bims-lysosi 2020-12-13 papers

bims-lysosi

Biomed News

on Lysosomes and signaling

Issue of 2020‒12‒13
23 papers selected by
Stephanie Fernandes
Max Planck Institute for Biology of Ageing

Direct lysosome-based autophagy of lipid droplets in hepatocytes.
Architecture of the Tuberous Sclerosis Protein Complex.
Inositol Polyphosphate Multikinase Inhibits Liquid-Liquid Phase Separation of TFEB to Negatively Regulate Autophagy Activity.
REV-ERBα alters circadian rhythms by modulating mTOR signaling.
A Conformational Change in the N Terminus of SLC38A9 Signals mTORC1 Activation.
Translation in amino acid-poor environments is limited by tRNAGln charging.
CNS-Targeting Therapies for Lysosomal Storage Diseases: Current Advances and Challenges.
Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors.
When lipid homeostasis runs havoc: lipotoxicity links lysosomal dysfunction to autophagy.
Current Evidence for a Bidirectional Loop Between the Lysosome and Alpha-Synuclein Proteoforms.
The Inhibitory Role of Rab11b in Osteoclastogenesis through Triggering Lysosome-Induced Degradation of c-Fms and RANK Surface Receptors.
Whole-exome sequencing reveals novel vacuolar ATPase genes' variants and variants in genes involved in lysosomal biology and autophagosomal formation in oral granular cell tumors.
Elevated Dkk1 Mediates Downregulation of the Canonical Wnt Pathway and Lysosomal Loss in an iPSC Model of Neuronopathic Gaucher Disease.
Out of Phase: How IPMK Inhibits TFEB.
Quantification and characterization of the 5'exonuclease activity of the lysosomal nuclease PLD3 by a novel cell-based assay.
Lysosomal storage disorders: Novel and frequent pathogenic variants in a large cohort of Indian patients of Pompe, Fabry, Gaucher and Hurler disease.
Getting Lost in the Cell-Lysosomal Entrapment of Chemotherapeutics.
Retinol binding protein 4 (Rbp4) mRNA translation in hepatocytes is enhanced by activation of mTORC1.
TFEB/Mitf links impaired nuclear import to autophagolysosomal dysfunction in C9-ALS.
A dual-labeling probe to track functional mitochondria-lysosome interactions in live cells.
Dual enzyme responsive mannose-6-phosphate based vesicle for controlled lysosomal delivery.
Late endosomes promote microglia migration via cytosolic translocation of immature protease cathD.
The role of lysosomes in cancer development and progression.

Proc Natl Acad Sci U S A. 2020 Dec 07. pii: 202011442. [Epub ahead of print]

Direct lysosome-based autophagy of lipid droplets in hepatocytes.

Ryan J Schulze, Eugene W Krueger, Shaun G Weller, Katherine M Johnson, Carol A Casey, Micah B Schott, Mark A McNiven.

  Hepatocytes metabolize energy-rich cytoplasmic lipid droplets (LDs) in the lysosome-directed process of autophagy. An organelle-selective form of this process (macrolipophagy) results in the engulfment of LDs within double-membrane delimited structures (autophagosomes) before lysosomal fusion. Whether this is an exclusive autophagic mechanism used by hepatocytes to catabolize LDs is unclear. It is also unknown whether lysosomes alone might be sufficient to mediate LD turnover in the absence of an autophagosomal intermediate. We performed live-cell microscopy of hepatocytes to monitor the dynamic interactions between lysosomes and LDs in real-time. We additionally used a fluorescent variant of the LD-specific protein (PLIN2) that exhibits altered fluorescence in response to LD interactions with the lysosome. We find that mammalian lysosomes and LDs undergo interactions during which proteins and lipids can be transferred from LDs directly into lysosomes. Electron microscopy (EM) of primary hepatocytes or hepatocyte-derived cell lines supports the existence of these interactions. It reveals a dramatic process whereby the lipid contents of the LD can be "extruded" directly into the lysosomal lumen under nutrient-limited conditions. Significantly, these interactions are not affected by perturbations to crucial components of the canonical macroautophagy machinery and can occur in the absence of double-membrane lipoautophagosomes. These findings implicate the existence of an autophagic mechanism used by mammalian cells for the direct transfer of LD components into the lysosome for breakdown. This process further emphasizes the critical role of lysosomes in hepatic LD catabolism and provides insights into the mechanisms underlying lipid homeostasis in the liver.

Keywords:  hepatocyte; lipid droplet; lipolysis; lysosome; microautophagy

DOI:  https://doi.org/10.1073/pnas.2011442117
J Mol Biol. 2020 Dec 08. pii: S0022-2836(20)30668-9. [Epub ahead of print] 166743

Architecture of the Tuberous Sclerosis Protein Complex.

Kailash Ramlaul, Wencheng Fu, Hua Li, Natàlia de Martin Garrido, Lin He, Manjari Trivedi, Wei Cui, Christopher H S Aylett, Geng Wu.

  The Tuberous Sclerosis Complex (TSC) protein complex (TSCC), comprising TSC1, TSC2, and TBC1D7, is widely recognised as a key integration hub for cell growth and intracellular stress signals upstream of the mammalian target of rapamycin complex 1 (mTORC1). The TSCC negatively regulates mTORC1 by acting as a GTPase-activating protein (GAP) towards the small GTPase Rheb. Both human TSC1 and TSC2 are important tumour suppressors, and mutations in them underlie the disease tuberous sclerosis. We used single-particle cryo-EM to reveal the organisation and architecture of the complete human TSCC. We show that TSCC forms an elongated scorpion-like structure, consisting of a central "body", with a "pincer" and a "tail" at the respective ends. The "body" is composed of a flexible TSC2 HEAT repeat dimer, along the surface of which runs the TSC1 coiled-coil backbone, breaking the symmetry of the dimer. Each end of the body is structurally distinct, representing the N- and C-termini of TSC1; a "pincer" is formed by the highly flexible N-terminal TSC1 core domains and a barbed "tail" makes up the TSC1 coiled-coil-TBC1D7 junction. The TSC2 GAP domain is found abutting the centre of the body on each side of the dimerisation interface, poised to bind a pair of Rheb molecules at a similar separation to the pair in activated mTORC1. Our architectural dissection reveals the mode of association and topology of the complex, casts light on the recruitment of Rheb to the TSCC, and also hints at functional higher order oligomerisation, which has previously been predicted to be important for Rheb-signalling suppression.

Keywords:  Cryo-EM; Hamartin; RapGAP; Tuberin; Tuberous sclerosis complex

DOI:  https://doi.org/10.1016/j.jmb.2020.166743
Dev Cell. 2020 Dec 07. pii: S1534-5807(20)30800-5. [Epub ahead of print]55(5): 588-602.e7

Inositol Polyphosphate Multikinase Inhibits Liquid-Liquid Phase Separation of TFEB to Negatively Regulate Autophagy Activity.

Di Chen, Zheng Wang, Yan G Zhao, Hui Zheng, Hongyu Zhao, Nan Liu, Hong Zhang.

  Liquid-liquid phase separation (LLPS) compartmentalizes transcriptional condensates for gene expression, but little is known about how this process is controlled. Here, we showed that depletion of IPMK, encoding inositol polyphosphate multikinase, promotes autophagy and lysosomal function and biogenesis in a TFEB-dependent manner. Cytoplasmic-nuclear trafficking of TFEB, a well-characterized mechanism by which diverse signaling pathways regulate TFEB activity, is not evidently altered by IPMK depletion. We demonstrated that nuclear TFEB forms distinct puncta that colocalize with the Mediator complex and with mRNAs of target lysosomal genes. TFEB undergoes LLPS in vitro. IPMK directly interacts with and inhibits LLPS of TFEB and also dissolves TFEB condensates. Depletion of IPMK increases the number of nuclear TFEB puncta and the co-localization of TFEB with Mediator and mRNAs of target genes. Our study reveals that nuclear-localized IPMK acts as a chaperone to inhibit LLPS of TFEB to negatively control its transcriptional activity.

Keywords:  IPMK; TFEB; autophagy; lysosome; phase separation

DOI:  https://doi.org/10.1016/j.devcel.2020.10.010
Mol Cell Endocrinol. 2020 Dec 04. pii: S0303-7207(20)30410-X. [Epub ahead of print] 111108

REV-ERBα alters circadian rhythms by modulating mTOR signaling.

Dadon-Freiberg Maayan, Nava Chapnik, Oren Froy.

  REV-ERBα is a nuclear receptor that inhibits Bmal1 transcription as part of the circadian clock molecular mechanism. Mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is a master regulator of cell and whole-body energy homeostasis, that serves as an important link between metabolism and circadian clock, in part, by regulating BMAL1 activity. While the connection of REV-ERBα to the circadian clock molecular mechanism is well characterized, the interaction between mTORC1, REV-ERBα and the circadian clock machinery is not very clear. We used leucine and rapamycin to modulate mTORC1 activation and evaluate this effect on circadian rhythms. In the liver, mTORC1 was inhibited by leucine. REV-ERBα overexpression activated the mTORC1 signaling pathway via transcription inhibition of mTORC1 inhibitor, Tsc1, antagonizing the effect of leucine, while its silencing downregulated mTORC1 signaling. Activation of mTORC1 led to increased levels of BMAL1 phosphorylation. Activation as well as inhibition of mTORC1 led to altered circadian rhythms in mouse muscle. Inhibition of liver mTORC1 by leucine or rapamycin led to low-amplitude circadian rhythms. In summary, our study shows that leucine inhibits liver mTORC1 pathway leading to dampened circadian rhythms. REV-ERBα activates the mTORC1 pathway, leading to phosphorylation of the clock protein BMAL1.

Keywords:  REV-ERB; circadian; clock; leucine; liver; mTOR

DOI:  https://doi.org/10.1016/j.mce.2020.111108
Structure. 2020 Dec 07. pii: S0969-2126(20)30426-3. [Epub ahead of print]

A Conformational Change in the N Terminus of SLC38A9 Signals mTORC1 Activation.

Hsiang-Ting Lei, Xuelang Mu, Johan Hattne, Tamir Gonen.

  mTORC1 is a central hub that integrates environmental cues, such as cellular stresses and nutrient availability to modulate metabolism and cellular responses. Recently, SLC38A9, a lysosomal amino acid transporter, emerged as a sensor for luminal arginine and as an activator of mTORC1. The amino acid-mediated activation of mTORC1 is regulated by the N-terminal domain of SLC38A9. Here, we determined the crystal structure of zebrafish SLC38A9 (drSLC38A9) and found the N-terminal fragment inserted deep within the transporter, bound in the substrate-binding pocket where normally arginine would bind. This represents a significant conformational change of the N-terminal domain (N-plug) when compared with our recent arginine-bound structure of drSLC38A9. We propose a ball-and-chain model for mTORC1 activation, where N-plug insertion and Rag GTPase binding with SLC38A9 is regulated by luminal arginine levels. This work provides important insights into nutrient sensing by SLC38A9 to activate the mTORC1 pathways in response to dietary amino acids.

Keywords:  SLC38A9; arginine transport; crystallography; mTORC1

DOI:  https://doi.org/10.1016/j.str.2020.11.014
Elife. 2020 Dec 08. pii: e62307. [Epub ahead of print]9

Translation in amino acid-poor environments is limited by tRNAGln charging.

Natalya N Pavlova, Bryan King, Rachel H Josselsohn, Sara Violante, Victoria L Macera, Santosha A Vardhana, Justin R Cross, Craig B Thompson.

  An inadequate supply of amino acids leads to accumulation of uncharged tRNAs, which can bind and activate GCN2 kinase to reduce translation. Here, we show that glutamine-specific tRNAs selectively become uncharged when extracellular amino acid availability is compromised. In contrast, all other tRNAs retain charging of their cognate amino acids in a manner that is dependent upon intact lysosomal function. In addition to GCN2 activation and reduced total translation, the reduced charging of tRNAGln in amino acid-deprived cells also leads to specific depletion of proteins containing polyglutamine tracts including core binding factor α1, mediator subunit 12, transcriptional coactivator CBP and TATA-box binding protein. Treating amino acid-deprived cells with exogenous glutamine or glutaminase inhibitors restores tRNAGln charging and the levels of polyglutamine-containing proteins. Together, these results demonstrate that the activation of GCN2 and the translation of polyglutamine-encoding transcripts serve as key sensors of glutamine availability in mammalian cells.

Keywords:  cell biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.62307
Front Mol Biosci. 2020 ;7 559804

CNS-Targeting Therapies for Lysosomal Storage Diseases: Current Advances and Challenges.

Mariola J Edelmann, Gustavo H B Maegawa.

  During the past decades, several therapeutic approaches have been developed and made rapidly available for many patients afflicted with lysosomal storage disorders (LSDs), inborn organelle disorders with broad clinical manifestations secondary to the progressive accumulation of undegraded macromolecules within lysosomes. These conditions are individually rare, but, collectively, their incidence ranges from 1 in 2,315 to 7,700 live-births. Most LSDs are manifested by neurological symptoms or signs, including developmental delay, seizures, acroparesthesia, motor weakness, and extrapyramidal signs. The chronic and later-onset clinical forms are at one end of the continuum spectrum and are characterized by a subtle and slow progression of neurological symptoms. Due to its inherent physiological properties, unfortunately, the blood-brain barrier (BBB) constitutes a significant obstacle for current and upcoming therapies to achieve the central nervous system (CNS) and treat neurological problems so prevalent in these conditions. To circumvent this limitation, several strategies have been developed to make the therapeutic agent achieve the CNS. This narrative will provide an overview of current therapeutic strategies under development to permeate the BBB, and address and unmet need for treatment of the progressive neurological manifestations, which are so prevalent in these inherited lysosomal disorders.

Keywords:  enzyme replacement therapy; exosomes; extracellular vesicles; gene therapy; liposomes; lysosomes; small molecules; therapy

DOI:  https://doi.org/10.3389/fmolb.2020.559804
Cells. 2020 Dec 03. pii: E2593. [Epub ahead of print]9(12):

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors.

Silvin Lito, Adama Sidibe, Sten Ilmjarv, Patricie Burda, Matthias Baumgartner, Bernhard Wehrle-Haller, Karl-Heinz Krause, Antoine Marteyn.

  Background: Mucopolysaccharidosis type I-Hurler (MPS1-H) is a severe genetic lysosomal storage disorder due to loss-of-function mutations in the IDUA gene. The subsequent complete deficiency of alpha l-iduronidase enzyme is directly responsible of a progressive accumulation of glycosaminoglycans (GAG) in lysosomes which affects the functions of many tissues. Consequently, MPS1 is characterized by systemic symptoms (multiorgan dysfunction) including respiratory and cardiac dysfunctions, skeletal abnormalities and early fatal neurodegeneration. Methods: To understand mechanisms underlying MPS1 neuropathology, we generated induced pluripotent stem cells (iPSC) from a MPS1-H patient with loss-of-function mutations in both IDUA alleles. To avoid variability due to different genetic background of iPSC, we established an isogenic control iPSC line by rescuing IDUA expression by a lentivectoral approach. Results: Marked differences between MPS1-H and IDUA-corrected isogenic controls were observed upon neural differentiation. A scratch assay revealed a strong migration defect of MPS1-H cells. Also, there was a massive impact of IDUA deficiency on gene expression (340 genes with an FDR <0.05). Conclusions: Our results demonstrate a hitherto unknown connection between lysosomal degradation, gene expression and neural motility, which might account at least in part for the phenotype of MPS1-H patients.

Keywords:  disease modelling; induced pluripotent stem cells; mucopolysaccharidosis I; neural migration; neurite outgrowth; neuronal differentiation

DOI:  https://doi.org/10.3390/cells9122593
Matrix Biol. 2020 Dec 05. pii: S0945-053X(20)30115-3. [Epub ahead of print]

When lipid homeostasis runs havoc: lipotoxicity links lysosomal dysfunction to autophagy.

Irmgard Tegeder, Donat Kögel.

  Autophagy is one of the major cellular degradation pathways, which prevents accumulation of cellular wastes including "hazardous" material such as oxidized proteins and lipids and allows removal of aggregates and dysfunctional organelles. Hence, autophagy is meant to preserve cell survival, and is mostly protective. However, autophagy may trigger a feedforward, exaggerated cycle in which cells continue to degrade proteins and organelles, finally leading to autophagy-dependent cell death (ADCD), a process that can be initiated with lysosomotropic detergents, which are protonated within the lysosome and cause a permeabilization of the membrane. Such drugs may be useful to combat cancer. In some paradigms of ADCD, there is evidence that the cellular fate is determined by the integrity of lysosomal membranes, transporters, enzymes and ion gradients. Detergent-like effects of lysosomotropic drugs can over-activate autophagy. A disruption of the lysosomal membrane barrier with leakage of lysosomal enzymes or lipids may trigger a vicious cycle via proteases and accumulation of lipids, which impair the functions of the plasma - and organelle membranes. This review summarizes the current evidence for a crosstalk between lysosomal dysfunction and autophagy and the lysosomal events, which progress toward ADCD with a focus on the role of sphingolipids and cholesterol as cargo and as regulators of ADCD.

Keywords:  Lysosomal leak; cell death; ceramides; cholesterol; sphingolipids

DOI:  https://doi.org/10.1016/j.matbio.2020.11.005
Front Cell Dev Biol. 2020 ;8 598446

Current Evidence for a Bidirectional Loop Between the Lysosome and Alpha-Synuclein Proteoforms.

Norelle C Wildburger, Anna-Sophia Hartke, Alina Schidlitzki, Franziska Richter.

  Cumulative evidence collected in recent decades suggests that lysosomal dysfunction contributes to neurodegenerative diseases, especially if amyloid proteins are involved. Among these, alpha-synuclein (aSyn) that progressively accumulates and aggregates in Lewy bodies is undisputedly a main culprit in Parkinson disease (PD) pathogenesis. Lysosomal dysfunction is evident in brains of PD patients, and mutations in lysosomal enzymes are a major risk factor of PD. At first glance, the role of protein-degrading lysosomes in a disease with pathological protein accumulation seems obvious and should guide the development of straightforward and rational therapeutic targets. However, our review demonstrates that the story is more complicated for aSyn. The protein can possess diverse posttranslational modifications, aggregate formations, and truncations, all of which contribute to a growing known set of proteoforms. These interfere directly or indirectly with lysosome function, reducing their own degradation, and thereby accelerating the protein aggregation and disease process. Conversely, unbalanced lysosomal enzymatic processes can produce truncated aSyn proteoforms that may be more toxic and prone to aggregation. This highlights the possibility of enhancing lysosomal function as a treatment for PD, if it can be confirmed that this approach effectively reduces harmful aSyn proteoforms and does not produce novel, toxic proteoforms.

Keywords:  GCase; Parkinson disease; alpha-synuclein; lysosome; proteoforms

DOI:  https://doi.org/10.3389/fcell.2020.598446
Int J Mol Sci. 2020 Dec 08. pii: E9352. [Epub ahead of print]21(24):

The Inhibitory Role of Rab11b in Osteoclastogenesis through Triggering Lysosome-Induced Degradation of c-Fms and RANK Surface Receptors.

Manh Tien Tran, Yuka Okusha, Yunxia Feng, Masatoshi Morimatsu, Penggong Wei, Chiharu Sogawa, Takanori Eguchi, Tomoko Kadowaki, Eiko Sakai, Hirohiko Okamura, Keiji Naruse, Takayuki Tsukuba, Kuniaki Okamoto.

  Rab11b, abundantly enriched in endocytic recycling compartments, is required for the establishment of the machinery of vesicle trafficking. Yet, no report has so far characterized the biological function of Rab11b in osteoclastogenesis. Using in vitro model of osteoclasts differentiated from murine macrophages like RAW-D cells or bone marrow-derived macrophages, we elucidated that Rab11b served as an inhibitory regulator of osteoclast differentiation sequentially via (i) abolishing surface abundance of RANK and c-Fms receptors; and (ii) attenuating nuclear factor of activated T-cells c1 (NFATc-1) upstream signaling cascades, following RANKL stimulation. Rab11b was localized in early and late endosomes, Golgi complex, and endoplasmic reticulum; moreover, its overexpression enlarged early and late endosomes. Upon inhibition of lysosomal function by a specific blocker, chloroquine (CLQ), we comprehensively clarified a novel function of lysosomes on mediating proteolytic degradation of c-Fms and RANK surface receptors, drastically ameliorated by Rab11b overexpression in RAW-D cell-derived osteoclasts. These findings highlight the key role of Rab11b as an inhibitor of osteoclastogenesis by directing the transport of c-Fms and RANK surface receptors to lysosomes for degradation via the axis of early endosomes-late endosomes-lysosomes, thereby contributing towards the systemic equilibrium of the bone resorption phase.

Keywords:  NFATc-1; RANK; Rab11b; c-Fms; osteoclasts; vesicular transport

DOI:  https://doi.org/10.3390/ijms21249352
J Oral Pathol Med. 2020 Dec 01.

Whole-exome sequencing reveals novel vacuolar ATPase genes' variants and variants in genes involved in lysosomal biology and autophagosomal formation in oral granular cell tumors.

Josiane Alves França, Tenzin Gayden, Eric Bareke, Jean Nunes Santos, Sílvia Ferreira de Sousa, Luciana Bastos-Rodrigues, Jacek Majewski, Nada Jabado, Ricardo Santiago Gomez, Carolina Cavalieri Gomes.

  BACKGROUND: Granular cell tumors (GCTs) are rare neuroectodermal soft tissue neoplasms that mainly affect the skin of the upper limbs and trunks and the oral cavity. GCTs are derived from Schwann cells and, ultrastructurally, their intracytoplasmic granules are considered autophagosomes or autophagolysosomes and are consistent with myelin accumulation.METHODS: In this study, a convenience set of 22 formalin-fixed, paraffin-embedded samples of oral GCTs, all but one sample located at the tongue, was screened for mutations by whole-exome sequencing.
RESULTS: Two novel variants in genes of the vacuolar ATPase (V-ATPase) complex: ATP6AP1 frameshift c.746_749del, leading to p.P249Hfs*4, and ATP6V1A nonsynonymous c.G868A, leading to p.D290N. Each of these mutations occurred in one case. With regard to the samples that were wild-type for these V-ATPase variants, at least two samples presented variants in genes that are part of endosomal/lysosomal/autophagosomal networks including ABCA8, ABCC6, AGAP3, ATG9A, CTSB, DNAJC13, GALC, NPC1, SLC15A3, SLC31A2 and TMEM104.
CONCLUSION: Although the mechanisms involved in oral GCT initiation and progression remains unclear, our results suggest that oral GCTs have V-ATPase variants similarly to GCTs from other tissues/organs, and additionally show variants in lysosomes/endosomes/autophagosomal genes.

Keywords:  Genetics; Lysosomes; Oral granular cell tumor; Soft tissue neoplasms; V‐ATPase

DOI:  https://doi.org/10.1111/jop.13148
Biomolecules. 2020 Dec 03. pii: E1630. [Epub ahead of print]10(12):

Elevated Dkk1 Mediates Downregulation of the Canonical Wnt Pathway and Lysosomal Loss in an iPSC Model of Neuronopathic Gaucher Disease.

Manasa P Srikanth, Ricardo A Feldman.

  Gaucher Disease (GD), which is the most common lysosomal storage disorder, is caused by bi-allelic mutations in GBA1-a gene that encodes the lysosomal hydrolase β-glucocerebrosidase (GCase). The neuronopathic forms of GD (nGD) are characterized by severe neurological abnormalities that arise during gestation or early in infancy. Using GD-induced pluripotent stem cell (iPSC)-derived neuronal progenitor cells (NPCs), we have previously reported that neuronal cells have neurodevelopmental defects associated with the downregulation of canonical Wnt signaling. In this study, we report that GD NPCs display elevated levels of Dkk1, which is a secreted Wnt antagonist that prevents receptor activation. Dkk1 upregulation in mutant NPCs resulted in an increased degradation of β-catenin, and there was a concomitant reduction in lysosomal numbers. Consistent with these results, incubation of the mutant NPCs with recombinant Wnt3a (rWnt3a) was able to outcompete the excess Dkk1, increasing β-catenin levels and rescuing lysosomal numbers. Furthermore, the incubation of WT NPCs with recombinant Dkk1 (rDkk1) phenocopied the mutant phenotype, recapitulating the decrease in β-catenin levels and lysosomal depletion seen in nGD NPCs. This study provides evidence that downregulation of the Wnt/β-catenin pathway in nGD neuronal cells involves the upregulation of Dkk1. As Dkk1 is an extracellular Wnt antagonist, our results suggest that the deleterious effects of Wnt/β-catenin downregulation in nGD may be ameliorated by the prevention of Dkk1 binding to the Wnt co-receptor LRP6, pointing to Dkk1 as a potential therapeutic target for GBA1-associated neurodegeneration.

Keywords:  Dkk1; Gaucher Disease; Wnt/β-catenin; Wnt3a; iPSC; lysosomes; neuronopathy

DOI:  https://doi.org/10.3390/biom10121630
Dev Cell. 2020 Dec 07. pii: S1534-5807(20)30880-7. [Epub ahead of print]55(5): 517-519

Out of Phase: How IPMK Inhibits TFEB.

Luca Ferrari, Sascha Martens.

The expression of autophagy and lysosomal genes is coordinated by the transcription factor EB (TFEB). In this issue of Developmental Cell, Chen et al. identify an evolutionary conserved mode of TFEB regulation, which entails the inhibition of TFEB phase separation in the nucleus by inositol polyphosphate multikinase.

DOI: https://doi.org/10.1016/j.devcel.2020.11.005
J Biol Chem. 2020 Dec 06. pii: jbc.RA120.015867. [Epub ahead of print]

Quantification and characterization of the 5'exonuclease activity of the lysosomal nuclease PLD3 by a novel cell-based assay.

Cedric Cappel, Adriana Carolina Gonzalez, Markus Damme.

  Phospholipase D3 (PLD3) and phospholipase D4 (PLD4), the most recently described lysosomal nucleases, are associated with Alzheimer`s disease, spinocerebellar ataxia, and systemic lupus erythematosus. They exhibit 5' exonuclease activity on single-stranded DNA, hydrolyzing it at the acidic pH associated with the lysosome. However, their full cellular function is inadequately understood. To examine these enzymes, we developed a robust and automatable cell-based assay based on fluorophore- and fluorescence-quencher coupled oligonucleotides for the quantitative determination of acidic 5' exonuclease activity. We validated the assay under knockout and PLD-overexpression conditions, and then applied it to characterize PLD3 and PLD4 biochemically. Our experiments revealed PLD3 as the principal acid 5' exonuclease in HeLa cells, where it showed a markedly higher specific activity compared to PLD4. We further used our newly developed assay to determine the substrate specificity and inhibitory profile of PLD3, and found that proteolytic processing of PLD3 is dispensable for its hydrolytic activity. We followed the expression, proteolytic processing, and intracellular distribution of genetic PLD3 variants previously associated with Alzheimer's disease and investigated each variant's effect on the 5' nuclease activity of PLD3, finding that some variants lead to reduced activity, but others not. The development of a PLD3/4-specific biochemical assay will be instrumental in understanding better both nucleases and their incompletely unknown roles in vitro and in vivo.

Keywords:  5' exonuclease; DNA enzyme; Lysosomal; PLD3; PLD4; fluorescence-quenched oligonucleotide; lysosomal glycoprotein; lysosome; nucleoside/nucleotide metabolism; substrate specificity; toll-like receptor (TLR)

DOI:  https://doi.org/10.1074/jbc.RA120.015867
Clin Biochem. 2020 Dec 07. pii: S0009-9120(20)30906-1. [Epub ahead of print]

Lysosomal storage disorders: Novel and frequent pathogenic variants in a large cohort of Indian patients of Pompe, Fabry, Gaucher and Hurler disease.

Divya C Thomas, Sandeepika Sharma, Ratna D Puri, I C Verma, Jyotsna Verma.

  OBJECTIVES: Diagnosis of lysosomal storage disorders (LSDs) remains challenging due to wide clinical, biochemical and molecular heterogeneity. The study applies a combined biochemical and genetic approach to diagnose symptomatic Indian patients of Pompe, Fabry, Gaucher and Hurler disease to generate a comprehensive dataset of pathogenic variants for these disorders. Design & Methods Symptomatic patients were biochemically diagnosed by fluorometric methods and molecular confirmation was carried out by gene sequencing. Genetic variants were analyzed according to the ACMG/AMP 2015 variant interpretation guidelines.RESULTS: Amongst the 2181 suspected patients, 285 (13%) were biochemically diagnosed. Of these, 22.5% (64/285) diagnosed with Pompe disease harboured c.1933G>A, c.1A>G, c.1927G>A and c.2783G>C as common and 10 novel pathogenic variants while 7.4% (21/285) patients diagnosed with Fabry disease carried c.851T>C , c.902G>A, c.905A>C and c.1212_1234del as frequent disease-causing variants along with 7 novel pathogenic variants. As many as 48.4% (138/285) patients were diagnosed with Gaucher disease and had c.1448T>C as the most common pathogenic variant followed by c.1342G>C and c.754T>C with 7 previously unreported disease-causing variants and in the 21.7% (62/285) diagnosed cases of Hurler disease, c.1469T>C, c.754delC c.568_581del and c.1898C>T were identified as the most common causative variants along with 21 novel pathogenic variants.
CONCLUSION: This comprehensive data set of disease-causing frequent and novel pathogenic variants reported for the first time in such a large patient cohort for each of these four LSDs from the Indian sub-continent, along with their biochemical and clinical spectrum will contribute towards providing definitive diagnosis and treatment, identifying carrier status, as well as in counselling prenatal cases to reduce the morbidity and mortality associated with these disorders.

Keywords:  Fabry; Gaucher; Hurler; Lysosomal storage disorders; Novel variants; Pompe

DOI:  https://doi.org/10.1016/j.clinbiochem.2020.12.002
Cancers (Basel). 2020 Dec 07. pii: E3669. [Epub ahead of print]12(12):

Getting Lost in the Cell-Lysosomal Entrapment of Chemotherapeutics.

Xingjian Zhai, Yassine El Hiani.

  Despite extensive research, resistance to chemotherapy still poses a major obstacle in clinical oncology. An exciting strategy to circumvent chemoresistance involves the identification and subsequent disruption of cellular processes that are aberrantly altered in oncogenic states. Upon chemotherapeutic challenges, lysosomes are deemed to be essential mediators that enable cellular adaptation to stress conditions. Therefore, lysosomes potentially hold the key to disarming the fundamental mechanisms of chemoresistance. This review explores modes of action of classical chemotherapeutic agents, adaptive response of the lysosomes to cell stress, and presents physiological and pharmacological insights pertaining to drug compartmentalization, sequestration, and extracellular clearance through the lens of lysosomes.

Keywords:  cancer therapy; chemoresistance; chemotherapeutics; lysosomal entrapment; lysosomes

DOI:  https://doi.org/10.3390/cancers12123669
Am J Physiol Endocrinol Metab. 2020 Dec 07.

Retinol binding protein 4 (Rbp4) mRNA translation in hepatocytes is enhanced by activation of mTORC1.

Jaclyn E Welles, Allyson L Toro, Siddharth Sunilkumar, Shaunaci A Stevens, Carson J Purnell, Scot R Kimball, Michael D Dennis.

  Increased expression of the peptide hormone retinol-binding protein 4 (RBP4) has been implicated in the development of insulin resistance, type 2 diabetes, and visual dysfunction. Prior investigations of the mechanisms that influence RBP4 synthesis have focused solely on changes in mRNA abundance. Yet, the production of many secreted proteins is controlled at the level of mRNA translation, as it allows for a rapid and reversible change in expression. Herein, we evaluated Rbp4 mRNA translation using sucrose density gradient centrifugation. In the liver of fasted rodents, Rbp4 mRNA translation was low. In response to re-feeding, Rbp4 mRNA translation was enhanced and RBP4 levels in serum were increased. In H4IIE cells, refreshing culture medium promoted Rbp4 mRNA translation and expression of the protein. Rbp4 mRNA abundance was not increased by either experimental manipulation. Enhanced Rbp4 mRNA translation was associated with activation of the kinase mTORC1 and enhanced phosphorylation of the translational repressor 4E-BP1. In H4IIE cells, expression of a 4E-BP1 variant that is unable to be phosphorylated by mTORC1 or suppression of mTORC1 with rapamycin attenuated activity of a luciferase reporter encoding the Rbp4 mRNA 5'-untranslated region (UTR). Purine substitutions to disrupt a terminal oligopyrimidine (TOP)-like sequence in the Rbp4 5'-UTRprevented the suppressive effect of rapamycin on reporter activity. Rapamycin also prevented upregulation of Rbp4 mRNA translation in the liver, and reduced serum levels of RBP4 in response to feeding. Overall, the findings support a model in which nutrient-induced activation of mTORC1 up regulates Rbp4 mRNA translation to promote RBP4 synthesis.

Keywords:  eukaryotic initiation factor; eukaryotic translation initiation; liver; retinol binding protein

DOI:  https://doi.org/10.1152/ajpendo.00494.2020
Elife. 2020 Dec 10. pii: e59419. [Epub ahead of print]9

TFEB/Mitf links impaired nuclear import to autophagolysosomal dysfunction in C9-ALS.

Kathleen M Cunningham, Kirstin Maulding, Kai Ruan, Mumine Senturk, Jonathan C Grima, Hyun Sung, Zhongyuan Zuo, Helen Song, Junli Gao, Sandeep Dubey, Jeffrey D Rothstein, Ke Zhang, Hugo J Bellen, Thomas E Lloyd.

  Disrupted nucleocytoplasmic transport (NCT) has been implicated in neurodegenerative disease pathogenesis; however, the mechanisms by which disrupted NCT causes neurodegeneration remain unclear. In a Drosophila screen, we identified ref(2)P/p62, a key regulator of autophagy, as a potent suppressor of neurodegeneration caused by the GGGGCC hexanucleotide repeat expansion (G4C2 HRE) in C9orf72 that causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We found that p62 is increased and forms ubiquitinated aggregates due to decreased autophagic cargo degradation. Immunofluorescence and electron microscopy of Drosophila tissues demonstrate an accumulation of lysosome-like organelles that precedes neurodegeneration. These phenotypes are partially caused by cytoplasmic mislocalization of Mitf/TFEB, a key transcriptional regulator of autophagolysosomal function. Additionally, TFEB is mislocalized and downregulated in human cells expressing GGGGCC repeats and in C9-ALS patient motor cortex. Our data suggest that the C9orf72-HRE impairs Mitf/TFEB nuclear import, thereby disrupting autophagy and exacerbating proteostasis defects in C9-ALS/FTD.

Keywords:  D. melanogaster; cell biology; neuroscience

DOI:  https://doi.org/10.7554/eLife.59419
Nat Commun. 2020 12 08. 11(1): 6290

A dual-labeling probe to track functional mitochondria-lysosome interactions in live cells.

Qixin Chen, Hongbao Fang, Xintian Shao, Zhiqi Tian, Shanshan Geng, Yuming Zhang, Huaxun Fan, Pan Xiang, Jie Zhang, Xiaohe Tian, Kai Zhang, Weijiang He, Zijian Guo, Jiajie Diao.

Mitochondria-lysosome interactions are essential for maintaining intracellular homeostasis. Although various fluorescent probes have been developed to visualize such interactions, they remain unable to label mitochondria and lysosomes simultaneously and dynamically track their interaction. Here, we introduce a cell-permeable, biocompatible, viscosity-responsive, small organic molecular probe, Coupa, to monitor the interaction of mitochondria and lysosomes in living cells. Through a functional fluorescence conversion, Coupa can simultaneously label mitochondria with blue fluorescence and lysosomes with red fluorescence, and the correlation between the red-blue fluorescence intensity indicates the progress of mitochondria-lysosome interplay during mitophagy. Moreover, because its fluorescence is sensitive to viscosity, Coupa allowed us to precisely localize sites of mitochondria-lysosome contact and reveal increases in local viscosity on mitochondria associated with mitochondria-lysosome contact. Thus, our probe represents an attractive tool for the localization and dynamic tracking of functional mitochondria-lysosome interactions in living cells.

DOI: https://doi.org/10.1038/s41467-020-20067-6
Chem Commun (Camb). 2020 Dec 08.

Dual enzyme responsive mannose-6-phosphate based vesicle for controlled lysosomal delivery.

Basudeb Mondal, Tahiti Dutta, Sayam Sen Gupta.

Dual enzyme responsive stable biomimetic vesicles composed of mannose-6-phosphate lipid can encapsulate and deliver dual dye/drug and protein/enzyme exclusively to the lysosome in HEK-293 cells. The release of the cargo from the vesicles can be temporally controlled due to the enzyme responsive morphology change of the M6P lipid assembly.

DOI: https://doi.org/10.1039/d0cc06169g
Sci Adv. 2020 Dec;pii: eaba5783. [Epub ahead of print]6(50):

Late endosomes promote microglia migration via cytosolic translocation of immature protease cathD.

Yi-Jun Liu, Ting Zhang, Daxiao Cheng, Junhua Yang, Sicong Chen, Xingyue Wang, Xia Li, Duo Duan, Huifang Lou, Liya Zhu, Jianhong Luo, Margaret S Ho, Xiao-Dong Wang, Shumin Duan.

Organelle transport requires dynamic cytoskeleton remodeling, but whether cytoskeletal dynamics are, in turn, regulated by organelles remains elusive. Here, we demonstrate that late endosomes, a type of prelysosomal organelles, facilitate actin-cytoskeleton remodeling via cytosolic translocation of immature protease cathepsin D (cathD) during microglia migration. After cytosolic translocation, late endosome-derived cathD juxtaposes actin filaments at the leading edge of lamellipodia. Suppressing cathD expression or blocking its cytosolic translocation impairs the maintenance but not the initiation of lamellipodial extension. Moreover, immature cathD balances the activity of the actin-severing protein cofilin to maintain globular-actin (G-actin) monomer pool for local actin recycling. Our study identifies cathD as a key lysosomal molecule that unconventionally contributes to actin cytoskeleton remodeling via cytosolic translocation during adenosine triphosphate-evoked microglia migration.

DOI: https://doi.org/10.1126/sciadv.aba5783
Cell Biosci. 2020 Nov 18. 10(1): 131

The role of lysosomes in cancer development and progression.

Tao Tang, Ze-Yu Yang, Di Wang, Xian-Yan Yang, Jun Wang, Lin Li, Qian Wen, Lei Gao, Xiu-Wu Bian, Shi-Cang Yu.

  Lysosomes are an important component of the inner membrane system and participate in numerous cell biological processes, such as macromolecular degradation, antigen presentation, intracellular pathogen destruction, plasma membrane repair, exosome release, cell adhesion/migration and apoptosis. Thus, lysosomes play important roles in cellular activity. In addition, previous studies have shown that lysosomes may play important roles in cancer development and progression through the abovementioned biological processes and that the functional status and spatial distribution of lysosomes are closely related to cancer cell proliferation, energy metabolism, invasion and metastasis, immune escape and tumor-associated angiogenesis. Therefore, identifying the factors and mechanisms that regulate the functional status and spatial distribution of lysosomes and elucidating the relationship between lysosomes and the development and progression of cancer can provide important information for cancer diagnosis and prognosis prediction and may yield new therapeutic targets. This study briefly reviews the above information and explores the potential value of lysosomes in cancer therapy.

Keywords:  Cancer; Energy metabolism; Lysosomes; Metastasis; Spatial distribution

DOI:  https://doi.org/10.1186/s13578-020-00489-x