bims-lysosi Biomed News
on Lysosomes and signaling
Issue of 2021‒04‒04
forty-nine papers selected by
Stephanie Fernandes
Max Planck Institute for Biology of Ageing
  1. Overlapping roles of JIP3 and JIP4 in promoting axonal transport of lysosomes in human iPSC-derived neurons.
  2. TFEB regulates pluripotency transcriptional network in mouse embryonic stem cells independent of autophagy-lysosomal biogenesis.
  3. GCase and LIMP2 Abnormalities in the Liver of Niemann Pick Type C Mice.
  4. EphB6 Regulates TFEB-Lysosomal Pathway and Survival of Disseminated Indolent Breast Cancer Cells.
  5. Fronto-temporal dementia risk gene TMEM106B has opposing effects in different lysosomal storage disorders.
  6. Exploiting the Potential of Drosophila Models in Lysosomal Storage Disorders: Pathological Mechanisms and Drug Discovery.
  7. Gene Expression-Related Changes in Morphologies of Organelles and Cellular Component Organization in Mucopolysaccharidoses.
  8. Inhibiting mTOR activity using AZD2014 increases autophagy in the mouse cerebral cortex.
  9. Long-term effects of sirolimus on human skin TSC2-null fibroblast-like cells.
  10. The P2X7 Receptor in Microglial Cells Modulates the Endolysosomal Axis, Autophagy, and Phagocytosis.
  11. Real-time tracking lysosomal pH changes under heatstroke and redox stress with a novel near-infrared emissive probe.
  12. Autophagy Triggers Tamoxifen Resistance in Human Breast Cancer Cells by Preventing Drug-Induced Lysosomal Damage.
  13. Muscle Proteomic Profile before and after Enzyme Replacement Therapy in Late-Onset Pompe Disease.
  14. Ccr4-Not as a mediator of environmental signaling: a jack of all trades and master of all.
  15. Hepatitis B Virus X Protein (HBx) Suppresses Transcription Factor EB (TFEB) Resulting in Stabilization of Integrin Beta 1 (ITGB1) in Hepatocellular Carcinoma Cells.
  16. A lysosomal enigma CLN5 and its significance in understanding neuronal ceroid lipofuscinosis.
  17. Changes in expression of lysosomal membrane proteins in leucocytes of cancer patients treated with tyrosine kinase inhibitors.
  18. Rapid and Progressive Loss of Multiple Retinal Cell Types in Cathepsin D-Deficient Mice-An Animal Model of CLN10 Disease.
  19. Lysosomal Calcium Channels in Autophagy and Cancer.
  20. Disparate bone anabolic cues activate bone formation by regulating the rapid lysosomal degradation of sclerostin protein.
  21. Lifelong restriction of dietary branched-chain amino acids has sex-specific benefits for frailty and lifespan in mice.
  22. Identification of new interactions between endolysosomal tethering factors.
  23. Development of Triantennary N-Acetylgalactosamine Conjugates as Degraders for Extracellular Proteins.
  24. Mechanistic Target of Rapamycin Inhibitors in Renal Cell Carcinoma: Potential, Limitations, and Perspectives.
  25. Phosphoproteome Profiling Revealed the Importance of mTOR Inhibition on CDK1 Activation to Further Regulate Cell Cycle Progression.
  26. Key Signaling Pathways in Aging and Potential Interventions for Healthy Aging.
  27. The Structural Basis of Akt PH Domain Interaction with Calmodulin.
  28. Modulation of Endosome Function, Vesicle Trafficking and Autophagy by Human Herpesviruses.
  29. Pathological mechanisms of vacuolar aggregate myopathy arising from a Casq1 mutation.
  30. Differential controls of MAIT cell effector polarization by mTORC1/mTORC2 via integrating cytokine and costimulatory signals.
  31. Phosphorus Availability Regulates TORC1 Signaling via LST8 in Chlamydomonas[OPEN].
  32. Loss of ARID1A activates mTOR signaling and SOX9 in gastric adenocarcinoma-rationale for targeting ARID1A deficiency.
  33. Autophagosome content profiling reveals receptor-specific cargo candidates.
  34. Rapid Identification of New Biomarkers for the Classification of GM1 Type 2 Gangliosidosis Using an Unbiased 1H NMR-Linked Metabolomics Strategy.
  35. BCKDK regulates the TCA cycle through PDC in the absence of PDK family during embryonic development.
  36. Defects in early secretory pathway transport machinery components and neurodevelopmental disorders.
  37. Activation of PI3K/AKT/mTOR Pathway Causes Drug Resistance in Breast Cancer.
  38. Hydrogen peroxide (H2O2) mediated activation of mTORC2 increases intracellular Na+ concentration in the renal medullary thick ascending limb of Henle.
  39. Therapeutic Potential of AAV1-Rheb(S16H) Transduction against Neurodegenerative Diseases.
  40. Upregulation of the pathogenic transcription factor SPI1/PU.1 in tuberous sclerosis complex and focal cortical dysplasia by oxidative stress.
  41. ATP13A2 Regulates Cellular α-Synuclein Multimerization, Membrane Association, and Externalization.
  42. The Role of Ribosomal Protein S6 Kinases in Plant Homeostasis.
  43. Synaptic activity controls autophagic vacuole motility and function in dendrites.
  44. Lysosomal Functions in Glia Associated with Neurodegeneration.
  45. TOR coordinates nucleotide availability with ribosome biogenesis in plants.
  46. The Uncovered Function of the Drosophila GBA1a-Encoded Protein.
  47. Serine metabolism antagonizes antiviral innate immunity by preventing ATP6V0d2-mediated YAP lysosomal degradation.
  48. LRRK2 at the Crossroad of Aging and Parkinson's Disease.
  49. Retention Using Selective Hooks (RUSH) Cargo Sorting Assay for Protein Vesicle Tracking in HeLa Cells.
  1. Mol Biol Cell. 2021 Mar 31. mbcE20060382
    Overlapping roles of JIP3 and JIP4 in promoting axonal transport of lysosomes in human iPSC-derived neurons.
    Swetha Gowrishankar, Lila Lyons, Nisha Mohd Rafiq, Agnes Roczniak-Ferguson, Pietro De Camilli, Shawn M Ferguson.
      The dependence of neurons on microtubule-based motors for the movement of lysosomes over long distances raises questions about adaptations that allow neurons to meet these demands. Recently, JIP3/MAPK8IP3, a neuronally enriched putative adaptor between lysosomes and motors, was identified as a critical regulator of axonal lysosome abundance. In this study, we establish a human induced pluripotent stem cell (iPSC)-derived neuron model for the investigation of axonal lysosome transport and maturation and show that loss of JIP3 results in the accumulation of axonal lysosomes and the Alzheimer's disease-related amyloid precursor protein (APP)-derived Aβ42 peptide. We furthermore reveal an overlapping role of the homologous JIP4 gene in lysosome axonal transport. These results establish a cellular model for investigating the relationship between lysosome axonal transport and amyloidogenic APP processing and more broadly demonstrate the utility of human iPSC-derived neurons for the investigation of neuronal cell biology and pathology. [Media: see text] [Media: see text] [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E20-06-0382
  2. Cell Death Dis. 2021 Apr 01. 12(4): 343
    TFEB regulates pluripotency transcriptional network in mouse embryonic stem cells independent of autophagy-lysosomal biogenesis.
    Anderson Tan, Renuka Prasad, Eek-Hoon Jho.
      Transcription factor EB (TFEB), a well-known master regulator of autophagy and lysosomal biogenesis, is a member of the microphthalmia family of transcription factors (MiT family). Over the years, TFEB has been shown to have diverse roles in various physiological processes such as clearance for intracellular pathogenic factors and having developmental functions such as dendritic maturation, as well as osteoclast, and endoderm differentiation. However, in the present study, we propose a novel mechanism for TFEB governing pluripotency of mouse ESCs (mESCs) by regulating the pluripotency transcriptional network (PTN) in these cells. We observed high levels of TFEB mRNA and protein levels in undifferentiated mESCs. Interestingly, we found a reduction of Nanog and Sox2 levels in TFEB knockout (KO) mESCs while pluripotency was maintained as there was an upregulation of TFE3, a potent stem cell maintenance factor. In consistent, double knockout of TFEB/TFE3 (TFEB/3 DKO) reduced mESC pluripotency, as indicated by the loss of ESC morphology, reduction of ESC markers, and the emergence of differentiation markers. We further discovered that Nanog was a TFEB target gene in undifferentiated mESCs. TFEB also promoted sex-determining region Y-box2 (Sox2) transcription by forming a heterodimer with Sox2 in mESCs. Notably, Sox2, Oct4, and Nanog were also binding to the TFEB promoter and thus generating a feed-forward loop in relation to TFEB. Although high levels of nuclear TFEB are expected to enhance autophagy-lysosomal activity, undifferentiated mESC remarkably displayed low basal autophagy-lysosomal activity. Overexpression or knockout of TFEB did not affect the expression of TFEB lysosomal-autophagy target genes and TFEB also had a lesser binding affinity to its own lysosomal promoter-target genes in mESCs compared to differentiated cells. Collectively, these findings define a newly incorporative, moonlighting function for TFEB in regulating PTN, independent of its autophagy-lysosomal biogenesis roles.
    DOI:  https://doi.org/10.1038/s41419-021-03632-9
  3. Int J Mol Sci. 2021 Mar 03. pii: 2532. [Epub ahead of print]22(5):
    GCase and LIMP2 Abnormalities in the Liver of Niemann Pick Type C Mice.
    Martijn J C van der Lienden, Jan Aten, André R A Marques, Ingeborg S E Waas, Per W B Larsen, Nike Claessen, Nicole N van der Wel, Roelof Ottenhoff, Marco van Eijk, Johannes M F G Aerts.
      The lysosomal storage disease Niemann-Pick type C (NPC) is caused by impaired cholesterol efflux from lysosomes, which is accompanied by secondary lysosomal accumulation of sphingomyelin and glucosylceramide (GlcCer). Similar to Gaucher disease (GD), patients deficient in glucocerebrosidase (GCase) degrading GlcCer, NPC patients show an elevated glucosylsphingosine and glucosylated cholesterol. In livers of mice lacking the lysosomal cholesterol efflux transporter NPC1, we investigated the expression of established biomarkers of lipid-laden macrophages of GD patients, their GCase status, and content on the cytosol facing glucosylceramidase GBA2 and lysosomal integral membrane protein type B (LIMP2), a transporter of newly formed GCase to lysosomes. Livers of 80-week-old Npc1-/- mice showed a partially reduced GCase protein and enzymatic activity. In contrast, GBA2 levels tended to be reciprocally increased with the GCase deficiency. In Npc1-/- liver, increased expression of lysosomal enzymes (cathepsin D, acid ceramidase) was observed as well as increased markers of lipid-stressed macrophages (GPNMB and galectin-3). Immunohistochemistry showed that the latter markers are expressed by lipid laden Kupffer cells. Earlier reported increase of LIMP2 in Npc1-/- liver was confirmed. Unexpectedly, immunohistochemistry showed that LIMP2 is particularly overexpressed in the hepatocytes of the Npc1-/- liver. LIMP2 in these hepatocytes seems not to only localize to (endo)lysosomes. The recent recognition that LIMP2 harbors a cholesterol channel prompts the speculation that LIMP2 in Npc1-/- hepatocytes might mediate export of cholesterol into the bile and thus protects the hepatocytes.
    Keywords:  GCase; GPNMB; LIMP2; NPC; NPC1; lysosome; macrophage; storage
    DOI:  https://doi.org/10.3390/ijms22052532
  4. Cancers (Basel). 2021 Mar 03. pii: 1079. [Epub ahead of print]13(5):
    EphB6 Regulates TFEB-Lysosomal Pathway and Survival of Disseminated Indolent Breast Cancer Cells.
    Manuela Zangrossi, Patrizia Romani, Probir Chakravarty, Colin D H Ratcliffe, Steven Hooper, Martina Dori, Mattia Forcato, Silvio Bicciato, Sirio Dupont, Erik Sahai, Marco Montagner.
      Late relapse of disseminated cancer cells is a common feature of breast and prostate tumors. Several intrinsic and extrinsic factors have been shown to affect quiescence and reawakening of disseminated dormant cancer cells (DDCCs); however, the signals and processes sustaining the survival of DDCCs in a foreign environment are still poorly understood. We have recently shown that crosstalk with lung epithelial cells promotes survival of DDCCs of estrogen receptor-positive (ER+) breast tumors. By using a lung organotypic system and in vivo dissemination assays, here we show that the TFEB-lysosomal axis is activated in DDCCs and that it is modulated by the pro-survival ephrin receptor EphB6. TFEB lysosomal direct targets are enriched in DDCCs in vivo and correlate with relapse in ER+ breast cancer patients. Direct coculture of DDCCs with alveolar type I-like lung epithelial cells and dissemination in the lung drive lysosomal accumulation and EphB6 induction. EphB6 contributes to survival, TFEB transcriptional activity, and lysosome formation in DDCCs in vitro and in vivo. Furthermore, signaling from EphB6 promotes the proliferation of surrounding lung parenchymal cells in vivo. Our data provide evidence that EphB6 is a key factor in the crosstalk between disseminated dormant cancer cells and the lung parenchyma and that the TFEB-lysosomal pathway plays an important role in the persistence of DDCCs.
    Keywords:  EphB6; Ephrin receptors; breast cancer; dormancy; lysosomes; metastasis; tumor microenvironment
    DOI:  https://doi.org/10.3390/cancers13051079
  5. Brain Commun. 2021 ;3(1): fcaa200
    Fronto-temporal dementia risk gene TMEM106B has opposing effects in different lysosomal storage disorders.
    Azucena Perez-Canamas, Hideyuki Takahashi, Jane A Lindborg, Stephen M Strittmatter.
      TMEM106B is a transmembrane protein localized to the endo-lysosomal compartment. Genome-wide association studies have identified TMEM106B as a risk modifier of Alzheimer's disease and frontotemporal lobar degeneration, especially with progranulin haploinsufficiency. We recently demonstrated that TMEM106B loss rescues progranulin null mouse phenotypes including lysosomal enzyme dysregulation, neurodegeneration and behavioural alterations. However, the reason whether TMEM106B is involved in other neurodegenerative lysosomal diseases is unknown. Here, we evaluate the potential role of TMEM106B in modifying the progression of lysosomal storage disorders using progranulin-independent models of Gaucher disease and neuronal ceroid lipofuscinosis. To study Gaucher disease, we employ a pharmacological approach using the inhibitor conduritol B epoxide in wild-type and hypomorphic Tmem106b-/- mice. TMEM106B depletion ameliorates neuronal degeneration and some behavioural abnormalities in the pharmacological model of Gaucher disease, similar to its effect on certain progranulin null phenotypes. In order to examine the role of TMEM106B in neuronal ceroid lipofuscinosis, we crossbred Tmem106b-/- mice with Ppt1-/-, a genetic model of the disease. In contrast to its conduritol B epoxide-rescuing effect, TMEM106B loss exacerbates Purkinje cell degeneration and motor deficits in Ppt1-/- mice. Mechanistically, TMEM106B is known to interact with subunits of the vacuolar ATPase and influence lysosomal acidification. In the pharmacological Gaucher disease model, the acidified lysosomal compartment is enhanced and TMEM106B loss rescues in vivo phenotypes. In contrast, gene-edited neuronal loss of Ppt1 causes a reduction in vacuolar ATPase levels and impairment of the acidified lysosomal compartment, and TMEM106B deletion exacerbates the mouse Ppt1-/- phenotype. Our findings indicate that TMEM106B differentially modulates the progression of the lysosomal storage disorders Gaucher disease and neuronal ceroid lipofuscinosis. The effect of TMEM106B in neurodegeneration varies depending on vacuolar ATPase state and modulation of lysosomal pH. These data suggest TMEM106B as a target for correcting lysosomal pH alterations, and in particular for therapeutic intervention in Gaucher disease and neuronal ceroid lipofuscinosis.
    Keywords:  Gaucher; TMEM106B; lysosome; neuronal ceroid lipofuscinosis; palmitoyl-protein thioesterase 1
    DOI:  https://doi.org/10.1093/braincomms/fcaa200
  6. Biomedicines. 2021 Mar 07. pii: 268. [Epub ahead of print]9(3):
    Exploiting the Potential of Drosophila Models in Lysosomal Storage Disorders: Pathological Mechanisms and Drug Discovery.
    Laura Rigon, Concetta De Filippis, Barbara Napoli, Rosella Tomanin, Genny Orso.
      Lysosomal storage disorders (LSDs) represent a complex and heterogeneous group of rare genetic diseases due to mutations in genes coding for lysosomal enzymes, membrane proteins or transporters. This leads to the accumulation of undegraded materials within lysosomes and a broad range of severe clinical features, often including the impairment of central nervous system (CNS). When available, enzyme replacement therapy slows the disease progression although it is not curative; also, most recombinant enzymes cannot cross the blood-brain barrier, leaving the CNS untreated. The inefficient degradative capability of the lysosomes has a negative impact on the flux through the endolysosomal and autophagic pathways; therefore, dysregulation of these pathways is increasingly emerging as a relevant disease mechanism in LSDs. In the last twenty years, different LSD Drosophila models have been generated, mainly for diseases presenting with neurological involvement. The fruit fly provides a large selection of tools to investigate lysosomes, autophagy and endocytic pathways in vivo, as well as to analyse neuronal and glial cells. The possibility to use Drosophila in drug repurposing and discovery makes it an attractive model for LSDs lacking effective therapies. Here, ee describe the major cellular pathways implicated in LSDs pathogenesis, the approaches available for their study and the Drosophila models developed for these diseases. Finally, we highlight a possible use of LSDs Drosophila models for drug screening studies.
    Keywords:  Drosophila melanogaster; animal model; autophagy; lysosomal storage disorders; lysosome; mucolipidosis; mucopolysaccharidosis; neuronal ceroid lipofuscinosis; sphingolipidosis
    DOI:  https://doi.org/10.3390/biomedicines9030268
  7. Int J Mol Sci. 2021 Mar 09. pii: 2766. [Epub ahead of print]22(5):
    Gene Expression-Related Changes in Morphologies of Organelles and Cellular Component Organization in Mucopolysaccharidoses.
    Lidia Gaffke, Karolina Pierzynowska, Estera Rintz, Zuzanna Cyske, Izabela Giecewicz, Grzegorz Węgrzyn.
      Mucopolysaccharidoses (MPS) are inherited metabolic diseases characterized by accumulation of incompletely degraded glycosaminoglycans (GAGs) in lysosomes. Although primary causes of these diseases are mutations in genes coding for enzymes involved in lysosomal GAG degradation, it was demonstrated that storage of these complex carbohydrates provokes a cascade of secondary and tertiary changes affecting cellular functions. Potentially, this might lead to appearance of cellular disorders which could not be corrected even if the primary cause of the disease is removed. In this work, we studied changes in cellular organelles in MPS fibroblasts relative to control cells. All 11 types and subtypes of MPS were included into this study to obtain a complex picture of changes in organelles in this group of diseases. Two experimental approaches were employed, transcriptomic analyses and electron microscopic assessment of morphology of organelles. We analyzed levels of transcripts of genes grouped into two terms included into the QuickGO database, 'Cellular component organization' (GO:0016043) and 'Cellular anatomical entity' (GO:0110165), to find that number of transcripts with significantly changed levels in MPS fibroblasts vs. controls ranged from 109 to 322 (depending on MPS type) in GO:0016043, and from 70 to 208 in GO:0110165. This dysregulation of expression of genes crucial for proper structures and functions of various organelles was accompanied by severe changes in morphologies of lysosomes, nuclei, mitochondria, Golgi apparatus, and endoplasmic reticulum. Interestingly, some observed changes occurred in all/most MPS types while others were specific to particular disease types/subtypes. We suggest that severe changes in organelles in MPS cells might arise from dysregulation of expression of a battery of genes involved in organelles' structures and functions. Intriguingly, normalization of GAG levels by using recombinant human enzymes specific to different MPS types corrected morphologies of some, but not all, organelles, while it failed to improve regulation of expression of selected genes. These results might suggest reasons for inability of enzyme replacement therapy to correct all MPS symptoms, particularly if initiated at advanced stages of the disease.
    Keywords:  electron microscopy; mucopolysaccharidoses; organelles; transcriptomic analyses
    DOI:  https://doi.org/10.3390/ijms22052766
  8. Neuropharmacology. 2021 Mar 29. pii: S0028-3908(21)00095-2. [Epub ahead of print] 108541
    Inhibiting mTOR activity using AZD2014 increases autophagy in the mouse cerebral cortex.
    Julien Bensalem, Célia Fourrier, Leanne K Hein, Sofia Hassiotis, Christopher G Proud, Timothy J Sargeant.
      Autophagy is a catabolic process that collects and degrades damaged or unwanted cellular materials such as protein aggregates. Defective brain autophagy has been linked to diseases such as Alzheimer's disease. Autophagy is regulated by the protein kinase mTOR (mechanistic target of rapamycin). Although already demonstrated in vitro, it remains contentious whether inhibiting mTOR can enhance autophagy in the brain. To address this, mice were intraperitoneally injected with the mTOR inhibitor AZD2014 for seven days. mTOR complex 1 (mTORC1) activity was decreased in liver and brain. Autophagic activity was increased by AZD2014 in both organs, as measured by immunoblotting for LC3 (microtubule-associated proteins-1A/1B light chain 3B) and measurement of autophagic flux in the cerebral cortex of transgenic mice expressing the EGFP-mRFP-LC3B transgene. mTOR activity was shown to correlate with changes in LC3. Thus, we show it is possible to promote autophagy in the brain using AZD2014, which will be valuable in tackling conditions associated with defective autophagy, especially neurodegeneration.
    Keywords:  AZD2014; Autophagy; HeLa cells; TF-LC3; Vistusertib; brain; lysosome; mTOR; mechanistic target of rapamycin kinase
    DOI:  https://doi.org/10.1016/j.neuropharm.2021.108541
  9. J Invest Dermatol. 2021 Mar 24. pii: S0022-202X(21)01120-9. [Epub ahead of print]
    Long-term effects of sirolimus on human skin TSC2-null fibroblast-like cells.
    Xiong Cai, Qingyuan Fan, Gi Soo Kang, Kelsey Grolig, Xiaoyan Shen, Eric M Billings, Gustavo Pacheco-Rodriguez, Thomas N Darling, Joel Moss.
      Tuberous sclerosis complex (TSC) is an autosomal-dominant disorder characterized by hamartomatous tumors of the skin, kidneys, brain, and lungs. TSC is caused by mutations in the TSC1 and TSC2 genes, which result in hyperactivation of the mechanistic Target of Rapamycin (mTOR), leading to dysregulated cell growth and autophagy. Rapamycin (sirolimus) shrinks TSC tumors but clinical benefits of sirolimus are not sustained after its withdrawal. Here, we studied cellular processes critical for tumor formation and growth, including proliferation and cell size. TSC2-/- and TSC2+/- cells were isolated from TSC skin tumors and normal-appearing skin, respectively. Cells were incubated with sirolimus for 72 hours. Withdrawal of sirolimus from TSC2-/- cells resulted in a highly proliferative phenotype and caused cells to enter the S-phase of the cell cycle, with persistent phosphorylation of mTOR, p70 S6 kinase, ribosomal protein S6, and 4EBP1, decreased cyclin D kinase inhibitors and transient hyperactivation of Akt. Sirolimus modulated the estrogen- and autophagy-dependent volume of TSC2-/- cells. These results suggest that sirolimus may decrease the size of TSC tumors by reducing TSC2-/- cell volume, altering cell cycle and reprogramming TSC2-null cells.
    Keywords:  Lymphangioleiomyomatosis; Sirolimus; Tuberous Sclerosis Complex
    DOI:  https://doi.org/10.1016/j.jid.2021.02.754
  10. Front Cell Neurosci. 2021 ;15 645244
    The P2X7 Receptor in Microglial Cells Modulates the Endolysosomal Axis, Autophagy, and Phagocytosis.
    Keith E Campagno, Claire H Mitchell.
      Microglial cells regulate neural homeostasis by coordinating both immune responses and clearance of debris, and the P2X7 receptor for extracellular ATP plays a central role in both functions. The P2X7 receptor is primarily known in microglial cells for its immune signaling and NLRP3 inflammasome activation. However, the receptor also affects the clearance of extracellular and intracellular debris through modifications of lysosomal function, phagocytosis, and autophagy. In the absence of an agonist, the P2X7 receptor acts as a scavenger receptor to phagocytose material. Transient receptor stimulation induces autophagy and increases LC3-II levels, likely through calcium-dependent phosphorylation of AMPK, and activates microglia to an M1 or mixed M1/M2 state. We show an increased expression of Nos2 and Tnfa and a decreased expression of Chil3 (YM1) from primary cultures of brain microglia exposed to high levels of ATP. Sustained stimulation can reduce lysosomal function in microglia by increasing lysosomal pH and slowing autophagosome-lysosome fusion. P2X7 receptor stimulation can also cause lysosomal leakage, and the subsequent rise in cytoplasmic cathepsin B activates the NLRP3 inflammasome leading to caspase-1 cleavage and IL-1β maturation and release. Support for P2X7 receptor activation of the inflammasome following lysosomal leakage comes from data on primary microglia showing IL-1β release following receptor stimulation is inhibited by cathepsin B blocker CA-074. This pathway bridges endolysosomal and inflammatory roles and may provide a key mechanism for the increased inflammation found in age-dependent neurodegenerations characterized by excessive lysosomal accumulations. Regardless of whether the inflammasome is activated via this lysosomal leakage or the better-known K+-efflux pathway, the inflammatory impact of P2X7 receptor stimulation is balanced between the autophagic reduction of inflammasome components and their increase following P2X7-mediated priming. In summary, the P2X7 receptor modulates clearance of extracellular debris by microglial cells and mediates lysosomal damage that can activate the NLRP3 inflammasome. A better understanding of how the P2X7 receptor alters phagocytosis, lysosomal health, inflammation, and autophagy can lead to therapies that balance the inflammatory and clearance roles of microglial cells.
    Keywords:  NLRP3; P2X7; autophagy; cathepsin B; lysosomes; microglia; neuroinflammation; phagocytosis
    DOI:  https://doi.org/10.3389/fncel.2021.645244
  11. Talanta. 2021 Jun 01. pii: S0039-9140(21)00105-3. [Epub ahead of print]228 122184
    Real-time tracking lysosomal pH changes under heatstroke and redox stress with a novel near-infrared emissive probe.
    Qingfeng Xia, Shumin Feng, Jiaxin Hong, Guoqiang Feng.
      Lysosomes are important subcellular organelles with acidic pH. The change of lysosomal pH can affect the normal function and activity of cells. To conveniently detect and visualize lysosomal pH changes, we designed herein a novel fluorescent probe NIR-Rh-LysopH. The probe is based on a Rhodamine 101 derivative, which was modified to include a fused tetrahydroquinoxaline ring to obtain near-infrared fluorescence and a methylcarbitol moiety to locate the lysosome. Based on the proton-induced spirolactam ring-opening mechanism, NIR-Rh-LysopH showed rapid, selective, sensitive, and reversible near-infrared fluorescence responses around 686 nm (Stokes shift 88 nm) with a pKa value of 5.70. From pH 7.4 to 4.0, about 285 folds of fluorescence enhancement was observed. Cell experiments showed that NIR-Rh-LysopH has low cytotoxicity and excellent lysosome-targeting ability. Moreover, NIR-Rh-LysopH was applied successfully to track lysosomal pH changes induced by drugs (such as chloroquine and dexamethasone), heatstroke, and redox stress. Thus, NIR-Rh-LysopH is very promising for conveniently tracking lysosomal pH changes and studying the related life processes.
    Keywords:  Heatstroke; Lysosomal pH; NIR emissive Probe; Redox stress; Rhodamine
    DOI:  https://doi.org/10.1016/j.talanta.2021.122184
  12. Cancers (Basel). 2021 Mar 12. pii: 1252. [Epub ahead of print]13(6):
    Autophagy Triggers Tamoxifen Resistance in Human Breast Cancer Cells by Preventing Drug-Induced Lysosomal Damage.
    Chiara Actis, Giuliana Muzio, Riccardo Autelli.
      Endocrine resistance is a major complication during treatment of estrogen receptor-positive breast cancer. Although autophagy has recently gained increasing consideration among the causative factors, the link between autophagy and endocrine resistance remains elusive. Here, we investigate the autophagy-based mechanisms of tamoxifen resistance in MCF7 cells. Tamoxifen (Tam) triggers autophagy and affects the lysosomal compartment of MCF7 cells, such that activated autophagy supports disposal of tamoxifen-damaged lysosomes by lysophagy. MCF7 cells resistant to 5 µM tamoxifen (MCF7-TamR) have a higher autophagic flux and an enhanced resistance to Tam-induced lysosomal alterations compared to parental cells, which suggests a correlation between the two events. MCF7-TamR cells overexpress messenger RNAs (mRNAs) for metallothionein 2A and ferritin heavy chain, and they are re-sensitized to Tam by inhibition of autophagy. Overexpressing these proteins in parental MCF7 cells protects lysosomes from Tam-induced damage and preserves viability, while inhibiting autophagy abrogates lysosome protection. Consistently, we also demonstrate that other breast cancer cells that overexpress selected mRNAs encoding iron-binding proteins are less sensitive to Tam-induced lysosomal damage when autophagy is activated. Collectively, our data demonstrate that autophagy triggers Tam resistance in breast cancer cells by favoring the lysosomal relocation of overexpressed factors that restrain tamoxifen-induced lysosomal damage.
    Keywords:  autophagy; breast cancer; endocrine resistance; iron-binding proteins; lysophagy; lysosomal membrane permeabilization
    DOI:  https://doi.org/10.3390/cancers13061252
  13. Int J Mol Sci. 2021 Mar 11. pii: 2850. [Epub ahead of print]22(6):
    Muscle Proteomic Profile before and after Enzyme Replacement Therapy in Late-Onset Pompe Disease.
    Manuela Moriggi, Daniele Capitanio, Enrica Torretta, Pietro Barbacini, Cinzia Bragato, Patrizia Sartori, Maurizio Moggio, Lorenzo Maggi, Marina Mora, Cecilia Gelfi.
      Mutations in the acidic alpha-glucosidase (GAA) coding gene cause Pompe disease. Late-onset Pompe disease (LOPD) is characterized by progressive proximal and axial muscle weakness and atrophy, causing respiratory failure. Enzyme replacement therapy (ERT), based on recombinant human GAA infusions, is the only available treatment; however, the efficacy of ERT is variable. Here we address the question whether proteins at variance in LOPD muscle of patients before and after 1 year of ERT, compared withhealthy age-matched subjects (CTR), reveal a specific signature. Proteins extracted from skeletal muscle of LOPD patients and CTR were analyzed by combining gel based (two-dimensional difference gel electrophoresis) and label-free (liquid chromatography-mass spectrometry) proteomic approaches, and ingenuity pathway analysis. Upstream regulators targeting autophagy and lysosomal tethering were assessed by immunoblotting. 178 proteins were changed in abundance in LOPD patients, 47 of them recovered normal level after ERT. Defects in oxidative metabolism, muscle contractile protein regulation, cytoskeletal rearrangement, and membrane reorganization persisted. Metabolic changes, ER stress and UPR (unfolded protein response) contribute to muscle proteostasis dysregulation with active membrane remodeling (high levels of LC3BII/LC3BI) and accumulation of p62, suggesting imbalance in the autophagic process. Active lysosome biogenesis characterizes both LOPD PRE and POST, unparalleled by molecules involved in lysosome tethering (VAMP8, SNAP29, STX17, and GORASP2) and BNIP3. In conclusion this study reveals a specific signature that suggests ERT prolongation and molecular targets to ameliorate patient's outcome.
    Keywords:  autophagy; mass spectrometry; pompe disease; proteomics; rare disease; sarcopenia
    DOI:  https://doi.org/10.3390/ijms22062850
  14. Curr Genet. 2021 Mar 31.
    Ccr4-Not as a mediator of environmental signaling: a jack of all trades and master of all.
    R Nicholas Laribee.
      The cellular response to environmental exposures, such as nutrient shifts and various forms of stress, requires the integration of the signaling apparatus that senses these environmental changes with the downstream gene regulatory machinery. Delineating this molecular circuitry remains essential for understanding how organisms adapt to environmental flux, and it is critical for determining how dysregulation of these mechanisms causes disease. Ccr4-Not is a highly conserved regulatory complex that controls all aspects of the gene expression process. Recent studies in budding yeast have identified novel roles for Ccr4-Not as a key regulator of core nutrient signaling pathways that control cell growth and proliferation, including signaling through the mechanistic target of rapamycin complex 1 (TORC1) pathway. Herein, I will review the current evidence that implicate Ccr4-Not in nutrient signaling regulation, and I will discuss important unanswered questions that should help guide future efforts to delineate Ccr4-Not's role in linking environmental signaling with the gene regulatory machinery. Ccr4-Not is highly conserved throughout eukaryotes, and increasing evidence indicates it is dysregulated in a variety of diseases. Determining how Ccr4-Not regulates these signaling pathways in model organisms such as yeast will provide a guide for defining how it controls these processes in human cells.
    Keywords:  Ccr4-Not; Lysosome; Nutrient signaling; TORC1; Transcription; V-ATPase
    DOI:  https://doi.org/10.1007/s00294-021-01180-5
  15. Cancers (Basel). 2021 Mar 09. pii: 1181. [Epub ahead of print]13(5):
    Hepatitis B Virus X Protein (HBx) Suppresses Transcription Factor EB (TFEB) Resulting in Stabilization of Integrin Beta 1 (ITGB1) in Hepatocellular Carcinoma Cells.
    Chunyan Zhang, Huan Yang, Liwei Pan, Guangfu Zhao, Ruofei Zhang, Tianci Zhang, Zhixiong Xiao, Ying Tong, Yi Zhang, Richard Hu, Stephen J Pandol, Yuan-Ping Han.
      Hepatitis B virus (HBV) infection is a major etiological risk for the incidence of hepatocellular carcinoma (HCC), and HBV X protein (HBx) is essential for oncogenic transformation. It is not known that if HBx can sabotage the lysosomal system for transformation and tumorigenesis, or its mechanism if it does have an effect. Examining clinical data, we observed that the downregulation of lysosomal components and transcription factor EB (TFEB) was associated with a poor prognosis of HCC patients. In HCC cells, we found that expression of HBx suppressed TFEB, impaired biogenesis of autophagic-lysosome, and promoted cellular dissemination. HBx mediated downregulation of TFEB led to impairment of autophagic/lysosomal biogenesis and flux, and consequently, accumulation of integrin beta 1 (ITGB1) for motility of HCC cells. Conversely, TFEB, in a steady-state condition, through induction of lysosomal biogenesis restrained ITGB1 levels and limited mobility of HCC cells. Specifically, overexpression of TFEB upregulated and activated the cysteine proteases including cathepsin L (CTSL) to degrade ITGB1. Conversely, expression of cystatin A (CSTA) or cystatin B (CSTB), the cellular inhibitors of lysosomal cysteine proteinases, spared ITGB1 from degradation and promoted dissemination of HCC cells. Taken together, this study suggests a potential mechanism for HBV-mediated malignancy, showing that HBx mediated downregulation of TFEB leads to accumulation of ITGB1 for HCC cell migration.
    Keywords:  HBx; ITGB1; TFEB; cysteine protease; hepatocellular carcinoma (HCC); lysosome biogenesis
    DOI:  https://doi.org/10.3390/cancers13051181
  16. Cell Mol Life Sci. 2021 Apr 01.
    A lysosomal enigma CLN5 and its significance in understanding neuronal ceroid lipofuscinosis.
    I Basak, H E Wicky, K O McDonald, J B Xu, J E Palmer, H L Best, S Lefrancois, S Y Lee, L Schoderboeck, S M Hughes.
      Neuronal Ceroid Lipofuscinosis (NCL), also known as Batten disease, is an incurable childhood brain disease. The thirteen forms of NCL are caused by mutations in thirteen CLN genes. Mutations in one CLN gene, CLN5, cause variant late-infantile NCL, with an age of onset between 4 and 7 years. The CLN5 protein is ubiquitously expressed in the majority of tissues studied and in the brain, CLN5 shows both neuronal and glial cell expression. Mutations in CLN5 are associated with the accumulation of autofluorescent storage material in lysosomes, the recycling units of the cell, in the brain and peripheral tissues. CLN5 resides in the lysosome and its function is still elusive. Initial studies suggested CLN5 was a transmembrane protein, which was later revealed to be processed into a soluble form. Multiple glycosylation sites have been reported, which may dictate its localisation and function. CLN5 interacts with several CLN proteins, and other lysosomal proteins, making it an important candidate to understand lysosomal biology. The existing knowledge on CLN5 biology stems from studies using several model organisms, including mice, sheep, cattle, dogs, social amoeba and cell cultures. Each model organism has its advantages and limitations, making it crucial to adopt a combinatorial approach, using both human cells and model organisms, to understand CLN5 pathologies and design drug therapies. In this comprehensive review, we have summarised and critiqued existing literature on CLN5 and have discussed the missing pieces of the puzzle that need to be addressed to develop an efficient therapy for CLN5 Batten disease.
    Keywords:  Batten disease; CLN5; Lysosome; Neurodegeneration; Neuronal ceroid lipofuscinosis
    DOI:  https://doi.org/10.1007/s00018-021-03813-x
  17. Cancer Chemother Pharmacol. 2021 Mar 30.
    Changes in expression of lysosomal membrane proteins in leucocytes of cancer patients treated with tyrosine kinase inhibitors.
    N Pastvova, J Havlasek, P Dolezel, K Kikalova, H Studentova, A Zemankova, B Melichar, P Mlejnek.
      Lysosomal sequestration of weak base drugs has been identified as one of the stress-related mechanisms that trigger in vitro lysosomal biogenesis controlled by transcription factor EB (TFEB). Whether such mechanism can induce lysosomal biogenesis in vivo is unknown. In this study, we addressed the question whether prolonged treatment with sunitinib (SUN) in patients with advanced renal cell carcinoma (n = 22) and with imatinib (IM) in those with gastrointestinal stromal tumor (n = 6) could induce lysosomal biogenesis in leukocytes. Lysosomal biogenesis was monitored using immunoblotting of three lysosomal membrane proteins: lysosome-associated membrane proteins 1 and 2 (LAMP1 and LAMP2) and vacuolar H+-ATPase, B2 subunit (ATP6V1B2). Present results indicate that prolonged treatment with SUN affects LAMP1 and LAMP2 expression only marginally in most patients. In contrast, changes in ATP6V1B2 expression were marked and resembled irregular oscillations. Very similar changes in the expression of lysosomal membrane proteins were also found in IM-treated patients. Conclusion: prolonged treatment of cancer patients with SUN and IM did not induce leucocyte lysosomal biogenesis but dramatically affected expression of ATP6V1B2.
    Keywords:  B2 subunit; Imatinib; LAMP1; LAMP2; Lysosmal membrane proteins; Sunitinib; Vacuolar H+-ATPase
    DOI:  https://doi.org/10.1007/s00280-021-04266-6
  18. Cells. 2021 Mar 21. pii: 696. [Epub ahead of print]10(3):
    Rapid and Progressive Loss of Multiple Retinal Cell Types in Cathepsin D-Deficient Mice-An Animal Model of CLN10 Disease.
    Mahmoud Bassal, Junling Liu, Wanda Jankowiak, Paul Saftig, Udo Bartsch.
      Vision loss is among the characteristic symptoms of neuronal ceroid lipofuscinosis (NCL), a fatal neurodegenerative lysosomal storage disorder. Here, we performed an in-depth analysis of retinal degeneration at the molecular and cellular levels in mice lacking the lysosomal aspartyl protease cathepsin D, an animal model of congenital CLN10 disease. We observed an early-onset accumulation of storage material as indicated by elevated levels of saposin D and subunit C of the mitochondrial ATP synthase. The accumulation of storage material was accompanied by reactive astrogliosis and microgliosis, elevated expression of the autophagy marker sequestosome 1/p62 and a dysregulated expression of several lysosomal proteins. The number of cone photoreceptor cells was reduced as early as at postnatal day 5. At the end stage of the disease, the outer nuclear layer was almost atrophied, and all cones were lost. A significant loss of rod and cone bipolar cells, amacrine cells and ganglion cells was found at advanced stages of the disease. Results demonstrate that cathepsin D deficiency results in an early-onset and rapidly progressing retinal dystrophy that involves all retinal cell types. Data of the present study will serve as a reference for studies aimed at developing treatments for retinal degeneration in CLN10 disease.
    Keywords:  bipolar cells; ganglion cells; lysosomal storage disorder; neuronal ceroid lipofuscinosis; photoreceptor cells; retinal degeneration; storage material
    DOI:  https://doi.org/10.3390/cells10030696
  19. Cancers (Basel). 2021 Mar 15. pii: 1299. [Epub ahead of print]13(6):
    Lysosomal Calcium Channels in Autophagy and Cancer.
    Yi Wu, Peng Huang, Xian-Ping Dong.
      Ca2+ is pivotal intracellular messenger that coordinates multiple cell functions such as fertilization, growth, differentiation, and viability. Intracellular Ca2+ signaling is regulated by both extracellular Ca2+ entry and Ca2+ release from intracellular stores. Apart from working as the cellular recycling center, the lysosome has been increasingly recognized as a significant intracellular Ca2+ store that provides Ca2+ to regulate many cellular processes. The lysosome also talks to other organelles by releasing and taking up Ca2+. In lysosomal Ca2+-dependent processes, autophagy is particularly important, because it has been implicated in many human diseases including cancer. This review will discuss the major components of lysosomal Ca2+ stores and their roles in autophagy and human cancer progression.
    Keywords:  autophagy; calcium; cancer; ion channel; lysosome
    DOI:  https://doi.org/10.3390/cancers13061299
  20. Elife. 2021 Mar 29. pii: e64393. [Epub ahead of print]10
    Disparate bone anabolic cues activate bone formation by regulating the rapid lysosomal degradation of sclerostin protein.
    Nicole R Gould, Katrina M Williams, Humberto C Joca, Olivia M Torre, James S Lyons, Jenna M Leser, Manasa P Srikanth, Marcus Hughes, Ramzi J Khairallah, Ricardo A Feldman, Christopher W Ward, Joseph P Stains.
      The down regulation of sclerostin in osteocytes mediates bone formation in response to mechanical cues and parathyroid hormone (PTH). To date, the regulation of sclerostin has been attributed exclusively to the transcriptional downregulation of the Sost gene hours after stimulation. Using mouse models and rodent cell lines, we describe the rapid, minutes-scale post-translational degradation of sclerostin protein by the lysosome following mechanical load and PTH. We present a model, integrating both new and established mechanically- and hormonally-activated effectors into the regulated degradation of sclerostin by lysosomes. Using a mouse forelimb mechanical loading model, we find transient inhibition of lysosomal degradation or the upstream mechano-signaling pathway controlling sclerostin abundance impairs subsequent load-induced bone formation by preventing sclerostin degradation. We also link dysfunctional lysosomes to aberrant sclerostin regulation using human Gaucher disease iPSCs. These results reveal how bone anabolic cues post-translationally regulate sclerostin abundance in osteocytes to regulate bone formation.
    Keywords:  cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.64393
  21. Nat Aging. 2021 Jan;1(1): 73-86
    Lifelong restriction of dietary branched-chain amino acids has sex-specific benefits for frailty and lifespan in mice.
    Nicole E Richardson, Elizabeth N Konon, Haley S Schuster, Alexis T Mitchell, Colin Boyle, Allison C Rodgers, Megan Finke, Lexington R Haider, Deyang Yu, Victoria Flores, Heidi H Pak, Soha Ahmad, Sareyah Ahmed, Abigail Radcliff, Jessica Wu, Elizabeth M Williams, Lovina Abdi, Dawn S Sherman, Timothy Hacker, Dudley W Lamming.
      Protein restricted (PR) diets promote health and longevity in many species. While the precise components of a PR diet that mediate the beneficial effects to longevity have not been defined, we recently showed that many metabolic effects of PR can be attributed to reduced dietary levels of the branched-chain amino acids (BCAAs) leucine, isoleucine, and valine. Here, we demonstrate that restricting dietary BCAAs increases the survival of two different progeroid mouse models, delays frailty and promotes the metabolic health of wild-type C57BL/6J mice when started in midlife, and leads to a 30% increase in lifespan and a reduction in frailty in male, but not female, wild-type mice when fed lifelong. Our results demonstrate that restricting dietary BCAAs can increase healthspan and longevity in mice, and suggest that reducing dietary BCAAs may hold potential as a translatable intervention to promote healthy aging.
    Keywords:  branched-chain amino acids; healthspan; lifespan; mTOR; mTORC1; progeria; protein restriction; rapamycin
    DOI:  https://doi.org/10.1038/s43587-020-00006-2
  22. J Mol Biol. 2021 Mar 26. pii: S0022-2836(21)00166-2. [Epub ahead of print] 166965
    Identification of new interactions between endolysosomal tethering factors.
    Zsófia Simon-Vecsei, Ármin Sőth, Péter Lőrincz, András Rubics, András Tálas, Péter István Kulcsár, Gábor Juhász.
      Proper functioning of the precisely controlled endolysosomal system is essential for maintaining the homeostasis of the entire cell. Tethering factors play pivotal roles in mediating the fusion of different transport vesicles, such as endosomes or autophagosomes with each other or with lysosomes. In this work, we uncover several new interactions between the endolysosomal tethering factors Rabenosyn-5 (Rbsn) and the HOPS and CORVET complexes. We find that Rbsn binds to the HOPS/CORVET complexes mainly via their shared subunit Vps18 and we mapped this interaction to the 773-854 region of Vps18. Based on genetic rescue experiments, the binding between Rbsn and Vps18 is required for endosomal transport and is dispensable for autophagy. Moreover, Vps18 seems to be important for β1 integrin recycling by binding to Rbsn and its known partner Vps45.
    Keywords:  CORVET; HOPS; Rabenosyn-5; Vps18; Vps45
    DOI:  https://doi.org/10.1016/j.jmb.2021.166965
  23. ACS Cent Sci. 2021 Mar 24. 7(3): 499-506
    Development of Triantennary N-Acetylgalactosamine Conjugates as Degraders for Extracellular Proteins.
    Yaxian Zhou, Peng Teng, Nathan T Montgomery, Xiaolei Li, Weiping Tang.
      Targeted protein degradation (TPD) technology has drawn significant attention from researchers in both academia and industry. It is rapidly evolved as a new therapeutic modality and also a useful chemical tool in selectively depleting various protein targets. As most efforts focus on cytosolic proteins using PROteolysis TArgeting Chimera (PROTAC), LYsosome TArgeting Chimera (LYTAC) recently emerged as a promising technology to deliver extracellular protein targets to lysosome for degradation through the cation-independent mannose-6-phosphate receptor (CI-M6PR). In this study, we exploited the potential of the asialoglycoprotein receptor (ASGPR), a lysosomal targeting receptor specifically expressed on liver cells, for the degradation of extracellular proteins including membrane proteins. The ligand of ASGPR, triantennary N-acetylgalactosamine (tri-GalNAc), was conjugated to biotin, antibodies, or fragments of antibodies to generate a new class of degraders. We demonstrated that the extracellular protein targets could be successfully internalized and delivered into lysosome for degradation in liver cell lines specifically by these degraders. This work will add a new dimension to TPD with cell type specificity.
    DOI:  https://doi.org/10.1021/acscentsci.1c00146
  24. Front Cell Dev Biol. 2021 ;9 636037
    Mechanistic Target of Rapamycin Inhibitors in Renal Cell Carcinoma: Potential, Limitations, and Perspectives.
    Seraina Faes, Nicolas Demartines, Olivier Dormond.
      Several elements highlight the importance of the mechanistic target of rapamycin (mTOR) in the biology of renal cell carcinoma (RCC). mTOR signaling pathway is indeed frequently activated in RCC, inducing cancer cell proliferation and survival. In addition, mTOR promotes tumor angiogenesis and regulates the expression of hypoxia-inducible factors that play an important role in a subset of RCC. Despite mTOR protumorigenic effects, mTOR inhibitors have failed to provide long-lasting anticancer benefits in RCC patients, highlighting the need to readdress their role in the treatment of RCC. This review aims to present the rationale and limitations of targeting mTOR in RCC. Future roles of mTOR inhibitors in the treatment of RCC are also discussed, in particular in the context of immunotherapies.
    Keywords:  HIF-α; angiogenesis; mTOR; rapalogs; renal cell carcinoma
    DOI:  https://doi.org/10.3389/fcell.2021.636037
  25. J Proteome Res. 2021 Apr 02.
    Phosphoproteome Profiling Revealed the Importance of mTOR Inhibition on CDK1 Activation to Further Regulate Cell Cycle Progression.
    Luqi Jin, Yu Chen, Chunlan Yan, Xiaoyuan Guo, Tingting Jiang, Ayiding Guli, Xinghui Song, Qun Wan, Qiang Shu, Shiping Ding.
      The mammalian target of rapamycin (mTOR) functions as a critical regulator of cell cycle progression. However, the underlying mechanism by which mTOR regulates cell cycle progression remains elusive. In this study, we used stable isotope labeling of amino acids in cell culture with a two-step strategy for phosphopeptide enrichment and high-throughput quantitative mass spectrometry to perform a global phosphoproteome analysis of mTOR inhibition by rapamycin. By monitoring the phosphoproteome alterations upon rapamycin treatment, downregulation of mTOR signaling pathway was detected and enriched. Further functional analysis of phosphoproteome revealed the involvement of cell cycle events. Specifically, the elevated profile of cell cycle-related substrates was observed, and the activation of CDK1, MAPK1, and MAPK3 kinases was determined. Second, pathway interrogation using kinase inhibitor treatment confirmed that CDK1 activation operated downstream from mTOR inhibition to further regulate cell cycle progression. Third, we found that the activation of CDK1 following 4-12 h of mTOR inhibition was accompanied by the activation of the Greatwall-endosulfine complex. In conclusion, we presented a high-confidence phosphoproteome map inside the cells upon mTOR inhibition by rapamycin. Our data implied that mTOR inhibition could contribute to CDK1 activation for further regulating cell cycle progression, which was mediated by the Greatwall-endosulfine complex.
    Keywords:  CDK1; cell cycle; mTOR; phosphoproteome; rapamycin
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00848
  26. Cells. 2021 Mar 16. pii: 660. [Epub ahead of print]10(3):
    Key Signaling Pathways in Aging and Potential Interventions for Healthy Aging.
    Mengdi Yu, Hongxia Zhang, Brian Wang, Yinuo Zhang, Xiaoying Zheng, Bei Shao, Qichuan Zhuge, Kunlin Jin.
      Aging is a fundamental biological process accompanied by a general decline in tissue function. Indeed, as the lifespan increases, age-related dysfunction, such as cognitive impairment or dementia, will become a growing public health issue. Aging is also a great risk factor for many age-related diseases. Nowadays, people want not only to live longer but also healthier. Therefore, there is a critical need in understanding the underlying cellular and molecular mechanisms regulating aging that will allow us to modify the aging process for healthy aging and alleviate age-related disease. Here, we reviewed the recent breakthroughs in the mechanistic understanding of biological aging, focusing on the adenosine monophosphate-activated kinase (AMPK), Sirtuin 1 (SIRT1) and mammalian target of rapamycin (mTOR) pathways, which are currently considered critical for aging. We also discussed how these proteins and pathways may potentially interact with each other to regulate aging. We further described how the knowledge of these pathways may lead to new interventions for antiaging and against age-related disease.
    Keywords:  AMPK; SIRT1; aging; health span; intervention; mTOR; senescence; signaling
    DOI:  https://doi.org/10.3390/cells10030660
  27. Biophys J. 2021 Mar 25. pii: S0006-3495(21)00248-4. [Epub ahead of print]
    The Structural Basis of Akt PH Domain Interaction with Calmodulin.
    Jackson Weako, Hyunbum Jang, Ozlem Keskin, Ruth Nussinov, Attila Gursoy.
      Akt plays a key role in the Ras/PI3K/Akt/mTOR signaling pathway. In breast cancer, Akt translocation to the plasma membrane is enabled by the interaction of its pleckstrin homology domain (PHD) with calmodulin (CaM). At the membrane, the conformational change promoted by PIP3 releases CaM and facilitates Thr308 and Ser473 phosphorylation and activation. Here, using modelling and molecular dynamics (MD) simulations we aim to figure out how CaM interacts with Akt's PHD at the atomic level. Our simulations show that the CaM-PHD interaction is thermodynamically stable and involves a β-strand, rather than an α-helix, in agreement with NMR data, and that electrostatic and hydrophobic interactions are critical. PHD interacts with CaM lobes; however, multiple modes are possible. IP4, the polar head of PIP3, weakens the CaM-PHD interaction, implicating the release mechanism at the plasma membrane. Recently, we unraveled the mechanism of PI3Kα activation at the atomistic level and the structural basis for Ras role in the activation. Here, our atomistic structural data clarify the mechanism of how CaM interacts, delivers, and releases Akt - the next node in the Ras/PI3K pathway - at the plasma membrane.
    Keywords:  Akt activation; CaM; MD Simulation; PH domain; PI3K; Phosphorylation; Ras; plasma membrane; signaling pathway
    DOI:  https://doi.org/10.1016/j.bpj.2021.03.018
  28. Cells. 2021 Mar 04. pii: 542. [Epub ahead of print]10(3):
    Modulation of Endosome Function, Vesicle Trafficking and Autophagy by Human Herpesviruses.
    Eduardo I Tognarelli, Antonia Reyes, Nicolás Corrales, Leandro J Carreño, Susan M Bueno, Alexis M Kalergis, Pablo A González.
      Human herpesviruses are a ubiquitous family of viruses that infect individuals of all ages and are present at a high prevalence worldwide. Herpesviruses are responsible for a broad spectrum of diseases, ranging from skin and mucosal lesions to blindness and life-threatening encephalitis, and some of them, such as Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), are known to be oncogenic. Furthermore, recent studies suggest that some herpesviruses may be associated with developing neurodegenerative diseases. These viruses can establish lifelong infections in the host and remain in a latent state with periodic reactivations. To achieve infection and yield new infectious viral particles, these viruses require and interact with molecular host determinants for supporting their replication and spread. Important sets of cellular factors involved in the lifecycle of herpesviruses are those participating in intracellular membrane trafficking pathways, as well as autophagic-based organelle recycling processes. These cellular processes are required by these viruses for cell entry and exit steps. Here, we review and discuss recent findings related to how herpesviruses exploit vesicular trafficking and autophagy components by using both host and viral gene products to promote the import and export of infectious viral particles from and to the extracellular environment. Understanding how herpesviruses modulate autophagy, endolysosomal and secretory pathways, as well as other prominent trafficking vesicles within the cell, could enable the engineering of novel antiviral therapies to treat these viruses and counteract their negative health effects.
    Keywords:  ESCRT; autophagy; endocytosis; exocytosis; human herpesviruses; lysosomes; trans-Golgi network; viral
    DOI:  https://doi.org/10.3390/cells10030542
  29. FASEB J. 2021 May;35(5): e21349
    Pathological mechanisms of vacuolar aggregate myopathy arising from a Casq1 mutation.
    Amy D Hanna, Chang Seok Lee, Lyle Babcock, Hui Wang, Joseph Recio, Susan L Hamilton.
      Mice with a mutation (D244G, DG) in calsequestrin 1 (CASQ1), analogous to a human mutation in CASQ1 associated with a delayed onset human myopathy (vacuolar aggregate myopathy), display a progressive myopathy characterized by decreased activity, decreased ability of fast twitch muscles to generate force and low body weight after one year of age. The DG mutation causes CASQ1 to partially dissociate from the junctional sarcoplasmic reticulum (SR) and accumulate in the endoplasmic reticulum (ER). Decreased junctional CASQ1 reduces SR Ca2+ release. Muscles from older DG mice display ER stress, ER expansion, increased mTOR signaling, inadequate clearance of aggregated proteins by the proteasomes, and elevation of protein aggregates and lysosomes. This study suggests that the myopathy associated with the D244G mutation in CASQ1 is driven by CASQ1 mislocalization, reduced SR Ca2+ release, CASQ1 misfolding/aggregation and ER stress. The subsequent maladaptive increase in protein synthesis and decreased protein aggregate clearance are likely to contribute to disease progression.
    Keywords:  EC coupling; ER stress; calsequestrin; myopathy; sarcoplasmic reticulum
    DOI:  https://doi.org/10.1096/fj.202001653RR
  30. Nat Commun. 2021 Apr 01. 12(1): 2029
    Differential controls of MAIT cell effector polarization by mTORC1/mTORC2 via integrating cytokine and costimulatory signals.
    Huishan Tao, Yun Pan, Shuai Chu, Lei Li, Jinhai Xie, Peng Wang, Shimeng Zhang, Srija Reddy, John W Sleasman, Xiao-Ping Zhong.
      Mucosal-associated invariant T (MAIT) cells have important functions in immune responses against pathogens and in diseases, but mechanisms controlling MAIT cell development and effector lineage differentiation remain unclear. Here, we report that IL-2/IL-15 receptor β chain and inducible costimulatory (ICOS) not only serve as lineage-specific markers for IFN-γ-producing MAIT1 and IL-17A-producing MAIT17 cells, but are also important for their differentiation, respectively. Both IL-2 and IL-15 induce mTOR activation, T-bet upregulation, and subsequent MAIT cell, especially MAIT1 cell, expansion. By contrast, IL-1β induces more MAIT17 than MAIT1 cells, while IL-23 alone promotes MAIT17 cell proliferation and survival, but synergizes with IL-1β to induce strong MAIT17 cell expansion in an mTOR-dependent manner. Moreover, mTOR is dispensable for early MAIT cell development, yet pivotal for MAIT cell effector differentiation. Our results thus show that mTORC2 integrates signals from ICOS and IL-1βR/IL-23R to exert a crucial role for MAIT17 differentiation, while the IL-2/IL-15R-mTORC1-T-bet axis ensures MAIT1 differentiation.
    DOI:  https://doi.org/10.1038/s41467-021-22162-8
  31. Plant Cell. 2020 Jan 10. 32(1): 69-80
    Phosphorus Availability Regulates TORC1 Signaling via LST8 in Chlamydomonas[OPEN].
    Inmaculada Couso, María Esther Pérez-Pérez, Megan M Ford, Enrique Martínez-Force, Leslie M Hicks, James G Umen, José L Crespo.
      Target of rapamycin complex 1 (TORC1) is a central regulator of cell growth. It balances anabolic and catabolic processes in response to nutrients, growth factors, and energy availability. Nitrogen- and carbon-containing metabolites have been shown to activate TORC1 in yeast, animals, and plants. Here, we show that phosphorus (P) regulates TORC1 signaling in the model green alga Chlamydomonas (Chlamydomonas reinhardtii) via LST8, a conserved TORC1 subunit that interacts with the kinase domain of TOR. P starvation results in a sharp decrease in LST8 abundance and downregulation of TORC1 activity. A hypomorphic lst8 mutation resulted in decreased LST8 abundance, and it both reduced TORC1 signaling and altered the cellular response to P starvation. Additionally, we found that LST8 levels and TORC1 activity were not properly regulated in a mutant defective in the transcription factor PSR1, which is the major mediator of P deprivation responses in Chlamydomonas. Unlike wild-type cells, the psr1 mutant failed to downregulate LST8 abundance and TORC1 activity when under P limitation. These results identify PSR1 as an upstream regulator of TORC1 and demonstrate that TORC1 is a key component in P signaling in Chlamydomonas.
    DOI:  https://doi.org/10.1105/tpc.19.00179
  32. Gut. 2021 Mar 30. pii: gutjnl-2020-322660. [Epub ahead of print]
    Loss of ARID1A activates mTOR signaling and SOX9 in gastric adenocarcinoma-rationale for targeting ARID1A deficiency.
    Xiaochuan Dong, Shumei Song, Yuan Li, Yibo Fan, Lulu Wang, Ruiping Wang, Longfei Huo, Ailing Scott, Yan Xu, Melissa Pool Pizzi, Lang Ma, Ying Wang, Jiangkang Jin, Wei Zhao, Xiaodan Yao, Randy L Johnson, Linghua Wang, Zhenning Wang, Guang Peng, Jaffer A Ajani.
      BACKGROUND: Gastric adenocarcinoma (GAC) is a lethal disease with limited therapeutic options. Genetic alterations in chromatin remodelling gene AT-rich interactive domain 1A (ARID1A) and mTOR pathway activation occur frequently in GAC. Targeting the mechanistic target of rapamycin (mTOR) pathway in unselected patients has failed to show survival benefit. A deeper understanding of GAC might identify a subset that can benefit from mTOR inhibition.METHODS: Genomic alterations in ARID1A were analysed in GAC. Mouse gastric epithelial cells from CK19-Cre-Arid1Afl/fl and wild-type mice were used to determine the activation of oncogenic genes due to loss of Arid1A. Functional studies were performed to determine the significance of loss of ARID1A and the sensitivity of ARID1A-deficient cancer cells to mTOR inhibition in GAC.
    RESULTS: More than 30% of GAC cases had alterations (mutations or deletions) of ARID1A and ARID1A expression was negatively associated with phosphorylation of S6 and SOX9 in GAC tissues and patient-derived xenografts (PDXs). Activation of mTOR signalling (increased pS6) and SOX9 nuclear expression were strongly increased in Arid1A-/- mouse gastric tissues which could be curtailed by RAD001, an mTOR inhibitor. Knockdown of ARID1A in GAC cell lines increased pS6 and nuclear SOX9 and increased sensitivity to an mTOR inhibitor which was further amplified by its combination with fluorouracil both in vitro and in vivo in PDXs.
    CONCLUSIONS: The loss of ARID1A activates pS6 and SOX9 in GAC, which can be effectively targeted by an mTOR inhibitor. Therefore, our studies suggest a new therapeutic strategy of clinically targeting the mTOR pathway in patients with GAC with ARID1A deficiency.
    Keywords:  cancer; gastric cancer; gastric neoplasia; gastrointestinal cancer; gene expression
    DOI:  https://doi.org/10.1136/gutjnl-2020-322660
  33. Autophagy. 2021 Mar 28.
    Autophagosome content profiling reveals receptor-specific cargo candidates.
    Susanne Zellner, Christian Behrends.
      Selective autophagy receptors have been implicated in the degradation of cellular constituents of various size and rigidity. However, the identity of protein cargo have largely remained elusive. In our recent study, we combined limited proteolysis-enhanced proximity biotinylation and organelle enrichment with quantitative proteomics to map the inventory of autophagosomes in a manner dependent on six different selective autophagy receptors, namely SQSTM1/p62, NBR1, CALCOCO2/NDP52, OPTN, TAX1BP1 and TOLLIP. Conducting this approach under basal and proteostasis-challenged conditions in mammalian cells led to the identification of various new autophagy substrates of which some were degraded through endosomal microautophagy rather than canonical autophagy dependent on the receptors TOLLIP and SQSTM1, respectively.
    Keywords:  (5-6): Selective autophagy receptors; APEX2; TOLLIP; endosomal microautophagy; proteostasis challenges; proximity proteomics
    DOI:  https://doi.org/10.1080/15548627.2021.1909410
  34. Cells. 2021 Mar 05. pii: 572. [Epub ahead of print]10(3):
    Rapid Identification of New Biomarkers for the Classification of GM1 Type 2 Gangliosidosis Using an Unbiased 1H NMR-Linked Metabolomics Strategy.
    Benita C Percival, Yvonne L Latour, Cynthia J Tifft, Martin Grootveld.
      Biomarkers currently available for the diagnosis, prognosis, and therapeutic monitoring of GM1 gangliosidosis type 2 (GM1T2) disease are mainly limited to those discovered in targeted proteomic-based studies. In order to identify and establish new, predominantly low-molecular-mass biomarkers for this disorder, we employed an untargeted, multi-analyte approach involving high-resolution 1H NMR analysis coupled to a range of multivariate analysis and computational intelligence technique (CIT) strategies to explore biomolecular distinctions between blood plasma samples collected from GM1T2 and healthy control (HC) participants (n = 10 and 28, respectively). The relationship of these differences to metabolic mechanisms underlying the pathogenesis of GM1T2 disorder was also investigated. 1H NMR-linked metabolomics analyses revealed significant GM1T2-mediated dysregulations in ≥13 blood plasma metabolites (corrected p < 0.04), and these included significant upregulations in 7 amino acids, and downregulations in lipoprotein-associated triacylglycerols and alanine. Indeed, results acquired demonstrated a profound distinctiveness between the GM1T2 and HC profiles. Additionally, employment of a genome-scale network model of human metabolism provided evidence that perturbations to propanoate, ethanol, amino-sugar, aspartate, seleno-amino acid, glutathione and alanine metabolism, fatty acid biosynthesis, and most especially branched-chain amino acid degradation (p = 10-12-10-5) were the most important topologically-highlighted dysregulated pathways contributing towards GM1T2 disease pathology. Quantitative metabolite set enrichment analysis revealed that pathological locations associated with these dysfunctions were in the order fibroblasts > Golgi apparatus > mitochondria > spleen ≈ skeletal muscle ≈ muscle in general. In conclusion, results acquired demonstrated marked metabolic imbalances and alterations to energy demand, which are consistent with GM1T2 disease pathogenesis mechanisms.
    Keywords:  GM1 gangliosidosis; NMR-based metabolomics; biomarkers; lysosomal storage disorders; metabolite set enrichment analysis; nuclear magnetic resonance (NMR) analysis; validation
    DOI:  https://doi.org/10.3390/cells10030572
  35. Dev Cell. 2021 Mar 23. pii: S1534-5807(21)00204-5. [Epub ahead of print]
    BCKDK regulates the TCA cycle through PDC in the absence of PDK family during embryonic development.
    Lia Heinemann-Yerushalmi, Lital Bentovim, Neta Felsenthal, Ron Carmel Vinestock, Nofar Michaeli, Sharon Krief, Alon Silberman, Marina Cohen, Shifra Ben-Dor, Ori Brenner, Rebecca Haffner-Krausz, Maxim Itkin, Sergey Malitsky, Ayelet Erez, Elazar Zelzer.
      Pyruvate dehydrogenase kinases (PDK1-4) inhibit the TCA cycle by phosphorylating pyruvate dehydrogenase complex (PDC). Here, we show that PDK family is dispensable for murine embryonic development and that BCKDK serves as a compensatory mechanism by inactivating PDC. First, we knocked out all four Pdk genes one by one. Surprisingly, Pdk total KO embryos developed and were born in expected ratios but died by postnatal day 4 because of hypoglycemia or ketoacidosis. Moreover, PDC was phosphorylated in these embryos, suggesting that another kinase compensates for PDK family. Bioinformatic analysis implicated branched-chain ketoacid dehydrogenase kinase (Bckdk), a key regulator of branched-chain amino acids (BCAAs) catabolism. Indeed, knockout of Bckdk and Pdk family led to the loss of PDC phosphorylation, an increase in PDC activity and pyruvate entry into the TCA cycle, and embryonic lethality. These findings reveal a regulatory crosstalk hardwiring BCAA and glucose catabolic pathways, which feed the TCA cycle.
    Keywords:  BCAA; BCKDK; PDC; PDK; TCA cycle; embryogenesis; glycolysis
    DOI:  https://doi.org/10.1016/j.devcel.2021.03.007
  36. Rev Neurosci. 2021 Mar 30.
    Defects in early secretory pathway transport machinery components and neurodevelopmental disorders.
    Bor Luen Tang.
      The early secretory pathway, provisionally comprising of vesicular traffic between the endoplasmic reticulum (ER) and the Golgi apparatus, occurs constitutively in mammalian cells. Critical for a constant supply of secretory and plasma membrane (PM) materials, the pathway is presumably essential for general cellular function and survival. Neurons exhibit a high intensity in membrane dynamics and protein/lipid trafficking, with differential and polarized trafficking towards the somatodendritic and axonal PM domains. Mutations in genes encoding early secretory pathway membrane trafficking machinery components are known to result in neurodevelopmental or neurological disorders with disease manifestation in early life. Here, such rare disorders associated with autosomal recessive mutations in coat proteins, membrane tethering complexes and membrane fusion machineries responsible for trafficking in the early secretory pathway are summarily discussed. These mutations affected genes encoding subunits of coat protein complex I and II, subunits of transport protein particle (TRAPP) complexes, members of the YIP1 domain family (YIPF) and a SNAP receptor (SNARE) family member. Why the ubiquitously present and constitutively acting early secretory pathway machinery components could specifically affect neurodevelopment is addressed, with the plausible underlying disease etiologies and neuropathological mechanisms resulting from these mutations explored.
    Keywords:  SNARE; YIP1-YIF1 complex; coat protein II (COPII); neurodevelopmental disorder; transport protein particle (TRAPP) complex
    DOI:  https://doi.org/10.1515/revneuro-2021-0020
  37. Front Pharmacol. 2021 ;12 628690
    Activation of PI3K/AKT/mTOR Pathway Causes Drug Resistance in Breast Cancer.
    Chao Dong, Jiao Wu, Yin Chen, Jianyun Nie, Ceshi Chen.
      Although chemotherapy, targeted therapy and endocrine therapy decrease rate of disease recurrence in most breast cancer patients, many patients exhibit acquired resistance. Hyperactivation of the PI3K/AKT/mTOR pathway is associated with drug resistance and cancer progression. Currently, a number of drugs targeting PI3K/AKT/mTOR are being investigated in clinical trials by combining them with standard therapies to overcome acquired resistance in breast cancer. In this review, we summarize the critical role of the PI3K/AKT/mTOR pathway in drug resistance, the development of PI3K/AKT/mTOR inhibitors, and strategies to overcome acquired resistance to standard therapies in breast cancer.
    Keywords:  PI3K; chemotherapy; drug resistance; endocrine therapy; targeted therapy
    DOI:  https://doi.org/10.3389/fphar.2021.628690
  38. Sci Rep. 2021 Mar 31. 11(1): 7300
    Hydrogen peroxide (H2O2) mediated activation of mTORC2 increases intracellular Na+ concentration in the renal medullary thick ascending limb of Henle.
    Nadezhda N Zheleznova, Vikash Kumar, Theresa Kurth, Allen W Cowley.
      Hydrogen peroxide (H2O2) production in the renal outer medulla is an important determinant of renal medullary blood flow and blood pressure (BP) salt-sensitivity in Dahl salt-sensitive (SS) rats. The mechanisms and pathways responsible for these actions are poorly understood. Recently, we have discovered that the mTOR complex 2 (mTORC2) plays a critical role in BP salt-sensitivity of SS rats by regulating Na+ homeostasis. PP242, an inhibitor of mTORC1/2 pathways exhibits potent natriuretic actions and completely prevented salt-induced hypertension in SS rats. In the present study, we have found that chronic infusion of H2O2 into the single remaining kidney of Sprague Dawley (SD) rats (3 days) stimulated the functional marker (pAKTSer473/AKT) of mTORC2 activity measured by Western Blot analysis. No changes in mTORC1 activity in OM were observed as determined by pS6Ser235/236/S6. Using fluorescent microscopy and the Na+ sensitive dye Sodium Green, we have shown that H2O2 (100 µM added in the bath) increased intracellular sodium concentration ([Na+]i) in renal medullary thick ascending limbs (mTALs) isolated from SD rats. These responses were almost completely abolished by pretreatment of mTAL with 10 µM PP242, indicating that mTORC1/2 pathways were involved in the H2O2 induced increase of [Na+]i. mTAL cell volume remained unchanged (± 1%) by H2O2 as determined by 3D reconstruction confocal laser scanning microscopy techniques. Consistent with the microscopy data, Western Blot analysis of proteins obtained from freshly isolated mTAL treated with 100 µM H2O2 exhibited increased activity/phosphorylation of AKT (pAKTSer473/AKT) that was inhibited by PP242. This was associated with increased protein activity of the apical membrane cotransporter Na+-K+-2Cl- (NKCC2) and the Na/H exchanger (NHE-3). Na+-K+-ATPase activity was increased as reflected an increase in the ratio of pNa+-K+-ATPaseSer16 to total Na+-K+-ATPase. Overall, the results indicate that H2O2 mediated activation of mTORC2 plays a key role in transducing the observed increases of cytosolic [Na+]i despite associated increases of basolateral pump activity.
    DOI:  https://doi.org/10.1038/s41598-021-86678-1
  39. Int J Mol Sci. 2021 Mar 17. pii: 3064. [Epub ahead of print]22(6):
    Therapeutic Potential of AAV1-Rheb(S16H) Transduction against Neurodegenerative Diseases.
    Youngpyo Nam, Gyeong Joon Moon, Sang Ryong Kim.
      Neurotrophic factors (NTFs) are essential for cell growth, survival, synaptic plasticity, and maintenance of specific neuronal population in the central nervous system. Multiple studies have demonstrated that alterations in the levels and activities of NTFs are related to the pathology and symptoms of neurodegenerative disorders, such as Parkinson's disease (PD), Alzheimer's disease (AD), and Huntington's disease. Hence, the key molecule that can regulate the expression of NTFs is an important target for gene therapy coupling adeno-associated virus vector (AAV) gene. We have previously reported that the Ras homolog protein enriched in brain (Rheb)-mammalian target of rapamycin complex 1 (mTORC1) axis plays a vital role in preventing neuronal death in the brain of AD and PD patients. AAV transduction using a constitutively active form of Rheb exerts a neuroprotective effect through the upregulation of NTFs, thereby promoting the neurotrophic interaction between astrocytes and neurons in AD conditions. These findings suggest the role of Rheb as an important regulator of the regulatory system of NTFs to treat neurodegenerative diseases. In this review, we present an overview of the role of Rheb in neurodegenerative diseases and summarize the therapeutic potential of AAV serotype 1 (AAV1)-Rheb(S16H) transduction in the treatment of neurodegenerative disorders, focusing on diseases, such as AD and PD.
    Keywords:  Alzheimer’s disease; Parkinson’s disease; Rheb(S16H); neurodegenerative disease; neurotrophic factor
    DOI:  https://doi.org/10.3390/ijms22063064
  40. Brain Pathol. 2021 Mar 30. e12949
    Upregulation of the pathogenic transcription factor SPI1/PU.1 in tuberous sclerosis complex and focal cortical dysplasia by oxidative stress.
    Till S Zimmer, Anatoly Korotkov, Susan Zwakenberg, Floor E Jansen, Fried J T Zwartkruis, Nicholas R Rensing, Michael Wong, Angelika Mühlebner, Erwin A van Vliet, Eleonora Aronica, James D Mills.
      Tuberous sclerosis complex (TSC) is a congenital disorder characterized by cortical malformations and concomitant epilepsy caused by loss-of-function mutations in the mTOR suppressors TSC1 or TSC2. While the underlying molecular changes caused by mTOR activation in TSC have previously been investigated, the drivers of these transcriptional change have not been fully elucidated. A better understanding of the perturbed transcriptional regulation could lead to the identification of novel pathways for therapeutic intervention not only in TSC, but other genetic epilepsies in which mTOR activation plays a key role, such as focal cortical dysplasia 2b (FCD). Here, we analyzed RNA sequencing data from cortical tubers and a tsc2-/- zebrafish. We identified differential expression of the transcription factors (TFs) SPI1/PU.1, IRF8, GBX2, and IKZF1 of which SPI1/PU.1 and IRF8 targets were enriched among the differentially expressed genes. Furthermore, for SPI1/PU.1 these findings were conserved in TSC zebrafish model. Next, we confirmed overexpression of SPI1/PU.1 on the RNA and protein level in a separate cohort of surgically resected TSC tubers and FCD tissue, in fetal TSC tissue, and a Tsc1GFAP-/- mouse model of TSC. Subsequently, we validated the expression of SPI1/PU.1 in dysmorphic cells with mTOR activation in TSC tubers. In fetal TSC, we detected SPI1/PU.1 expression prenatally and elevated RNA Spi1 expression in Tsc1GFAP-/- mice before the development of seizures. Finally, in vitro, we identified that in astrocytes and neurons SPI1 transcription was driven by H2 O2 -induced oxidative stress, independent of mTOR. We identified SPI1/PU.1 as a novel TF involved in the pro-inflammatory gene expression of malformed cells in TSC and FCD 2b. This transcriptional program is activated in response to oxidative stress and already present prenatally. Importantly, SPI1/PU.1 protein appears to be strictly limited to malformed cells, as we did not find SPI1/PU.1 protein expression in mice nor in our in vitro models.
    Keywords:  brain inflammation; epilepsy; focal cortical dysplasia; mTOR; oxidative stress; tuberous sclerosis complex
    DOI:  https://doi.org/10.1111/bpa.12949
  41. Int J Mol Sci. 2021 Mar 07. pii: 2689. [Epub ahead of print]22(5):
    ATP13A2 Regulates Cellular α-Synuclein Multimerization, Membrane Association, and Externalization.
    Jianmin Si, Chris Van den Haute, Evy Lobbestael, Shaun Martin, Sarah van Veen, Peter Vangheluwe, Veerle Baekelandt.
      ATP13A2, a late endo-/lysosomal polyamine transporter, is implicated in a variety of neurodegenerative diseases, including Parkinson's disease and Kufor-Rakeb syndrome, an early-onset atypical form of parkinsonism. Loss-of-function mutations in ATP13A2 result in lysosomal deficiency as a consequence of impaired lysosomal export of the polyamines spermine/spermidine. Furthermore, accumulating evidence suggests the involvement of ATP13A2 in regulating the fate of α-synuclein, such as cytoplasmic accumulation and external release. However, no consensus has yet been reached on the mechanisms underlying these effects. Here, we aimed to gain more insight into how ATP13A2 is linked to α-synuclein biology in cell models with modified ATP13A2 activity. We found that loss of ATP13A2 impairs lysosomal membrane integrity and induces α-synuclein multimerization at the membrane, which is enhanced in conditions of oxidative stress or exposure to spermine. In contrast, overexpression of ATP13A2 wildtype (WT) had a protective effect on α-synuclein multimerization, which corresponded with reduced αsyn membrane association and stimulation of the ubiquitin-proteasome system. We also found that ATP13A2 promoted the secretion of α-synuclein through nanovesicles. Interestingly, the catalytically inactive ATP13A2 D508N mutant also affected polyubiquitination and externalization of α-synuclein multimers, suggesting a regulatory function independent of the ATPase and transport activity. In conclusion, our study demonstrates the impact of ATP13A2 on α-synuclein multimerization via polyamine transport dependent and independent functions.
    Keywords:  ATP13A2; Parkinson’s disease; spermine; α-synuclein; α-synuclein multimerization
    DOI:  https://doi.org/10.3390/ijms22052689
  42. Front Mol Biosci. 2021 ;8 636560
    The Role of Ribosomal Protein S6 Kinases in Plant Homeostasis.
    Irabonosi Obomighie, Kestutis Lapenas, Billy E Murphy, Alexander M C Bowles, Ulrike Bechtold, Filippo Prischi.
      The p70 ribosomal S6 kinase (S6K) family is a group of highly conserved kinases in eukaryotes that regulates cell growth, cell proliferation, and stress response via modulating protein synthesis and ribosomal biogenesis. S6Ks are downstream effectors of the Target of Rapamycin (TOR) pathway, which connects nutrient and energy signaling to growth and homeostasis, under normal and stress conditions. The plant S6K family includes two isoforms, S6K1 and S6K2, which, despite their high level of sequence similarity, have distinct functions and regulation mechanisms. Significant advances on the characterization of human S6Ks have occurred in the past few years, while studies on plant S6Ks are scarce. In this article, we review expression and activation of the two S6K isoforms in plants and we discuss their roles in mediating responses to stresses and developmental cues.
    Keywords:  abiotic stress; cell signaling; plant homeostasis; ribosomal protein S6 kinases; stress response
    DOI:  https://doi.org/10.3389/fmolb.2021.636560
  43. J Cell Biol. 2021 Jun 07. pii: e202002084. [Epub ahead of print]220(6):
    Synaptic activity controls autophagic vacuole motility and function in dendrites.
    Vineet Vinay Kulkarni, Anip Anand, Jessica Brandt Herr, Christina Miranda, Maria Chalokh Vogel, Sandra Maday.
      Macroautophagy (hereafter "autophagy") is a lysosomal degradation pathway that is important for learning and memory, suggesting critical roles for autophagy at the neuronal synapse. Little is known, however, about the molecular details of how autophagy is regulated with synaptic activity. Here, we used live-cell confocal microscopy to define the autophagy pathway in primary hippocampal neurons under various paradigms of synaptic activity. We found that synaptic activity regulates the motility of autophagic vacuoles (AVs) in dendrites. Stimulation of synaptic activity dampens AV motility, whereas silencing synaptic activity induces AV motility. Activity-dependent effects on dendritic AV motility are local and reversible. Importantly, these effects are compartment specific, occurring in dendrites and not in axons. Most strikingly, synaptic activity increases the presence of degradative autolysosomes in dendrites and not in axons. On the basis of our findings, we propose a model whereby synaptic activity locally controls AV dynamics and function within dendrites that may regulate the synaptic proteome.
    DOI:  https://doi.org/10.1083/jcb.202002084
  44. Biomolecules. 2021 Mar 09. pii: 400. [Epub ahead of print]11(3):
    Lysosomal Functions in Glia Associated with Neurodegeneration.
    Conlan Kreher, Jacob Favret, Malabika Maulik, Daesung Shin.
      Lysosomes are cellular organelles that contain various acidic digestive enzymes. Despite their small size, they have multiple functions. Lysosomes remove or recycle unnecessary cell parts. They repair damaged cellular membranes by exocytosis. Lysosomes also sense cellular energy status and transmit signals to the nucleus. Glial cells are non-neuronal cells in the nervous system and have an active role in homeostatic support for neurons. In response to dynamic cues, glia use lysosomal pathways for the secretion and uptake of regulatory molecules, which affect the physiology of neighboring neurons. Therefore, functional aberration of glial lysosomes can trigger neuronal degeneration. Here, we review lysosomal functions in oligodendrocytes, astrocytes, and microglia, with emphasis on neurodegeneration.
    Keywords:  astrocytes; autophagy; glia; lysosomes; microglia; neurodegenerative diseases; oligodendrocytes; synapse
    DOI:  https://doi.org/10.3390/biom11030400
  45. Plant Cell. 2021 Feb 04. pii: koab043. [Epub ahead of print]
    TOR coordinates nucleotide availability with ribosome biogenesis in plants.
    Michael Busche, M Regina Scarpin, Robert Hnasko, Jacob O Brunkard.
      TARGET OF RAPAMYCIN (TOR) is a conserved eukaryotic Ser/Thr protein kinase that coordinates growth and metabolism with nutrient availability. We conducted a medium-throughput functional genetic screen to discover essential genes that promote TOR activity in plants, and identified a critical regulatory enzyme, cytosolic phosphoribosyl pyrophosphate (PRPP) synthetase (PRS4). PRS4 synthesizes cytosolic PRPP, a key upstream metabolite in nucleotide synthesis and salvage pathways. We found that prs4 knockouts are embryo-lethal in Arabidopsis thaliana, and that silencing PRS4 expression in Nicotiana benthamiana causes pleiotropic developmental phenotypes, including dwarfism, aberrant leaf shape, and delayed flowering. Transcriptomic analysis revealed that ribosome biogenesis is among the most strongly repressed processes in prs4 knockdowns. Building on these results, we discovered that TOR activity is inhibited by chemical or genetic disruption of nucleotide biosynthesis, but that this effect can be reversed by supplying plants with nucleobases. Finally, we show that TOR transcriptionally promotes nucleotide biosynthesis to support the demands of ribosomal RNA synthesis. We propose that TOR coordinates ribosome biogenesis with nucleotide availability in plants to maintain metabolic homeostasis and support growth.
    DOI:  https://doi.org/10.1093/plcell/koab043
  46. Cells. 2021 Mar 12. pii: 630. [Epub ahead of print]10(3):
    The Uncovered Function of the Drosophila GBA1a-Encoded Protein.
    Or Cabasso, Sumit Paul, Gali Maor, Metsada Pasmanik-Chor, Wouter Kallemeijn, Johannes Aerts, Mia Horowitz.
      Human GBA1 encodes lysosomal acid β-glucocerebrosidase (GCase), which hydrolyzes cleavage of the beta-glucosidic linkage of glucosylceramide (GlcCer). Mutations in this gene lead to reduced GCase activity, accumulation of glucosylceramide and glucosylsphingosine, and development of Gaucher disease (GD). Drosophila melanogaster has two GBA1 orthologs. Thus far, GBA1b was documented as a bone fide GCase-encoding gene, while the role of GBA1a encoded protein remained unclear. In the present study, we characterized a mutant variant of the fly GBA1a, which underwent ERAD and mildly activated the UPR machinery. RNA-seq analyses of homozygous mutant flies revealed upregulation of inflammation-associated as well as of cell-cycle related genes and reduction in programmed cell death (PCD)-associated genes, which was confirmed by qRT-PCR. We also observed compromised cell death in the midgut of homozygous larvae and a reduction in pupation. Our results strongly indicated that GBA1a-encoded protein plays a role in midgut maturation during larvae development.
    Keywords:  GBA1; Gaucher disease; acid β-glucocerebrosidase; inflammation; unfolded protein response
    DOI:  https://doi.org/10.3390/cells10030630
  47. Cell Metab. 2021 Mar 26. pii: S1550-4131(21)00113-3. [Epub ahead of print]
    Serine metabolism antagonizes antiviral innate immunity by preventing ATP6V0d2-mediated YAP lysosomal degradation.
    Long Shen, Penghui Hu, Yanan Zhang, Zemin Ji, Xiao Shan, Lina Ni, Na Ning, Jing Wang, He Tian, Guanghou Shui, Yukang Yuan, Guoli Li, Hui Zheng, Xiang-Ping Yang, Dandan Huang, Xiangling Feng, Mulin Jun Li, Zhe Liu, Ting Wang, Qiujing Yu.
      Serine metabolism promotes tumor oncogenesis and regulates immune cell functions, but whether it also contributes to antiviral innate immunity is unknown. Here, we demonstrate that virus-infected macrophages display decreased expression of serine synthesis pathway (SSP) enzymes. Suppressing the SSP key enzyme phosphoglycerate dehydrogenase (PHGDH) by genetic approaches or by treatment with the pharmaceutical inhibitor CBR-5884 and by exogenous serine restriction enhanced IFN-β-mediated antiviral innate immunity in vitro and in vivo. Mechanistic experiments showed that virus infection or serine metabolism deficiency increased the expression of the V-ATPase subunit ATP6V0d2 by inhibiting S-adenosyl methionine-dependent H3K27me3 occupancy at the promoter. ATP6V0d2 promoted YAP lysosomal degradation to relieve YAP-mediated blockade of the TBK1-IRF3 axis and, thus, enhance IFN-β production. These findings implicate critical functions of PHGDH and the key immunometabolite serine in blunting antiviral innate immunity and also suggest manipulation of serine metabolism as a therapeutic strategy against virus infection.
    Keywords:  ATP6V0d2; H3K27me3; PHGDH; SAM; YAP; antiviral; serine metabolism
    DOI:  https://doi.org/10.1016/j.cmet.2021.03.006
  48. Genes (Basel). 2021 Mar 29. pii: 505. [Epub ahead of print]12(4):
    LRRK2 at the Crossroad of Aging and Parkinson's Disease.
    Eun-Mi Hur, Byoung Dae Lee.
      Parkinson's disease (PD) is a heterogeneous neurodegenerative disease characterized by the progressive loss of dopaminergic neurons in the substantia nigra pars compacta and the widespread occurrence of proteinaceous inclusions known as Lewy bodies and Lewy neurites. The etiology of PD is still far from clear, but aging has been considered as the highest risk factor influencing the clinical presentations and the progression of PD. Accumulating evidence suggests that aging and PD induce common changes in multiple cellular functions, including redox imbalance, mitochondria dysfunction, and impaired proteostasis. Age-dependent deteriorations in cellular dysfunction may predispose individuals to PD, and cellular damages caused by genetic and/or environmental risk factors of PD may be exaggerated by aging. Mutations in the LRRK2 gene cause late-onset, autosomal dominant PD and comprise the most common genetic causes of both familial and sporadic PD. LRRK2-linked PD patients show clinical and pathological features indistinguishable from idiopathic PD patients. Here, we review cellular dysfunctions shared by aging and PD-associated LRRK2 mutations and discuss how the interplay between the two might play a role in PD pathologies.
    Keywords:  LRRK2; Parkinson’s disease; ROS; aging; autophagy; lysosome; mitochondria
    DOI:  https://doi.org/10.3390/genes12040505
  49. Bio Protoc. 2021 Mar 05. 11(5): e3936
    Retention Using Selective Hooks (RUSH) Cargo Sorting Assay for Protein Vesicle Tracking in HeLa Cells.
    Natalia Pacheco-Fernandez, Mehrshad Pakdel, Julia Von Blume.
      Monitoring vesicle trafficking is an excellent tool for the evaluation of protein dynamics in living cells. Such study is key for the understanding of protein sorting and secretion. Recent developments in microscopy, as well as new methodologies developed to study synchronized trafficking of proteins, allowed a better understanding of signaling, regulation and trafficking dynamics at the secretory pathway. One of the most helpful tools so far developed is the Retention Using Selective Hooks (RUSH) system, a methodology that facilitates the evaluation of synchronized cargo trafficking by monitoring fluorescent vesicles in cells upon biotin addition. Here we present a protocol that allows the quantitative evaluation of protein cargo trafficking at different fixed time points and an analytic approach that enables a better examination of specific cargo trafficking dynamics at the secretory pathway. Graphic abstract: Schematic representation of RUSH sorting assay in mammalian cells.
    Keywords:  Cargo sorting; Confocal microscopy; Protein trafficking; RUSH; Vesicle tracking
    DOI:  https://doi.org/10.21769/BioProtoc.3936
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