bims-lysosi 2020-12-27 papers

bims-lysosi

Biomed News

on Lysosomes and signaling

Issue of 2020–12–27
ten papers selected by
Stephanie Fernandes, Max Planck Institute for Biology of Ageing

Impaired autophagy: The collateral damage of lysosomal storage disorders.
Mitochondrial Threonyl-tRNA Synthetase TARS2 Is Required for Threonine-Sensitive mTORC1 Activation.
Cancer-secreted miRNAs regulate amino-acid-induced mTORC1 signaling and fibroblast protein synthesis.
In Vivo Evidence for Serine Biosynthesis-Defined Sensitivity of Lung Metastasis, but Not of Primary Breast Tumors, to mTORC1 Inhibition.
Cathepsin B is an executioner of ferroptosis.
The SARS-CoV-2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules.
Formation of retromer transport carriers is disrupted by the Parkinson disease-linked Vps35 D620N variant.
Lack of Annexin A6 exacerbates liver dysfunction and reduces lifespan of NPC1-deficient mice.
Function of the Endolysosomal Network in Cholesterol Homeostasis and Metabolic Associated Fatty Liver Disease (MAFLD).
Cathepsins in Bacteria-Macrophage Interaction: Defenders or Victims of Circumstance?

EBioMedicine. 2020 Dec 17. pii: S2352-3964(20)30542-9. [Epub ahead of print]63 103166

Impaired autophagy: The collateral damage of lysosomal storage disorders.

Rachel Myerowitz, Rosa Puertollano, Nina Raben.

  Lysosomal storage disorders (LSDs), which number over fifty, are monogenically inherited and caused by mutations in genes encoding proteins that are involved in lysosomal function. Lack of the functional protein results in storage of a distinctive material within the lysosomes, which for years was thought to determine the pathophysiology of the disorder. However, our current view posits that the primary storage material disrupts the normal role of the lysosome in the autophagic pathway resulting in the secondary storage of autophagic debris. It is this "collateral damage" which is common to the LSDs but nonetheless intricately nuanced in each. We have selected five LSDs resulting from defective proteins that govern widely different lysosomal functions including glycogen degradation (Pompe), lysosomal transport (Cystinosis), lysosomal trafficking (Danon), glycolipid degradation (Gaucher) and an unidentified function (Batten) and argue that despite the disparate functions, these proteins, when mutant, all impair the autophagic process uniquely.

Keywords:  Autophagy; Batten disease; Cystinosis; Danon disease; Gaucher disease; Lysosome; Pompe disease

DOI:  https://doi.org/10.1016/j.ebiom.2020.103166
Mol Cell. 2020 Dec 10. pii: S1097-2765(20)30836-4. [Epub ahead of print]

Mitochondrial Threonyl-tRNA Synthetase TARS2 Is Required for Threonine-Sensitive mTORC1 Activation.

Sung-Hoon Kim, Jung-Hyun Choi, Peng Wang, Christopher D Go, Geoffrey G Hesketh, Anne-Claude Gingras, Seyed Mehdi Jafarnejad, Nahum Sonenberg.

  Mechanistic target of rapamycin complex 1 (mTORC1) controls cell growth and proliferation by sensing fluctuations in environmental cues such as nutrients, growth factors, and energy levels. The Rag GTPases (Rags) serve as a critical module that signals amino acid (AA) availability to modulate mTORC1 localization and activity. Recent studies have demonstrated how AAs regulate mTORC1 activity through Rags. Here, we uncover an unconventional pathway that activates mTORC1 in response to variations in threonine (Thr) levels via mitochondrial threonyl-tRNA synthetase TARS2. TARS2 interacts with inactive Rags, particularly GTP-RagC, leading to increased GTP loading of RagA. mTORC1 activity in cells lacking TARS2 is resistant to Thr repletion, showing that TARS2 is necessary for Thr-dependent mTORC1 activation. The requirement of TARS2, but not cytoplasmic threonyl-tRNA synthetase TARS, for this effect demonstrates an additional layer of complexity in the regulation of mTORC1 activity.

Keywords:  Rag GTPases; TARS2; amino acid; aminoacyl-tRNA synthetase; mTORC1; threonine

DOI:  https://doi.org/10.1016/j.molcel.2020.11.036
EMBO Rep. 2020 Dec 20. e51239

Cancer-secreted miRNAs regulate amino-acid-induced mTORC1 signaling and fibroblast protein synthesis.

Miranda Y Fong, Wei Yan, Majid Ghassemian, Xiwei Wu, Xin Zhou, Minghui Cao, Li Jiang, Jessica Wang, Xuxiang Liu, Jin Zhang, Shizhen Emily Wang.

  Metabolic reprogramming of non-cancer cells residing in a tumor microenvironment, as a result of the adaptations to cancer-derived metabolic and non-metabolic factors, is an emerging aspect of cancer-host interaction. We show that in normal and cancer-associated fibroblasts, breast cancer-secreted extracellular vesicles suppress mTOR signaling upon amino acid stimulation to globally reduce mRNA translation. This is through delivery of cancer-derived miR-105 and miR-204, which target RAGC, a component of Rag GTPases that regulate mTORC1 signaling. Following amino acid starvation and subsequent re-feeding, 13 C-arginine labeling of de novo synthesized proteins shows selective translation of proteins that cluster to specific cellular functional pathways. The repertoire of these newly synthesized proteins is altered in fibroblasts treated with cancer-derived extracellular vesicles, in addition to the overall suppressed protein synthesis. In human breast tumors, RAGC protein levels are inversely correlated with miR-105 in the stroma. Our results suggest that through educating fibroblasts to reduce and re-prioritize mRNA translation, cancer cells rewire the metabolic fluxes of amino acid pool and dynamically regulate stroma-produced proteins during periodic nutrient fluctuations.

Keywords:  breast cancer; extracellular vesicles; mRNA translation; mTORC1; microRNA

DOI:  https://doi.org/10.15252/embr.202051239
Mol Cell. 2020 Dec 15. pii: S1097-2765(20)30827-3. [Epub ahead of print]

In Vivo Evidence for Serine Biosynthesis-Defined Sensitivity of Lung Metastasis, but Not of Primary Breast Tumors, to mTORC1 Inhibition.

Gianmarco Rinaldi, Erica Pranzini, Joke Van Elsen, Dorien Broekaert, Cornelius M Funk, Mélanie Planque, Ginevra Doglioni, Patricia Altea-Manzano, Matteo Rossi, Vincent Geldhof, Shao Thing Teoh, Christina Ross, Kent W Hunter, Sophia Y Lunt, Thomas G P Grünewald, Sarah-Maria Fendt.

  In tumors, nutrient availability and metabolism are known to be important modulators of growth signaling. However, it remains elusive whether cancer cells that are growing out in the metastatic niche rely on the same nutrients and metabolic pathways to activate growth signaling as cancer cells within the primary tumor. We discovered that breast-cancer-derived lung metastases, but not the corresponding primary breast tumors, use the serine biosynthesis pathway to support mTORC1 growth signaling. Mechanistically, pyruvate uptake through Mct2 supported mTORC1 signaling by fueling serine biosynthesis-derived α-ketoglutarate production in breast-cancer-derived lung metastases. Consequently, expression of the serine biosynthesis enzyme PHGDH was required for sensitivity to the mTORC1 inhibitor rapamycin in breast-cancer-derived lung tumors, but not in primary breast tumors. In summary, we provide in vivo evidence that the metabolic and nutrient requirements to activate growth signaling differ between the lung metastatic niche and the primary breast cancer site.

Keywords:  MCT2; PHGDH; breast cancer; lung environment; mTORC1; metastasis formation; pyruvate; serine biosynthesis; α-ketoglutarate

DOI:  https://doi.org/10.1016/j.molcel.2020.11.027
Biochim Biophys Acta Mol Cell Res. 2020 Dec 16. pii: S0167-4889(20)30286-X. [Epub ahead of print] 118928

Cathepsin B is an executioner of ferroptosis.

Pandian Nagakannan, Md Imamul Islam, Marcus Conrad, Eftekhar Eftekharpour.

  Ferroptosis is a necrotic form of cell death caused by inactivation of the glutathione system and uncontrolled iron-mediated lipid peroxidation. Increasing evidence implicates ferroptosis in a wide range of diseases from neurotrauma to cancer, highlighting the importance of identifying an executioner system that can be exploited for clinical applications. In this study, using pharmacological and genetic models of ferroptosis, we observed that lysosomal membrane permeabilization and cytoplasmic leakage of cathepsin B unleashes structural and functional changes in mitochondria and promotes a not previously reported cleavage of histone H3. Inhibition of cathepsin-B robustly rescued cellular membrane integrity and chromatin degradation. We show that these protective effects are independent of glutathione peroxidase-4 and are mediated by preventing lysosomal membrane damage. This was further confirmed when cathepsin B knockout primary fibroblasts remained unaffected in response to various ferroptosis inducers. Our work identifies new and yet-unrecognized aspects of ferroptosis and identifies cathepsin B as a mediator of ferroptotic cell death.

Keywords:  GPX4; Histone H3; autophagy; glutathione; lipid peroxidation; lysosomes

DOI:  https://doi.org/10.1016/j.bbamcr.2020.118928
ACS Infect Dis. 2020 Dec 21.

The SARS-CoV-2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules.

Kirill Gorshkov, Catherine Z Chen, Robert Bostwick, Lynn Rasmussen, Bruce Nguyen Tran, Yu-Shan Cheng, Miao Xu, Manisha Pradhan, Mark Henderson, Wei Zhu, Eunkeu Oh, Kimihiro Susumu, Mason Wolak, Khalida Shamim, Wenwei Huang, Xin Hu, Min Shen, Carleen Klumpp-Thomas, Zina Itkin, Paul Shinn, Juan Carlos de la Torre, Anton Simeonov, Sam G Michael, Matthew D Hall, Donald C Lo, Wei Zheng.

  Understanding the SARS-CoV-2 virus' pathways of infection, virus-host-protein interactions, and mechanisms of virus-induced cytopathic effects will greatly aid in the discovery and design of new therapeutics to treat COVID-19. Chloroquine and hydroxychloroquine, extensively explored as clinical agents for COVID-19, have multiple cellular effects including alkalizing lysosomes and blocking autophagy as well as exhibiting dose-limiting toxicities in patients. Therefore, we evaluated additional lysosomotropic compounds to identify an alternative lysosome-based drug repurposing opportunity. We found that six of these compounds blocked the cytopathic effect of SARS-CoV-2 in Vero E6 cells with half-maximal effective concentration (EC50) values ranging from 2.0 to 13 μM and selectivity indices (SIs; SI = CC50/EC50) ranging from 1.5- to >10-fold. The compounds (1) blocked lysosome functioning and autophagy, (2) prevented pseudotyped particle entry, (3) increased lysosomal pH, and (4) reduced (ROC-325) viral titers in the EpiAirway 3D tissue model. Consistent with these findings, the siRNA knockdown of ATP6V0D1 blocked the HCoV-NL63 cytopathic effect in LLC-MK2 cells. Moreover, an analysis of SARS-CoV-2 infected Vero E6 cell lysate revealed significant dysregulation of autophagy and lysosomal function, suggesting a contribution of the lysosome to the life cycle of SARS-CoV-2. Our findings suggest the lysosome as a potential host cell target to combat SARS-CoV-2 infections and inhibitors of lysosomal function could become an important component of drug combination therapies aimed at improving treatment and outcomes for COVID-19.

Keywords:  SARS-CoV-2; autophagy; coronavirus; cytopathic effect; small molecule inhibitors

DOI:  https://doi.org/10.1021/acsinfecdis.0c00349
Traffic. 2020 Dec 21.

Formation of retromer transport carriers is disrupted by the Parkinson disease-linked Vps35 D620N variant.

Yi Cui, Zhe Yang, Neftali Flores-Rodriguez, Jordan Follett, Nicholas Ariotti, Adam A Wall, Robert G Parton, Rohan D Teasdale.

  Retromer core complex is an endosomal scaffold that plays a critical role in orchestrating protein trafficking within the endosomal system. Here we characterized the effect of the Parkinson's disease-linked Vps35 D620N in the endo-lysosomal system using Vps35 D620N rescue cell models. Vps35 D620N fully rescues the lysosomal and autophagy defects caused by retromer knock-out. Analogous to Vps35 knock out cells, the endosome-to-TGN transport of cation-independent mannose 6-phosphate receptor (CI-M6PR) is impaired in Vps35 D620N rescue cells due to a reduced capacity to form endosome transport carriers. Cells expressing the Vps35 D620N variant have altered endosomal morphology, resulting in smaller, rounder structures with less tubule-like branches. At the molecular level retromer incorporating Vps35 D620N variant has a decreased binding to retromer associated proteins WASH and SNX3 which are known to associate with retromer to form that endosome transport carriers. Hence, the partial defects on retrograde protein trafficking carriers in the presence of Vps35 D620N represents an altered cellular state able to cause Parkinson's disease. This article is protected by copyright. All rights reserved.

Keywords:  Parkinson’s disease; Protein trafficking; WASH complex; endosomal trafficking; retromer

DOI:  https://doi.org/10.1111/tra.12779
Am J Pathol. 2020 Dec 17. pii: S0002-9440(20)30564-2. [Epub ahead of print]

Lack of Annexin A6 exacerbates liver dysfunction and reduces lifespan of NPC1-deficient mice.

Elsa Meneses-Salas, Marta Garcia-Forn, Carla Castany-Pladevall, Albert Lu, Alba Fajardo, Jaimy Jose, Mohamed Wahba, Marta Bosch, Albert Pol, Francesc Tebar, Andrés D Klein, Silvana Zanlungo, Esther Pérez-Navarro, Thomas Grewal, Carlos Enrich, Carles Rentero.

Niemann-Pick type C disease (NP-C) is a lysosomal storage disorder characterized by cholesterol accumulation caused by loss-of-function mutations in the Npc1 gene. NP-C disease primarily affects the brain, causing neuronal damage and affecting motor coordination. In addition, considerable liver malfunction in NP-C disease is common. Recently, we demonstrated that the depletion of annexin A6 (ANXA6), which is most abundant in the liver and involved in cholesterol transport, ameliorated cholesterol accumulation in Npc1 mutant cells. To evaluate the potential contribution of ANXA6 in the progression of NP-C disease, double-knockout mice (Npc1-/-/Anxa6-/-) were generated and examined for lifespan, neurological and hepatic functions, as well as liver histology and ultrastructure. Strikingly, lack of ANXA6 in NPC1-deficient animals did not prevent the cerebellar degeneration phenotype but further deteriorated their compromised hepatic functions and reduced lifespan. Moreover, livers of Npc1-/-/Anxa6-/- mice contained a significantly elevated number of foam cells congesting the sinusoidal space, a feature commonly associated with inflammation. We hypothesize that ANXA6 deficiency in Npc1-/- mice do not reverse neurological and motor dysfunction and it further worsens overall liver function, exacerbating hepatic failure in NP-C disease.

DOI: https://doi.org/10.1016/j.ajpath.2020.12.009
Mol Metab. 2020 Dec 18. pii: S2212-8778(20)30220-9. [Epub ahead of print] 101146

Function of the Endolysosomal Network in Cholesterol Homeostasis and Metabolic Associated Fatty Liver Disease (MAFLD).

Dyonne Y Vos, Bart van de Sluis.

   BACKGROUND: Metabolic associated fatty liver disease (MAFLD), also known as non-alcoholic fatty liver disease, has become the leading cause of chronic liver disease worldwide. Besides hepatic accumulation of triglycerides, dysregulated cholesterol metabolism is an important contributor to the pathogenesis of MAFLD. Maintenance of cholesterol homeostasis is highly dependent on cellular cholesterol uptake, and subsequently cholesterol transport to other membrane compartments, such as the endocytic reticulum (ER).
SCOPE OF REVIEW: The endolysosomal network is key for regulating cellular homeostasis and adaptation, and emerging evidence has shown that the endolysosomal network is crucial to maintain metabolic homeostasis. In this review, we will summarize our current understanding of the role of the endolysosomal network in cholesterol homeostasis and its implications in MAFLD pathogenesis.
MAJOR CONCLUSIONS: Although multiple endolysosomal proteins have been identified in the regulation of cholesterol uptake, intracellular transport, and degradation, their physiological role is incompletely understood. Further research should elucidate their role in controlling metabolic homeostasis and development of fatty liver disease.

Keywords:  LDLR; NAFLD; PCSK9; cholesterol transport; endosomal sorting; endosome and lysosome

DOI:  https://doi.org/10.1016/j.molmet.2020.101146
Front Cell Infect Microbiol. 2020 ;10 601072

Cathepsins in Bacteria-Macrophage Interaction: Defenders or Victims of Circumstance?

Lidia Szulc-Dąbrowska, Magdalena Bossowska-Nowicka, Justyna Struzik, Felix N Toka.

  Macrophages are the first encounters of invading bacteria and are responsible for engulfing and digesting pathogens through phagocytosis leading to initiation of the innate inflammatory response. Intracellular digestion occurs through a close relationship between phagocytic/endocytic and lysosomal pathways, in which proteolytic enzymes, such as cathepsins, are involved. The presence of cathepsins in the endo-lysosomal compartment permits direct interaction with and killing of bacteria, and may contribute to processing of bacterial antigens for presentation, an event necessary for the induction of antibacterial adaptive immune response. Therefore, it is not surprising that bacteria can control the expression and proteolytic activity of cathepsins, including their inhibitors - cystatins, to favor their own intracellular survival in macrophages. In this review, we summarize recent developments in defining the role of cathepsins in bacteria-macrophage interaction and describe important strategies engaged by bacteria to manipulate cathepsin expression and activity in macrophages. Particularly, we focus on specific bacterial species due to their clinical relevance to humans and animal health, i.e., Mycobacterium, Mycoplasma, Staphylococcus, Streptococcus, Salmonella, Shigella, Francisella, Chlamydia, Listeria, Brucella, Helicobacter, Neisseria, and other genera.

Keywords:  bacteria; cathepsins; immune invasion; macrophages; modulation of immune function

DOI:  https://doi.org/10.3389/fcimb.2020.601072