia. Moreover, growth pathways are identified with delay in reactivation of mTOR that deregulate termination of autophagy and reformation of lysosomes. Insulin resistance caused by changes in lipids rafts has been described in different LSDs. While the genetic and biochemical bases of deficient proteins in LSDs are well understood, the secondary molecular mechanisms that disrupt wider biological processes associated with LSDs are only now becoming clearer. Therefore, we explored how specific signaling pathways can be related to specific LSDs, showing that a system medicine approach could be a valuable tool for the better understanding of LSD pathogenesis. This article is categorized under: Metabolic Diseases > Molecular and Cellular Physiology.

Keywords:  Hh pathway; LSDs; insulin; mTOR; systems medicine

DOI:  https://doi.org/10.1002/wsbm.1521
PLoS One. 2021 ;16(11): e0259556

The SQSTM1/p62 UBA domain regulates Ajuba localisation, degradation and NF-κB signalling function.

Melanie A Sultana, Carmel Cluning, Wai-Sin Kwong, Nicole Polain, Nathan J Pavlos, Thomas Ratajczak, John P Walsh, Jiake Xu, Sarah L Rea.

The LIM-domain containing protein Ajuba and the scaffold protein SQSTM1/p62 regulate signalling of NF-κB, a transcription factor involved in osteoclast differentiation and survival. The ubiquitin-associated domain of SQSTM1/p62 is frequently mutated in patients with Paget's disease of bone. Here, we report that Ajuba activates NF-κB activity in HEK293 cells, and that co-expression with SQSTM1/p62 inhibits this activation in an UBA domain-dependent manner. SQSTM1/p62 regulates proteins by targeting them to the ubiquitin-proteasome system or the autophagy-lysosome pathway. We show that Ajuba is degraded by autophagy, however co-expression with SQSTM1/p62 (wild type or UBA-deficient) protects Ajuba levels both in cells undergoing autophagy and those exposed to proteasomal stress. Additionally, in unstressed cells co-expression of SQSTM1/p62 reduces the amount of Ajuba present in the nucleus. SQSTM1/p62 with an intact ubiquitin-associated domain forms holding complexes with Ajuba that are not destined for degradation yet inhibit signalling. Thus, in situations with altered levels and localization of SQSTM1/p62 expression, such as osteoclasts in Paget's disease of bone and various cancers, SQSTM1/p62 may compartmentalize Ajuba and thereby impact its cellular functions and disease pathogenesis. In Paget's, ubiquitin-associated domain mutations may lead to increased or prolonged Ajuba-induced NF-κB signalling leading to increased osteoclastogenesis. In cancer, Ajuba expression promotes cell survival. The increased levels of SQSTM1/p62 observed in cancer may enhance Ajuba-mediated cancer cell survival.

DOI: https://doi.org/10.1371/journal.pone.0259556
Autophagy. 2021 Nov 05. 1-13

Salicylic acid and the viral virulence factor 2b regulate the divergent roles of autophagy during cucumber mosaic virus infection.

Aayushi Shukla, Gesa Hoffmann, Nirbhay Kumar Kushwaha, Silvia López-González, Daniel Hofius, Anders Hafrén.

  Macroautophagy/autophagy is a conserved intracellular degradation pathway that has recently emerged as an integral part of plant responses to virus infection. The known mechanisms of autophagy range from the selective degradation of viral components to a more general attenuation of disease symptoms. In addition, several viruses are able to manipulate the autophagy machinery and counteract autophagy-dependent resistance. Despite these findings, the complex interplay of autophagy activities, viral pathogenicity factors, and host defense pathways in disease development remains poorly understood. In the current study, we analyzed the interaction between autophagy and cucumber mosaic virus (CMV) in Arabidopsis thaliana. We show that autophagy is induced during CMV infection and promotes the turnover of the major virulence protein and RNA silencing suppressor 2b. Intriguingly, autophagy induction is mediated by salicylic acid (SA) and dampened by the CMV virulence factor 2b. In accordance with 2b degradation, we found that autophagy provides resistance against CMV by reducing viral RNA accumulation in an RNA silencing-dependent manner. Moreover, autophagy and RNA silencing attenuate while SA promotes CMV disease symptoms, and epistasis analysis suggests that autophagy-dependent disease and resistance are uncoupled. We propose that autophagy counteracts CMV virulence via both 2b degradation and reduced SA-responses, thereby increasing plant fitness with the viral trade-off arising from increased RNA silencing-mediated resistance.

Keywords:  CMV; RNA silencing; host-pathogen trade-off; plant immunity; plant virus; viral disease; viral effector protein; virus self-attenuation; virus transmission

DOI:  https://doi.org/10.1080/15548627.2021.1987674
Autophagy. 2021 Nov 05. 1-17

GNS561, a clinical-stage PPT1 inhibitor, is efficient against hepatocellular carcinoma via modulation of lysosomal functions.

Sonia Brun, Eloïne Bestion, Eric Raymond, Firas Bassissi, Zuzana Macek Jilkova, Soraya Mezouar, Madani Rachid, Marie Novello, Jennifer Tracz, Ahmed Hamaï, Gilles Lalmanach, Lise Vanderlynden, Raphael Legouffe, Jonathan Stauber, Thomas Schubert, Maximilian G Plach, Jérôme Courcambeck, Cyrille Drouot, Guillaume Jacquemot, Cindy Serdjebi, Gael Roth, Jean-Pierre Baudoin, Christelle Ansaldi, Thomas Decaens, Philippe Halfon.

  Hepatocellular carcinoma is the most frequent primary liver cancer. Macroautophagy/autophagy inhibitors have been extensively studied in cancer but, to date, none has reached efficacy in clinical trials. In this study, we demonstrated that GNS561, a new autophagy inhibitor, whose anticancer activity was previously linked to lysosomal cell death, displayed high liver tropism and potent antitumor activity against a panel of human cancer cell lines and in two hepatocellular carcinoma in vivo models. We showed that due to its lysosomotropic properties, GNS561 could reach and specifically inhibited its enzyme target, PPT1 (palmitoyl-protein thioesterase 1), resulting in lysosomal unbound Zn2+ accumulation, impairment of cathepsin activity, blockage of autophagic flux, altered location of MTOR (mechanistic target of rapamycin kinase), lysosomal membrane permeabilization, caspase activation and cell death. Accordingly, GNS561, for which a global phase 1b clinical trial in liver cancers was just successfully achieved, represents a promising new drug candidate and a hopeful therapeutic strategy in cancer treatment.Abbreviations: ANXA5:annexin A5; ATCC: American type culture collection; BafA1: bafilomycin A1; BSA: bovine serum albumin; CASP3: caspase 3; CASP7: caspase 7; CASP8: caspase 8; CCND1: cyclin D1; CTSB: cathepsin B; CTSD: cathepsin D; CTSL: cathepsin L; CQ: chloroquine; iCCA: intrahepatic cholangiocarcinoma; DEN: diethylnitrosamine; DMEM: Dulbelcco's modified Eagle medium; FBS: fetal bovine serum; FITC: fluorescein isothiocyanate; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HCC: hepatocellular carcinoma; HCQ: hydroxychloroquine; HDSF: hexadecylsulfonylfluoride; IC50: mean half-maximal inhibitory concentration; LAMP: lysosomal associated membrane protein; LC3-II: phosphatidylethanolamine-conjugated form of MAP1LC3; LMP: lysosomal membrane permeabilization; MALDI: matrix assisted laser desorption ionization; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MKI67: marker of proliferation Ki-67; MTOR: mechanistic target of rapamycin kinase; MRI: magnetic resonance imaging; NH4Cl: ammonium chloride; NtBuHA: N-tert-butylhydroxylamine; PARP: poly(ADP-ribose) polymerase; PBS: phosphate-buffered saline; PPT1: palmitoyl-protein thioesterase 1; SD: standard deviation; SEM: standard error mean; vs, versus; Zn2+: zinc ion; Z-Phe: Z-Phe-Tyt(tBu)-diazomethylketone; Z-VAD-FMK: carbobenzoxy-valyl-alanyl-aspartyl-[O-methyl]- fluoromethylketone.

Keywords:  Antitumor; PPT1; autophagy; liver cancer; lysosome; mtor

DOI:  https://doi.org/10.1080/15548627.2021.1988357
Autophagy. 2021 Oct 31. 1-19

Newcastle disease virus degrades SIRT3 via PINK1-PRKN-dependent mitophagy to reprogram energy metabolism in infected cells.

Yabin Gong, Ning Tang, Panrao Liu, Yingjie Sun, Shanxin Lu, Weiwei Liu, Lei Tan, Cuiping Song, Xusheng Qiu, Ying Liao, Shengqing Yu, Xiufan Liu, Shu-Hai Lin, Chan Ding.

  Lacking a self-contained metabolism network, viruses have evolved multiple mechanisms for rewiring the metabolic system of their host to hijack the host's metabolic resources for replication. Newcastle disease virus (NDV) is a paramyxovirus, as an oncolytic virus currently being developed for cancer treatment. However, how NDV alters cellular metabolism is still far from fully understood. In this study, we show that NDV infection reprograms cell metabolism by increasing glucose utilization in the glycolytic pathway. Mechanistically, NDV induces mitochondrial damage, elevated mitochondrial reactive oxygen species (mROS) and ETC dysfunction. Infection of cells depletes nucleotide triphosphate levels, resulting in elevated AMP:ATP ratios, AMP-activated protein kinase (AMPK) phosphorylation, and MTOR crosstalk mediated autophagy. In a time-dependent manner, NDV shifts the balance of mitochondrial dynamics from fusion to fission. Subsequently, PINK1-PRKN-dependent mitophagy was activated, forming a ubiquitin chain with MFN2 (mitofusin 2), and molecular receptor SQSTM1/p62 recognized damaged mitochondria. We also found that NDV infection induces NAD+-dependent deacetylase SIRT3 loss via mitophagy to engender HIF1A stabilization, leading to the switch from oxidative phosphorylation (OXPHOS) to aerobic glycolysis. Overall, these studies support a model that NDV modulates host cell metabolism through PINK1-PRKN-dependent mitophagy for degrading SIRT3.Abbreviations: AMPK: AMP-activated protein kinase; CCCP: carbonyl cyanide 3-chlorophenylhydrazone; ECAR: extracellular acidification rate; hpi: hours post infection LC-MS: liquid chromatography-mass spectrometry; mito-QC: mCherry-GFP-FIS1[mt101-152]; MFN2: mitofusin 2; MMP: mitochondrial membrane potential; mROS: mitochondrial reactive oxygen species; MOI: multiplicity of infection; 2-NBDG: 2-(N-(7-nitrobenz-2-oxa-1, 3-diazol-4-yl) amino)-2-deoxyglucose; NDV: newcastle disease virus; OCR: oxygen consumption rate; siRNA: small interfering RNA; SIRT3: sirtuin 3; TCA: tricarboxylic acid; TCID50: tissue culture infective doses.

Keywords:  Cellular metabolism; SIRT3; glycolysis; mitochondrial fission; mitophagy; newcastle disease virus

DOI:  https://doi.org/10.1080/15548627.2021.1990515
Circ Res. 2021 Nov 02.

Alternative Mitophagy Protects the Heart Against Obesity-Associated Cardiomyopathy.

Mingming Tong, Toshiro Saito, Peiyong Zhai, Shin-Ichi Oka, Wataru Mizushima, Michinari Nakamura, Shohei Ikeda, Akihiro Shirakabe, Junichi Sadoshima.

Rationale: Obesity-associated cardiomyopathy characterized by hypertrophy and mitochondrial dysfunction. Mitochondrial quality control mechanisms, including mitophagy, are essential for the maintenance of cardiac function in obesity-associated cardiomyopathy. However, autophagic flux peaks at around 6 weeks of high fat diet (HFD) consumption and declines thereafter. Objective: We investigated whether mitophagy is activated during the chronic phase of cardiomyopathy associated with obesity (obesity cardiomyopathy) after general autophagy is downregulated and, if so, what the underlying mechanism and the functional significance are. Methods and Results: Mice were fed either a normal diet (ND) or a HFD (60 kcal % fat). Mitophagy, evaluated using Mito-Keima, was increased after 3 weeks of HFD consumption and continued to increase after conventional mechanisms of autophagy were inactivated, at least until 24 weeks. HFD consumption time-dependently up-regulated both Ser555-phosphorylated Ulk1 and Rab9 in the mitochondrial fraction. Mitochondria were sequestrated by Rab9-positive ring-like structures in cardiomyocytes isolated from mice after 20 weeks of HFD consumption, consistent with the activation of alternative mitophagy. Increases in mitophagy induced by HFD consumption for 20 weeks were abolished in cardiac-specific ulk1 knockout mouse hearts, in which both diastolic and systolic dysfunction were exacerbated. Rab9 S179A knock-in mice, in which alternative mitophagy is selectively suppressed, exhibited impaired mitophagy and more severe cardiac dysfunction than control mice following HFD consumption for 20 weeks. Overexpression of Rab9 in the heart increased mitophagy and protected against cardiac dysfunction during HFD consumption. HFD-induced activation of Rab9-dependent mitophagy was accompanied by upregulation of TFE3, which plays an essential role in transcriptional activation of mitophagy. Conclusions: Ulk1-Rab9-dependent alternative mitophagy is activated during the chronic phase of HFD consumption and serves as an essential mitochondrial quality control mechanism, thereby protecting the heart against obesity cardiomyopathy.

DOI: https://doi.org/10.1161/CIRCRESAHA.121.319377
World J Gastrointest Oncol. 2021 Oct 15. 13(10): 1244-1262

Role of autophagy in gastric carcinogenesis.

Apostolis Papaefthymiou, Gregory Christodoulidis, Apostolos Koffas, Michael Doulberis, Stergios A Polyzos, Anastasios Manolakis, Spyros Potamianos, Andreas Kapsoritakis, Jannis Kountouras.

  Gastric cancer represents a common and highly fatal malignancy, and thus a pathophysiology-based reconsideration is necessary, given the absence of efficient therapeutic regimens. In this regard, emerging data reveal a significant role of autophagy in gastric oncogenesis, progression, metastasis and chemoresistance. Although autophagy comprises a normal primordial process, ensuring cellular homeostasis under energy depletion and stress conditions, alterations at any stage of the complex regulatory system could stimulate a tumorigenic and promoting cascade. Among others, Helicobacter pylori infection induces a variety of signaling molecules modifying autophagy, during acute infection or after chronic autophagy degeneration. Subsequently, defective autophagy allows malignant transformation and upon cancer establishment, an overactive autophagy is stimulated. This overexpressed autophagy provides energy supplies and resistance mechanisms to gastric cancer cells against hosts defenses and anticancer treatment. This review interprets the implicated autophagic pathways in normal cells and in gastric cancer to illuminate the potential preventive, therapeutic and prognostic benefits of understanding and intervening autophagy.

Keywords:  Autophagy; Chemoresistance; Gastric cancer; Helicobacter pylori; Prognosis

DOI:  https://doi.org/10.4251/wjgo.v13.i10.1244
Front Cell Dev Biol. 2021 ;9 766142

Autophagy in Viral Infection and Pathogenesis.

Shan Liang, Yun-Shan Wu, Dong-Yi Li, Ji-Xin Tang, Hua-Feng Liu.

  As an evolutionarily conserved cellular process, autophagy plays an essential role in the cellular metabolism of eukaryotes as well as in viral infection and pathogenesis. Under physiological conditions, autophagy is able to meet cellular energy needs and maintain cellular homeostasis through degrading long-lived cellular proteins and recycling damaged organelles. Upon viral infection, host autophagy could degrade invading viruses and initial innate immune response and facilitate viral antigen presentation, all of which contribute to preventing viral infection and pathogenesis. However, viruses have evolved a variety of strategies during a long evolutionary process, by which they can hijack and subvert host autophagy for their own benefits. In this review, we highlight the function of host autophagy in the key regulatory steps during viral infections and pathogenesis and discuss how the viruses hijack the host autophagy for their life cycle and pathogenesis. Further understanding the function of host autophagy in viral infection and pathogenesis contributes to the development of more specific therapeutic strategies to fight various infectious diseases, such as the coronavirus disease 2019 epidemic.

Keywords:  antigen presentation; autophagy; inflammation and immunity; innate immune response; viral infection; virophagy; xenophagy

DOI:  https://doi.org/10.3389/fcell.2021.766142
Nat Commun. 2021 Nov 04. 12(1): 6409

Constitutive activation of the PI3K-Akt-mTORC1 pathway sustains the m.3243 A > G mtDNA mutation.

Chih-Yao Chung, Kritarth Singh, Vassilios N Kotiadis, Gabriel E Valdebenito, Jee Hwan Ahn, Emilie Topley, Joycelyn Tan, William D Andrews, Benoit Bilanges, Robert D S Pitceathly, Gyorgy Szabadkai, Mariia Yuneva, Michael R Duchen.

Mutations of the mitochondrial genome (mtDNA) cause a range of profoundly debilitating clinical conditions for which treatment options are very limited. Most mtDNA diseases show heteroplasmy - tissues express both wild-type and mutant mtDNA. While the level of heteroplasmy broadly correlates with disease severity, the relationships between specific mtDNA mutations, heteroplasmy, disease phenotype and severity are poorly understood. We have carried out extensive bioenergetic, metabolomic and RNAseq studies on heteroplasmic patient-derived cells carrying the most prevalent disease related mtDNA mutation, the m.3243 A > G. These studies reveal that the mutation promotes changes in metabolites which are associated with the upregulation of the PI3K-Akt-mTORC1 axis in patient-derived cells and tissues. Remarkably, pharmacological inhibition of PI3K, Akt, or mTORC1 reduced mtDNA mutant load and partially rescued cellular bioenergetic function. The PI3K-Akt-mTORC1 axis thus represents a potential therapeutic target that may benefit people suffering from the consequences of the m.3243 A > G mutation.

DOI: https://doi.org/10.1038/s41467-021-26746-2
Plant Cell. 2021 Oct 30. pii: koab263. [Epub ahead of print]

FYVE2, a phosphatidylinositol 3-phosphate effector, interacts with the COPII machinery to control autophagosome formation in Arabidopsis.

Jeong Hun Kim, Han Nim Lee, Xiao Huang, Hyera Jung, Marisa S Otegui, Faqiang Li, Taijoon Chung.

Autophagy is an intracellular trafficking mechanism by which cytosolic macromolecules and organelles are sequestered into autophagosomes for degradation inside the vacuole. In various eukaryotes including yeast, metazoans, and plants, the precursor of the autophagosome, termed the phagophore, nucleates in the vicinity of the endoplasmic reticulum (ER) with the participation of phosphatidylinositol 3-phosphate (PI3P) and the coat protein complex II (COPII). Here we show that Arabidopsis thaliana FYVE2, a plant-specific PI3P-binding protein, provides a functional link between the COPII machinery and autophagy. FYVE2 interacts with the small GTPase SAR1, which is essential for the budding of COPII vesicles. FYVE2 also interacts with ATG18A, another PI3P effector on the phagophore membrane. Fluorescently tagged FYVE2 localized to autophagic membranes near the ER and was delivered to vacuoles. SAR1 fusion proteins were also targeted to the vacuole via FYVE2-dependent autophagy. Either mutations in FYVE2 or the expression of dominant-negative mutant SAR1B proteins resulted in reduced autophagic flux and the accumulation of autophagic organelles. We propose that FYVE2 regulates autophagosome biogenesis through its interaction with ATG18A and the COPII machinery, acting downstream of ATG2.

DOI: https://doi.org/10.1093/plcell/koab263
Cell Mol Immunol. 2021 Nov 02.

Autophagy takes the STING out of DNA sensing.

Carlos Maluquer de Motes.

DOI: https://doi.org/10.1038/s41423-021-00797-3
J Cell Biol. 2022 Jan 03. pii: e202103033. [Epub ahead of print]221(1):

CHMP2B regulates TDP-43 phosphorylation and cytotoxicity independent of autophagy via CK1.

Xue Deng, Xing Sun, Wenkai Yue, Yongjia Duan, Rirong Hu, Kai Zhang, Jiangxia Ni, Jihong Cui, Qiangqiang Wang, Yelin Chen, Ang Li, Yanshan Fang.

The ESCRT protein CHMP2B and the RNA-binding protein TDP-43 are both associated with ALS and FTD. The pathogenicity of CHMP2B has mainly been considered a consequence of autophagy-endolysosomal dysfunction, whereas protein inclusions containing phosphorylated TDP-43 are a pathological hallmark of ALS and FTD. Intriguingly, TDP-43 pathology has not been associated with the FTD-causing CHMP2BIntron5 mutation. In this study, we identify CHMP2B as a modifier of TDP-43-mediated neurodegeneration in a Drosophila screen. Down-regulation of CHMP2B reduces TDP-43 phosphorylation and toxicity in flies and mammalian cells. Surprisingly, although CHMP2BIntron5 causes dramatic autophagy dysfunction, disturbance of autophagy does not alter TDP-43 phosphorylation levels. Instead, we find that inhibition of CK1, but not TTBK1/2 (all of which are kinases phosphorylating TDP-43), abolishes the modifying effect of CHMP2B on TDP-43 phosphorylation. Finally, we uncover that CHMP2B modulates CK1 protein levels by negatively regulating ubiquitination and the proteasome-mediated turnover of CK1. Together, our findings propose an autophagy-independent role and mechanism of CHMP2B in regulating CK1 abundance and TDP-43 phosphorylation.

DOI: https://doi.org/10.1083/jcb.202103033
Chem Commun (Camb). 2021 Nov 03.

Visualization of lipophagy using a supramolecular FRET pair.

Ara Lee, Meng Li, Young Ho Ko, Sanghwang Park, Jongcheol Seo, Kyeng Min Park, Kimoon Kim.

A rationally designed supramolecular FRET pair consisting of cyanine3-cucurbit[7]uril (Cy3-CB[7]) and boron-dipyrromethene 630/650-adamantylammonium (BDP-AdA) can be used to visualize organelle-specific autophagy events. The intracellular accumulations of Cy3-CB[7] in lysosomes and BDP-AdA in lipid droplets (LDs) and the formation of an intracellular host-guest complex between Cy3-CB[7] and BDP-AdA resulting in FRET signals allow us to visualize the fusion of LDs with lysosomes, namely, lipophagy. This study demonstrates the potential of supramolecular imaging based on bio-orthogonal host-guest interactions in the investigation of selective autophagy events.

DOI: https://doi.org/10.1039/d1cc04779e
Sci Adv. 2021 Nov 05. 7(45): eabg3897

TSC1 loss increases risk for tauopathy by inducing tau acetylation and preventing tau clearance via chaperone-mediated autophagy.

Carolina Alquezar, Kathleen M Schoch, Ethan G Geier, Eliana Marisa Ramos, Aurora Scrivo, Kathy H Li, Andrea R Argouarch, Elisabeth E Mlynarski, Beth Dombroski, Michael DeTure, Dennis W Dickson, Jennifer S Yokoyama, Ana M Cuervo, Alma L Burlingame, Gerard D Schellenberg, Timothy M Miller, Bruce L Miller, Aimee W Kao.

[Figure: see text].

DOI: https://doi.org/10.1126/sciadv.abg3897
Front Cell Neurosci. 2021 ;15 760422

Autophagy Regulates the Survival of Hair Cells and Spiral Ganglion Neurons in Cases of Noise, Ototoxic Drug, and Age-Induced Sensorineural Hearing Loss.

Lingna Guo, Wei Cao, Yuguang Niu, Shuangba He, Renjie Chai, Jianming Yang.

  Inner ear hair cells (HCs) and spiral ganglion neurons (SGNs) are the core components of the auditory system. However, they are vulnerable to genetic defects, noise exposure, ototoxic drugs and aging, and loss or damage of HCs and SGNs results in permanent hearing loss due to their limited capacity for spontaneous regeneration in mammals. Many efforts have been made to combat hearing loss including cochlear implants, HC regeneration, gene therapy, and antioxidant drugs. Here we review the role of autophagy in sensorineural hearing loss and the potential targets related to autophagy for the treatment of hearing loss.

Keywords:  autophagy; hair cells; hearing loss; mechanism; spiral ganglion neurons

DOI:  https://doi.org/10.3389/fncel.2021.760422
Ann Transl Med. 2021 Sep;9(18): 1474

Induction of osteoclast formation by LOX mutant (LOXG473A) through regulation of autophagy.

Bo Zhang, Chenglin Luo, Wenjin Xiao.

   Background: Lysyl oxidase (LOX) has been identified to modulate osteoclast activity, so we explored the role of LOXG473A, the highest frequency single nucleotide polymorphism in LOX, in osteoclast formation and its potential relationship to autophagy.
Methods: The ability of the LOX mutant, LOXG473A, to promote autophagy and osteoclast formation was evaluated in the pre-osteoclast cell line RAW264.7. Furthermore, autophagy-related protein expression and autophagosomes were detected by western blot and electron microscopy, respectively. Simultaneously, osteoclast formation and resorption ability were also detected using TRAP staining assay and bone resorption assay. In addition, the osteoclast-related proteins and mRNAs, as well as p-AMPKα and p-mTOR proteins, were further evaluated by western blot and qPCR assays.
Results: Autophagy inhibitor 3-MA suppressed the Beclin-1 and ATG5 protein levels and the ratio of LC3-II to LC3-I, as well as autophagosome formation in RAW264.7 transfected with the MUT plasmid and enhanced p62 protein expression. Simultaneously, 3-MA also reduced osteoclast formation and resorption, as well as the F-actin ring level of osteoclasts. In addition, 3-MA inhibited osteoclast-related protein and mRNA expression, including NFATC1, ACP5, CTSK. And the autophagy-related pathway protein p-AMPKα was increased and p-mTOR was reduced by 3-MA treatment. However, autophagy agonist RAPA reversed the effect of 3-MA on RAW264.7 with LOXG473A mutation, indicating that promoting autophagy could enhance the ability of LOXG473A to induce osteoclast formation.
Conclusions: LOX mutant (LOXG473A) might promote osteoclast formation for RAW264.7 by enhancing autophagy via the AMPK/mTOR pathway, which is a new direction for bone disease research.

Keywords:  Autophagy; LOXG473A; RAW264.7; lysyl oxidase (LOX); osteoclast formation

DOI:  https://doi.org/10.21037/atm-21-4474
Mol Biol Rep. 2021 Nov 05.

Hormetic effect of low doses of rapamycin triggers anti-aging cascades in WRL-68 cells by modulating an mTOR-mitochondria cross-talk.

R Mahalakshmi, J Priyanga, Dipita Bhakta-Guha, Gunjan Guha.

   BACKGROUND: Rapamycin is hormetic in nature-it demonstrates contrasting effects at high and low doses. It is toxic at moderate/high doses, while it can restrain aging and extend lifespan at low doses. However, it is not fully understood how rapamycin governs cellular aging. On the other hand, aging is putatively correlated to mitochondrial dysregulation. Although previous studies have suggested that hormetic (low) doses of rapamycin can cause partial/incomplete inhibition of mTOR, the actual modus operandi of how such partial mTOR inhibition might modulate the mTOR-mitochondria cross-talk remained to be deciphered in the context of cellular aging. The present study was designed to understand the hormetic effects of rapamycin on cellular factors that govern aging-associated changes in mitochondrial facets, such as functional and metabolic homeostases, sustenance of membrane potential, biogenesis, mitophagy, and oxidative injury to mitochondrial macromolecules.
METHODS AND RESULTS: WRL-68 cells treated (24 h) with variable doses of rapamycin were studied for estimating their viability, apoptosis, senescence, mitochondrial density and Δψm. Expression levels of key functional proteins were estimated by immunofluorescence/immunoblots. Oxidative damage to mtDNA/mtRNA/proteins was measured in mitochondrial lysates. We demonstrated that hormetic doses (0.1 and 1 nM) of rapamycin can alleviate aging-associated mitochondrial dyshomeostasis in WRL-68 cells, such as oxidative injury to mitochondrial nucleic acids and proteins, as well as disequilibrium of mitochondrial density, membrane potential, biogenesis, mitophagy and overall metabolism.
CONCLUSIONS: We established that low doses of rapamycin can hormetically amend the mTOR-mitochondria cross-talk, and can consequently promote anti-aging outcome in cells.

Keywords:  Anti-aging; Hormesis; Mitochondria; Oxidative stress; Rapamycin; mTOR

DOI:  https://doi.org/10.1007/s11033-021-06898-6
Mol Cancer Ther. 2021 Nov 01. pii: molcanther.1103.2021. [Epub ahead of print]

Radiosensitizing pancreatic cancer via effective autophagy inhibition.

Taha Yazal, Justine Bailleul, Yangjingyi Ruan, David Sung, Fang-I Chu, Daisy Palomera, Amy Dao, Anahita Sehgal, Vibha Gurunathan, Laila Aryan, Mansoureh Eghbali, Erina Vlashi.

Despite aggressive treatments, pancreatic ductal adenocarcinoma (PDAC) remains an intractable disease, largely because it is refractory to therapeutic interventions. To overcome its nutrient-poor microenvironment, PDAC heavily relies on autophagy for metabolic needs to promote tumor growth and survival. Here, we explore autophagy inhibition as a method to enhance the effects of radiation therapy (RT) on PDAC tumors. Hydroxychloroquine (HCQ) is an autophagy inhibitor at the focus of many PDAC clinical trials, including in combination with RT. However, its acid-labile properties likely reduce its intratumoral efficacy. Here, we demonstrate that EAD1, a synthesized analogue of HCQ, is a more effective therapeutic for sensitizing PDAC tumors of various KRAS mutations to RT. Specifically, in vitro models show that EAD1 is an effective inhibitor of autophagic flux in PDAC cells, accompanied by a potent inhibition of proliferation. When combined with RT, EAD1 is consistently superior to HCQ not only as a single agent, but also in radiosensitizing PDAC cells, and perhaps most importantly, in decreasing the self-renewal capacity of PDAC cancer stem cells (PCSCs). The more pronounced sensitizing effects of autophagy inhibitors on pancreatic stem over differentiated cells points to a new understanding that PCSCs may be more dependent on autophagy to counter the effects of radiation toxicity, a potential mechanism explaining the resistance of PCSCs to RT. Finally, in vivo sub-cutaneous tumor models demonstrate that combination of RT and EAD1 is the most successful at controlling tumor growth. The models also confirmed a similar toxicity profile between EAD1 and HCQ.

DOI: https://doi.org/10.1158/1535-7163.MCT-20-1103
Front Neurol. 2021 ;12 754045

The Genetic Basis of Phenotypic Heterogeneity in the Neuronal Ceroid Lipofuscinoses.

Emily Gardner, Sara E Mole.

  The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders that affect children and adults. They share some similar clinical features and the accumulation of autofluorescent storage material. Since the discovery of the first causative genes, more than 530 mutations have been identified across 13 genes in cases diagnosed with NCL. These genes encode a variety of proteins whose functions have not been fully defined; most are lysosomal enzymes, or transmembrane proteins of the lysosome or other organelles. Many mutations in these genes are associated with a typical NCL disease phenotype. However, increasing numbers of variant disease phenotypes are being described, affecting age of onset, severity or progression, and including some distinct clinical phenotypes. This data is collated by the NCL Mutation Database which allows analysis from many perspectives. This article will summarise and interpret current knowledge and understanding of their genetic basis and phenotypic heterogeneity.

Keywords:  CLN; NCL; batten disease; gene; lysosomal disease; mutation; neuronal ceroid lipofuscinosis

DOI:  https://doi.org/10.3389/fneur.2021.754045
J Physiol Biochem. 2021 Nov 06.

Calcium/calmodulin-dependent protein kinase IV regulates vascular autophagy and insulin signaling through Akt/mTOR/CREB pathway in ob/ob mice.

Jiali Liu, Yue Li, Ning Gao, Jing Ji, Qian He.

  Calcium/calmodulin-dependent protein kinase IV (CaMKIV) has recently emerged as an important regulator of glucose metabolism and vascular function, but the underlying mechanism is not fully understood. Recently, we revealed that CaMKIV limits metabolic disorder and liver insulin resistance and regulates autophagy in high-fat diet-induced obese mice. In the present study, we demonstrated that CaMKIV was not only associated with improvement of glucose tolerance and insulin sensitivity in ob/ob mice but also involved in the regulation of vascular autophagy and mitochondrial biogenesis. Our in vitro data indicated that CaMKIV reversed autophagic imbalance and restored insulin sensitivity in palmitate-induced A7r5 cells with insulin resistance. However, the protective effects of CaMKIV were nullified by suppression of Akt, mTOR, or CREB, suggesting that CaMKIV inhibits autophagy and improves insulin signaling in insulin resistance cell models in an Akt/mTOR/CREB-dependent manner. CaMKIV reversed autophagic imbalance and insulin sensitivity in vascular tissues and vascular cells through Akt/mTOR/CREB signaling, which could be regarded as a novel opportunity for the treatment of insulin resistance.

Keywords:  Akt/mTOR signaling; CREB; CaMKIV; Vascular function

DOI:  https://doi.org/10.1007/s13105-021-00853-6
Autophagy. 2021 Oct 31. 1-17

FAIM regulates autophagy through glutaminolysis in lung adenocarcinoma.

Tianyu Han, Pengcheng Wang, Yanan Wang, Wenze Xun, Jiapeng Lei, Tao Wang, Zhuo Lu, Mingxi Gan, Wei Zhang, Bentong Yu, Jian-Bin Wang.

  Altered glutamine metabolism is an important aspect of cancer metabolic reprogramming. The GLS isoform GAC (glutaminase C), the rate-limiting enzyme in glutaminolysis, plays a vital role in cancer initiation and progression. Our previous studies demonstrated that phosphorylation of GAC was essential for its high enzymatic activity. However, the molecular mechanisms for GAC in maintaining its high enzymatic activity and protein stability still need to be further clarified. FAIM/FAIM1 (Fas apoptotic inhibitory molecule) is known as an important anti-apoptotic protein, but little is known about its function in tumorigenesis. Here, we found that knocking down FAIM induced macroautophagy/autophagy through suppressing the activation of the MTOR pathway in lung adenocarcinoma. Further studies demonstrated that FAIM could promote the tetramer formation of GAC through increasing PRKCE/PKCε-mediated phosphorylation. What's more, FAIM also stabilized GAC through sequestering GAC from degradation by protease ClpXP. These effects increased the production of α-ketoglutarate, leading to the activation of MTOR. Besides, FAIM also promoted the association of ULK1 and MTOR and this further suppressed autophagy induction. These findings discovered new functions of FAIM and elucidated an important molecular mechanism for GAC in maintaining its high enzymatic activity and protein stability.

Keywords:  Autophagy; Fas apoptosis inhibitory molecule 1; glutaminase C; protein stability; tetramer formation

DOI:  https://doi.org/10.1080/15548627.2021.1987672
Immunity. 2021 Oct 23. pii: S1074-7613(21)00446-5. [Epub ahead of print]

Plasmacytoid dendritic cell activation is dependent on coordinated expression of distinct amino acid transporters.

Katarzyna M Grzes, David E Sanin, Agnieszka M Kabat, Michal A Stanczak, Joy Edwards-Hicks, Mai Matsushita, Alexandra Hackl, Fabian Hässler, Kristin Knoke, Sophie Zahalka, Matteo Villa, David M Kofler, Reinhard E Voll, Paola Zigrino, Mario Fabri, Erika L Pearce, Edward J Pearce.

  Human plasmacytoid dendritic cells (pDCs) are interleukin-3 (IL-3)-dependent cells implicated in autoimmunity, but the role of IL-3 in pDC biology is poorly understood. We found that IL-3-induced Janus kinase 2-dependent expression of SLC7A5 and SLC3A2, which comprise the large neutral amino acid transporter, was required for mammalian target of rapamycin complex 1 (mTORC1) nutrient sensor activation in response to toll-like receptor agonists. mTORC1 facilitated increased anabolic activity resulting in type I interferon, tumor necrosis factor, and chemokine production and the expression of the cystine transporter SLC7A11. Loss of function of these amino acid transporters synergistically blocked cytokine production by pDCs. Comparison of in vitro-activated pDCs with those from lupus nephritis lesions identified not only SLC7A5, SLC3A2, and SLC7A11 but also ectonucleotide pyrophosphatase-phosphodiesterase 2 (ENPP2) as components of a shared transcriptional signature, and ENPP2 inhibition also blocked cytokine production. Our data identify additional therapeutic targets for autoimmune diseases in which pDCs are implicated.

Keywords:  GM-CSF; IL-3; JAK-STAT signaling; amino acid transporters; autoimmunity; cytokines; mTORC1; metabolism; plasmacytoid dendritic cells

DOI:  https://doi.org/10.1016/j.immuni.2021.10.009
Nature. 2021 Nov 03.

Mice with disrupted mitochondria used to model Parkinson's disease.

Zak Doric, Ken Nakamura.



Keywords:  Neurodegeneration; Parkinson's disease

DOI:  https://doi.org/10.1038/d41586-021-02955-z