bims-lysosi Biomed News
on Lysosomes and signaling
Issue of 2022‒02‒20
forty papers selected by
Stephanie Fernandes
Max Planck Institute for Biology of Ageing
  1. Lysosomal cystine mobilization shapes the response of TORC1 and tissue growth to fasting.
  2. Lysosomal ceramides regulate Cathepsin B-mediated processing of saposin C and glucocerebrosidase activity.
  3. A lysosomal biogenesis map reveals the cargo spectrum of yeast vacuolar protein targeting pathways.
  4. Regulation of lysosomal trafficking of progranulin by sortilin and prosaposin.
  5. An AMPKα2-specific phospho-switch controls lysosomal targeting for activation.
  6. Impact of Organelle Transport Deficits on Mitophagy and Autophagy in Niemann-Pick Disease Type C.
  7. The Role of the Lysosomal Cl-/H+ Antiporter ClC-7 in Osteopetrosis and Neurodegeneration.
  8. MTOR-mediates hepatic lipid metabolism through an autophagic SNARE complex.
  9. Autophagy and Lysosomal Functionality in CMT2B Fibroblasts Carrying the RAB7K126R Mutation.
  10. NPRL2 Inhibition of mTORC1 Controls Sodium Channel Expression and Brain Amino Acid Homeostasis.
  11. Assessment of FDA-Approved Drugs as a Therapeutic Approach for Niemann-Pick Disease Type C1 Using Patient-Specific iPSC-Based Model Systems.
  12. Bur1 functions with TORC1 for vacuole-mediated cell cycle progression.
  13. ATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1.
  14. ETV2 regulates PARP-1 binding protein to induce ER stress-mediated death in tuberin-deficient cells.
  15. Predominant Role of mTOR Signaling in Skin Diseases with Therapeutic Potential.
  16. PERK activation by SB202190 ameliorates amyloidogenesis via the TFEB-induced autophagy-lysosomal pathway.
  17. Mitochondrial Dynamics and Mitochondria-Lysosome Contacts in Neurogenetic Diseases.
  18. mTOR Signaling Components in Tumor Mechanobiology.
  19. Non-canonical roles of ATG8 for TFEB activation.
  20. CDK6 increases glycolysis and suppresses autophagy by mTORC1-HK2 pathway activation in cervical cancer cells.
  21. Exosomal miR-673-5p from fibroblasts promotes Schwann cell-mediated peripheral neuron myelination by targeting the TSC2/mTORC1/SREBP2 axis.
  22. Downregulation of NAGLU in VEC Increases Abnormal Accumulation of Lysosomes and Represents a Predictive Biomarker in Early Atherosclerosis.
  23. Peripheral Inflammatory Cytokine Signature Mirrors Motor Deficits in Mucolipidosis IV.
  24. Improved Cathepsin Probes for Sensitive Molecular Imaging.
  25. Modulating mTOR Signaling as a Promising Therapeutic Strategy for Atherosclerosis.
  26. Involvement of Gtr1p in the oxidative stress response in yeast Saccharomyces cerevisiae.
  27. Defective Cystinosin, Aberrant Autophagy-Endolysosome Pathways, and Storage Disease: Towards Assembling the Puzzle.
  28. Loss of miR-34 in Drosophila dysregulates protein translation and protein turnover in the aging brain.
  29. Ultrarapid lytic granule release from CTLs activates Ca2+-dependent synaptic resistance pathways in melanoma cells.
  30. Effect of FKBP12-Derived Intracellular Peptides on Rapamycin-Induced FKBP-FRB Interaction and Autophagy.
  31. A generation of human induced pluripotent stem cell line (MUi031-A) from a type-3 Gaucher disease patient carrying homozygous mutation on GBA1 gene.
  32. Cathepsin B - A Neuronal Death Mediator in Alzheimer's Disease Leads to Neurodegeneration.
  33. Role of ARHGEF3 as a GEF and mTORC2 Regulator.
  34. Chaperone Therapy in Fabry Disease.
  35. The AUTOTAC chemical biology platform for targeted protein degradation via the autophagy-lysosome system.
  36. Rag GTPases regulate cellular amino acid homeostasis.
  37. Linking a nuclear lncRNA to cytoplasmic lysosome integrity and cell death.
  38. TOR complex 2 contributes to regulation of gene expression via inhibiting Gcn5 recruitment to subtelomeric and DNA replication stress genes.
  39. p70 S6 kinase as a therapeutic target in cancers: More than just an mTOR effector.
  40. Lung-selective mRNA delivery of synthetic lipid nanoparticles for the treatment of pulmonary lymphangioleiomyomatosis.
  1. Science. 2022 Feb 18. 375(6582): eabc4203
    Lysosomal cystine mobilization shapes the response of TORC1 and tissue growth to fasting.
    Patrick Jouandin, Zvonimir Marelja, Yung-Hsin Shih, Andrey A Parkhitko, Miriam Dambowsky, John M Asara, Ivan Nemazanyy, Christian C Dibble, Matias Simons, Norbert Perrimon.
      Adaptation to nutrient scarcity involves an orchestrated response of metabolic and signaling pathways to maintain homeostasis. We find that in the fat body of fasting Drosophila, lysosomal export of cystine coordinates remobilization of internal nutrient stores with reactivation of the growth regulator target of rapamycin complex 1 (TORC1). Mechanistically, cystine was reduced to cysteine and metabolized to acetyl-coenzyme A (acetyl-CoA) by promoting CoA metabolism. In turn, acetyl-CoA retained carbons from alternative amino acids in the form of tricarboxylic acid cycle intermediates and restricted the availability of building blocks required for growth. This process limited TORC1 reactivation to maintain autophagy and allowed animals to cope with starvation periods. We propose that cysteine metabolism mediates a communication between lysosomes and mitochondria, highlighting how changes in diet divert the fate of an amino acid into a growth suppressive program.
    DOI:  https://doi.org/10.1126/science.abc4203
  2. Hum Mol Genet. 2022 Feb 19. pii: ddac047. [Epub ahead of print]
    Lysosomal ceramides regulate Cathepsin B-mediated processing of saposin C and glucocerebrosidase activity.
    Myung Jong Kim, Hyunkyung Jeong, Dimitri Krainc.
      Variants in multiple lysosomal enzymes increase Parkinson's disease risk, including the genes encoding glucocerebrosidase (GCase), acid sphingomyelinase and galactosylceramidase. Each of these enzymes generate ceramide by hydrolysis of sphingolipids in lysosomes, but the role of this common pathway in PD pathogenesis has not yet been explored. Variations in GBA1, the gene encoding GCase, are the most common genetic risk factor for Parkinson's disease (PD). The lysosomal enzyme Cathepsin B has recently been implicated as an important genetic modifier of disease penetrance in individuals harboring GBA1 variants, suggesting a mechanistic link between these enzymes. Here, we found that ceramide activates cathepsin B, and identified a novel role for cathepsin B in mediating prosaposin cleavage to form saposin C, the lysosomal coactivator of GCase. Interestingly, this pathway was disrupted in Parkin-linked PD models, and upon treatment with inhibitor of acid sphingomyelinase which resulted in decreased ceramide production. Conversely, increasing ceramide production by inhibiting acid ceramidase activity, was sufficient to upregulate cathepsin B and saposin C-mediated activation of GCase. These results highlight a mechanistic link between ceramide and cathepsin B in regulating GCase activity, and suggest that targeting lysosomal ceramide or cathepsin B represents an important therapeutic strategy for activating GCase in Parkinson's and related disorders.
    DOI:  https://doi.org/10.1093/hmg/ddac047
  3. J Cell Biol. 2022 Apr 04. pii: e202107148. [Epub ahead of print]221(4):
    A lysosomal biogenesis map reveals the cargo spectrum of yeast vacuolar protein targeting pathways.
    Sebastian Eising, Bianca Esch, Mike Wälte, Prado Vargas Duarte, Stefan Walter, Christian Ungermann, Maria Bohnert, Florian Fröhlich.
      The lysosome is the major catabolic organelle in the cell that has been established as a key metabolic signaling center. Mutations in many lysosomal proteins have catastrophic effects and cause neurodegeneration, cancer, and age-related diseases. The vacuole is the lysosomal analog of Saccharomyces cerevisiae that harbors many evolutionary conserved proteins. Proteins reach vacuoles via the Vps10-dependent endosomal vacuolar protein sorting pathway, via the alkaline phosphatase (ALP or AP-3) pathway, and via the cytosol-to-vacuole transport (CVT) pathway. A systematic understanding of the cargo spectrum of each pathway is completely lacking. Here, we use quantitative proteomics of purified vacuoles to generate the yeast lysosomal biogenesis map. This dataset harbors information on the cargo-receptor relationship of almost all vacuolar proteins. We map binding motifs of Vps10 and the AP-3 complex and identify a novel cargo of the CVT pathway under nutrient-rich conditions. Our data show how organelle purification and quantitative proteomics can uncover fundamental insights into organelle biogenesis.
    DOI:  https://doi.org/10.1083/jcb.202107148
  4. Brain Commun. 2022 ;4(1): fcab310
    Regulation of lysosomal trafficking of progranulin by sortilin and prosaposin.
    Huan Du, Xiaolai Zhou, Tuancheng Feng, Fenghua Hu.
      Haploinsufficiency of the progranulin protein is a leading cause of frontotemporal lobar degeneration. Accumulating evidence support a crucial role of progranulin in the lysosome. Progranulin comprises 7.5 granulin repeats and is known to traffic to lysosomes via direct interactions with prosaposin or sortilin. Within the lysosome, progranulin gets processed into granulin peptides. Here, we report that sortilin and prosaposin independently regulate lysosomal trafficking of progranulin in vivo. The deletion of either prosaposin or sortilin alone results in a significant decrease in the ratio of granulin peptides versus full-length progranulin in mouse brain lysates. This decrease is further augmented by the deficiency of both prosaposin and sortilin. A concomitant increase in the levels of secreted progranulin in the serum was observed. Interestingly, while the deletion of both prosaposin and sortilin totally abolishes lysosomal localization of progranulin in neurons, it has a limited effect on lysosomal trafficking of progranulin in microglia, suggesting the existence of a novel sortilin and prosaposin independent pathway mediating progranulin lysosomal trafficking. In summary, our studies shed light on the regulation of lysosomal trafficking and processing of progranulin in vivo.
    Keywords:  frontotemporal lobar degeneration; lysosome; progranulin; prosaposin; sortilin
    DOI:  https://doi.org/10.1093/braincomms/fcab310
  5. Cell Rep. 2022 02 15. pii: S2211-1247(22)00086-9. [Epub ahead of print]38(7): 110365
    An AMPKα2-specific phospho-switch controls lysosomal targeting for activation.
    Kaitlin R Morrison, William J Smiles, Naomi X Y Ling, Ashfaqul Hoque, Gabrielle Shea, Kevin R W Ngoei, Dingyi Yu, Lisa Murray-Segal, John W Scott, Sandra Galic, Bruce E Kemp, Janni Petersen, Jonathan S Oakhill.
      AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin complex 1 (mTORC1) are metabolic kinases that co-ordinate nutrient supply with cell growth. AMPK negatively regulates mTORC1, and mTORC1 reciprocally phosphorylates S345/7 in both AMPK α-isoforms. We report that genetic or torin1-induced loss of α2-S345 phosphorylation relieves suppression of AMPK signaling; however, the regulatory effect does not translate to α1-S347 in HEK293T or MEF cells. Dephosphorylation of α2-S345, but not α1-S347, transiently targets AMPK to lysosomes, a cellular site for activation by LKB1. By mass spectrometry, we find that α2-S345 is basally phosphorylated at 2.5-fold higher stoichiometry than α1-S347 in HEK293T cells and, unlike α1, phosphorylation is partially retained after prolonged mTORC1 inhibition. Loss of α2-S345 phosphorylation in endogenous AMPK fails to sustain growth of MEFs under amino acid starvation conditions. These findings uncover an α2-specific mechanism by which AMPK can be activated at lysosomes in the absence of changes in cellular energy.
    Keywords:  AMPK; energy homeostasis; kinase; lysosome; mTORC1; metabolic signaling; phosphorylation
    DOI:  https://doi.org/10.1016/j.celrep.2022.110365
  6. Cells. 2022 Feb 01. pii: 507. [Epub ahead of print]11(3):
    Impact of Organelle Transport Deficits on Mitophagy and Autophagy in Niemann-Pick Disease Type C.
    Maik Liedtke, Christin Völkner, Andreas Hermann, Moritz J Frech.
      Defective mitochondria are pathophysiological features of a number of neurodegenerative diseases. Here, we investigated mitochondrial dysfunction in the context of the rare lysosomal storage diseases Niemann-Pick disease type C1 and type C2 (NP-C1 and NP-C2). Mutations in either the NPC1 or NPC2 gene lead to cholesterol accumulation in late endosomes and lysosomes, resulting in impaired cholesterol homeostasis. The extent to which this may lead to mitochondrial dysfunction has been poorly studied so far. Therefore, we investigated the morphology, function, and transport of mitochondria, as well as their degradation via mitophagy, in a disease-associated human neural cell model of NP-C. By performing live cell imaging, we observed markedly reduced mitochondrial transport, although morphology and function were not appreciably altered. However, we observed a defective mitophagy induction shown by a reduced capability to elevate parkin expression and engulf mitochondria in autophagosomes after treatment with carbonyl cyanide 3-chlorophenylhydrazone (CCCP). This was accompanied by defects in autophagy induction, exhibited by a hampered p62 expression and progression, shown by increased LC3BII levels and a defective fusion of autophagosomes and lysosomes. The latter might have been additionally influenced by the observed reduced lysosomal transport. Hence, we hypothesized that a reduced recycling of mitochondria contributes to the pathophysiology of NP-C.
    Keywords:  NPC1; NPC2; iPSCs; induced pluripotent stem cells; lysosomal storage disorder; mitochondria
    DOI:  https://doi.org/10.3390/cells11030507
  7. Cells. 2022 Jan 21. pii: 366. [Epub ahead of print]11(3):
    The Role of the Lysosomal Cl-/H+ Antiporter ClC-7 in Osteopetrosis and Neurodegeneration.
    Giovanni Zifarelli.
      CLC proteins comprise Cl- channels and anion/H+ antiporters involved in several fundamental physiological processes. ClC-7 is a lysosomal Cl-/H+ antiporter that together with its beta subunit Ostm1 has a critical role in the ionic homeostasis of lysosomes and of the osteoclasts' resorption lacuna, although the specific underlying mechanism has so far remained elusive. Mutations in ClC-7 cause osteopetrosis, but also a form of lysosomal storage disease and neurodegeneration. Interestingly, both loss-of- and gain-of-function mutations of ClC-7 can be pathogenic, but the mechanistic implications of this finding are still unclear. This review will focus on the recent advances in our understanding of the biophysical properties of ClC-7 and of its role in human diseases with a focus on osteopetrosis and neurodegeneration.
    Keywords:  bone; chloride transport; lysosomal storage disease; lysosome; organellar transporter; osteoclast; osteopetrosis; proton transport
    DOI:  https://doi.org/10.3390/cells11030366
  8. Autophagy. 2022 Feb 17. 1-3
    MTOR-mediates hepatic lipid metabolism through an autophagic SNARE complex.
    Qinqin Ouyang, Rong Liu.
      The STX17-SNAP29-VAMP8 SNARE complex mediates autophagosome-lysosome fusion. Our recent study showed that MTOR directly phosphorylates VAMP8's T48 residue in nutrient-rich conditions. Phosphorylated VAMP8 inhibits autophagosome-lysosome fusion by blocking STX17-SNAP29-VAMP8 SNARE complex formation. Our study also showed that SCFD1 is a previously unrecognized macroautophagy/autophagy regulatory protein, which can be recruited by VAMP8 (in its non-phosphorylated form) to autolysosomes, where it promotes STX17-SNAP29-VAMP8 complex assembly - and consequently promotes autophagosome-lysosome fusion. Moreover, we observed that mice harboring a phosphomimic VAMP8 variant accumulate aberrantly high lipid levels in their livers. VAMP8 phosphorylation can disrupt autophagosome-lysosome fusion in the liver and thereby dysregulate lipid metabolism. Beyond providing insights into the molecular mechanisms of autophagosome maturation, our study suggests that modulating autophagic SNARE function may help treat liver lipid disorders.
    Keywords:  Autophagosome-lysosome fusion; MTORC1; SCFD1; VAMP8; phosphorylation
    DOI:  https://doi.org/10.1080/15548627.2022.2037853
  9. Cells. 2022 Jan 31. pii: 496. [Epub ahead of print]11(3):
    Autophagy and Lysosomal Functionality in CMT2B Fibroblasts Carrying the RAB7K126R Mutation.
    Roberta Romano, Victoria Stefania Del Fiore, Paola Saveri, Ilaria Elena Palamà, Chiara Pisciotta, Davide Pareyson, Cecilia Bucci, Flora Guerra.
      Charcot-Marie-Tooth type 2B (CMT2B) disease is a dominant axonal peripheral neuropathy caused by five mutations in the RAB7A gene. Autophagy and late endocytic trafficking were already characterized in CMT2B. Indeed, impairment of autophagy and an increase in lysosomal degradative activity were found in cells expressing the mutant proteins. Recently, we described a novel RAB7 mutation associated with predominantly motor CMT2 and impaired EGFR trafficking. With the aim to analyze the autophagy process and lysosomal activity in CMT2B fibroblasts carrying the p.K126R RAB7 novel mutation and to investigate further the causes of the different phenotype, we have performed Western blot, immunofluorescence and cytometric analyses monitoring autophagic markers and endocytic proteins. Moreover, we investigated lipophagy by analyzing accumulation of lipid droplets and their co-localization with endolysosomal degradative compartments. We found that cells expressing the RAB7K126R mutant protein were characterized by impairment of autophagy and lipophagy processes and by a moderate increase in lysosomal activity compared to the previously studied cells carrying the RAB7V162M mutation. Thus, we concluded that EGFR trafficking alterations and a moderate increase in lysosomal activity with concomitant impairment of autophagy could induce the specific predominantly motor phenotype observed in K126R patients.
    Keywords:  Charcot-Marie-Tooth; RAB7A; autophagy; lipid droplets; lipophagy; lysosome
    DOI:  https://doi.org/10.3390/cells11030496
  10. eNeuro. 2022 Feb 11. pii: ENEURO.0317-21.2022. [Epub ahead of print]
    NPRL2 Inhibition of mTORC1 Controls Sodium Channel Expression and Brain Amino Acid Homeostasis.
    Jeremy B Hui, Jose Cesar Hernandez Silva, Mari Carmen Pelaez, Myriam Sévigny, Janani Priya Venkatasubramani, Quentin Plumereau, Mohamed Chahine, Christophe D Proulx, Chantelle F Sephton, Paul A Dutchak.
      Genetic mutations in nitrogen permease regulator-like 2 (NPRL2) are associated with a wide spectrum of familial focal epilepsies, autism, and sudden unexpected death of epileptics (SUDEP), but the mechanisms by which NPRL2 contributes to these effects are not well known. NPRL2 is a requisite subunit of the Gap Activity TOward Rags 1 (GATOR1) complex, which functions as a negative regulator of mammalian Target Of Rapamycin Complex 1 (mTORC1) kinase when intracellular amino acids are low. Here we show that loss of NPRL2 expression in mouse excitatory glutamatergic neurons causes seizures prior to death, consistent with SUDEP in humans with epilepsy. Additionally, the absence of NPRL2 expression increases mTORC1-dependent signal transduction and significantly alters amino acid homeostasis in the brain. Loss of NPRL2 reduces dendritic branching and increases the strength of electrically stimulated action potentials in neurons. The increased action potential strength is consistent with elevated expression of epilepsy-linked, voltage-gated sodium channels in the NPRL2-deficient brain. Targeted deletion of NPRL2 in primary neurons increases the expression of sodium channel Scn1A, whereas treatment with the pharmacological mTORC1 inhibitor called rapamycin prevents Scn1A upregulation. These studies demonstrate a novel role of NPRL2 and mTORC1 signaling in the regulation of sodium channels, which can contribute to seizures and early lethality.Significance StatementNPRL2 is a requisite subunit of the epilepsy-linked GATOR1 complex that functions as a negative regulator of mTORC1 kinase when intracellular amino acids are limited. Here we report the generation and characterization of a new neurological model of GATOR1-dependent mTORopathy, caused by the loss of NPRL2 function in glutamatergic neurons. Loss of NPRL2 increases mTORC1 signal transduction, significantly alters amino acid homeostasis in the brain, and causes SUDEP. In addition, loss of NPRL2 increases the strength of electrically stimulated action potentials and the expression of epilepsy-linked sodium channels. These data reveal an unanticipated link between intracellular amino acid signaling by NPRL2 and a novel mTORC1-dependent regulation of sodium-channel expression in epilepsy.
    Keywords:  GATOR1; NPRL2; epilepsy; mTORC1; neurometabolism; sodium channels
    DOI:  https://doi.org/10.1523/ENEURO.0317-21.2022
  11. Cells. 2022 Jan 18. pii: 319. [Epub ahead of print]11(3):
    Assessment of FDA-Approved Drugs as a Therapeutic Approach for Niemann-Pick Disease Type C1 Using Patient-Specific iPSC-Based Model Systems.
    Christin Völkner, Supansa Pantoom, Maik Liedtke, Jan Lukas, Andreas Hermann, Moritz J Frech.
      Niemann-Pick type C1 (NP-C1) is a fatal, progressive neurodegenerative disease caused by mutations in the NPC1 gene. Mutations of NPC1 can result in a misfolded protein that is subsequently marked for proteasomal degradation. Such loss-of-function mutations lead to cholesterol accumulation in late endosomes and lysosomes. Pharmacological chaperones (PCs) are described to protect misfolded proteins from proteasomal degradation and are being discussed as a treatment strategy for NP-C1. Here, we used a combinatorial approach of high-throughput in silico screening of FDA-approved drugs and in vitro biochemical assays to identify potential PCs. The effects of the hit compounds identified by molecular docking were compared in vitro with 25-hydroxycholesterol (25-HC), which is known to act as a PC for NP-C1. We analyzed cholesterol accumulation, NPC1 protein content, and lysosomal localization in patient-specific fibroblasts, as well as in neural differentiated and hepatocyte-like cells derived from patient-specific induced pluripotent stem cells (iPSCs). One compound, namely abiraterone acetate, showed comparable results to 25-HC and restored NPC1 protein level, corrected the intracellular localization of NPC1, and consequently decreased cholesterol accumulation in NPC1-mutated fibroblasts and iPSC-derived neural differentiated and hepatocyte-like cells. The discovered PC altered not only the pathophysiological phenotype of cells carrying the I1061T mutation- known to be responsive to treatment with PCs-but an effect was also observed in cells carrying other NPC1 missense mutations. Therefore, we hypothesize that the PCs studied here may serve as an effective treatment strategy for a large group of NP-C1 patients.
    Keywords:  NPC1; in silico screening; induced pluripotent stem cells; molecular docking; pharmacological chaperones
    DOI:  https://doi.org/10.3390/cells11030319
  12. EMBO Rep. 2022 Feb 15. e53477
    Bur1 functions with TORC1 for vacuole-mediated cell cycle progression.
    Yui Jin, Natsuko Jin, Yu Oikawa, Ron Benyair, Michiko Koizumi, Thomas E Wilson, Yoshinori Ohsumi, Lois S Weisman.
      The vacuole/lysosome plays essential roles in the growth and proliferation of many eukaryotic cells via the activation of target of rapamycin complex 1 (TORC1). Moreover, the yeast vacuole/lysosome is necessary for progression of the cell division cycle, in part via signaling through the TORC1 pathway. Here, we show that an essential cyclin-dependent kinase, Bur1, plays a critical role in cell cycle progression in cooperation with TORC1. A mutation in BUR1 combined with a defect in vacuole inheritance shows a synthetic growth defect. Importantly, the double mutant, as well as a bur1-267 mutant on its own, has a severe defect in cell cycle progression from G1 phase. In further support that BUR1 functions with TORC1, mutation of bur1 alone results in high sensitivity to rapamycin, a TORC1 inhibitor. Mechanistic insight for Bur1 function comes from the findings that Bur1 directly phosphorylates Sch9, a target of TORC1, and that both Bur1 and TORC1 are required for the activation of Sch9. Together, these discoveries suggest that multiple signals converge on Sch9 to promote cell cycle progression.
    Keywords:   SCH9 ; SGV1 ; lysosome; rapamycin; yeast
    DOI:  https://doi.org/10.15252/embr.202153477
  13. Nat Commun. 2022 Feb 18. 13(1): 967
    ATF-4 and hydrogen sulfide signalling mediate longevity in response to inhibition of translation or mTORC1.
    Cyril Statzer, Jin Meng, Richard Venz, Monet Bland, Stacey Robida-Stubbs, Krina Patel, Dunja Petrovic, Raffaella Emsley, Pengpeng Liu, Ianessa Morantte, Cole Haynes, William B Mair, Alban Longchamp, Milos R Filipovic, T Keith Blackwell, Collin Y Ewald.
      Inhibition of the master growth regulator mTORC1 (mechanistic target of rapamycin complex 1) slows ageing across phyla, in part by reducing protein synthesis. Various stresses globally suppress protein synthesis through the integrated stress response (ISR), resulting in preferential translation of the transcription factor ATF-4. Here we show in C. elegans that inhibition of translation or mTORC1 increases ATF-4 expression, and that ATF-4 mediates longevity under these conditions independently of ISR signalling. ATF-4 promotes longevity by activating canonical anti-ageing mechanisms, but also by elevating expression of the transsulfuration enzyme CTH-2 to increase hydrogen sulfide (H2S) production. This H2S boost increases protein persulfidation, a protective modification of redox-reactive cysteines. The ATF-4/CTH-2/H2S pathway also mediates longevity and increased stress resistance from mTORC1 suppression. Increasing H2S levels, or enhancing mechanisms that H2S influences through persulfidation, may represent promising strategies for mobilising therapeutic benefits of the ISR, translation suppression, or mTORC1 inhibition.
    DOI:  https://doi.org/10.1038/s41467-022-28599-9
  14. Life Sci Alliance. 2022 May;pii: e202201369. [Epub ahead of print]5(5):
    ETV2 regulates PARP-1 binding protein to induce ER stress-mediated death in tuberin-deficient cells.
    Shikshya Shrestha, Anthony Lamattina, Gustavo Pacheco-Rodriguez, Julie Ng, Xiaoli Liu, Abhijeet Sonawane, Jewel Imani, Weiliang Qiu, Kosmas Kosmas, Pierce Louis, Anne Hentschel, Wendy K Steagall, Rieko Onishi, Helen Christou, Elizabeth P Henske, Kimberly Glass, Mark A Perrella, Joel Moss, Kelan Tantisira, Souheil El-Chemaly.
      Lymphangioleiomyomatosis (LAM) is a rare progressive disease, characterized by mutations in the tuberous sclerosis complex genes (TSC1 or TSC2) and hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1). Here, we report that E26 transformation-specific (ETS) variant transcription factor 2 (ETV2) is a critical regulator of Tsc2-deficient cell survival. ETV2 nuclear localization in Tsc2-deficient cells is mTORC1-independent and is enhanced by spleen tyrosine kinase (Syk) inhibition. In the nucleus, ETV2 transcriptionally regulates poly(ADP-ribose) polymerase 1 binding protein (PARPBP) mRNA and protein expression, partially reversing the observed down-regulation of PARPBP expression induced by mTORC1 blockade during treatment with both Syk and mTORC1 inhibitors. In addition, silencing Etv2 or Parpbp in Tsc2-deficient cells induced ER stress and increased cell death in vitro and in vivo. We also found ETV2 expression in human cells with loss of heterozygosity for TSC2, lending support to the translational relevance of our findings. In conclusion, we report a novel ETV2 signaling axis unique to Syk inhibition that promotes a cytocidal response in Tsc2-deficient cells and therefore maybe a potential alternative therapeutic target in LAM.
    DOI:  https://doi.org/10.26508/lsa.202201369
  15. Int J Mol Sci. 2022 Feb 01. pii: 1693. [Epub ahead of print]23(3):
    Predominant Role of mTOR Signaling in Skin Diseases with Therapeutic Potential.
    Fani Karagianni, Antreas Pavlidis, Lina S Malakou, Christina Piperi, Evangelia Papadavid.
      The serine/threonine kinase mechanistic target of rapamycin (mTOR) plays a pivotal role in the regulation of cell proliferation, survival, and motility in response to availability of energy and nutrients as well as mitogens. The mTOR signaling axis regulates important biological processes, including cellular growth, metabolism, and survival in many tissues. In the skin, dysregulation of PI3K/AKT/mTOR pathway may lead to severe pathological conditions characterized by uncontrolled proliferation and inflammation, including skin hyperproliferative as well as malignant diseases. Herein, we provide an update on the current knowledge regarding the pathogenic implication of the mTOR pathway in skin diseases with inflammatory features (such as psoriasis, atopic dermatitis, pemphigus, and acne) and malignant characteristics (such as cutaneous T cell lymphoma and melanoma) while we critically discuss current and future perspectives for therapeutic targeting of mTOR axis in clinical practice.
    Keywords:  acne; atopic dermatitis; cutaneous T cell lymphoma; inhibitors; mTOR signaling pathway; melanoma; pemphigus; psoriasis; therapy
    DOI:  https://doi.org/10.3390/ijms23031693
  16. Aging (Albany NY). 2022 Feb 15. 14(undefined):
    PERK activation by SB202190 ameliorates amyloidogenesis via the TFEB-induced autophagy-lysosomal pathway.
    Mihyang Do, Jeongmin Park, Yubing Chen, So-Young Rah, Thu-Hang Thi Nghiem, Jeong Heon Gong, Seong-A Ju, Byung-Sam Kim, Rina Yu, Jeong Woo Park, Stefan W Ryter, Young-Joon Surh, Uh-Hyun Kim, Yeonsoo Joe, Hun Taeg Chung.
      The protein kinase R (PKR)-like endoplasmic reticulum (ER) kinase (PERK), a key ER stress sensor of the unfolded protein response (UPR), can confer beneficial effects by facilitating the removal of cytosolic aggregates through the autophagy-lysosome pathway (ALP). In neurodegenerative diseases, the ALP ameliorates the accumulation of intracellular protein aggregates in the brain. Transcription factor-EB (TFEB), a master regulator of the ALP, positively regulates key genes involved in the cellular degradative pathway. However, in neurons, the role of PERK activation in mitigating amyloidogenesis by ALP remains unclear. In this study, we found that SB202190 selectively activates PERK independently of its inhibition of p38 mitogen-activated protein kinase, but not inositol-requiring transmembrane kinase/endoribonuclease-1α (IRE1α) or activating transcription factor 6 (ATF6), in human neuroblastoma cells. PERK activation by SB202190 was dependent on mitochondrial ROS production and promoted Ca2+-calcineurin activation. The activation of the PERK-Ca2+-calcineurin axis by SB202190 positively affects TFEB activity to increase ALP in neuroblastoma cells. Collectively, our study reveals a novel physiological mechanism underlying ALP activation, dependent on PERK activation, for ameliorating amyloidogenesis in neurodegenerative diseases.
    Keywords:  PERK; amyloidogenesis; autophagy-lysosome pathway; mitochondrial reactive oxygen species; transcription factor-EB
    DOI:  https://doi.org/10.18632/aging.203899
  17. Front Neurosci. 2022 ;16 784880
    Mitochondrial Dynamics and Mitochondria-Lysosome Contacts in Neurogenetic Diseases.
    Jordi Pijuan, Lara Cantarero, Daniel Natera-de Benito, Arola Altimir, Anna Altisent-Huguet, Yaiza Díaz-Osorio, Laura Carrera-García, Jessica Expósito-Escudero, Carlos Ortez, Andrés Nascimento, Janet Hoenicka, Francesc Palau.
      Mitochondrial network is constantly in a dynamic and regulated balance of fusion and fission processes, which is known as mitochondrial dynamics. Mitochondria make physical contacts with almost every other membrane in the cell thus impacting cellular functions. Mutations in mitochondrial dynamics genes are known to cause neurogenetic diseases. To better understand the consequences on the cellular phenotype and pathophysiology of neurogenetic diseases associated with defective mitochondrial dynamics, we have compared the fibroblasts phenotypes of (i) patients carrying pathogenic variants in genes involved in mitochondrial dynamics such as DRP1 (also known as DNM1L), GDAP1, OPA1, and MFN2, and (ii) patients carrying mutated genes that their dysfunction affects mitochondria or induces a mitochondrial phenotype, but that are not directly involved in mitochondrial dynamic network, such as FXN (encoding frataxin, located in the mitochondrial matrix), MED13 (hyperfission phenotype), and CHKB (enlarged mitochondria phenotype). We identified mitochondrial network alterations in all patients' fibroblasts except for CHKB Q198*/Q198*. Functionally, all fibroblasts showed mitochondrial oxidative stress, without membrane potential abnormalities. The lysosomal area and distribution were abnormal in GDAP1 W67L/W67L, DRP1 K75E/+, OPA1 F570L/+, and FXN R165C/GAA fibroblasts. These lysosomal alterations correlated with mitochondria-lysosome membrane contact sites (MCSs) defects in GDAP1 W67L/W67L exclusively. The study of mitochondrial contacts in all samples further revealed a significant decrease in MFN2 R104W/+ fibroblasts. GDAP1 and MFN2 are outer mitochondrial membrane (OMM) proteins and both are related to Charcot-Marie Tooth neuropathy. Here we identified their constitutive interaction as well as MFN2 interaction with LAMP-1. Therefore MFN2 is a new mitochondria-lysosome MCSs protein. Interestingly, GDAP1 W67L/W67L and MFN2 R104W/+ fibroblasts carry pathogenic changes that occur in their catalytic domains thus suggesting a functional role of GDAP1 and MFN2 in mitochondria-lysosome MCSs. Finally, we observed starvation-induced autophagy alterations in DRP1 K75E/+, GDAP1 W67L/W67L, OPA1 F570L/+, MFN2 R104W/+, and CHKB Q198*/Q198* fibroblasts. These genes are related to mitochondrial membrane structure or lipid composition, which would associate the OMM with starvation-induced autophagy. In conclusion, the study of mitochondrial dynamics and mitochondria-lysosome axis in a group of patients with different neurogenetic diseases has deciphered common and unique cellular phenotypes of degrading and non-degrading pathways that shed light on pathophysiological events, new biomarkers and pharmacological targets for these disorders.
    Keywords:  lysosome; membrane contact sites (MCSs); mitochondria; mitochondrial dynamics; neurogenetic diseases
    DOI:  https://doi.org/10.3389/fnins.2022.784880
  18. Int J Mol Sci. 2022 Feb 05. pii: 1825. [Epub ahead of print]23(3):
    mTOR Signaling Components in Tumor Mechanobiology.
    Antonios N Gargalionis, Kostas A Papavassiliou, Efthimia K Basdra, Athanasios G Papavassiliou.
      Mechanistic target of rapamycin (mTOR) is a central signaling hub that integrates networks of nutrient availability, cellular metabolism, and autophagy in eukaryotic cells. mTOR kinase, along with its upstream regulators and downstream substrates, is upregulated in most human malignancies. At the same time, mechanical forces from the tumor microenvironment and mechanotransduction promote cancer cells' proliferation, motility, and invasion. mTOR signaling pathway has been recently found on the crossroads of mechanoresponsive-induced signaling cascades to regulate cell growth, invasion, and metastasis in cancer cells. In this review, we examine the emerging association of mTOR signaling components with certain protein tools of tumor mechanobiology. Thereby, we highlight novel mechanisms of mechanotransduction, which regulate tumor progression and invasion, as well as mechanisms related to the therapeutic efficacy of antitumor drugs.
    Keywords:  Akt; PI3K; extracellular matrix; integrin; mTOR; matrix stiffness; mechanotransduction; tumor mechanobiology
    DOI:  https://doi.org/10.3390/ijms23031825
  19. Biochem Soc Trans. 2022 Feb 15. pii: BST20210813. [Epub ahead of print]
    Non-canonical roles of ATG8 for TFEB activation.
    Shuhei Nakamura, Shiori Akayama, Tamotsu Yoshimori.
      Autophagy is an evolutionally conserved cytoplasmic degradation pathway in which the double membrane structure, autophagosome sequesters cytoplasmic material and delivers them to lysosomes for degradation. Many autophagy related (ATG) proteins participate in the regulation of the several steps of autophagic process. Among ATGs, ubiquitin-like protein, ATG8 plays a pivotal role in autophagy. ATG8 is directly conjugated on lipid in autophagosome membrane upon induction of autophagy thus providing a good marker to monitor and analyze autophagy process. However, recent discoveries suggest that ATG8 has autophagy independent non-canonical functions and ATG8 positive structures are not always autophagosomes. This review briefly overviews canonical and non-canonical roles of ATG8 and introduce novel function of ATG8 to activate Transcriptional Factor EB(TFEB), a master transcription factor of autophagy and lysosome function during lysosomal damage.
    Keywords:  ATG8; TFEB; autophagy; lysosomes
    DOI:  https://doi.org/10.1042/BST20210813
  20. Cell Cycle. 2022 Feb 15. 1-19
    CDK6 increases glycolysis and suppresses autophagy by mTORC1-HK2 pathway activation in cervical cancer cells.
    Xiaoxi Zhang, Yunxia Sun, Siyao Cheng, Yanjing Yao, Xintao Hua, Yueyue Shi, Xiaoqin Jin, Jieli Pan, Miaofen G Hu, Pian Ying, Xiaoli Hou, Daozong Xia.
      Cervical carcinoma is a leading malignant tumor among women worldwide, characterized by the dysregulation of cell cycle. Cyclin-dependent kinase 6 (CDK6) plays important roles in the cell cycle progression, cell differentiation, and tumorigenesis. However, the role of CDK6 in cervical cancer remains controversial. Here, we found that loss of CDK6 in cervical adenocarcinoma HeLa cell line inhibited cell proliferation but induced apoptosis as well as autophagy, accompanied by attenuated expression of mammalian target of rapamycin complex 1 (mTORC1) and hexokinase 2 (HK2), reduced glycolysis, and production of protein, nucleotide, and lipid. Similarly, we showed that CDK6 knockout inhibited the survival of CDK6-high CaSki but not CDK6-low SiHa cervical cancer cells by regulation of glycolysis and autophagy process. Collectively, our studies indicate that CDK6 is a critical regulator of human cervical cancer cells, especially with high CDK6 level, through its ability to regulate cellular apoptosis and metabolism. Thus, inhibition of CDK6 kinase activity could be a powerful therapeutic avenue used to treat cervical cancers.
    Keywords:  CDK6; Cervical carcinoma; apoptosis; autophagy; glycolysis; mTOR
    DOI:  https://doi.org/10.1080/15384101.2022.2039981
  21. J Biol Chem. 2022 Feb 10. pii: S0021-9258(22)00158-2. [Epub ahead of print] 101718
    Exosomal miR-673-5p from fibroblasts promotes Schwann cell-mediated peripheral neuron myelination by targeting the TSC2/mTORC1/SREBP2 axis.
    Yahong Zhao, Yunyun Liang, Zhixin Xu, Jina Liu, Xiaoyu Liu, Jinyu Ma, Cheng Sun, Yumin Yang.
      Peripheral myelination is a complicated process, wherein Schwann cells (SCs) promote the formation of the myelin sheath around the axons of peripheral neurons. Fibroblasts are the second resident cells in the peripheral nerves; however, the precise function of fibroblasts in SC-mediated myelination has rarely been examined. Here, we show that exosomes derived from fibroblasts boost myelination-related gene expression in SCs. We used exosome sequencing, together with bioinformatic analysis, to demonstrate that exosomal microRNA miR-673-5p is capable of stimulating myelin gene expression in SCs. Subsequent functional studies revealed that miR-673-5p targets the regulator of mTOR complex 1 (mTORC1) TSC2 in SCs, leading to the activation of downstream signaling pathways including mTORC1 and SREBP2. In vivo experiments further confirmed that miR-673-5p activates the TSC2/mTORC1/SREBP2 axis, thus promoting the synthesis of cholesterol and related lipids and subsequently accelerating myelin sheath maturation in peripheral nerves. Overall, our findings revealed exosome-mediated crosstalk between fibroblasts and SCs that plays a pivotal role in peripheral myelination. We propose that exosomes derived from fibroblasts and miR-673-5p might be useful for promoting peripheral myelination in translational medicine.
    Keywords:  Exosomes; Fibroblasts; Lipid synthesis; Myelination; Peripheral nerve regeneration; Schwann cells
    DOI:  https://doi.org/10.1016/j.jbc.2022.101718
  22. Front Cell Dev Biol. 2021 ;9 797047
    Downregulation of NAGLU in VEC Increases Abnormal Accumulation of Lysosomes and Represents a Predictive Biomarker in Early Atherosclerosis.
    Changchang Xing, Zhongyi Jiang, Yi Wang.
      Cardiovascular diseases (CVDs), predominantly caused by atherosclerosis (AS), are the leading cause of mortality worldwide. Although a great number of previous studies have attempted to reveal the molecular mechanism of AS, the underlying mechanism has not been fully elucidated. The aberrant expression profiling of vascular endothelial cells (VECs) gene in early atherosclerosis (EAS) was analyzed according to the dataset (GSE132651) downloaded from the Gene Expression Omnibus (GEO) database. We primarily performed functional annotation analysis on the downregulated genes (DRGs). We further identified that α-N-acetylglucosaminidase (NAGLU), one of the DRGs, played a critical role in the progression of EAS. NAGLU is a key enzyme for the degradation of heparan sulfate (HS), and its deficiency could cause lysosomal accumulation and lead to dysfunctions of VECs. We found that siRNA knockdown of NAGLU in human umbilical vein endothelial cell (HUVEC) aggravated the abnormal accumulation of lysosomes and HS. In addition, the expression of NAGLU was reduced in the EAS model constructed by ApoE -/- mice. Furthermore, we also showed that heparin-binding EGF-like growth factor (HB-EGF) protein was upregulated while NAGLU knockdown in HUVEC could specifically bind to vascular endothelial growth factor receptor 2 (VEGFR2) and promote its phosphorylation, ultimately activating the phosphorylation levels of extracellular signal-regulated kinases (ERKs). However, the application of selective VEGFR2 and ERKs inhibitors, SU5614 and PD98059, respectively, could reverse the abnormal lysosomal storage caused by NAGLU knockdown. These results indicated that downregulation of NAGLU in HUVEC increases the abnormal accumulation of lysosomes and may be a potential biomarker for the diagnosis of EAS.
    Keywords:  ERK; NAGLU; VEGFR2; bioinformatics analysis; early atherosclerosis; lysosome; vascular endothelial cell
    DOI:  https://doi.org/10.3389/fcell.2021.797047
  23. Cells. 2022 Feb 04. pii: 546. [Epub ahead of print]11(3):
    Peripheral Inflammatory Cytokine Signature Mirrors Motor Deficits in Mucolipidosis IV.
    Albert L Misko, Laura D Weinstock, Sitara B Sankar, Amanda Furness, Yulia Grishchuk, Levi B Wood.
      BACKGROUND: Mucolipidosis IV (MLIV) is an autosomal recessive pediatric disease that leads to motor and cognitive deficits and loss of vision. It is caused by a loss of function of the lysosomal channel transient receptor potential mucolipin-1 and is associated with an early pro-inflammatory brain phenotype, including increased cytokine expression. The goal of the current study was to determine whether blood cytokines are linked to motor dysfunction in patients with MLIV and reflect brain inflammatory changes observed in an MLIV mouse model.METHODS: To determine the relationship between blood cytokines and motor function, we collected plasma from MLIV patients and parental controls concomitantly with assessment of motor function using the Brief Assessment of Motor Function and Modified Ashworth scales. We then compared these profiles with cytokine profiles in brain and plasma samples collected from the Mcoln1-/- mouse model of MLIV.
    RESULTS: We found that MLIV patients had prominently increased cytokine levels compared to familial controls and identified profiles of cytokines correlated with motor dysfunction, including IFN-γ, IFN-α2, and IP-10. We found that IP-10 was a key differentiating factor separating MLIV cases from controls based on data from human plasma, mouse plasma, and mouse brain.
    CONCLUSIONS: Our data indicate that MLIV is characterized by increased blood cytokines, which are strongly related to underlying neurological and functional deficits in MLIV patients. Moreover, our data identify the interferon pro-inflammatory axis in both human and mouse signatures, suggesting that interferon signaling is an important aspect of MLIV pathology.
    Keywords:  biomarkers; blood; cytokines; lysosomal storage disorder; motor function; mucolipidosis; plasma
    DOI:  https://doi.org/10.3390/cells11030546
  24. Molecules. 2022 Jan 27. pii: 842. [Epub ahead of print]27(3):
    Improved Cathepsin Probes for Sensitive Molecular Imaging.
    Yonit Yitzhak, Hanmant Gaikwad, Tommy Weiss-Sadan, Emmanuelle Merquiol, Boris Turk, Galia Blum.
      Cysteine cathepsin proteases are found under normal conditions in the lysosomal compartments of cells, where they play pivotal roles in a variety of cellular processes such as protein and lipid metabolism, autophagy, antigen presentation, and cell growth and proliferation. As a consequence, aberrant localization and activity contribute to several pathologic conditions such as a variety of malignancies, cardiovascular diseases, osteoporosis, and other diseases. Hence, there is a resurgence of interest to expand the toolkit to monitor intracellular cathepsin activity and better ascertain their functions under these circumstances. Previous fluorescent activity-based probes (ABPs) that target cathepsins B, L, and S enabled detection of their activity in intact cells as well as non-invasive detection in animal disease models. However, their binding potency is suboptimal compared to the cathepsin inhibitor on which they were based, as the P1 positive charge was capped by a reporter tag. Here, we show the development of an improved cathepsin ABP that has a P1 positive charge by linking the tag on an additional amino acid at the end of the probe. While enhancing potency towards recombinant cathepsins, the new probe had reduced cell permeability due to additional peptide bonds. At a second phase, the probe was trimmed; the fluorophore was linked to an extended carbobenzoxy moiety, leading to enhanced cell permeability and superb detection of cathepsin activity in intact cells. In conclusion, this work introduces a prototype design for the next generation of highly sensitive ABPs that have excellent detection of cellular cathepsin activity.
    Keywords:  activity-based probes; cathepsin; cell permeability
    DOI:  https://doi.org/10.3390/molecules27030842
  25. Int J Mol Sci. 2022 Jan 21. pii: 1153. [Epub ahead of print]23(3):
    Modulating mTOR Signaling as a Promising Therapeutic Strategy for Atherosclerosis.
    Anastasia V Poznyak, Vasily N Sukhorukov, Alexander Zhuravlev, Nikolay A Orekhov, Vladislav Kalmykov, Alexander N Orekhov.
      For more than a decade, atherosclerosis has been one of the leading causes of death in developed countries. The issue of treatment and prevention of the disease is especially acute. Despite the huge amount of basic and clinical research, a significant number of gaps remain in our understanding of the pathogenesis of atherosclerosis, and only their closure will bring us closer to understanding the causes of the disease at the cellular and molecular levels and, accordingly, to the development of an effective treatment. One of the seemingly well-studied elements of atherogenesis is the mTOR signaling pathway. However, more and more new details are still being clarified. Therapeutic strategies associated with rapamycin have worked well in a number of different diseases, and there is every reason to believe that targeting components of the mTOR pathway may pay off in atherosclerosis as well.
    Keywords:  atherosclerosis; cardiovascular disease; mTOR; rapamycin
    DOI:  https://doi.org/10.3390/ijms23031153
  26. Biochem Biophys Res Commun. 2022 Feb 08. pii: S0006-291X(22)00198-X. [Epub ahead of print]598 107-112
    Involvement of Gtr1p in the oxidative stress response in yeast Saccharomyces cerevisiae.
    Takeshi Sekiguchi, Takashi Ishii, Yoshiaki Kamada, Minoru Funakoshi, Hideki Kobayashi, Nobuaki Furuno.
      Yeast Gtr1p is a GTPase that forms a heterodimer with Gtr2p, another GTPase; it is involved in regulating TORC1 activity in nutrient signaling, including amino acid availability and growth control. Gtr1p is a positive regulator of TORC1, a kinase that regulates various cellular functions (e.g., protein synthesis and autophagy) under specific nutrient and environmental conditions, including oxidative stress. In this study, we examined the roles of Gtr1p in oxidative stress responses. We found that yeast cells expressing guanosine diphosphatase (GDP)-bound Gtr1p (Gtr1-S20Lp) were resistant to hydrogen peroxide (H2O2), whereas guanosine triphosphate (GTP)-bound Gtr1p (Gtr1-Q65Lp) was sensitive to H2O2 compared with the wild type. Consistent with these findings, yeast cells lacking Iml1p, a component of the GTPase-activating protein complex for Gtr1p, exhibited the H2O2-sensitive phenotype. In gtr1S20L cells, autophagy was highly induced under oxidative stress. gtr1Q65L cells showed decreased expression of the SNQ2 gene, which encodes a multidrug transporter involved in resistance to oxidative stress, and the overexpression of SNQ2 rescued the oxidative stress sensitivity of gtr1Q65L cells. These results suggest that Gtr1p is involved in oxidative stress responses through mechanisms that include autophagy and SNQ2 expression.
    Keywords:  Autophagy; Gtr1p; Oxidative stress; SNQ2; TORC1
    DOI:  https://doi.org/10.1016/j.bbrc.2022.02.016
  27. Cells. 2022 Jan 19. pii: 326. [Epub ahead of print]11(3):
    Defective Cystinosin, Aberrant Autophagy-Endolysosome Pathways, and Storage Disease: Towards Assembling the Puzzle.
    Laura Rita Rega, Ester De Leo, Daniela Nieri, Alessandro Luciani.
      Epithelial cells that form the kidney proximal tubule (PT) rely on an intertwined ecosystem of vesicular membrane trafficking pathways to ensure the reabsorption of essential nutrients-a key requisite for homeostasis. The endolysosome stands at the crossroads of this sophisticated network, internalizing molecules through endocytosis, sorting receptors and nutrient transporters, maintaining cellular quality control via autophagy, and toggling the balance between PT differentiation and cell proliferation. Dysregulation of such endolysosome-guided trafficking pathways might thus lead to a generalized dysfunction of PT cells, often causing chronic kidney disease and life-threatening complications. In this review, we highlight the biological functions of endolysosome-residing proteins from the perspectives of understanding-and potentially reversing-the pathophysiology of rare inherited diseases affecting the kidney PT. Using cystinosis as a paradigm of endolysosome disease causing PT dysfunction, we discuss how the endolysosome governs the homeostasis of specialized epithelial cells. This review also provides a critical analysis of the molecular mechanisms through which defects in autophagy pathways can contribute to PT dysfunction, and proposes potential interventions for affected tissues. These insights might ultimately accelerate the discovery and development of new therapeutics, not only for cystinosis, but also for other currently intractable endolysosome-related diseases, eventually transforming our ability to regulate homeostasis and health.
    Keywords:  autophagy; endolysosome; epithelial cell differentiation; homeostasis; kidney proximal tubule; lysosomal storage diseases; mitochondrial distress
    DOI:  https://doi.org/10.3390/cells11030326
  28. Aging Cell. 2022 Feb 15. e13559
    Loss of miR-34 in Drosophila dysregulates protein translation and protein turnover in the aging brain.
    Ananth R Srinivasan, Tracy T Tran, Nancy M Bonini.
      Aging is a risk factor for neurodegenerative disease, but precise mechanisms that influence this relationship are still under investigation. Work in Drosophila melanogaster identified the microRNA miR-34 as a modifier of aging and neurodegeneration in the brain. MiR-34 mutants present aspects of early aging, including reduced lifespan, neurodegeneration, and a buildup of the repressive histone mark H3K27me3. To better understand how miR-34 regulated pathways contribute to age-associated phenotypes in the brain, here we transcriptionally profiled the miR-34 mutant brain. This identified that genes associated with translation are dysregulated in the miR-34 mutant. The brains of these animals show increased translation activity, accumulation of protein aggregation markers, and altered autophagy activity. To determine if altered H3K27me3 was responsible for this proteostasis dysregulation, we studied the effects of increased H3K27me3 by mutating the histone demethylase Utx. Reduced Utx activity enhanced neurodegeneration and mimicked the protein accumulation seen in miR-34 mutant brains. However, unlike the miR-34 mutant, Utx mutant brains did not show similar altered autophagy or translation activity, suggesting that additional miR-34-targeted pathways are involved. Transcriptional analysis of predicted miR-34 targets identified Lst8, a subunit of Tor Complex 1 (TORC1), as a potential target. We confirmed that miR-34 regulates the 3' UTR of Lst8 and identified several additional predicted miR-34 targets that may be critical for maintaining proteostasis and brain health. Together, these results present novel understanding of the brain and the role of the conserved miRNA miR-34 in impacting proteostasis in the brain with age.
    Keywords:   miR-34 ; aging; autophagy; neurodegeneration; proteostasis; translation
    DOI:  https://doi.org/10.1111/acel.13559
  29. Sci Adv. 2022 Feb 18. 8(7): eabk3234
    Ultrarapid lytic granule release from CTLs activates Ca2+-dependent synaptic resistance pathways in melanoma cells.
    Liza Filali, Marie-Pierre Puissegur, Kevin Cortacero, Sylvain Cussat-Blanc, Roxana Khazen, Nathalie Van Acker, François-Xavier Frenois, Arnaud Abreu, Laurence Lamant, Nicolas Meyer, Béatrice Vergier, Sabina Müller, Brienne McKenzie, Salvatore Valitutti.
      Human cytotoxic T lymphocytes (CTLs) exhibit ultrarapid lytic granule secretion, but whether melanoma cells mobilize defense mechanisms with commensurate rapidity remains unknown. We used single-cell time-lapse microscopy to offer high spatiotemporal resolution analyses of subcellular events in melanoma cells upon CTL attack. Target cell perforation initiated an intracellular Ca2+ wave that propagated outward from the synapse within milliseconds and triggered lysosomal mobilization to the synapse, facilitating membrane repair and conferring resistance to CTL induced cytotoxicity. Inhibition of Ca2+ flux and silencing of synaptotagmin VII limited synaptic lysosomal exposure and enhanced cytotoxicity. Multiplexed immunohistochemistry of patient melanoma nodules combined with automated image analysis showed that melanoma cells facing CD8+ CTLs in the tumor periphery or peritumoral area exhibited significant lysosomal enrichment. Our results identified synaptic Ca2+ entry as the definitive trigger for lysosomal deployment to the synapse upon CTL attack and highlighted an unpredicted defensive topology of lysosome distribution in melanoma nodules.
    DOI:  https://doi.org/10.1126/sciadv.abk3234
  30. Cells. 2022 Jan 24. pii: 385. [Epub ahead of print]11(3):
    Effect of FKBP12-Derived Intracellular Peptides on Rapamycin-Induced FKBP-FRB Interaction and Autophagy.
    Carolina A Parada, Ivan Pires de Oliveira, Mayara C F Gewehr, João Agostinho Machado-Neto, Keli Lima, Rosangela A S Eichler, Lucia R Lopes, Luiz R G Bechara, Julio C B Ferreira, William T Festuccia, Luciano Censoni, Ivarne Luis S Tersariol, Emer S Ferro.
      Intracellular peptides (InPeps) generated by proteasomes were previously suggested as putative natural regulators of protein-protein interactions (PPI). Here, the main aim was to investigate the intracellular effects of intracellular peptide VFDVELL (VFD7) and related peptides on PPI. The internalization of the peptides was achieved using a C-terminus covalently bound cell-penetrating peptide (cpp; YGRKKRRQRRR). The possible inhibition of PPI was investigated using a NanoBiT® luciferase structural complementation reporter system, with a pair of plasmids vectors each encoding, simultaneously, either FK506-binding protein (FKBP) or FKBP-binding domain (FRB) of mechanistic target of rapamycin complex 1 (mTORC1). The interaction of FKBP-FRB within cells occurs under rapamycin induction. Results shown that rapamycin-induced interaction between FKBP-FRB within human embryonic kidney 293 (HEK293) cells was inhibited by VFD7-cpp (10-500 nM) and FDVELLYGRKKRRQRRR (VFD6-cpp; 1-500 nM); additional VFD7-cpp derivatives were either less or not effective in inhibiting FKBP-FRB interaction induced by rapamycin. Molecular dynamics simulations suggested that selected peptides, such as VFD7-cpp, VFD6-cpp, VFAVELLYGRKKKRRQRRR (VFA7-cpp), and VFEVELLYGRKKKRRQRRR (VFA7-cpp), bind to FKBP and to FRB protein surfaces. However, only VFD7-cpp and VFD6-cpp induced changes on FKBP structure, which could help with understanding their mechanism of PPI inhibition. InPeps extracted from HEK293 cells were found mainly associated with macromolecular components (i.e., proteins and/or nucleic acids), contributing to understanding InPeps' intracellular proteolytic stability and mechanism of action-inhibiting PPI within cells. In a model of cell death induced by hypoxia-reoxygenation, VFD6-cpp (1 µM) increased the viability of mouse embryonic fibroblasts cells (MEF) expressing mTORC1-regulated autophagy-related gene 5 (Atg5), but not in autophagy-deficient MEF cells lacking the expression of Atg5. These data suggest that VFD6-cpp could have therapeutic applications reducing undesired side effects of rapamycin long-term treatments. In summary, the present report provides further evidence that InPeps have biological significance and could be valuable tools for the rational design of therapeutic molecules targeting intracellular PPI.
    Keywords:  edgotype; intracellular peptides; mTORC1; protein–protein interaction
    DOI:  https://doi.org/10.3390/cells11030385
  31. Stem Cell Res. 2022 Feb 02. pii: S1873-5061(22)00047-2. [Epub ahead of print]60 102698
    A generation of human induced pluripotent stem cell line (MUi031-A) from a type-3 Gaucher disease patient carrying homozygous mutation on GBA1 gene.
    Tanapat Pornsukjantra, Kitsada Kangboonruang, Pirut Tong-Ngam, Thipwimol Tim-Aroon, Duangrurdee Wattanasirichaigoon, Usanarat Anurathapan, Suradej Hongeng, Alisa Tubsuwan, Kanit Bhukhai, Nithi Asavapanumas.
      Gaucher disease (GD) is one of the most prevalent lysosomal storage diseases caused by mutation of glucocerebrosidase (GBA1) gene. GD patients develop symptoms in various organs of the body; however, the underlying mechanisms causing pathology are still elusive. Thus, a suitable disease model is important in order to facilitate subsequent investigations. Here, we established MUi031-A human induced pluripotent stem cell (hiPSC) line from CD34+ hematopoietic stem cells of a female type-3 GD patient with homozygous c.1448 T > C (L444P) mutation. The cells exhibited embryonic stem cell-like characteristics and expressed pluripotency markers with capability to differentiate into three germ layers.
    DOI:  https://doi.org/10.1016/j.scr.2022.102698
  32. Mini Rev Med Chem. 2022 Feb 14.
    Cathepsin B - A Neuronal Death Mediator in Alzheimer's Disease Leads to Neurodegeneration.
    Anjali Sharma, Rayala Swetha, Nilesh Gajanan Bajad, Ankit Ganeshpurkar, Ravi Singh, Ashok Kumar, Sushil Kumar Singh.
      The lysosomal cysteine protease enzyme, named Cathepsin B, mainly degrades the protein and manages its average turnover in our body. The Cathepsin B active form is mostly present inside the lysosomal part at a cellular level, providing the slightly acidic medium for its activation. Multiple findings on Cathepsin B reveal its involvement in neurons' degeneration and a possible role as a neuronal death mediator in several neurodegenerative diseases. In this review article, we highlight the participation of Cathepsin B in the etiology/progress of AD, along with various other factors. The enzyme is involved in producing neurotoxic Aβ amyloid in the AD brain by acting as the β-secretase enzyme in the regulated secretory pathways responsible for APP processing. Aβ amyloid accumulation and amyloid plaque formation lead to neuronal degeneration, one of the prominent pathological hallmarks of AD. Cathepsin B is also involved in the production of PGlu-Aβ, which is a truncated and highly neurotoxic form of Aβ. Some of the findings also revealed that Cathepsin B specific gene deletion decreases the level of PGlu-Aβ inside the brain of experimental mice. Therefore, neurotoxicity might be considered a new pathological indication of AD due to the involvement of Cathepsin B. It also damages neurons present in the CNS region by producing inflammatory responses and generating mitochondrial ROS. However, Cathepsin B inhibitors, i.e., CA-074, can prevent neuronal death in AD patients. The other natural inhibitors are also equally effective against neuronal damage with higher selectivity. Its synthetic inhibitors are specific for their target; however, they lose their selectivity in the presence of quite a few reducing agents. Therefore, a humanized monoclonal antibody is used as a selective Cathepsin B inhibitor to overcome the problem experienced. The use of Cathepsin B for the treatment of AD and other neurodegenerative diseases could be considered a rational therapeutic target.
    Keywords:  Alzheimer's disease; Cathepsin B; Pyroglutamate amyloid- β (PGlu-Aβ); humanized antibody; neuroinflammation; regulated secretory pathway; β-amyloid
    DOI:  https://doi.org/10.2174/1389557522666220214095859
  33. Front Cell Dev Biol. 2021 ;9 806258
    Role of ARHGEF3 as a GEF and mTORC2 Regulator.
    Sana Abdul Khaliq, Zobia Umair, Mee-Sup Yoon.
      Guanine nucleotide exchange factors (GEFs) activate GTPases by stimulating the release of guanosine diphosphate to permit the binding of guanosine triphosphate. ARHGEF3 or XPLN (exchange factor found in platelets, leukemic, and neuronal tissues) is a selective guanine nucleotide exchange factor for Rho GTPases (RhoGEFs) that activates RhoA and RhoB but not RhoC, RhoG, Rac1, or Cdc42. ARHGEF3 contains the diffuse B-cell lymphoma homology and pleckstrin homology domains but lacks similarity with other known functional domains. ARHGEF3 also binds the mammalian target of rapamycin complex 2 (mTORC2) and subsequently inhibits mTORC2 and Akt. In vivo investigation has also indicated the communication between ARHGEF3 and autophagy-related muscle pathologies. Moreover, studies on genetic variation in ARHGEF3 and genome-wide association studies have predicted exciting novel roles of ARHGEF3 in controlling bone mineral density, platelet formation and differentiation, and Hirschsprung disease. In conclusion, we hypothesized that additional biochemical and functional studies are required to elucidate the detailed mechanism of ARHGEF3-related pathologies and therapeutics.
    Keywords:  ARHGEF3; Akt; XPLN; mTORC2; rho guanine nucleotide exchange factors
    DOI:  https://doi.org/10.3389/fcell.2021.806258
  34. Int J Mol Sci. 2022 Feb 08. pii: 1887. [Epub ahead of print]23(3):
    Chaperone Therapy in Fabry Disease.
    Frank Weidemann, Ana Jovanovic, Ken Herrmann, Irfan Vardarli.
      Fabry disease is an X-linked lysosomal multisystem storage disorder induced by a mutation in the alpha-galactosidase A (GLA) gene. Reduced activity or deficiency of alpha-galactosidase A (AGAL) leads to escalating storage of intracellular globotriaosylceramide (GL-3) in numerous organs, including the kidneys, heart and nerve system. The established treatment for 20 years is intravenous enzyme replacement therapy. Lately, oral chaperone therapy was introduced and is a therapeutic alternative in patients with amenable mutations. Early starting of therapy is essential for long-term improvement. This review describes chaperone therapy in Fabry disease.
    Keywords:  Fabry disease; chaperone; therapy
    DOI:  https://doi.org/10.3390/ijms23031887
  35. Nat Commun. 2022 Feb 16. 13(1): 904
    The AUTOTAC chemical biology platform for targeted protein degradation via the autophagy-lysosome system.
    Chang Hoon Ji, Hee Yeon Kim, Min Ju Lee, Ah Jung Heo, Daniel Youngjae Park, Sungsu Lim, Seulgi Shin, Woo Seung Yang, Chang An Jung, Kun Young Kim, Eun Hye Jeong, Sun Ho Park, Su Bin Kim, Su Jin Lee, Jeong Eun Na, Ji In Kang, Hyung Min Chi, Hyun Tae Kim, Yun Kyung Kim, Bo Yeon Kim, Yong Tae Kwon.
      Targeted protein degradation allows targeting undruggable proteins for therapeutic applications as well as eliminating proteins of interest for research purposes. While several degraders that harness the proteasome or the lysosome have been developed, a technology that simultaneously degrades targets and accelerates cellular autophagic flux is still missing. In this study, we develop a general chemical tool and platform technology termed AUTOphagy-TArgeting Chimera (AUTOTAC), which employs bifunctional molecules composed of target-binding ligands linked to autophagy-targeting ligands. AUTOTACs bind the ZZ domain of the otherwise dormant autophagy receptor p62/Sequestosome-1/SQSTM1, which is activated into oligomeric bodies in complex with targets for their sequestration and degradation. We use AUTOTACs to degrade various oncoproteins and degradation-resistant aggregates in neurodegeneration at nanomolar DC50 values in vitro and in vivo. AUTOTAC provides a platform for selective proteolysis in basic research and drug development.
    DOI:  https://doi.org/10.1038/s41467-022-28520-4
  36. Proc Natl Acad Sci U S A. 2022 Feb 22. pii: e2200788119. [Epub ahead of print]119(8):
    Rag GTPases regulate cellular amino acid homeostasis.
    Ken Inoki, Kun-Liang Guan.
      
    DOI:  https://doi.org/10.1073/pnas.2200788119
  37. Proc Natl Acad Sci U S A. 2022 Feb 22. pii: e2123082119. [Epub ahead of print]119(8):
    Linking a nuclear lncRNA to cytoplasmic lysosome integrity and cell death.
    Haibin Liu, Zhi-Ming Zheng.
      
    DOI:  https://doi.org/10.1073/pnas.2123082119
  38. PLoS Genet. 2022 Feb 14. 18(2): e1010061
    TOR complex 2 contributes to regulation of gene expression via inhibiting Gcn5 recruitment to subtelomeric and DNA replication stress genes.
    Adiel Cohen, Emese Pataki, Martin Kupiec, Ronit Weisman.
      The fission yeast TOR complex 2 (TORC2) is required for gene silencing at subtelomeric regions and for the induction of gene transcription in response to DNA replication stress. Thus, TORC2 affects transcription regulation both negatively and positively. Whether these two TORC2-dependent functions share a common molecular mechanism is currently unknown. Here, we show that Gad8 physically interacts with proteins that regulate transcription, including subunits of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and the BET bromodomain protein Bdf2. We demonstrate that in the absence of TORC2, Gcn5, the histone acetyltransferase subunit of SAGA, accumulates at subtelomeric genes and at non-induced promoters of DNA replication genes. Remarkably, the loss of Gcn5 in TORC2 mutant cells restores gene silencing as well as transcriptional induction in response to DNA replication stress. Loss of Bdf2 alleviates excess of Gcn5 binding in TORC2 mutant cells and also rescues the aberrant regulation of transcription in these cells. Furthermore, the loss of either SAGA or Bdf2 suppresses the sensitivity of TORC2 mutant cells to a variety of stresses, including DNA replication, DNA damage, temperature and nutrient stresses. We suggest a role of TORC2 in transcriptional regulation that is critical for gene silencing and gene induction in response to stress and involves the binding of Gcn5 to the chromatin.
    DOI:  https://doi.org/10.1371/journal.pgen.1010061
  39. Cancer Lett. 2022 Feb 14. pii: S0304-3835(22)00068-4. [Epub ahead of print] 215593
    p70 S6 kinase as a therapeutic target in cancers: More than just an mTOR effector.
    Margarita Artemenko, Sophia S W Zhong, Sally K Y To, Alice S T Wong.
      p70 S6 kinase (p70S6K) is best-known for its regulatory roles in protein synthesis and cell growth by phosphorylating its primary substrate, ribosomal protein S6, upon mitogen stimulation. The enhanced expression/activation of p70S6K has been correlated with poor prognosis in some cancer types, suggesting that it may serve as a biomarker for disease monitoring. p70S6K is a critical downstream effector of the oncogenic PI3K/Akt/mTOR pathway and its activation is tightly regulated by an ordered cascade of Ser/Thr phosphorylation events. Nonetheless, it should be noted that other upstream mechanisms regulating p70S6K at both the post-translational and post-transcriptional levels also exist. Activated p70S6K could promote various aspects of cancer progression such as epithelial-mesenchymal transition, cancer stemness and drug resistance. Importantly, novel evidence showing that p70S6K may also regulate different cellular components in the tumor microenvironment will be discussed. Therapeutic targeting of p70S6K alone or in combination with traditional chemotherapies or other microenvironmental-based drugs such as immunotherapy may represent promising approaches against cancers with aberrant p70S6K signaling. Currently, the only clinically available p70S6K inhibitors are rapamycin analogs (rapalogs) which target mTOR. However, there are emerging p70S6K-selective drugs which are going through active preclinical or clinical trial phases. Moreover, various screening strategies have been used for the discovery of novel p70S6K inhibitors, hence bringing new insights for p70S6K-targeted therapy.
    Keywords:  Cancer; Drug development; Tumor microenvironment; p70 S6 kinase
    DOI:  https://doi.org/10.1016/j.canlet.2022.215593
  40. Proc Natl Acad Sci U S A. 2022 Feb 22. pii: e2116271119. [Epub ahead of print]119(8):
    Lung-selective mRNA delivery of synthetic lipid nanoparticles for the treatment of pulmonary lymphangioleiomyomatosis.
    Min Qiu, Yan Tang, Jinjin Chen, Rachel Muriph, Zhongfeng Ye, Changfeng Huang, Jason Evans, Elizabeth P Henske, Qiaobing Xu.
      Safe and efficacious systemic delivery of messenger RNA (mRNA) to specific organs and cells in vivo remains the major challenge in the development of mRNA-based therapeutics. Targeting of systemically administered lipid nanoparticles (LNPs) coformulated with mRNA has largely been confined to the liver and spleen. Using a library screening approach, we identified that N-series LNPs (containing an amide bond in the tail) are capable of selectively delivering mRNA to the mouse lung, in contrast to our previous discovery that O-series LNPs (containing an ester bond in the tail) that tend to deliver mRNA to the liver. We analyzed the protein corona on the liver- and lung-targeted LNPs using liquid chromatography-mass spectrometry and identified a group of unique plasma proteins specifically absorbed onto the surface that may contribute to the targetability of these LNPs. Different pulmonary cell types can also be targeted by simply tuning the headgroup structure of N-series LNPs. Importantly, we demonstrate here the success of LNP-based RNA therapy in a preclinical model of lymphangioleiomyomatosis (LAM), a destructive lung disease caused by loss-of-function mutations in the Tsc2 gene. Our lung-targeting LNP exhibited highly efficient delivery of the mouse tuberous sclerosis complex 2 (Tsc2) mRNA for the restoration of TSC2 tumor suppressor in tumor and achieved remarkable therapeutic effect in reducing tumor burden. This research establishes mRNA LNPs as a promising therapeutic intervention for the treatment of LAM.
    Keywords:  lipid nanoparticles; lung-targeted delivery; lymphangioleiomyomatosis; mRNA; tuberous sclerosis complex
    DOI:  https://doi.org/10.1073/pnas.2116271119
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