bims-lysosi 2021-10-03 papers

bims-lysosi

Biomed News

on Lysosomes and signaling

Issue of 2021‒10‒03
forty-three papers selected by
Stephanie Fernandes
Max Planck Institute for Biology of Ageing

GABARAP sequesters the FLCN-FNIP tumor suppressor complex to couple autophagy with lysosomal biogenesis.
Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy.
Insights into the Interaction of Lysosomal Amino Acid Transporters SLC38A9 and SLC36A1 Involved in mTORC1 Signaling in C2C12 Cells.
Substrate Reduction Therapy Reverses Mitochondrial, mTOR, and Autophagy Alterations in a Cell Model of Gaucher Disease.
Treatment trials in Niemann-Pick type C disease.
A human iPSC-derived inducible neuronal model of Niemann-Pick disease, type C1.
Lysosomes and the pathogenesis of merosin-deficient congenital muscular dystrophy.
Persistent mTORC1 activation via Depdc5 deletion results in spontaneous hepatocellular carcinoma but does not exacerbate carcinogen- and high-fat diet-induced hepatic carcinogenesis in mice.
The role of lysosomal membrane proteins in glucose and lipid metabolism.
A Review of APOE Genotype-Dependent Autophagic Flux Regulation in Alzheimer's Disease.
AMPK-mTOR Signaling and Cellular Adaptations in Hypoxia.
Design and Validation of a Custom NGS Panel Targeting a Set of Lysosomal Storage Diseases Candidate for NBS Applications.
IP3R-driven increases in mitochondrial Ca2+ promote neuronal death in NPC disease.
Alpha-Synuclein and the Endolysosomal System in Parkinson's Disease: Guilty by Association.
Exercise and Sestrin Mediate Speed and Lysosomal Activity in Drosophila by Partially Overlapping Mechanisms.
Carnitine is a pharmacological allosteric chaperone of the human lysosomal α-glucosidase.
Preprint Highlight: ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA- dependent STING signaling.
On the cusp of cures: Breakthroughs in Batten disease research.
Pathogenesis and Molecular Mechanisms of Anderson-Fabry Disease and Possible New Molecular Addressed Therapeutic Strategies.
Parsing Fabry Disease Metabolic Plasticity Using Metabolomics.
mTOR Signaling: The Interface Linking Cellular Metabolism and Hepatitis B Virus Replication.
Loss of mTORC2-induced metabolic reprogramming in monocytes uncouples migration and maturation from production of proinflammatory mediators.
Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase.
Autophagy and the Hallmarks of Aging.
TBK1 has a new Akt.
Asymmetric organelle positioning during epithelial polarization of C. elegans intestinal cells.
Lipid Droplet-Organelle Contact Sites as Hubs for Fatty Acid Metabolism, Trafficking, and Metabolic Channeling.
Oxidative Stress in Mucopolysaccharidoses: Pharmacological Implications.
Selective Autophagy as a Potential Therapeutic Target in Age-Associated Pathologies.
Redefining the Scope of Targeted Protein Degradation: Translational Opportunities in Hijacking the Autophagy-Lysosome Pathway.
Vacuolar-type proton ATPase is required for maintenance of apicobasal polarity of embryonic visceral endoderm.
An ancient RAB5 governs the formation of additional vacuoles and cell shape in petunia petals.
Crosstalk between miRNA and PI3K/AKT/mTOR signaling pathway in cancer.
C5a Activates a Pro-Inflammatory Gene Expression Profile in Human Gaucher iPSC-Derived Macrophages.
The Role of Sch9 and the V-ATPase in the Adaptation Response to Acetic Acid and the Consequences for Growth and Chronological Lifespan.
Covalently Engineered Nanobody Chimeras for Targeted Membrane Protein Degradation.
Advances in Intracellular Calcium Signaling Reveal Untapped Targets for Cancer Therapy.
Cathepsin S Evokes PAR2-Dependent Pain in Oral Squamous Cell Carcinoma Patients and Preclinical Mouse Models.
ATP-binding cassette transporters mediate differential biosynthesis of glycosphingolipid species.
Structural basis for the specificity of PPM1H phosphatase for Rab GTPases.
A genetic model of methionine restriction extends Drosophila health- and lifespan.
Cooperative regulation of endocytic vesicle transport by yeast Eps15-like protein Pan1p and epsins.
AMPK CA(R)Sts a new light on amino acid sensing.

Sci Adv. 2021 Oct;7(40): eabj2485

GABARAP sequesters the FLCN-FNIP tumor suppressor complex to couple autophagy with lysosomal biogenesis.

Jonathan M Goodwin, Ward G Walkup, Kirsty Hooper, Taoyingnan Li, Chieko Kishi-Itakura, Aylwin Ng, Timothy Lehmberg, Archana Jha, Sravya Kommineni, Katherine Fletcher, Jorge Garcia-Fortanet, Yaya Fan, Qing Tang, Menghao Wei, Asmita Agrawal, Sagar R Budhe, Sreekanth R Rouduri, Dan Baird, Jeff Saunders, Janna Kiselar, Mark R Chance, Andrea Ballabio, Brent A Appleton, John H Brumell, Oliver Florey, Leon O Murphy.

[Figure: see text].

DOI: https://doi.org/10.1126/sciadv.abj2485
Elife. 2021 Sep 29. pii: e72328. [Epub ahead of print]10

Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy.

Vinay V Eapen, Sharan Swarup, Melissa J Hoyer, Joao A Paulo, Wade Harper.

  Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the damaged organelle, prior to fusion with the degradative lysosomal compartment. Lysosomes themselves are also prone to damage and are degraded through the process of lysophagy. While early steps involve recognition of ruptured lysosomal membranes by glycan-binding Galectins and ubiquitylation of transmembrane lysosomal proteins, many steps in the process, and their inter-relationships, remain poorly understood, including the role and identity of cargo receptors required for completion of lysophagy. Here, we employ quantitative organelle capture and proximity biotinylation proteomics of autophagy adaptors, cargo receptors, and Galectins in response to acute lysosomal damage, thereby revealing the landscape of lysosome-associated proteome remodeling during lysophagy. Among proteins dynamically recruited to damaged lysosomes were ubiquitin-binding autophagic cargo receptors. Using newly developed lysophagic flux reporters including Lyso-Keima, we demonstrate that TAX1BP1, together with its associated kinase TBK1, are both necessary and sufficient to promote lysophagic flux in both HeLa cells and induced neurons (iNeurons). While the related receptor OPTN can drive damage-dependent lysophagy when overexpressed, cells lacking either OPTN or CALCOCO2 still maintain significant lysophagic flux in HeLa cells. Mechanistically, TAX1BP1-driven lysophagy requires its N-terminal SKICH domain, which binds both TBK1 and the autophagy regulatory factor RB1CC1, and requires upstream ubiquitylation events for efficient recruitment and lysophagic flux. These results identify TAX1BP1 as a central component in the lysophagy pathway and provide a proteomic resource for future studies of the lysophagy process.

Keywords:  biochemistry; cell biology; chemical biology; human

DOI:  https://doi.org/10.7554/eLife.72328
Biomolecules. 2021 Sep 06. pii: 1314. [Epub ahead of print]11(9):

Insights into the Interaction of Lysosomal Amino Acid Transporters SLC38A9 and SLC36A1 Involved in mTORC1 Signaling in C2C12 Cells.

Dan Wang, Xuebin Wan, Xiaoli Du, Zhuxia Zhong, Jian Peng, Qi Xiong, Jin Chai, Siwen Jiang.

  Amino acids are critical for mammalian target of rapamycin complex 1 (mTORC1) activation on the lysosomal surface. Amino acid transporters SLC38A9 and SLC36A1 are the members of the lysosomal amino acid sensing machinery that activates mTORC1. The current study aims to clarify the interaction of SLC38A9 and SLC36A1. Here, we discovered that leucine increased expressions of SLC38A9 and SLC36A1, leading to mTORC1 activation. SLC38A9 interacted with SLC36A1 and they enhanced each other's expression levels and locations on the lysosomal surface. Additionally, the interacting proteins of SLC38A9 in C2C12 cells were identified to participate in amino acid sensing mechanism, mTORC1 signaling pathway, and protein synthesis, which provided a resource for future investigations of skeletal muscle mass.

Keywords:  SLC36A1; SLC38A9; amino acid transporter; leucine; lysosome; mTORC1 signaling pathway

DOI:  https://doi.org/10.3390/biom11091314
Cells. 2021 Sep 02. pii: 2286. [Epub ahead of print]10(9):

Substrate Reduction Therapy Reverses Mitochondrial, mTOR, and Autophagy Alterations in a Cell Model of Gaucher Disease.

Yanyan Peng, Benjamin Liou, Yi Lin, Venette Fannin, Wujuan Zhang, Ricardo A Feldman, Kenneth D R Setchell, Gregory A Grabowski, Ying Sun.

  Substrate reduction therapy (SRT) in clinic adequately manages the visceral manifestations in Gaucher disease (GD) but has no direct effect on brain disease. To understand the molecular basis of SRT in GD treatment, we evaluated the efficacy and underlying mechanism of SRT in an immortalized neuronal cell line derived from a Gba knockout (Gba-/-) mouse model. Gba-/- neurons accumulated substrates, glucosylceramide, and glucosylsphingosine. Reduced cell proliferation was associated with altered lysosomes and autophagy, decreased mitochondrial function, and activation of the mTORC1 pathway. Treatment of the Gba-/- neurons with venglustat analogue GZ452, a central nervous system-accessible SRT, normalized glucosylceramide levels in these neurons and their isolated mitochondria. Enlarged lysosomes were reduced in the treated Gba-/- neurons, accompanied by decreased autophagic vacuoles. GZ452 treatment improved mitochondrial membrane potential and oxygen consumption rate. Furthermore, GZ452 diminished hyperactivity of selected proteins in the mTORC1 pathway and improved cell proliferation of Gba-/- neurons. These findings reinforce the detrimental effects of substrate accumulation on mitochondria, autophagy, and mTOR in neurons. A novel rescuing mechanism of SRT was revealed on the function of mitochondrial and autophagy-lysosomal pathways in GD. These results point to mitochondria and the mTORC1 complex as potential therapeutic targets for treatment of GD.

Keywords:  cell biology; glucosylceramide; glucosylsphingosine; lysosomal storage disorders; neurons

DOI:  https://doi.org/10.3390/cells10092286
Metab Brain Dis. 2021 Oct 01.

Treatment trials in Niemann-Pick type C disease.

Dominika Sitarska, Anna Tylki-Szymańska, Agnieszka Ługowska.

  Niemann-Pick type C (NPC) disease is a genetically determined neurodegenerative metabolic disease. It belongs to the lysosomal storage diseases and its main cause is impaired cholesterol transport in late endosomes or lysosomes. It is an autosomal recessive inherited disease that results from mutations in the NPC1 or NPC2 genes. The treatment efforts are focused on the slowing its progression. The only registered drug, devoted for NPC patients is Miglustat. Effective treatment is still under development. NPC disease mainly affects the nervous system, and the crossing of the blood-brain barrier by medicines is still a challenge, therefore the combination therapies of several compounds are increasingly being worked on. The aim of this paper is to present the possibilities in treatment of Niemann-Pick type C disease. The discussed research results relate to animal studies.

Keywords:  Arimoclomol; Gene Therapy; HP-β-CD; Miglustat; NPC; Niemann-Pick Type C disease; Therapy; Vorinostat

DOI:  https://doi.org/10.1007/s11011-021-00842-0
BMC Biol. 2021 Oct 01. 19(1): 218

A human iPSC-derived inducible neuronal model of Niemann-Pick disease, type C1.

Anika V Prabhu, Insung Kang, Raffaella De Pace, Christopher A Wassif, Hideji Fujiwara, Pamela Kell, Xuntian Jiang, Daniel S Ory, Juan S Bonifacino, Michael E Ward, Forbes D Porter.

  BACKGROUND: Niemann-Pick disease, type C (NPC) is a childhood-onset, lethal, neurodegenerative disorder caused by autosomal recessive mutations in the genes NPC1 or NPC2 and characterized by impaired cholesterol homeostasis, a lipid essential for cellular function. Cellular cholesterol levels are tightly regulated, and mutations in either NPC1 or NPC2 lead to deficient transport and accumulation of unesterified cholesterol in the late endosome/lysosome compartment, and progressive neurodegeneration in affected individuals. Previous cell-based studies to understand the NPC cellular pathophysiology and screen for therapeutic agents have mainly used patient fibroblasts. However, these do not allow modeling the neurodegenerative aspect of NPC disease, highlighting the need for an in vitro system that permits understanding the cellular mechanisms underlying neuronal loss and identifying appropriate therapies. This study reports the development of a novel human iPSC-derived, inducible neuronal model of Niemann-Pick disease, type C1 (NPC1).RESULTS: We generated a null i3Neuron (inducible × integrated × isogenic) (NPC1-/- i3Neuron) iPSC-derived neuron model of NPC1. The NPC1-/- and the corresponding isogenic NPC1+/+ i3Neuron cell lines were used to efficiently generate homogenous, synchronized neurons that can be used in high-throughput screens. NPC1-/- i3Neurons recapitulate cardinal cellular NPC1 pathological features including perinuclear endolysosomal storage of unesterified cholesterol, accumulation of GM2 and GM3 gangliosides, mitochondrial dysfunction, and impaired axonal lysosomal transport. Cholesterol storage, mitochondrial dysfunction, and axonal trafficking defects can be ameliorated by treatment with 2-hydroxypropyl-β-cyclodextrin, a drug that has shown efficacy in NPC1 preclinical models and in a phase 1/2a trial.
CONCLUSION: Our data demonstrate the utility of this new cell line in high-throughput drug/chemical screens to identify potential therapeutic agents. The NPC1-/- i3Neuron line will also be a valuable tool for the NPC1 research community to explore the pathological mechanisms contributing to neuronal degeneration.

Keywords:  Human induced pluripotent stem cells; Human neurons; Lysosomal disease; NPC1; Neurodegeneration; Niemann-Pick disease, type C1

DOI:  https://doi.org/10.1186/s12915-021-01133-x
Hum Mol Genet. 2021 Sep 25. pii: ddab278. [Epub ahead of print]

Lysosomes and the pathogenesis of merosin-deficient congenital muscular dystrophy.

Sarah J Smith, Lacramioara Fabian, Adeel Sheikh, Ramil Noche, Xiucheng Cui, Steven A Moore, James J Dowling.

  Congenital muscular dystrophy type 1A (MDC1A), the most common congenital muscular dystrophy in Western countries, is caused by recessive mutations in LAMA2, the gene encoding laminin alpha 2. Currently, no cure or disease modifying therapy has been successfully developed for MDC1A. Examination of patient muscle biopsies revealed altered distribution of lysosomes. We hypothesized that this redistribution was a novel and potentially druggable aspect of disease pathogenesis. We explored this hypothesis using candyfloss (caf), a zebrafish model of MDC1A.We found that lysosome distribution in caf zebrafish was also abnormal. This altered localization was significantly associated with fiber detachment and could be prevented by blocking myofiber detachment. Overexpression of TFEB, a transcription factor that promotes lysosomal biogenesis, led to increased lysosome content and decreased fiber detachment. We conclude that genetic manipulation of the lysosomal compartment is able to alter the caf zebrafish disease process, suggesting that lysosome function may be a target for disease modification.

Keywords:  laminin alpha 2lysosomesmuscular dystrophyMDC1A

DOI:  https://doi.org/10.1093/hmg/ddab278
Biochem Biophys Res Commun. 2021 Sep 20. pii: S0006-291X(21)01329-2. [Epub ahead of print]578 142-149

Persistent mTORC1 activation via Depdc5 deletion results in spontaneous hepatocellular carcinoma but does not exacerbate carcinogen- and high-fat diet-induced hepatic carcinogenesis in mice.

Lin Xu, Chenyan Yang, Jing Wang, Zun Li, Rong Huang, Honghui Ma, Jie Ma, Qingzhi Wang, Xiwen Xiong.

  The mechanistic target of rapamycin complex 1 (mTORC1) acts as a central regulator of metabolic pathways that drive cellular growth. Abnormal activation of mTORC1 occurs at high frequency in human and mouse hepatocellular carcinoma (HCC). DEP domain-containing protein 5 (DEPDC5), a component of GATOR1 complex, is a repressor of amino acid-sensing branch of the mTORC1 pathway. In the current study, we found that persistent activation of hepatic mTORC1 signaling caused by Depdc5 ablation was sufficient to induce a pathological program of liver damage, inflammation and fibrosis that triggers spontaneous HCC development. Take advantage of the combinatory treatment with a single dose of diethylnitrosamine (DEN) and chronic feeding with high-fat diet (HFD), we demonstrated that hepatic depdc5 deletion did not aggravate DEN&HFD induced liver tumorigenesis, probably due to its protective effects on diet-induced liver steatosis. In addition, we further showed that chronic rapamycin treatment did not have any apparent tumor-suppressing effects on DEN&HFD treated control mice, whereas it dramatically reduced the tumor burden in mice with hepatic Depdc5 ablation. This study provides the novel in vivo evidence for Depdc5 deletion mediated mTORC1 hyperactivation in liver tumorigenesis caused by aging or DEN&HFD treatment. Moreover, our findings also propose that pharmacological inhibition of mTORC1 signaling maybe a promising strategy to treat HCC patients with mutations in DEPDC5 gene.

Keywords:  DEPDC5; Diethylnitrosamine (DEN); Hepatocellular carcinoma (HCC); High-fat diet (HFD); Liver; mTORC1

DOI:  https://doi.org/10.1016/j.bbrc.2021.09.036
FASEB J. 2021 Oct;35(10): e21848

The role of lysosomal membrane proteins in glucose and lipid metabolism.

Jing Gu, Mengya Geng, Mengxiang Qi, Lizhuo Wang, Yao Zhang, Jialin Gao.

  Lysosomes have long been regarded as the "garbage dump" of the cell. More recently, however, researchers have revealed novel roles for lysosomal membranes in autophagy, ion transport, nutrition sensing, and membrane fusion and repair. With active research into lysosomal membrane proteins (LMP), increasing evidence has become available showing that LMPs are inextricably linked to glucose and lipid metabolism, and this relationship represents mutual influence and regulation. In this review, we summarize the roles of LMPs in relation to glucose and lipid metabolism, and describe their roles in glucose transport, glycolysis, cholesterol transport, and lipophagy. The role of transport proteins can be traced back to the original discoveries of GLUT8, NPC1, and NPC2, which were all found to have significant roles in the pathways involved in glucose and lipid metabolism. CLC-5 and SIDT2-knockout animals show serious phenotypic disorders of metabolism, and V-ATPase and LAMP-2 have been found to interact with proteins related to glucose and lipid metabolism. These findings all emphasize the critical role of LMPs in glycolipid metabolism and help to strengthen our understanding of the independent and close relationship between LMPs and glycolipid metabolism.

Keywords:  glucose metabolism; lipid metabolism; lysosomal membrane protein

DOI:  https://doi.org/10.1096/fj.202002602R
J Alzheimers Dis. 2021 Sep 22.

A Review of APOE Genotype-Dependent Autophagic Flux Regulation in Alzheimer's Disease.

Huiyi Chen, Feng Chen, Miaoping Zhang, Yanting Chen, Lili Cui, Chunmei Liang.

  Autophagy is a basic physiological process maintaining cell renewal, the degradation of dysfunctional organelles, and the clearance of abnormal proteins and has recently been identified as a main mechanism underlying the onset and progression of Alzheimer's disease (AD). The APOE ɛ4 genotype is the strongest genetic determinant of AD pathogenesis and initiates autophagic flux at different times. This review synthesizes the current knowledge about the potential pathogenic effects of ApoE4 on autophagy and describes its associations with the biological hallmarks of autophagy and AD from a novel perspective. Via a remarkable variety of widely accepted signaling pathway markers, such as mTOR, TFEB, SIRT1, LC3, p62, LAMP1, LAMP2, CTSD, Rabs, and V-ATPase, ApoE isoforms differentially modulate autophagy initiation; membrane expansion, recruitment, and enclosure; autophagosome and lysosome fusion; and lysosomal degradation. Although the precise pathogenic mechanism varies for different genes and proteins, the dysregulation of autophagic flux is a key mechanism on which multiple pathogenic processes converge.

Keywords:  Alzheimer’s disease; apolipoproteins E; autophagy; neurodegenerative diseases

DOI:  https://doi.org/10.3233/JAD-210602
Int J Mol Sci. 2021 Sep 09. pii: 9765. [Epub ahead of print]22(18):

AMPK-mTOR Signaling and Cellular Adaptations in Hypoxia.

Yoomi Chun, Joungmok Kim.

  Cellular energy is primarily provided by the oxidative degradation of nutrients coupled with mitochondrial respiration, in which oxygen participates in the mitochondrial electron transport chain to enable electron flow through the chain complex (I-IV), leading to ATP production. Therefore, oxygen supply is an indispensable chapter in intracellular bioenergetics. In mammals, oxygen is delivered by the bloodstream. Accordingly, the decrease in cellular oxygen level (hypoxia) is accompanied by nutrient starvation, thereby integrating hypoxic signaling and nutrient signaling at the cellular level. Importantly, hypoxia profoundly affects cellular metabolism and many relevant physiological reactions induce cellular adaptations of hypoxia-inducible gene expression, metabolism, reactive oxygen species, and autophagy. Here, we introduce the current knowledge of hypoxia signaling with two-well known cellular energy and nutrient sensing pathways, AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin complex 1 (mTORC1). Additionally, the molecular crosstalk between hypoxic signaling and AMPK/mTOR pathways in various hypoxic cellular adaptions is discussed.

Keywords:  AMPK; hypoxia; hypoxia-inducible factor (HIF); hypoxic cellular adaptations; mTORC1

DOI:  https://doi.org/10.3390/ijms22189765
Int J Mol Sci. 2021 Sep 17. pii: 10064. [Epub ahead of print]22(18):

Design and Validation of a Custom NGS Panel Targeting a Set of Lysosomal Storage Diseases Candidate for NBS Applications.

Valentina La Cognata, Maria Guarnaccia, Giovanna Morello, Martino Ruggieri, Agata Polizzi, Sebastiano Cavallaro.

  Lysosomal storage diseases (LSDs) are a heterogeneous group of approximately 70 monogenic metabolic disorders whose diagnosis represents an arduous challenge for clinicians due to their variability in phenotype penetrance, clinical manifestations, and high allelic heterogeneity. In recent years, the approval of disease-specific therapies and the rapid emergence of novel rapid diagnostic methods has opened, for a set of selected LSDs, the possibility for inclusion in extensive national newborn screening (NBS) programs. Herein, we evaluated the clinical utility and diagnostic validity of a targeted next-generation sequencing (tNGS) panel (called NBS_LSDs), designed ad hoc to scan the coding regions of six genes (GBA, GAA, SMPD1, IDUA1, GLA, GALC) relevant for a group of LSDs candidate for inclusion in national NBS programs (MPSI, Pompe, Fabry, Krabbe, Niemann Pick A-B and Gaucher diseases). A standard group of 15 samples with previously known genetic mutations was used to test and validate the entire flowchart. Analytical accuracy, sensitivity, and specificity, as well as turnaround time and costs, were assessed. Results showed that the Ion AmpliSeq and Ion Chef System-based high-throughput NBS_LSDs tNGS panel is a fast, accurate, and cost-effective process. The introduction of this technology into routine NBS procedures as a second-tier test along with primary biochemical assays will allow facilitating the identification and management of selected LSDs and reducing diagnostic delay.

Keywords:  lysosomal storage disease (LSDs); newborn screening (NBS); targeted next-generation sequencing (tNGS)

DOI:  https://doi.org/10.3390/ijms221810064
Proc Natl Acad Sci U S A. 2021 Oct 05. pii: e2110629118. [Epub ahead of print]118(40):

IP3R-driven increases in mitochondrial Ca2+ promote neuronal death in NPC disease.

Scott A Tiscione, Maria Casas, Jonathan D Horvath, Vincent Lam, Keiko Hino, Daniel S Ory, L Fernando Santana, Sergi Simó, Rose E Dixon, Eamonn J Dickson.

  Ca2+ is the most ubiquitous second messenger in neurons whose spatial and temporal elevations are tightly controlled to initiate and orchestrate diverse intracellular signaling cascades. Numerous neuropathologies result from mutations or alterations in Ca2+ handling proteins; thus, elucidating molecular pathways that shape Ca2+ signaling is imperative. Here, we report that loss-of-function, knockout, or neurodegenerative disease-causing mutations in the lysosomal cholesterol transporter, Niemann-Pick Type C1 (NPC1), initiate a damaging signaling cascade that alters the expression and nanoscale distribution of IP3R type 1 (IP3R1) in endoplasmic reticulum membranes. These alterations detrimentally increase Gq-protein coupled receptor-stimulated Ca2+ release and spontaneous IP3R1 Ca2+ activity, leading to mitochondrial Ca2+ cytotoxicity. Mechanistically, we find that SREBP-dependent increases in Presenilin 1 (PS1) underlie functional and expressional changes in IP3R1. Accordingly, expression of PS1 mutants recapitulate, while PS1 knockout abrogates Ca2+ phenotypes. These data present a signaling axis that links the NPC1 lysosomal cholesterol transporter to the damaging redistribution and activity of IP3R1 that precipitates cell death in NPC1 disease and suggests that NPC1 is a nanostructural disease.

Keywords:  GPCR; IP3R; NPC1; calcium; neurodegeneration

DOI:  https://doi.org/10.1073/pnas.2110629118
Biomolecules. 2021 Sep 09. pii: 1333. [Epub ahead of print]11(9):

Alpha-Synuclein and the Endolysosomal System in Parkinson's Disease: Guilty by Association.

Maxime Teixeira, Razan Sheta, Walid Idi, Abid Oueslati.

  Abnormal accumulation of the protein α- synuclein (α-syn) into proteinaceous inclusions called Lewy bodies (LB) is the neuropathological hallmark of Parkinson's disease (PD) and related disorders. Interestingly, a growing body of evidence suggests that LB are also composed of other cellular components such as cellular membrane fragments and vesicular structures, suggesting that dysfunction of the endolysosomal system might also play a role in LB formation and neuronal degeneration. Yet the link between α-syn aggregation and the endolysosomal system disruption is not fully elucidated. In this review, we discuss the potential interaction between α-syn and the endolysosomal system and its impact on PD pathogenesis. We propose that the accumulation of monomeric and aggregated α-syn disrupt vesicles trafficking, docking, and recycling, leading to the impairment of the endolysosomal system, notably the autophagy-lysosomal degradation pathway. Reciprocally, PD-linked mutations in key endosomal/lysosomal machinery genes (LRRK2, GBA, ATP13A2) also contribute to increasing α-syn aggregation and LB formation. Altogether, these observations suggest a potential synergistic role of α-syn and the endolysosomal system in PD pathogenesis and represent a viable target for the development of disease-modifying treatment for PD and related disorders.

Keywords:  Parkinson’s disease; aggregation; alpha-synuclein; endolysosomal system; trafficking; vesicles

DOI:  https://doi.org/10.3390/biom11091333
Cells. 2021 Sep 19. pii: 2479. [Epub ahead of print]10(9):

Exercise and Sestrin Mediate Speed and Lysosomal Activity in Drosophila by Partially Overlapping Mechanisms.

Alyson Sujkowski, Robert Wessells.

  Chronic exercise is widely recognized as an important contributor to healthspan in humans and in diverse animal models. Recently, we have demonstrated that Sestrins, a family of evolutionarily conserved exercise-inducible proteins, are critical mediators of exercise benefits in flies and mice. Knockout of Sestrins prevents exercise adaptations to endurance and flight in Drosophila, and similarly prevents benefits to endurance and metabolism in exercising mice. In contrast, overexpression of dSestrin in muscle mimics several of the molecular and physiological adaptations characteristic of endurance exercise. Here, we extend those observations to examine the impact of dSestrin on preserving speed and increasing lysosomal activity. We find that dSestrin is a critical factor driving exercise adaptations to climbing speed, but is not absolutely required for exercise to increase lysosomal activity in Drosophila. The role of Sestrin in increasing speed during chronic exercise requires both the TORC2/AKT axis and the PGC1α homolog spargel, while dSestrin requires interactions with TORC1 to cell-autonomously increase lysosomal activity. These results highlight the conserved role of Sestrins as key factors that drive diverse physiological adaptations conferred by chronic exercise.

Keywords:  Drosophila; Sestrin; exercise

DOI:  https://doi.org/10.3390/cells10092479
J Enzyme Inhib Med Chem. 2021 Dec;36(1): 2068-2079

Carnitine is a pharmacological allosteric chaperone of the human lysosomal α-glucosidase.

Roberta Iacono, Nadia Minopoli, Maria Carmina Ferrara, Antonietta Tarallo, Carla Damiano, Caterina Porto, Sandra Strollo, Véronique Roig-Zamboni, Gianfranco Peluso, Gerlind Sulzenbacher, Beatrice Cobucci-Ponzano, Giancarlo Parenti, Marco Moracci.

  Pompe disease is an inherited metabolic disorder due to the deficiency of the lysosomal acid α-glucosidase (GAA). The only approved treatment is enzyme replacement therapy with the recombinant enzyme (rhGAA). Further approaches like pharmacological chaperone therapy, based on the stabilising effect induced by small molecules on the target enzyme, could be a promising strategy. However, most known chaperones could be limited by their potential inhibitory effects on patient's enzymes. Here we report on the discovery of novel chaperones for rhGAA, L- and D-carnitine, and the related compound acetyl-D-carnitine. These drugs stabilise the enzyme at pH and temperature without inhibiting the activity and acted synergistically with active-site directed pharmacological chaperones. Remarkably, they enhanced by 4-fold the acid α-glucosidase activity in fibroblasts from three Pompe patients with added rhGAA. This synergistic effect of L-carnitine and rhGAA has the potential to be translated into improved therapeutic efficacy of ERT in Pompe disease.

Keywords:  carbohydrate active enzymes; glycogen storage disease type 2; lysosomal disease; orphan drugs; α-Glucosidase

DOI:  https://doi.org/10.1080/14756366.2021.1975694
Mol Biol Cell. 2021 Oct 01. 32(20): 1110

Preprint Highlight: ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA- dependent STING signaling.

Luis Bonet-Ponce.

Loss-of-function mutations in VPS13C cause familial Parkinson's disease (PD) and increase the risk to develop the sporadic form of the disease. However, the underlying disease mechanisms remain unclear. It has been previously established that VPS13C tethers lysosomes with the endoplasmic reticulum (ER) and promotes lipid interchange between both organelles. This study provides a cellular role of VPS13C, specifically regulating the cGAS/STING pathway and contributing to the innate immune response. The authors generate VPS13C knockout HeLa cells and use confocal microscopy and biochemical approaches to show loss of VPS13C leads to altered lysosome lipid composition and mitochondrial DNA leakage. Understanding how VPS13C preserves cellular homeostasis is an exciting discovery for scientists working on neurodegeneration and for cell biologists interested in lysosome-to-mitochondria cross-talk.

DOI: https://doi.org/10.1091/mbc.E21-10-0125p
Curr Opin Neurobiol. 2021 Sep 24. pii: S0959-4388(21)00094-5. [Epub ahead of print]72 48-54

On the cusp of cures: Breakthroughs in Batten disease research.

Jon J Brudvig, Jill M Weimer.

Batten disease is a family of rare, lysosomal disorders caused by mutations in one of at least 13 genes, which encode a diverse set of lysosomal and extralysosomal proteins. Despite decades of research, the development of effective therapies has remained intractable. But now, the field is experiencing rapid, unprecedented progress on multiple fronts. New tools are providing insights into previously unsolvable problems, with molecular functions now known for nine Batten disease proteins. Protein interactome data are uncovering potential functional overlap between several Batten disease proteins, providing long-sought links between seemingly disparate proteins. Understanding of cellular etiology is elucidating contributions from and interactions between various CNS cell types. Collectively, this explosion in insight is hastening an unparalleled period of therapeutic breakthroughs, with multiple therapies showing great promise in preclinical and clinical studies. The coming years will provide a continuation of this rapid progress, with the promise of effective treatments giving patients hope.

DOI: https://doi.org/10.1016/j.conb.2021.08.003
Int J Mol Sci. 2021 Sep 18. pii: 10088. [Epub ahead of print]22(18):

Pathogenesis and Molecular Mechanisms of Anderson-Fabry Disease and Possible New Molecular Addressed Therapeutic Strategies.

Antonino Tuttolomondo, Irene Simonetta, Renata Riolo, Federica Todaro, Tiziana Di Chiara, Salvatore Miceli, Antonio Pinto.

  Anderson-Fabry disease (AFD) is a rare disease with an incidenceof approximately 1:117,000 male births. Lysosomal accumulation of globotriaosylceramide (Gb3) is the element characterizing Fabry disease due to a hereditary deficiency α-galactosidase A (GLA) enzyme. The accumulation of Gb3 causes lysosomal dysfunction that compromises cell signaling pathways. Deposition of sphingolipids occurs in the autonomic nervous system, dorsal root ganglia, kidney epithelial cells, vascular system cells, and myocardial cells, resulting in organ failure. This manuscript will review the molecular pathogenetic pathways involved in Anderson-Fabry disease and in its organ damage. Some studies reported that inhibition of mitochondrial function and energy metabolism plays a significant role in AFD cardiomyopathy and in kidney disease of AFD patients. Furthermore, mitochondrial dysfunction has been reported as linked to the dysregulation of the autophagy-lysosomal pathway which inhibits the mechanistic target of rapamycin kinase (mTOR) mediated control of mitochondrial metabolism in AFD cells. Cerebrovascular complications due to AFD are caused by cerebral micro vessel stenosis. These are caused by wall thickening resulting from the intramural accumulation of glycolipids, luminal occlusion or thrombosis. Other pathogenetic mechanisms involved in organ damage linked to Gb3 accumulation are endocytosis and lysosomal degradation of endothelial calcium-activated intermediate-conductance potassium ion channel 3.1 (KCa3.1) via a clathrin-dependent process. This process represents a crucial event in endothelial dysfunction. Several studies have identified the deacylated form of Gb3, globotriaosylsphingosine (Lyso-Gb3), as the main catabolite that increases in plasma and urine in patients with AFD. The mean concentrations of Gb3 in all organs and plasma of Galactosidase A knockout mice were significantly higher than those of wild-type mice. The distributions of Gb3 isoforms vary from organ to organ. Various Gb3 isoforms were observed mainly in the kidneys, and kidney-specific Gb3 isoforms were hydroxylated. Furthermore, the action of Gb3 on the KCa3.1 channel suggests a possible contribution of this interaction to the Fabry disease process, as this channel is expressed in various cells, including endothelial cells, fibroblasts, smooth muscle cells in proliferation, microglia, and lymphocytes. These molecular pathways could be considered a potential therapeutic target to correct the enzyme in addition to the traditional enzyme replacement therapies (ERT) or drug chaperone therapy.

Keywords:  Anderson–Fabry disease; KCa3.1 activity; endothelial dysfunction; globotriaosylceramide; miR-1307-5p; miR-152-5p; miR-21-5p; miR-26a-5p; podocyturia; valvular dysfunction

DOI:  https://doi.org/10.3390/ijms221810088
J Pers Med. 2021 Sep 08. pii: 898. [Epub ahead of print]11(9):

Parsing Fabry Disease Metabolic Plasticity Using Metabolomics.

Franklin Ducatez, Wladimir Mauhin, Agnès Boullier, Carine Pilon, Tony Pereira, Raphaël Aubert, Olivier Benveniste, Stéphane Marret, Olivier Lidove, Soumeya Bekri, Abdellah Tebani.

  BACKGROUND: Fabry disease (FD) is an X-linked lysosomal disease due to a deficiency in the activity of the lysosomal α-galactosidase A (GalA), a key enzyme in the glycosphingolipid degradation pathway. FD is a complex disease with a poor genotype-phenotype correlation. FD could involve kidney, heart or central nervous system impairment that significantly decreases life expectancy. The advent of omics technologies offers the possibility of a global, integrated and systemic approach well-suited for the exploration of this complex disease.MATERIALS AND METHODS: Sixty-six plasmas of FD patients from the French Fabry cohort (FFABRY) and 60 control plasmas were analyzed using liquid chromatography and mass spectrometry-based targeted metabolomics (188 metabolites) along with the determination of LysoGb3 concentration and GalA enzymatic activity. Conventional univariate analyses as well as systems biology and machine learning methods were used.
RESULTS: The analysis allowed for the identification of discriminating metabolic profiles that unambiguously separate FD patients from control subjects. The analysis identified 86 metabolites that are differentially expressed, including 62 Glycerophospholipids, 8 Acylcarnitines, 6 Sphingomyelins, 5 Aminoacids and 5 Biogenic Amines. Thirteen consensus metabolites were identified through network-based analysis, including 1 biogenic amine, 2 lysophosphatidylcholines and 10 glycerophospholipids. A predictive model using these metabolites showed an AUC-ROC of 0.992 (CI: 0.965-1.000).
CONCLUSION: These results highlight deep metabolic remodeling in FD and confirm the potential of omics-based approaches in lysosomal diseases to reveal clinical and biological associations to generate pathophysiological hypotheses.

Keywords:  Fabry disease; inborn errors of metabolism; lysosomal storage diseases; machine learning; metabolomics; systems biology

DOI:  https://doi.org/10.3390/jpm11090898
Virol Sin. 2021 Sep 28.

mTOR Signaling: The Interface Linking Cellular Metabolism and Hepatitis B Virus Replication.

Xueyu Wang, Zhiqiang Wei, Yongfang Jiang, Zhongji Meng, Mengji Lu.

  Mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that includes mTOR complex (mTORC) 1 and mTORC2. The mTOR pathway is activated in viral hepatitis, including hepatitis B virus (HBV) infection-induced hepatitis. Currently, chronic HBV infection remains one of the most serious public health issues worldwide. The unavailability of effective therapeutic strategies for HBV suggests that clarification of the pathogenesis of HBV infection is urgently required. Increasing evidence has shown that HBV infection can activate the mTOR pathway, indicating that HBV utilizes or hijacks the mTOR pathway to benefit its own replication. Therefore, the mTOR signaling pathway might be a crucial target for controlling HBV infection. Here, we summarize and discuss the latest findings from model biology research regarding the interaction between the mTOR signaling pathway and HBV replication.

Keywords:  Autophagy; Hepatitis B virus (HBV); Mammalian target of rapamycin (mTOR); Metabolism

DOI:  https://doi.org/10.1007/s12250-021-00450-3
J Leukoc Biol. 2021 Sep 29.

Loss of mTORC2-induced metabolic reprogramming in monocytes uncouples migration and maturation from production of proinflammatory mediators.

Maryam Jangani, Juho Vuononvirta, Lamya Yamani, Eleanor Ward, Melania Capasso, Suchita Nadkarni, Frances Balkwill, Federica Marelli-Berg.

  Monocyte migration to the sites of inflammation and maturation into macrophages are key steps for their immune effector function. Here, we show that mechanistic target of rapamycin complex 2 (mTORC2)-dependent Akt activation is instrumental for metabolic reprogramming at the early stages of macrophage-mediated immunity. Despite an increased production of proinflammatory mediators, monocytes lacking expression of the mTORC2 component Rictor fail to efficiently migrate to inflammatory sites and fully mature into macrophages, resulting in reduced inflammatory responses in vivo. The mTORC2-dependent phosphorylation of Akt is instrumental for the enhancement of glycolysis and mitochondrial respiration, required to sustain monocyte maturation and motility. These observations are discussed in the context of therapeutic strategies aimed at selective inhibition of mTORC2 activity.

Keywords:  cell metabolism; mTORC2; macrophage; metabolism; monocyte

DOI:  https://doi.org/10.1002/JLB.1A0920-588R
Mol Biol Cell. 2021 Sep 29. mbcE21040219

Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase.

Natalya Pashkova, Liping Yu, Nicholas J Schnicker, Chun-Che Tseng, Lokesh Gakhar, David J Katzmann, Robert C Piper.

The family of Bro1 proteins coordinates the activity of the Endosomal Sorting Complexes Required for Transport (ESCRTs) to mediate a number of membrane remodeling events. These events culminate in membrane scission catalyzed by ESCRT-III, whose polymerization and disassembly is controlled by the AAA-ATPase, Vps4. Bro1-family members Alix and HD-PTP as well as yeast Bro1 have a central 'V' domains that non-covalently bind Ub and connect ubiquitinated proteins to ESCRT-driven functions such as the incorporation of ubiquitinated membrane proteins into intralumenal vesicles of multivesicular bodies. Recently, it was discovered that the V domain of yeast Bro1 binds the MIT domain of Vps4 to stimulate its ATPase activity. Here we determine the structural basis for how the V domain of human HD-PTP binds ubiquitin. The HD-PTP V domain also binds the MIT domain of Vps4 and ubiquitin-binding to the HD-PTP V domain enhances its ability to stimulate Vps4 ATPase activity. Additionally, we found V domains of both HD-PTP and Bro1 bind CHMP5 and Vps60, respectively, providing another potential molecular mechanism to alter Vps4 activity. These data support a model whereby contacts between ubiquitin, ESCRT-III, and Vps4 by V domains of the Bro1 family may coordinate late events in ESCRT-driven membrane remodeling events.

DOI: https://doi.org/10.1091/mbc.E21-04-0219
Ageing Res Rev. 2021 Sep 23. pii: S1568-1637(21)00215-4. [Epub ahead of print] 101468

Autophagy and the Hallmarks of Aging.

Susmita Kaushik, Inmaculada Tasset, Esperanza Arias, Olatz Pampliega, Esther Wong, Marta Martinez-Vicente, Ana Maria Cuervo.

  Autophagy, an essential cellular process that mediates degradation of proteins and organelles in lysosomes, has been tightly linked to cellular quality control for its role as part of the proteostasis network. The current interest in identifying the cellular and molecular determinants of aging, has highlighted the important contribution of malfunctioning of autophagy with age to the loss of proteostasis that characterizes all old organisms. However, the diversity of cellular functions of the different types of autophagy and the often reciprocal interactions of autophagy with other determinants of aging, is placing autophagy at the center of the aging process. In this work, we summarize evidence for the contribution of autophagy to health- and lifespan and provide examples of the bidirectional interplay between autophagic pathways and several of the so-called hallmarks of aging. This central role of autophagy in aging, and the dependence on autophagy of many geroprotective interventions, has motivated a search for direct modulators of autophagy that could be used to slow aging and extend healthspan. Here, we review some of those ongoing therapeutic efforts and comment on the potential of targeting autophagy in aging.

Keywords:  aging; chaperones; lysosomes; organelle turnover; proteolysis; proteostasis

DOI:  https://doi.org/10.1016/j.arr.2021.101468
J Biol Chem. 2021 Sep 23. pii: S0021-9258(21)01047-4. [Epub ahead of print] 101244

TBK1 has a new Akt.

Leslie M Shaw.

  TANK-binding kinase 1 (TBK1) is a non-canonical IκB kinase that plays an essential role in the innate immune response to foreign pathogens. Recent studies have highlighted additional roles for TBK1 in the regulation of metabolism, although the mechanisms of this regulation have not been well characterized. In a recent issue, Tooley et al demonstrated that TBK1-dependent activation of downstream kinase Akt is mediated via mTOR complex 2 (mTORC2). This novel action of TBK1 reveals a key role for this kinase in the regulation of cellular metabolism and growth by diverse environmental inputs.

Keywords:  AKT; TBK1; mTORC2

DOI:  https://doi.org/10.1016/j.jbc.2021.101244
Dev Biol. 2021 Sep 28. pii: S0012-1606(21)00216-5. [Epub ahead of print]

Asymmetric organelle positioning during epithelial polarization of C. elegans intestinal cells.

James N Brandt, Laura Voss, Fiona M Rambo, Katelyn Nicholson, Jackson R Thein, Lydia Fairchild, Laurence Seabrook, Danielia Lewis, Lali Guevara-Hernandez, Matthew L White, Luca Sax, Victoria Eichten, Logan Harper, Greg J Hermann.

  While the epithelial cell cortex displays profound asymmetries in protein distribution and morphology along the apico-basal axis, the extent to which the cytoplasm is similarly polarized within epithelial cells remains relatively unexplored. We show that cytoplasmic organelles within C. elegans embryonic intestinal cells develop extensive apico-basal polarity at the time they establish cortical asymmetry. Nuclei and conventional endosomes, including early endosomes, late endosomes, and lysosomes, become polarized apically. Lysosome-related gut granules, yolk platelets, and lipid droplets become basally enriched. Removal of par-3 activity does not disrupt organelle positioning, indicating that cytoplasmic apico-basal asymmetry is independent of the PAR polarity pathway. Blocking the apical migration of nuclei leads to the apical positioning of gut granules and yolk platelets, whereas the asymmetric localization of conventional endosomes and lipid droplets is unaltered. This suggests that nuclear positioning organizes some, but not all, cytoplasmic asymmetries in this cell type. We show that gut granules become apically enriched when WHT-2 and WHT-7 function is disrupted, identifying a novel role for ABCG transporters in gut granule positioning during epithelial polarization. Analysis of WHT-2 and WHT-7 ATPase mutants is consistent with a WHT-2/WHT-7 heterodimer acting as a transporter in gut granule positioning. In wht-2(-) mutants the polarized distribution of other organelles is not altered and gut granules do not take on characteristics of conventional endosomes that could have explained their apical mispositioning. During epithelial polarization wht-2(-) gut granules exhibit a loss of the Rab32/38 family member GLO-1 and ectopic expression of GLO-1 is sufficient to rescue the basal positioning of wht-2(-) and wht-7(-) gut granules. Furthermore, depletion of GLO-1 causes the mislocalization of the endolysosomal RAB-7 to gut granules and RAB-7 drives the apical mispositioning of gut granules when GLO-1, WHT-2, or WHT-7 function is disrupted. We suggest that ABC transporters residing on gut granules can regulate Rab dynamics to control organelle positioning during epithelial polarization.

Keywords:  ABC transporter; C. elegans; Epithelial polarization; Organelle positioning; Rab GTPase

DOI:  https://doi.org/10.1016/j.ydbio.2021.09.007
Front Cell Dev Biol. 2021 ;9 726261

Lipid Droplet-Organelle Contact Sites as Hubs for Fatty Acid Metabolism, Trafficking, and Metabolic Channeling.

Mike F Renne, Hanaa Hariri.

  Cells prepare for fluctuations in nutrient availability by storing energy in the form of neutral lipids in organelles called Lipid Droplets (LDs). Upon starvation, fatty acids (FAs) released from LDs are trafficked to different cellular compartments to be utilized for membrane biogenesis or as a source of energy. Despite the biochemical pathways being known in detail, the spatio-temporal regulation of FA synthesis, storage, release, and breakdown is not completely understood. Recent studies suggest that FA trafficking and metabolism are facilitated by inter-organelle contact sites that form between LDs and other cellular compartments such as the Endoplasmic Reticulum (ER), mitochondria, peroxisomes, and lysosomes. LD-LD contact sites are also sites where FAs are transferred in a directional manner to support LD growth and expansion. As the storage site of neutral lipids, LDs play a central role in FA homeostasis. In this mini review, we highlight the role of LD contact sites with other organelles in FA trafficking, channeling, and metabolism and discuss the implications for these pathways on cellular lipid and energy homeostasis.

Keywords:  contact sites; fatty acids; lipid droplets; metabolism; organelles

DOI:  https://doi.org/10.3389/fcell.2021.726261
Molecules. 2021 Sep 16. pii: 5616. [Epub ahead of print]26(18):

Oxidative Stress in Mucopolysaccharidoses: Pharmacological Implications.

Karolina Pierzynowska, Lidia Gaffke, Zuzanna Cyske, Grzegorz Węgrzyn, Brigitta Buttari, Elisabetta Profumo, Luciano Saso.

  Although mucopolysaccharidoses (MPS) are caused by mutations in genes coding for enzymes responsible for degradation of glycosaminoglycans, storage of these compounds is crucial but is not the only pathomechanism of these severe, inherited metabolic diseases. Among various factors and processes influencing the course of MPS, oxidative stress appears to be a major one. Oxidative imbalance, occurring in MPS and resulting in increased levels of reactive oxidative species, causes damage of various biomolecules, leading to worsening of symptoms, especially in the central nervous system (but not restricted to this system). A few therapeutic options are available for some types of MPS, including enzyme replacement therapy and hematopoietic stem cell transplantation, however, none of them are fully effective in reducing all symptoms. A possibility that molecules with antioxidative activities might be useful accompanying drugs, administered together with other therapies, is discussed in light of the potential efficacy of MPS treatment.

Keywords:  antioxidants; mucopolysaccharidoses; oxidative stress

DOI:  https://doi.org/10.3390/molecules26185616
Metabolites. 2021 Aug 31. pii: 588. [Epub ahead of print]11(9):

Selective Autophagy as a Potential Therapeutic Target in Age-Associated Pathologies.

Margarita-Elena Papandreou, Nektarios Tavernarakis.

  Progressive accumulation of damaged cellular constituents contributes to age-related diseases. Autophagy is the main catabolic process, which recycles cellular material in a multitude of tissues and organs. Autophagy is activated upon nutrient deprivation, and oncogenic, heat or oxidative stress-induced stimuli to selectively degrade cell constituents and compartments. Specificity and accuracy of the autophagic process is maintained via the precision of interaction of autophagy receptors or adaptors and substrates by the intricate, stepwise orchestration of specialized integrating stimuli. Polymorphisms in genes regulating selective autophagy have been linked to aging and age-associated disorders. The involvement of autophagy perturbations in aging and disease indicates that pharmacological agents balancing autophagic flux may be beneficial, in these contexts. Here, we introduce the modes and mechanisms of selective autophagy, and survey recent experimental evidence of dysfunctional autophagy triggering severe pathology. We further highlight identified pharmacological targets that hold potential for developing therapeutic interventions to alleviate cellular autophagic cargo burden and associated pathologies.

Keywords:  age-related disease; aggrephagy; aging; mitophagy; neurodegeneration; nucleophagy; pexophagy; rapamycin; selective autophagy

DOI:  https://doi.org/10.3390/metabo11090588
Biochemistry. 2021 Sep 27.

Redefining the Scope of Targeted Protein Degradation: Translational Opportunities in Hijacking the Autophagy-Lysosome Pathway.

Katelyn Cassidy, Heng Zhao.

The advent of multi-specific targeted protein degradation (TPD) therapies has made it possible to drug targets that have long been considered to be inaccessible. For this reason, the foremost TPD modalities - molecular glues and proteolysis targeting chimeras (PROTACs) -have been widely adopted and developed in therapeutic programs across the pharmaceutical and biotechnology industries. While there are many clear advantages to these two approaches, there are also blind spots. Specifically, PROTACs and molecular glues are inherently mechanistically analogous in that targets of both are degraded via the 26s proteasome; however, not all disease-relevant targets are suitable for ubiquitin proteasome system (UPS)-mediated degradation. The alternative mammalian protein degradation pathway, the autophagy-lysosome system (or ALS), is capable of degrading targets that elude the UPS such as long-lived proteins, insoluble protein aggregates, and even abnormal organelles. Emerging TPD strategies- such as ATTEC, AUTAC, and LYTAC- take advantage of the substrate diversity of the ALS to greatly expand the clinical utility of TPD. In this Perspective, we will discuss the array of current TPD modalities, with a focus on critical evaluation of these novel ALS-mediated degradation techniques.

DOI: https://doi.org/10.1021/acs.biochem.1c00330
Sci Rep. 2021 Sep 29. 11(1): 19355

Vacuolar-type proton ATPase is required for maintenance of apicobasal polarity of embryonic visceral endoderm.

Ge-Hong Sun-Wada, Hiroyuki Tabata, Yoh Wada.

The endocytic compartments keep their interior acidic through the inward flow of protons and anions from the cytosol. Acidification is mediated by a proton pump known as vacuolar-type ATPase (V-ATPase) and transporters conferring anion conductance to the organellar membrane. In this study, we analysed the phenotype of mouse embryos lacking the V-ATPase c-subunit. The mutant embryos differentiated embryonic epithelial tissues, primitive endoderm, epiblast, and extraembryonic ectoderm; however, the organisation of these epithelia was severely affected. The apical-basal polarity in the visceral endoderm layer was not properly established in the mutant embryos, resulting in abnormal epithelial morphology. Thus, the function of V-ATPase is imperative for the establishment and/or maintenance of epithelial cell polarity, which is required for early embryogenesis.

DOI: https://doi.org/10.1038/s41598-021-98952-3
Cell Rep. 2021 Sep 28. pii: S2211-1247(21)01203-1. [Epub ahead of print]36(13): 109749

An ancient RAB5 governs the formation of additional vacuoles and cell shape in petunia petals.

Shuangjiang Li, Martina Cerri, Pamela Strazzer, Yanbang Li, Cornelis Spelt, Mattijs Bliek, Michiel Vandenbussche, Enric Martínez-Calvó, Biao Lai, Lara Reale, Ronald Koes, Francesca M Quattrocchio.

  Homologous ("canonical") RAB5 proteins regulate endosomal trafficking to lysosomes in animals and to the central vacuole in plants. Epidermal petal cells contain small vacuoles (vacuolinos) that serve as intermediate stations for proteins on their way to the central vacuole. Here, we show that transcription factors required for vacuolino formation in petunia induce expression of RAB5a. RAB5a defines a previously unrecognized clade of canonical RAB5s that is evolutionarily and functionally distinct from ARA7-type RAB5s, which act in trafficking to the vacuole. Loss of RAB5a reduces cell height and abolishes vacuolino formation, which cannot be rescued by the ARA7 homologs, whereas constitutive RAB5a (over)expression alters the conical cell shape and promotes homotypic vacuolino fusion, resulting in oversized vacuolinos. These findings provide a rare example of how gene duplication and neofunctionalization increased the complexity of membrane trafficking during evolution and suggest a mechanism by which cells may form multiple vacuoles with distinct content and function.

Keywords:  MBW complex; RAB GTPase; conical cell shape; endosome trafficking; flower; petunia; vacuole; vacuolino

DOI:  https://doi.org/10.1016/j.celrep.2021.109749
Life Sci. 2021 Sep 27. pii: S0024-3205(21)00971-1. [Epub ahead of print] 119984

Crosstalk between miRNA and PI3K/AKT/mTOR signaling pathway in cancer.

Maryam Akbarzadeh, Ainaz Mihanfar, Shabnam Akbarzadeh, Bahman Yousefi, Maryam Majidinia.

  Phosphoinositide-3 kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) signaling pathway is one of the most important proliferative signaling pathways with critical undeniable function in various aspects of cancer initiation/progression, including proliferation, apoptosis, metastasis, angiogenesis, and drug resistance. On the other hand, numerous genetic alterations in the key genes involved in the PI3K/AKT/mTOR signaling pathway have been identified in multiple solid and hematological tumors. In addition, accumulating recent evidences have demonstrated a reciprocal interaction between this signaling pathway and microRNAs, a large group of small non-coding RNAs. Therefore, in this review, it was attempted to discuss about the interaction between key components of PI3K/AKT/mTOR signaling pathway with various miRNAs and their importance in cancer biology.

Keywords:  Angiogenesis; Cancer; Drug resistance; Metastasis; PI3K/AKT/mTOR; miRNA

DOI:  https://doi.org/10.1016/j.lfs.2021.119984
Int J Mol Sci. 2021 Sep 14. pii: 9912. [Epub ahead of print]22(18):

C5a Activates a Pro-Inflammatory Gene Expression Profile in Human Gaucher iPSC-Derived Macrophages.

Jacquelyn C Serfecz, Afsoon Saadin, Clayton P Santiago, Yuji Zhang, Søren M Bentzen, Stefanie N Vogel, Ricardo A Feldman.

  Gaucher disease (GD) is an autosomal recessive disorder caused by bi-allelic GBA1 mutations that reduce the activity of the lysosomal enzyme β-glucocerebrosidase (GCase). GCase catalyzes the conversion of glucosylceramide (GluCer), a ubiquitous glycosphingolipid, to glucose and ceramide. GCase deficiency causes the accumulation of GluCer and its metabolite glucosylsphingosine (GluSph) in a number of tissues and organs. In the immune system, GCase deficiency deregulates signal transduction events, resulting in an inflammatory environment. It is known that the complement system promotes inflammation, and complement inhibitors are currently being considered as a novel therapy for GD; however, the mechanism by which complement drives systemic macrophage-mediated inflammation remains incompletely understood. To help understand the mechanisms involved, we used human GD-induced pluripotent stem cell (iPSC)-derived macrophages. We found that GD macrophages exhibit exacerbated production of inflammatory cytokines via an innate immune response mediated by receptor 1 for complement component C5a (C5aR1). Quantitative RT-PCR and ELISA assays showed that in the presence of recombinant C5a (rC5a), GD macrophages secreted 8-10-fold higher levels of TNF-α compared to rC5a-stimulated control macrophages. PMX53, a C5aR1 blocker, reversed the enhanced GD macrophage TNF-α production, indicating that the observed effect was predominantly C5aR1-mediated. To further analyze the extent of changes induced by rC5a stimulation, we performed gene array analysis of the rC5a-treated macrophage transcriptomes. We found that rC5a-stimulated GD macrophages exhibit increased expression of genes involved in TNF-α inflammatory responses compared to rC5a-stimulated controls. Our results suggest that rC5a-induced inflammation in GD macrophages activates a unique immune response, supporting the potential use of inhibitors of the C5a-C5aR1 receptor axis to mitigate the chronic inflammatory abnormalities associated with GD.

Keywords:  C5a; GBA1; TNF-alpha; complement; gaucher disease; gene arrays; induced pluripotent stem cells (iPSC); inflammation; macrophages; β-glucocerebrosidase

DOI:  https://doi.org/10.3390/ijms22189912
Microorganisms. 2021 Sep 03. pii: 1871. [Epub ahead of print]9(9):

The Role of Sch9 and the V-ATPase in the Adaptation Response to Acetic Acid and the Consequences for Growth and Chronological Lifespan.

Marie-Anne Deprez, Jeroen M Maertens, Lisbeth Olsson, Maurizio Bettiga, Joris Winderickx.

  Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9Δ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan.

Keywords:  acetic acid stress; chronological lifespan; growth; lipidomics; nutrient signalling; pH homeostasis

DOI:  https://doi.org/10.3390/microorganisms9091871
J Am Chem Soc. 2021 Oct 01.

Covalently Engineered Nanobody Chimeras for Targeted Membrane Protein Degradation.

Heng Zhang, Yu Han, Yuanfan Yang, Feng Lin, Kexin Li, Linghao Kong, Hongxiang Liu, Yongjun Dang, Jian Lin, Peng R Chen.

The targeted degradation of membrane proteins would afford an attractive and general strategy for treating various diseases that remain difficult with the current proteolysis-targeting chimera (PROTAC) methodology. We herein report a covalent nanobody-based PROTAC strategy, termed GlueTAC, for targeted membrane protein degradation with high specificity and efficiency. We first established a mass-spectrometry-based screening platform for the rapid development of a covalent nanobody (GlueBody) that allowed proximity-enabled cross-linking with surface antigens on cancer cells. By conjugation with a cell-penetrating peptide and a lysosomal-sorting sequence, the resulting GlueTAC chimera triggered the internalization and degradation of programmed death-ligand 1 (PD-L1), which provides a new avenue to target and degrade cell-surface proteins.

DOI: https://doi.org/10.1021/jacs.1c08521
Biomedicines. 2021 Aug 24. pii: 1077. [Epub ahead of print]9(9):

Advances in Intracellular Calcium Signaling Reveal Untapped Targets for Cancer Therapy.

Aarushi Sharma, Grace T Ramena, Randolph C Elble.

  Intracellular Ca2+ distribution is a tightly regulated process. Numerous Ca2+ chelating, storage, and transport mechanisms are required to maintain normal cellular physiology. Ca2+-binding proteins, mainly calmodulin and calbindins, sequester free intracellular Ca2+ ions and apportion or transport them to signaling hubs needing the cations. Ca2+ channels, ATP-driven pumps, and exchangers assist the binding proteins in transferring the ions to and from appropriate cellular compartments. Some, such as the endoplasmic reticulum, mitochondria, and lysosomes, act as Ca2+ repositories. Cellular Ca2+ homeostasis is inefficient without the active contribution of these organelles. Moreover, certain key cellular processes also rely on inter-organellar Ca2+ signaling. This review attempts to encapsulate the structure, function, and regulation of major intracellular Ca2+ buffers, sensors, channels, and signaling molecules before highlighting how cancer cells manipulate them to survive and thrive. The spotlight is then shifted to the slow pace of translating such research findings into anticancer therapeutics. We use the PubMed database to highlight current clinical studies that target intracellular Ca2+ signaling. Drug repurposing and improving the delivery of small molecule therapeutics are further discussed as promising strategies for speeding therapeutic development in this area.

Keywords:  IP3R; MCU; ORAI; PNCA; SERCA; SOCE; STIM; STIMATE; TRP; VGCC; calmodulin

DOI:  https://doi.org/10.3390/biomedicines9091077
Cancers (Basel). 2021 Sep 19. pii: 4697. [Epub ahead of print]13(18):

Cathepsin S Evokes PAR2-Dependent Pain in Oral Squamous Cell Carcinoma Patients and Preclinical Mouse Models.

Nguyen Huu Tu, Kenji Inoue, Elyssa Chen, Bethany M Anderson, Caroline M Sawicki, Nicole N Scheff, Hung D Tran, Dong H Kim, Robel G Alemu, Lei Yang, John C Dolan, Cheng Z Liu, Malvin N Janal, Rocco Latorre, Dane D Jensen, Nigel W Bunnett, Laura E Edgington-Mitchell, Brian L Schmidt.

  Oral squamous cell carcinoma (SCC) pain is more prevalent and severe than pain generated by any other form of cancer. We previously showed that protease-activated receptor-2 (PAR2) contributes to oral SCC pain. Cathepsin S is a lysosomal cysteine protease released during injury and disease that can activate PAR2. We report here a role for cathepsin S in PAR2-dependent cancer pain. We report that cathepsin S was more active in human oral SCC than matched normal tissue, and in an orthotopic xenograft tongue cancer model than normal tongue. The multiplex immunolocalization of cathepsin S in human oral cancers suggests that carcinoma and macrophages generate cathepsin S in the oral cancer microenvironment. After cheek or paw injection, cathepsin S evoked nociception in wild-type mice but not in mice lacking PAR2 in Nav1.8-positive neurons (Par2Nav1.8), nor in mice treated with LY3000328 or an endogenous cathepsin S inhibitor (cystatin C). The human oral SCC cell line (HSC-3) with homozygous deletion of the gene for cathepsin S (CTSS) with CRISPR/Cas9 provoked significantly less mechanical allodynia and thermal hyperalgesia, as did those treated with LY3000328, compared to the control cancer mice. Our results indicate that cathepsin S is activated in oral SCC, and that cathepsin S contributes to cancer pain through PAR2 on neurons.

Keywords:  PAR2; cancer pain; cathepsin S; oral cancer; oral squamous cell carcinoma; pain; protease-activated receptor-2

DOI:  https://doi.org/10.3390/cancers13184697
J Lipid Res. 2021 Sep 28. pii: S0022-2275(21)00110-3. [Epub ahead of print] 100128

ATP-binding cassette transporters mediate differential biosynthesis of glycosphingolipid species.

Monique Budani, Christiane Auray-Blais, Clifford Lingwood.

  The cytosolic-oriented glucosylceramide (GlcCer) synthase is enigmatic, requiring nascent GlcCer translocation to the luminal Golgi membrane to access glycosphingolipid (GSL) anabolic glycosyltransferases. The mechanism by which GlcCer is flipped remains unclear. To investigate the role of GlcCer binding partners in this process, we previously made cleavable, biotinylated, photoreactive GlcCer analogs in which the reactive nitrene was closely apposed to the GlcCer head group, while maintaining a C16-acyl chain. GlcCer binding protein specificity was validated for both photoprobes. Using one probe, XLB, here we identified ATP-binding cassette (ABC) transporters ABCA3, ABCB4, and ABCB10 as unfractionated microsomal GlcCer-binding proteins in DU-145 prostate tumor cells. siRNA knockdown (KD) of these transporters differentially blocked GSL synthesis assessed in toto and via metabolic labelling. KD of ABCA3 reduced acid/neutral GSL levels, but increased those of LacCer, while KD of ABCB4 preferentially reduced neutral GSL levels, and KD of ABCB10 reduced levels of both neutral and acidic GSLs. Depletion of ABCA12, implicated in GlcCer transport, preferentially decreased neutral GSL levels, while ABCB1 KD preferentially reduced gangliosides, but increased neutral GSL Gb3. These results imply that multiple ABC transporters may provide distinct but overlapping GlcCer and LacCer pools within the Golgi lumen for anabolism of different GSL series by metabolic channeling. Differential ABC family member usage may fine tune GSL biosynthesis depending on cell/tissue type. We conclude that ABC transporters provide a new tool for the regulation of GSL biosynthesis and serve as potential targets to reduce selected GSL species/subsets in diseases in which GSLs are dysregulated.

Keywords:  ABC transporter; GSL anabolism; GlcCer pools; GlcCer synthase; LacCer; glucosylceramide flippase; glycosphingolipid; metabolic channeling; metabolic labelling; photoprobes

DOI:  https://doi.org/10.1016/j.jlr.2021.100128
EMBO Rep. 2021 Sep 28. e52675

Structural basis for the specificity of PPM1H phosphatase for Rab GTPases.

Dieter Waschbüsch, Kerryn Berndsen, Pawel Lis, Axel Knebel, Yuko Py Lam, Dario R Alessi, Amir R Khan.

  LRRK2 serine/threonine kinase is associated with inherited Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal-dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110-residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3-D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab-specific interaction domain within a conserved phosphatase fold.

Keywords:  LRRK2 kinase; PPM1H phosphatase; Rab GTPase; crystal structure; membrane trafficking

DOI:  https://doi.org/10.15252/embr.202152675
Proc Natl Acad Sci U S A. 2021 Oct 05. pii: e2110387118. [Epub ahead of print]118(40):

A genetic model of methionine restriction extends Drosophila health- and lifespan.

Andrey A Parkhitko, Lin Wang, Elizabeth Filine, Patrick Jouandin, Dmitry Leshchiner, Richard Binari, John M Asara, Joshua D Rabinowitz, Norbert Perrimon.

  Loss of metabolic homeostasis is a hallmark of aging and is characterized by dramatic metabolic reprogramming. To analyze how the fate of labeled methionine is altered during aging, we applied 13C5-Methionine labeling to Drosophila and demonstrated significant changes in the activity of different branches of the methionine metabolism as flies age. We further tested whether targeted degradation of methionine metabolism components would "reset" methionine metabolism flux and extend the fly lifespan. Specifically, we created transgenic flies with inducible expression of Methioninase, a bacterial enzyme capable of degrading methionine and revealed methionine requirements for normal maintenance of lifespan. We also demonstrated that microbiota-derived methionine is an alternative and important source in addition to food-derived methionine. In this genetic model of methionine restriction (MetR), we also demonstrate that either whole-body or tissue-specific Methioninase expression can dramatically extend Drosophila health- and lifespan and exerts physiological effects associated with MetR. Interestingly, while previous dietary MetR extended lifespan in flies only in low amino acid conditions, MetR from Methioninase expression extends lifespan independently of amino acid levels in the food. Finally, because impairment of the methionine metabolism has been previously associated with the development of Alzheimer's disease, we compared methionine metabolism reprogramming between aging flies and a Drosophila model relevant to Alzheimer's disease, and found that overexpression of human Tau caused methionine metabolism flux reprogramming similar to the changes found in aged flies. Altogether, our study highlights Methioninase as a potential agent for health- and lifespan extension.

Keywords:  13C-Methionine labeling; Alzheimer’s disease; Methioninase; aging; methionine restriction

DOI:  https://doi.org/10.1073/pnas.2110387118
J Biol Chem. 2021 Sep 27. pii: S0021-9258(21)01057-7. [Epub ahead of print] 101254

Cooperative regulation of endocytic vesicle transport by yeast Eps15-like protein Pan1p and epsins.

Nao Yoshida, Ippo Ogura, Makoto Nagano, Tadashi Ando, Junko Y Toshima, Jiro Toshima.

  Dynamic actin filaments are required for the formation and internalization of endocytic vesicles. Yeast actin cables serve as a track for the translocation of endocytic vesicles to early endosomes, but the molecular mechanisms regulating the interaction between vesicles and the actin cables remain ambiguous. Previous studies have demonstrated that the yeast Eps15-like protein Pan1p plays an important role in this interaction, and that interaction is not completely lost even after deletion of the Pan1p actin-binding domain, suggesting that additional proteins mediate association of the vesicle with the actin cable. Other candidates for mediating the interaction are endocytic coat proteins Sla2p (yeast Hip1R) and Ent1p/2p (yeast epsins), as these proteins can bind to both the plasma membrane and the actin filament. Here we investigated the degree of redundancy in the actin-binding activities of Pan1p, Sla2p, and Ent1p/2p involved in the internalization and transport of endocytic vesicles. Expression of the non-phosphorylatable form of Pan1p, Pan1-18TA, caused abnormal accumulation of both actin cables and endocytic vesicles, and this accumulation was additively suppressed by deletion of the actin-binding domains of both Pan1p and Ent1p. Interestingly, deletion of the actin-binding domains of Pan1p and Ent1p in cells lacking the ENT2 gene resulted in severely defective internalization of endocytic vesicles and recruitment of actin cables to the site of endocytosis. These results suggest that Pan1p and Ent1p/2p cooperatively regulate interaction between the endocytic vesicle and the actin cable.

Keywords:  actin; endocytosis; imaging; membrane transport

DOI:  https://doi.org/10.1016/j.jbc.2021.101254
EMBO J. 2021 Sep 28. e109575

AMPK CA(R)Sts a new light on amino acid sensing.

Kristin K Brown.

AMP-activated protein kinase (AMPK) is recognized as a critical regulator of cellular energy metabolism impacted by AMP/ATP and ADP/ATP ratios, or glucose- and fatty acid-derived metabolites. However, its ability to sense alterations in amino acid levels is poorly understood. Recent work by Yuan et al (2021) identifies a novel mechanism of AMPK regulation responsive to changes in availability of the sulfur-containing amino acid cysteine.

DOI: https://doi.org/10.15252/embj.2021109575