bims-lysosi Biomed News
on Lysosomes and signaling
Issue of 2021–12–12
forty papers selected by
Stephanie Fernandes, Max Planck Institute for Biology of Ageing
  1. Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.
  2. Wnt5a Promotes Lysosomal Cholesterol Egress and Protects Against Atherosclerosis.
  3. The mTOR-lysosome axis at the centre of ageing.
  4. Conformational dynamics of free and membrane-bound human Hsp70 in model cytosolic and endo-lysosomal environments.
  5. An unexpected tumor suppressor role of SQSTM1/p62 in liver tumorigenesis.
  6. Pharmacological Chaperone Therapy for Pompe Disease.
  7. GBA mutations, glucosylceramide and Parkinson's disease.
  8. Novel Dual-Organelle-Targeting Probe (RCPP) for Simultaneous Measurement of Organellar Acidity and Alkalinity in Living Cells.
  9. Cholesterol transport in the late endocytic pathway: Roles of ORP family proteins.
  10. Disturbance of lipid homeostasis in lysosomal lipase deficiency – pathomechanism, diagnosis and treatment
  11. Drug-Induced Lysosomal Impairment Is Associated with the Release of Extracellular Vesicles Carrying Autophagy Markers.
  12. Pathological α-syn aggregation is mediated by glycosphingolipid chain length and the physiological state of α-syn in vivo.
  13. Krabbe Disease: Prospects of Finding a Cure Using AAV Gene Therapy.
  14. Proteolysis of Amyloid β by Lysosomal Enzymes as a Function of Fibril Morphology.
  15. A molecular genetics view on Mucopolysaccharidosis Type II.
  16. Reproduction in Animal Models of Lysosomal Storage Diseases: A Scoping Review.
  17. Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis.
  18. Protocol for quantification of the lysosomal degradation of extracellular proteins into mammalian cells.
  19. The mTORC1-eIF4F axis controls paused pluripotency.
  20. Editorial: Coordination of mRNA Transport and Translation With Vesicle and Organelle Trafficking and Dynamics.
  21. The Association Between Lysosomal Storage Disorder Genes and Parkinson's Disease: A Large Cohort Study in Chinese Mainland Population.
  22. The Cross Talk Between p53 and mTOR Pathways in Response to Physiological and Genotoxic Stresses.
  23. Perinuclear positioning of endosomes can affect PS-ASO activities.
  24. C-X-C Motif Chemokine Ligand 9 and Its CXCR3 Receptor Are the Salt and Pepper for T Cells Trafficking in a Mouse Model of Gaucher Disease.
  25. Real-Time and High-Fidelity Tracking of Lysosomal Dynamics with a Dicyanoisophorone-Based Fluorescent Probe.
  26. Glitazone Treatment Rescues Phenotypic Deficits in a Fly Model of Gaucher/Parkinson's Disease.
  27. A Rapid and Simple UHPLC-MS/MS Method for Quantification of Plasma Globotriaosylsphingosine (lyso-Gb3).
  28. Exercise increases phosphorylation of the putative mTORC2 activity readout NDRG1 in human skeletal muscle.
  29. A Novel CLN6 Variant Associated With Juvenile Neuronal Ceroid Lipofuscinosis in Patients With Absence of Visual Loss as a Presenting Feature.
  30. Acid Sphingomyelinase Deficiency: A Clinical and Immunological Perspective.
  31. The role of Alzheimer's disease risk genes in endolysosomal pathways.
  32. Altered protein secretion in Batten disease.
  33. Cargo sorting at the trans-Golgi network at a glance.
  34. Dynamic eIF3a O-GlcNAcylation controls translation reinitiation during nutrient stress.
  35. Dual Targeting by Inhibition of Phosphoinositide-3-Kinase and Mammalian Target of Rapamycin Attenuates the Neuroinflammatory Responses in Murine Hippocampal Cells and Seizures in C57BL/6 Mice.
  36. A viral protein disrupts vacuolar acidification to facilitate virus infection in plants.
  37. Pre-steady-state Kinetic Analysis of Amino Acid Transporter SLC6A14 Reveals Rapid Turnover Rate and Substrate Translocation.
  38. Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution.
  39. Autophagy inhibition mediated by MCOLN1/TRPML1 suppresses cancer metastasis via regulating a ROS-driven TP53/p53 pathway.
  40. The Salmonella effector SifA initiates a kinesin-1 and kinesin-3 recruitment process mirroring that mediated by Arl8a/b.
  1. Nucleic Acids Res. 2021 Dec 06. pii: gkab1157. [Epub ahead of print]
    Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.
    Jonathan Bohlen, Mykola Roiuk, Aurelio A Teleman.
      Phosphorylation of Ribosomal Protein S6 (RPS6) was the first post-translational modification of the ribosome to be identified and is a commonly-used readout for mTORC1 activity. Although the cellular and organismal functions of RPS6 phosphorylation are known, the molecular consequences of RPS6 phosphorylation on translation are less well understood. Here we use selective ribosome footprinting to analyze the location of ribosomes containing phosphorylated RPS6 on endogenous mRNAs in cells. We find that RPS6 becomes progressively dephosphorylated on ribosomes as they translate an mRNA. As a consequence, average RPS6 phosphorylation is higher on mRNAs with short coding sequences (CDSs) compared to mRNAs with long CDSs. We test whether RPS6 phosphorylation differentially affects mRNA translation based on CDS length by genetic removal of RPS6 phosphorylation. We find that RPS6 phosphorylation promotes translation of mRNAs with short CDSs more strongly than mRNAs with long CDSs. Interestingly, RPS6 phosphorylation does not promote translation of mRNAs with 5' TOP motifs despite their short CDS lengths, suggesting they are translated via a different mode. In sum this provides a dynamic view of RPS6 phosphorylation on ribosomes as they translate mRNAs and the functional consequence on translation.
    DOI:  https://doi.org/10.1093/nar/gkab1157
  2. Circ Res. 2021 Dec 10.
    Wnt5a Promotes Lysosomal Cholesterol Egress and Protects Against Atherosclerosis.
    Sara Awan, Magalie Lambert, Ali Imtiaz, Fabien Alpy, Catherine Tomasetto, Mustapha Oulad-Abdelghani, Christine Schaeffer, Chloé Moritz, Diane Julien-David, Souad Najib, Laurent O Martinez, Rachel L Matz, Xavier Collet, Roberto Silva-Rojas, Johann Böhm, Joachim Herz, Jérome Terrand, Philippe Boucher.
      Background: Impairment of cellular cholesterol trafficking is at the heart of atherosclerotic lesions formation. This involves egress of cholesterol from the lysosomes and two lysosomal proteins, the Niemann-Pick C1 (NPC1) and NPC2 that promotes cholesterol trafficking. However, movement of cholesterol out the lysosome and how disrupted cholesterol trafficking leads to atherosclerosis is unclear. As the Wnt ligand, Wnt5a inhibits the intracellular accumulation of cholesterol in multiple cell types, we tested whether Wnt5a interacts with the lysosomal cholesterol export machinery and studied its role in atherosclerotic lesions formation. Methods: We generated mice deleted for the Wnt5a gene in vascular smooth muscle cells (VSMCs). To establish whether Wnt5a also protects against cholesterol accumulation in human VSMCs, we used a CRISPR/Cas9 guided nuclease approach to generate human VSMCs knockout for Wnt5a. Results: We show that Wnt5a is a crucial component of the lysosomal cholesterol export machinery. By increasing lysosomal acid lipase expression, decreasing metabolic signaling by the mTORC1 kinase, and through binding to NPC1 and NPC2, Wnt5a senses changes in dietary cholesterol supply and promotes lysosomal cholesterol egress to the endoplasmic reticulum (ER). Consequently, loss of Wnt5a decoupled mTORC1 from variations in lysosomal sterol levels, disrupted lysosomal function, decreased cholesterol content in the ER, and promoted atherosclerosis. Conclusions: These results reveal an unexpected function of the Wnt5a pathway as essential for maintaining cholesterol homeostasis in vivo.
    DOI:  https://doi.org/10.1161/CIRCRESAHA.121.318881
  3. FEBS Open Bio. 2021 Dec 08.
    The mTOR-lysosome axis at the centre of ageing.
    Julian M Carosi, Celia Fourrier, Julien Bensalem, Timothy J Sargeant.
      Age-related diseases represent some of largest unmet clinical needs of our time. While treatment of specific disease-related signs has had some success (for example the effect of statin drugs on slowing progression of atherosclerosis), slowing biological ageing itself represents a target that could significantly increase health-span and reduce the prevalence of multiple age-related diseases. Mechanistic target of rapamycin complex 1 (mTORC1) is known to control fundamental processes in ageing: inhibiting this signalling complex slows biological ageing, reduces age-related disease pathology, and increases lifespan in model organisms. How mTORC1 inhibition achieves this is still subject to ongoing research. However, one mechanism by which mTORC1 inhibition is thought to slow ageing is by activating the autophagy-lysosome pathway. In this review we examine the special bi-directional relationship between mTORC1 and the lysosome. In cells, mTORC1 is located on lysosomes. From this advantageous position, it directly controls the autophagy-lysosome pathway. However, the lysosome also controls mTORC1 activity in numerous ways, creating a special two-way relationship. We then explore specific examples of how inhibition of mTORC1 and activation of the autophagy-lysosome pathway slow the molecular hallmarks of ageing. This body of literature demonstrates that the autophagy-lysosome pathway represents an excellent target for treatments that seek to slow biological ageing and increase health-span in humans.
    Keywords:  Lysosome; age-related disease; aging; autophagy; lysophagy; mTOR
    DOI:  https://doi.org/10.1002/2211-5463.13347
  4. Commun Biol. 2021 12 07. 4(1): 1369
    Conformational dynamics of free and membrane-bound human Hsp70 in model cytosolic and endo-lysosomal environments.
    Valeria Calvaresi, Line T Truelsen, Sidsel B Larsen, Nikolaj H T Petersen, Thomas Kirkegaard, Kasper D Rand.
      The binding of the major stress-inducible human 70-kDa heat shock protein (Hsp70) to the anionic phospholipid bis-(monoacylglycero)-phosphate (BMP) in the lysosomal membrane is crucial for its impact on cellular pathology in lysosomal storage disorders. However, the conformational features of this protein-lipid complex remain unclear. Here, we apply hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the dynamics of the full-length Hsp70 in the cytosol and its conformational changes upon translocation into lysosomes. Using wild-type and W90F mutant proteins, we also map and discriminate the interaction of Hsp70 with BMP and other lipid components of the lysosomal membrane. We identify the N-terminal of the nucleotide binding domain (residues 87-118) as the primary orchestrator of BMP interaction. We show that the conformation of this domain is significantly reorganized in the W90F mutant, explaining its inability to stabilize lysosomal membranes. Overall, our results reveal important new molecular details of the protective effect of Hsp70 in lysosomal storage diseases, which, in turn, could guide future drug development.
    DOI:  https://doi.org/10.1038/s42003-021-02892-7
  5. Autophagy. 2021 Dec 06. 1-3
    An unexpected tumor suppressor role of SQSTM1/p62 in liver tumorigenesis.
    Xiaojuan Chao, Hong-Min Ni, Wen-Xing Ding.
      SQSTM1/p62 (sequestosome 1) is a macroautophagy/autophagy receptor protein that is degraded by selective autophagy. Intracellular accumulation of SQSTM1 activates multiple cell survival signaling pathways including NFΚB/NF-κB (nuclear factor kappa B), MTOR (mechanistic target of rapamycin kinase) and NFE2L2/Nrf2 (nuclear factor, erythroid derived 2, like 2). Both SQSTM1 and NFE2L2 have been considered as oncogenic, and increased accumulation of SQSTM1 and NFE2L2 activation have been frequently observed in various cancers including hepatocellular carcinoma. In a recent study, we found that deletion of Sqstm1 improved hepatic metabolic reprogramming and cell repopulation resulting in the attenuation of liver injury in mice with liver-specific deletion of Atg5 and Tsc1 that have defective hepatic autophagy and persistent MTOR complex 1 (MTORC1) activation. To our surprise, hepatocytic deletion of Sqstm1 promotes liver tumorigenesis in liver-specific atg5 and tsc1 double-knockout mice. Overall, these findings reveal a complex interplay among autophagy, SQSTM1 and MTORC1 and their differential roles either as oncogenic or tumor suppressor in liver tumorigenesis depending on the disease stage and context.
    Keywords:  ATG5; MTOR; Nrf2; Tsc1; autophagy; hepatocellular carcinoma
    DOI:  https://doi.org/10.1080/15548627.2021.2008693
  6. Molecules. 2021 Nov 29. pii: 7223. [Epub ahead of print]26(23):
    Pharmacological Chaperone Therapy for Pompe Disease.
    Marc Borie-Guichot, My Lan Tran, Yves Génisson, Stéphanie Ballereau, Cécile Dehoux.
      Pompe disease (PD), a lysosomal storage disease, is caused by mutations of the GAA gene, inducing deficiency in the acid alpha-glucosidase (GAA). This enzymatic impairment causes glycogen burden in lysosomes and triggers cell malfunctions, especially in cardiac, smooth and skeletal muscle cells and motor neurons. To date, the only approved treatment available for PD is enzyme replacement therapy (ERT) consisting of intravenous administration of rhGAA. The limitations of ERT have motivated the investigation of new therapies. Pharmacological chaperone (PC) therapy aims at restoring enzymatic activity through protein stabilization by ligand binding. PCs are divided into two classes: active site-specific chaperones (ASSCs) and the non-inhibitory PCs. In this review, we summarize the different pharmacological chaperones reported against PD by specifying their PC class and activity. An emphasis is placed on the recent use of these chaperones in combination with ERT.
    Keywords:  Pompe disease; lysosomal storage disease; pharmacological chaperone
    DOI:  https://doi.org/10.3390/molecules26237223
  7. Curr Opin Neurobiol. 2021 Dec 06. pii: S0959-4388(21)00131-8. [Epub ahead of print]72 148-154
    GBA mutations, glucosylceramide and Parkinson's disease.
    Ivan Milenkovic, Shani Blumenreich, Anthony H Futerman.
      Mutations in GBA, which encodes the lysosomal enzyme glucocerebrosidase, are the highest genetic risk factor for Parkinson's disease (PD), although the mechanistic link between GBA mutations and PD is unknown. An attractive hypothesis is that the lipid substrate of glucocerebrosidase, glucosylceramide, accumulates in patients with PD with a GBA mutation (PD-GBA). Despite the availability of new and accurate methods to quantitatively measure brain glucosylceramide levels, there is little evidence that glucosylceramide, or its deacetylated derivative, glucosylsphingosine, accumulates in human PD or PD-GBA brain or cerebrospinal fluid. Thus, a straightforward association between glucosylceramide levels and the development of PD does not appear valid, necessitating the involvement of other cellular pathways to explain this association, which could involve defects in lysosomal function.
    DOI:  https://doi.org/10.1016/j.conb.2021.11.004
  8. ACS Omega. 2021 Nov 30. 6(47): 31447-31456
    Novel Dual-Organelle-Targeting Probe (RCPP) for Simultaneous Measurement of Organellar Acidity and Alkalinity in Living Cells.
    Nazmiye B Yapici, Xiang Gao, Xin Yan, Shanshan Hou, Steffen Jockusch, Lillian Lesniak, K Michael Gibson, Lanrong Bi.
      Many organelles, such as lysosomes and mitochondria, maintain a pH that is different from the cytoplasmic pH. These pH differences have important functional ramifications for those organelles. Many cellular events depend upon a well-compartmentalized distribution of H+ ions spanning the membrane for the optimal function. Cells have developed a variety of mechanisms that enable the regulation of organelle pH. However, the measurement of organellar acidity/alkalinity in living cells has remained a challenge. Currently, most existing probes for the estimation of intracellular pH show a single -organelle targeting capacity. Such probes provide data that fails to comprehensively reveal the pathological and physiological roles and connections between mitochondria and lysosomes in different species. Mitochondrial and lysosomal functions are closely related and important for regulating cellular homeostasis. Accordingly, the design of a single fluorescent probe that can simultaneously target mitochondria and lysosomes is highly desirable, enabling a better understanding of the crosstalk between these organelles. We report the development of a novel fluorescent sensor, rhodamine-coumarin pH probe (RCPP), for detection of organellar acidity/alkalinity. RCPP simultaneously moves between mitochondrion and lysosome subcellular locations, facilitating the simultaneous monitoring of pH alterations in mitochondria and lysosomes.
    DOI:  https://doi.org/10.1021/acsomega.1c03087
  9. J Steroid Biochem Mol Biol. 2021 Dec 02. pii: S0960-0760(21)00233-8. [Epub ahead of print] 106040
    Cholesterol transport in the late endocytic pathway: Roles of ORP family proteins.
    Vesa M Olkkonen, Elina Ikonen.
      Oxysterol-binding protein (OSBP) homologues, designated ORP or OSBPL proteins, constitute one of the largest families of intracellular lipid-binding/transfer proteins (LTP). This review summarizes the mounting evidence that several members of this family participate in the machinery facilitating cholesterol trafficking in the late endocytic pathway. There are indications that OSBP, besides acting as a cholesterol/phosphatidylinositol 4-phosphate (PI4P) exchanger at the endoplasmic reticulum (ER)-trans-Golgi network (TGN) membrane contact sites (MCS), also exchanges these lipids at ER-lysosome (Lys) contacts, increasing Lys cholesterol content. The long isoform of ORP1 (ORP1 L), which also targets ER-late endosome (LE)/Lys MCS, has the capacity to mediate cholesterol transport either from ER to LE or in the opposite direction. Moreover, it regulates the motility, positioning and fusion of LE as well as autophagic flux. ORP2, the closest relative of ORP1, is mainly cytosolic, but also targets PI(4,5)P2-rich endosomal compartments. Our latest data suggest that ORP2 transfers cholesterol from LE to recycling endosomes (RE) in exchange for PI(4,5)P2, thus stimulating the recruitment of focal adhesion kinase (FAK) on the RE and cell adhesion. FAK activates phosphoinositide kinase on the RE to enhance PI(4,5)P2 synthesis. ORP2 in turn transfers PI(4,5)P2 from RE to LE, thus regulating LE tubule formation and transport activity.
    Keywords:  cholesterol; late endosome; lipid transport; lysosome; membrane contact site; phosphoinositide
    DOI:  https://doi.org/10.1016/j.jsbmb.2021.106040
  10. Postepy Biochem. 2021 09 30. 67(3): 231-235
    Disturbance of lipid homeostasis in lysosomal lipase deficiency – pathomechanism, diagnosis and treatment
    Patryk Lipiński, Anna Tylki-Szymańska.
      Lysosomal acid lipase (LAL) plays a key role in lipid metabolism through the hydrolysis of cholesteryl esters and triglycerides in lysosomes. LAL deficiency is a rare autosomal recessive lysosomal storage disease caused by deleterious mutations in the LIPA gene. In the case of LAL deficiency, cholesteryl esters and triglycerides accumulate within the lysosomes. The up-regulation of endogenous cholesterol production, increased synthesis of apolipoprotein B (ApoB) and increased production of very-low-density lipoprotein cholesterol (VLDL-C) is observed. The diagnosis is easy due to the currently available method of testing the enzyme activity in a dry blood spot. Molecular analysis is necessary to verify the clinical and biochemical diagnosis and to analyze the genotype-phenotype correlation. Sebelipase alfa is a recombinant human lysosomal lipase intended for use in enzyme replacement therapy in patients with LAL deficiency.
    DOI:  https://doi.org/10.18388/pb.2021_389
  11. Int J Mol Sci. 2021 Nov 29. pii: 12922. [Epub ahead of print]22(23):
    Drug-Induced Lysosomal Impairment Is Associated with the Release of Extracellular Vesicles Carrying Autophagy Markers.
    Krizia Sagini, Sandra Buratta, Federica Delo, Roberto Maria Pellegrino, Stefano Giovagnoli, Lorena Urbanelli, Carla Emiliani.
      Amiodarone is a cationic amphiphilic drug used as an antiarrhythmic agent. It induces phospholipidosis, i.e., the accumulation of phospholipids within organelles of the endosomal-lysosomal system. Extracellular vesicles (EVs) are membrane-enclosed structures released by any type of cell and retrieved in every fluid of the body. EVs have been initially identified as a system to dispose cell waste, but they are also considered to be an additional manner to transmit intercellular signals. To understand the role of EVs in drug-induced phospholipidosis, we investigated EVs release in amiodarone-treated HEK-293 cells engineered to produce fluorescently labelled EVs. We observed that amiodarone induces the release of a higher number of EVs, mostly of a large/medium size. EVs released upon amiodarone treatment do not display significant morphological changes or altered size distribution, but they show a dose-dependent increase in autophagy associated markers, indicating a higher release of EVs with an autophagosome-like phenotype. Large/medium EVs also show a higher content of phospholipids. Drugs inducing lysosomal impairment such as chloroquine and bafilomycin A1 similarly prompt a higher release of EVs enriched in autophagy markers. This result suggests a mechanism associated with amiodarone-induced lysosomal impairment more than a connection with the accumulation of specific undigested substrates. Moreover, the implementation of the lysosomal function by overexpressing TFEB, a master gene regulator of lysosomal biogenesis, prevents the amiodarone-induced release of EVs, suggesting that this could be a feasible target to attenuate drug-induced abnormalities.
    Keywords:  TFEB; amiodarone; bafilomycin A1; chloroquine; exosomes; extracellular vesicles; lysosomal storage disorders; microvesicles; phospholipidosis; secretory autophagy
    DOI:  https://doi.org/10.3390/ijms222312922
  12. Proc Natl Acad Sci U S A. 2021 Dec 14. pii: e2108489118. [Epub ahead of print]118(50):
    Pathological α-syn aggregation is mediated by glycosphingolipid chain length and the physiological state of α-syn in vivo.
    Kristina Fredriksen, Stefanos Aivazidis, Karan Sharma, Kevin J Burbidge, Caleb Pitcairn, Friederike Zunke, Eilrayna Gelyana, Joseph R Mazzulli.
      GBA1 mutations that encode lysosomal β-glucocerebrosidase (GCase) cause the lysosomal storage disorder Gaucher disease (GD) and are strong risk factors for synucleinopathies, including Parkinson's disease and Lewy body dementia. Only a subset of subjects with GBA1 mutations exhibit neurodegeneration, and the factors that influence neurological phenotypes are unknown. We find that α-synuclein (α-syn) neuropathology induced by GCase depletion depends on neuronal maturity, the physiological state of α-syn, and specific accumulation of long-chain glycosphingolipid (GSL) GCase substrates. Reduced GCase activity does not initiate α-syn aggregation in neonatal mice or immature human midbrain cultures; however, adult mice or mature midbrain cultures that express physiological α-syn oligomers are aggregation prone. Accumulation of long-chain GSLs (≥C22), but not short-chain species, induced α-syn pathology and neurological dysfunction. Selective reduction of long-chain GSLs ameliorated α-syn pathology through lysosomal cathepsins. We identify specific requirements that dictate synuclein pathology in GD models, providing possible explanations for the phenotypic variability in subjects with GCase deficiency.
    Keywords:  Gaucher disease; Parkinson’s disease; glycosphingolipids; lysosomal storage disease; α-synuclein
    DOI:  https://doi.org/10.1073/pnas.2108489118
  13. Front Med (Lausanne). 2021 ;8 760236
    Krabbe Disease: Prospects of Finding a Cure Using AAV Gene Therapy.
    Gibran Nasir, Rajiv Chopra, Fiona Elwood, Seemin S Ahmed.
      Krabbe Disease (KD) is an autosomal metabolic disorder that affects both the central and peripheral nervous systems. It is caused by a functional deficiency of the lysosomal enzyme, galactocerebrosidase (GALC), resulting in an accumulation of the toxic metabolite, psychosine. Psychosine accumulation affects many different cellular pathways, leading to severe demyelination. Although there is currently no effective therapy for Krabbe disease, recent gene therapy-based approaches in animal models have indicated a promising outlook for clinical treatment. This review highlights recent findings in the pathogenesis of Krabbe disease, and evaluates AAV-based gene therapy as a promising strategy for treating this devastating pediatric disease.
    Keywords:  Krabbe disease (globoid cell leukodystrophy); adeno-associated virus; galactocerebrosidase; gene therapy; leukodystrophies; psychosine
    DOI:  https://doi.org/10.3389/fmed.2021.760236
  14. ACS Omega. 2021 Nov 30. 6(47): 31520-31527
    Proteolysis of Amyloid β by Lysosomal Enzymes as a Function of Fibril Morphology.
    Tyler R Lambeth, Ryan R Julian.
      Aggregation of amyloid-β (Aβ) into extracellular plaques is a well-known hallmark of Alzheimer's disease (AD). Similarly, autophagic vacuoles, autophagosomes, and other residual bodies within dystrophic neurites, though more difficult to detect, are characteristic features of AD. To explore the potential intersection between these observations, we conducted experiments to assess whether Aβ fibril formation disrupts proteolysis by lysosomal enzymes. Fibrils constituted by either Aβ 1-40 or Aβ 1-42 were grown under both neutral and acidic pH. The extent of proteolysis by individual cathepsins (L, D, B, and H) was monitored by both thioflavin T fluorescence and liquid chromatography combined with mass spectrometry. The results show that all Aβ fibril morphologies are resistant to cathepsin digestion, with significant amounts of the undigested material remaining for samples grown in either neutral or acidic pH. Further analysis revealed that the neutral-grown fibrils are proteolytically resistant throughout the sequence, while the acid-grown fibrils prevented digestion primarily in the C-terminal portion of the sequence. Fibrils grown from Aβ 1-42 are generally more resistant to degradation compared to Aβ 1-40. Overall, the results indicate that Aβ fibrils formed in the neutral pH environments found in intracellular or extracellular spaces may pose the greatest difficulty for complete digestion by the lysosome, particularly when the fibrils are comprised of Aβ 1-42.
    DOI:  https://doi.org/10.1021/acsomega.1c03915
  15. Mutat Res Rev Mutat Res. 2021 Jul-Dec;788:pii: S1383-5742(21)00029-6. [Epub ahead of print]788 108392
    A molecular genetics view on Mucopolysaccharidosis Type II.
    Shalja Verma, Supansa Pantoom, Janine Petters, Anand Kumar Pandey, Andreas Hermann, Jan Lukas.
      Mucopolysaccharidosis Type II (MPS II) is an X-linked recessive genetic disorder that primarily affects male patients. With an incidence of 1 in 100,000 male live births, the disease is one of the orphan diseases. MPS II symptoms are caused by mutations in the lysosomal iduronate-2-sulfatase (IDS) gene. The mutations cause a loss of enzymatic performance and result in the accumulation of glycosaminoglycans (GAGs), heparan sulfate and dermatan sulfate, which are no longer degradable. This inadvertent accumulation causes damage in multiple organs and leads either to a severe neurological course or to an attenuated course of the disease, although the exact relationship between mutation, extent of GAG accumulation and disease progression is not yet fully understood. This review is intended to present current diagnostic procedures and therapeutic interventions. In times when the genetic profile of patients plays an increasingly important role in the assessment of therapeutic success and future drug design, we chose to further elucidate the impact of genetic diversity within the IDS gene on disease phenotype and potential implications in current diagnosis, prognosis and therapy. We report recent advances in the structural biological elucidation of I2S enzyme that that promises to improve our future understanding of the molecular damage of the hundreds of IDS gene variants and will aid damage prediction of novel mutations in the future.
    Keywords:  Genotype-phenotype correlation; Hunter syndrome; Iduronate-2-sulfatase; Individualized medicine; Lysosomal storage disease; Missense mutations
    DOI:  https://doi.org/10.1016/j.mrrev.2021.108392
  16. Front Mol Biosci. 2021 ;8 773384
    Reproduction in Animal Models of Lysosomal Storage Diseases: A Scoping Review.
    Daniela Vuolo, Cinthia Castro Do Nascimento, Vânia D'Almeida.
      Background: Lysosomal storage diseases (LSDs) are caused by a mutation in a specific gene. Enzymatic dysfunction results in a progressive storage of substrates that gradually affects lysosomal, cellular and tissue physiology. Their pathophysiological consequences vary according to the nature of the stored substrate, making LSDs complex and multisystemic diseases. Some LSDs result in near normal life expectancies, and advances in treatments mean that more people reach the age to have children, so considering the effects of LSDs on fertility and the risks associated with having children is of growing importance. Objectives: As there is a lack of clinical studies describing the effect of LSDs on the physiology of reproductivity, we undertook a scoping review of studies using animal models of LSDs focusing on reproductive parameters. Methods: We searched six databases: MEDLINE, LILACS, Scopus, Web of Science, Embase and SciELO, and identified 49 articles that met our inclusion criteria. Results: The majority of the studies used male animal models, and a number reported severe morphological and physiological damage in gametes and gonads in models of sphingolipidoses. Models of other LSDs, such as mucopolysaccharidoses, presented important morphological damage. Conclusion: Many of the models found alterations in reproductive systems. Any signs of subfertility or morphological damage in animal models are important, particularly in rodents which are extremely fertile, and may have implications for individuals with LSDs. We suggest the use of more female animal models to better understand the physiopathology of the diseases, and the use of clinical case studies to further explore the risks of individuals with LSDs having children.
    Keywords:  lipidosis; lysosomal storage diseases; mucopolysaccharidosis; ovary; reproduction; sperm; sphingolipidosis; testis
    DOI:  https://doi.org/10.3389/fmolb.2021.773384
  17. JCI Insight. 2021 Dec 08. pii: e150120. [Epub ahead of print]6(23):
    Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis.
    Linda Mc Koene, Eva Niggl, Ilse Wallaard, Martina Proietti-Onori, Diana C Rotaru, Ype Elgersma.
      Tuberous sclerosis complex (TSC), caused by heterozygous mutations in TSC1 or TSC2, frequently results in intractable epilepsy. Here, we made use of an inducible Tsc1-knockout mouse model, allowing us to study electrophysiological and molecular changes of Tsc1-induced epileptogenesis over time. We recorded from pyramidal neurons in the hippocampus and somatosensory cortex (L2/L3) and combined this with an analysis of transcriptome changes during epileptogenesis. Deletion of Tsc1 resulted in hippocampus-specific changes in excitability and adaptation, which emerged before seizure onset and progressed over time. All phenotypes were rescued after early treatment with rapamycin, an mTOR inhibitor. Later in epileptogenesis, we observed a hippocampal increase of excitation-to-inhibition ratio. These cellular changes were accompanied by dramatic transcriptional changes, especially after seizure onset. Most of these changes were rescued upon rapamycin treatment. Of the genes encoding ion channels or belonging to the Gene Ontology term action potential, 27 were differentially expressed just before seizure onset, suggesting a potential driving role in epileptogenesis. Our data highlight the complex changes driving epileptogenesis in TSC, including the changed expression of multiple ion channels. Our study emphasizes inhibition of the TSC/mTOR signaling pathway as a promising therapeutic approach to target epilepsy in patients with TSC.
    Keywords:  Epilepsy; Ion channels; Neuroscience; Transcription
    DOI:  https://doi.org/10.1172/jci.insight.150120
  18. STAR Protoc. 2021 Dec 17. 2(4): 100975
    Protocol for quantification of the lysosomal degradation of extracellular proteins into mammalian cells.
    Ayaka Tomihari, Momoka Chiba, Akira Matsuura, Eisuke Itakura.
      Endocytic internalization of extracellular proteins plays roles in signaling, nutrient uptake, immunity, and extracellular protein quality control. However, there are few protocols for analyzing the lysosomal degradation of extracellular protein. Here, we purified secreted proteins fused with pH-sensitive GFP and acid- and protease-resistant RFP from mammalian cells and describe an internalization assay for mammalian cells. This protocol enables quantification of cellular uptake and lysosomal degradation of protein-of-interest (POI) via cell biological and biochemical analyses. For full details on the use and execution of this protocol, please refer to Itakura et al. (2020).
    Keywords:  Cell Biology; Cell-based Assays; Flow Cytometry/Mass Cytometry; Molecular/Chemical Probes; Protein expression and purification
    DOI:  https://doi.org/10.1016/j.xpro.2021.100975
  19. EMBO Rep. 2021 Dec 06. e53081
    The mTORC1-eIF4F axis controls paused pluripotency.
    Xueting Xu, Tanveer Ahmed, Lulu Wang, Xintao Cao, Zeyu Zhang, Ming Wang, Yuan Lv, Shahzina Kanwal, Muqddas Tariq, Runxia Lin, Hui Zhang, Yinghua Huang, Hao Peng, Danni Lin, Xue Shi, Didi Geng, Baohua Liu, Xiaofei Zhang, Wen Yi, Yan Qin, Miguel A Esteban, Baoming Qin.
      Mouse embryonic stem cells (mESCs) can self-renew indefinitely and maintain pluripotency. Inhibition of mechanistic target of rapamycin (mTOR) by the kinase inhibitor INK128 is known to induce paused pluripotency in mESCs cultured with traditional serum/LIF medium (SL), but the underlying mechanisms remain unclear. In this study, we demonstrate that mTOR complex 1 (mTORC1) but not complex 2 (mTORC2) mediates mTOR inhibition-induced paused pluripotency in cells grown in both SL and 2iL medium (GSK3 and MEK inhibitors and LIF). We also show that mTORC1 regulates self-renewal in both conditions mainly through eIF4F-mediated translation initiation that targets mRNAs of both cytosolic and mitochondrial ribosome subunits. Moreover, inhibition of mitochondrial translation is sufficient to induce paused pluripotency. Interestingly, eIF4F also regulates maintenance of pluripotency in an mTORC1-independent but MEK/ERK-dependent manner in SL, indicating that translation of pluripotency genes is controlled differently in SL and 2iL. Our study reveals a detailed picture of how mTOR governs self-renewal in mESCs and uncovers a context-dependent function of eIF4F in pluripotency regulation.
    Keywords:  eIF4F; mTORC1; mitochondrial translation; pluripotency; self-renewal
    DOI:  https://doi.org/10.15252/embr.202153081
  20. Front Cell Dev Biol. 2021 ;9 800136
    Editorial: Coordination of mRNA Transport and Translation With Vesicle and Organelle Trafficking and Dynamics.
    Anni Vedeler, Clive R Bramham.
      
    Keywords:  RNP granule; endosomes; extracellular vesicles; lysosomes; mRNA
    DOI:  https://doi.org/10.3389/fcell.2021.800136
  21. Front Aging Neurosci. 2021 ;13 749109
    The Association Between Lysosomal Storage Disorder Genes and Parkinson's Disease: A Large Cohort Study in Chinese Mainland Population.
    Yu-Wen Zhao, Hong-Xu Pan, Zhenhua Liu, Yige Wang, Qian Zeng, Zheng-Huan Fang, Teng-Fei Luo, Kun Xu, Zheng Wang, Xun Zhou, Runcheng He, Bin Li, Guihu Zhao, Qian Xu, Qi-Ying Sun, Xin-Xiang Yan, Jie-Qiong Tan, Jin-Chen Li, Ji-Feng Guo, Bei-Sha Tang.
      Background: Recent years have witnessed an increasing number of studies indicating an essential role of the lysosomal dysfunction in Parkinson's disease (PD) at the genetic, biochemical, and cellular pathway levels. In this study, we investigated the association between rare variants in lysosomal storage disorder (LSD) genes and Chinese mainland PD. Methods: We explored the association between rare variants of 69 LSD genes and PD in 3,879 patients and 2,931 controls from Parkinson's Disease & Movement Disorders Multicenter Database and Collaborative Network in China (PD-MDCNC) using next-generation sequencing, which were analyzed by using the optimized sequence kernel association test. Results: We identified the significant burden of rare putative LSD gene variants in Chinese mainland patients with PD. This association was robust in familial or sporadic early-onset patients after excluding the GBA variants but not in sporadic late-onset patients. The burden analysis of variant sets in genes of LSD subgroups revealed a suggestive significant association between variant sets in genes of sphingolipidosis deficiency disorders and familial or sporadic early-onset patients. In contrast, variant sets in genes of sphingolipidoses, mucopolysaccharidoses, and post-translational modification defect disorders were suggestively associated with sporadic late-onset patients. Then, SMPD1 and other four novel genes (i.e., GUSB, CLN6, PPT1, and SCARB2) were suggestively associated with sporadic early-onset or familial patients, whereas GALNS and NAGA were suggestively associated with late-onset patients. Conclusion: Our findings supported the association between LSD genes and PD and revealed several novel risk genes in Chinese mainland patients with PD, which confirmed the importance of lysosomal mechanisms in PD pathogenesis. Moreover, we identified the genetic heterogeneity in early-onset and late-onset of patients with PD, which may provide valuable suggestions for the treatment.
    Keywords:  GBA; Parkinson’s disease; lysosomal storage disorders; lysosome; rare putative damaging variants
    DOI:  https://doi.org/10.3389/fnagi.2021.749109
  22. Front Cell Dev Biol. 2021 ;9 775507
    The Cross Talk Between p53 and mTOR Pathways in Response to Physiological and Genotoxic Stresses.
    Danrui Cui, Ruirui Qu, Dian Liu, Xiufang Xiong, Tingbo Liang, Yongchao Zhao.
      The tumor suppressor p53 is activated upon multiple cellular stresses, including DNA damage, oncogene activation, ribosomal stress, and hypoxia, to induce cell cycle arrest, apoptosis, and senescence. Mammalian target of rapamycin (mTOR), an evolutionarily conserved serine/threonine protein kinase, serves as a central regulator of cell growth, proliferation, and survival by coordinating nutrients, energy, growth factors, and oxygen levels. p53 dysfunction and mTOR pathway hyperactivation are hallmarks of human cancer. The balance between response to stresses or commitment to cell proliferation and survival is governed by various regulatory loops between the p53 and mTOR pathways. In this review, we first briefly introduce the tumor suppressor p53 and then describe the upstream regulators and downstream effectors of the mTOR pathway. Next, we discuss the role of p53 in regulating the mTOR pathway through its transcriptional and non-transcriptional effects. We further describe the complicated role of the mTOR pathway in modulating p53 activity. Finally, we discuss the current knowledge and future perspectives on the coordinated regulation of the p53 and mTOR pathways.
    Keywords:  MDM2; mTOR; miRNA; p53; post-translation; transcription; tumorigenesis
    DOI:  https://doi.org/10.3389/fcell.2021.775507
  23. Nucleic Acids Res. 2021 Dec 08. pii: gkab1198. [Epub ahead of print]
    Perinuclear positioning of endosomes can affect PS-ASO activities.
    Xue-Hai Liang, Joshua G Nichols, Dario Tejera, Stanley T Crooke.
      Phosphorothioate (PS) modified antisense oligonucleotide (ASO) drugs that act on cellular RNAs must enter cells and be released from endocytic organelles to elicit antisense activity. It has been shown that PS-ASOs are mainly released by late endosomes. However, it is unclear how endosome movement in cells contributes to PS-ASO activity. Here, we show that PS-ASOs in early endosomes display Brownian type motion and migrate only short distances, whereas PS-ASOs in late endosomes (LEs) move linearly along microtubules with substantial distances. In cells with normal microtubules and LE movement, PS-ASO-loaded LEs tend to congregate perinuclearly. Disruption of perinuclear positioning of LEs by reduction of dynein 1 decreased PS-ASO activity, without affecting PS-ASO cellular uptake. Similarly, disruption of perinuclear positioning of PS-ASO-LE foci by reduction of ER tethering proteins RNF26, SQSTM1 and UBE2J1, or by overexpression of P50 all decreased PS-ASO activity. However, enhancing perinuclear positioning through reduction of USP15 or over-expression of RNF26 modestly increased PS-ASO activity, indicating that LE perinuclear positioning is required for ensuring efficient PS-ASO release. Together, these observations suggest that LE movement along microtubules and perinuclear positioning affect PS-ASO productive release.
    DOI:  https://doi.org/10.1093/nar/gkab1198
  24. Int J Mol Sci. 2021 Nov 24. pii: 12712. [Epub ahead of print]22(23):
    C-X-C Motif Chemokine Ligand 9 and Its CXCR3 Receptor Are the Salt and Pepper for T Cells Trafficking in a Mouse Model of Gaucher Disease.
    Albert Frank Magnusen, Reena Rani, Mary Ashley McKay, Shelby Loraine Hatton, Tsitsi Carol Nyamajenjere, Daniel Nii Aryee Magnusen, Jörg Köhl, Gregory Alex Grabowski, Manoj Kumar Pandey.
      Gaucher disease is a lysosomal storage disease, which happens due to mutations in GBA1/Gba1 that encodes the enzyme termed as lysosomal acid β-glucosidase. The major function of this enzyme is to catalyze glucosylceramide (GC) into glucose and ceramide. The deficiency of this enzyme and resultant abnormal accumulation of GC cause altered function of several of the innate and adaptive immune cells. For example, augmented infiltration of T cells contributes to the increased production of pro-inflammatory cytokines, (e.g., IFNγ, TNFα, IL6, IL12p40, IL12p70, IL23, and IL17A/F). This leads to tissue damage in a genetic mouse model (Gba19V/-) of Gaucher disease. The cellular mechanism(s) by which increased tissue infiltration of T cells occurs in this disease is not fully understood. Here, we delineate role of the CXCR3 receptor and its exogenous C-X-C motif chemokine ligand 9 (CXCL9) in induction of increased tissue recruitment of CD4+ T and CD8+ T cells in Gaucher disease. Intracellular FACS staining of macrophages (Mϕs) and dendritic cells (DCs) from Gba19V/- mice showed elevated production of CXCL9. Purified CD4+ T cells and the CD8+ T cells from Gba19V/- mice showed increased expression of CXCR3. Ex vivo and in vivo chemotaxis experiments showed CXCL9 involvement in the recruitment of Gba19V/- T cells. Furthermore, antibody blockade of the CXCL9 receptor (CXCR3) on T cells caused marked reduction in CXCL9- mediated chemotaxis of T cells in Gba19V/- mice. These data implicate abnormalities of the CXCL9-CXCR3 axis leading to enhanced tissue recruitment of T cells in Gaucher disease. Such results provide a rationale for blockade of the CXCL9/CXCR3 axis as potential new therapeutic targets for the treatment of inflammation in Gaucher disease.
    Keywords:  chemokine; chemokine receptor; inflammation; lysosomal storage disease
    DOI:  https://doi.org/10.3390/ijms222312712
  25. Anal Chem. 2021 Dec 07.
    Real-Time and High-Fidelity Tracking of Lysosomal Dynamics with a Dicyanoisophorone-Based Fluorescent Probe.
    Jiaxin Hong, Qianhua Li, Qingfeng Xia, Guoqiang Feng.
      The development of high-performance probes that can visualize and track the dynamic changes of lysosomes is very important for the in-depth study of lysosomes. Herein, we report that a dicyanoisophorone-based probe (named DCIP) can be used for high-fidelity imaging of lysosomes and lysosomal dynamics. DCIP can be easily prepared and shows strong far-red to near-infrared emissions centered at 653 nm in water with a huge Stokes shift (224 nm), high quantum yield (Φ = 0.15), high pKa value (∼8.79), and good biocompatibility. DCIP also shows good cell permeability and can label lysosomes rapidly with bright fluorescence without a time-consuming washing process before imaging. DCIP also possesses good photostability and negligible background, making it effective for long-term and high spatiotemporal resolution (0.44 s of exposure) imaging of lysosomes. Moreover, DCIP achieved high-fidelity tracking of lysosomal dynamics at an extremely low concentration (1 nM). Finally, we also demonstrated that DCIP could real-time track the interactions of lysosomes with other organelles (damaged mitochondria as a model) and image the drug-escape processes from lysosomes. All of the results show that DCIP holds broad prospects in lysosome-related research.
    DOI:  https://doi.org/10.1021/acs.analchem.1c04341
  26. Int J Mol Sci. 2021 Nov 25. pii: 12740. [Epub ahead of print]22(23):
    Glitazone Treatment Rescues Phenotypic Deficits in a Fly Model of Gaucher/Parkinson's Disease.
    Oluwanifemi Shola-Dare, Shelby Bailess, Carlos C Flores, William M Vanderheyden, Jason R Gerstner.
      Parkinson's Disease (PD) is the most common movement disorder, and the strongest genetic risk factor for PD is mutations in the glucocerebrosidase gene (GBA). Mutations in GBA also lead to the development of Gaucher Disease (GD), the most common type of lysosomal storage disorder. Current therapeutic approaches fail to address neurological GD symptoms. Therefore, identifying therapeutic strategies that improve the phenotypic traits associated with GD/PD in animal models may provide an opportunity for treating neurological manifestations of GD/PD. Thiazolidinediones (TZDs, also called glitazones) are a class of compounds targeted for the treatment of type 2 diabetes, and have also shown promise for the treatment of neurodegenerative disease, including PD. Here, we tested the efficacy of glitazone administration during development in a fly GD model with deletions in the GBA homolog, dGBA1b (GBA1ΔTT/ΔTT). We observed an optimal dose of pioglitazone (PGZ) at a concentration of 1 μM that reduced sleep deficits, locomotor impairments, climbing defects, and restoration of normal protein levels of Ref(2)P, a marker of autophagic flux, in GBA1ΔTT/ΔTT mutant flies, compared to GBA1+/+ control flies. These data suggest that PGZ may represent a potential compound with which to treat GD/PD by improving function of lysosomal-autophagy pathways, a cellular process that removes misfolded or aggregated proteins.
    Keywords:  Lewy body; autophagy; dementia; neurodegeneration; p62; β-acid glucosidase 1
    DOI:  https://doi.org/10.3390/ijms222312740
  27. Molecules. 2021 Dec 03. pii: 7358. [Epub ahead of print]26(23):
    A Rapid and Simple UHPLC-MS/MS Method for Quantification of Plasma Globotriaosylsphingosine (lyso-Gb3).
    Alessandro Perrone, Susan Mohamed, Vincenzo Donadio, Rocco Liguori, Manuela Contin.
      Fabry disease (FD) is a rare X-linked lysosomal storage disorder caused by α-galactosidase A gene (GLA) mutations, resulting in loss of activity of the lysosomal hydrolase, α-galactosidase A (α-Gal A). As a result, the main glycosphingolipid substrates, globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3), accumulate in plasma, urine, and tissues. Here, we propose a simple, fast, and sensitive method for plasma quantification of lyso-Gb3, the most promising secondary screening target for FD. Assisted protein precipitation with methanol using Phree cartridges was performed as sample pre-treatment and plasma concentrations were measured using UHPLC-MS/MS operating in MRM positive electrospray ionization. Method validation provided excellent results for the whole calibration range (0.25-100 ng/mL). Intra-assay and inter-assay accuracy and precision (CV%) were calculated as <10%. The method was successfully applied to 55 plasma samples obtained from 34 patients with FD, 5 individuals carrying non-relevant polymorphisms of the GLA gene, and 16 healthy controls. Plasma lyso-Gb3 concentrations were larger in both male and female FD groups compared to healthy subjects (p < 0.001). Normal levels of plasma lyso-Gb3 were observed for patients carrying non-relevant mutations of the GLA gene compared to the control group (p = 0.141). Dropping the lower limit of quantification (LLOQ) to 0.25 ng/mL allowed us to set the optimal plasma lyso-Gb3 cut-off value between FD patients and healthy controls at 0.6 ng/mL, with a sensitivity of 97.1%, specificity of 100%, and accuracy of 0.998 expressed by the area under the ROC curve (C.I. 0.992 to 1.000, p-value < 0.001). Based on the results obtained, this method can be a reliable tool for early phenotypic assignment, assessing diagnoses in patients with borderline GalA activity, and confirming non-relevant mutations of the GLA gene.
    Keywords:  Fabry disease; UHPLC-MS/MS; lyso-Gb3; protein precipitation
    DOI:  https://doi.org/10.3390/molecules26237358
  28. Am J Physiol Endocrinol Metab. 2021 Dec 06.
    Exercise increases phosphorylation of the putative mTORC2 activity readout NDRG1 in human skeletal muscle.
    Jonas Roland Knudsen, Kaspar W Persson, Jaroslawna Meister, Christian Strini Carl, Steffen H Raun, Nicoline R Andersen, Lykke Sylow, Bente Kiens, Thomas E Jensen, Erik A Richter, Maximilian Kleinert.
      In mice, exercise is suggested to activate the mechanistic target of rapamycin complex 2 (mTORC2) in skeletal muscle, and mTORC2 is required for normal muscle glucose uptake during exercise. Whether this translates to human skeletal muscle and what signaling pathways facilitate the exercise-induced mTORC2 activation is unknown but important to determine given the important role of mTORC2 in metabolism. We herein tested the hypothesis that exercise increases mTORC2 activity in human skeletal muscle and investigated if β2-adrenergic receptor (AR) activation mediates exercise-induced mTORC2 activation. We examined several mTORC2 activity readouts (p-NDRG1 Thr346, p-Akt Ser473, p-mTOR S2481, and p-Akt Thr450) in human skeletal muscle biopsies after uphill walking or cycling exercise. In mouse muscles, we assessed mTORC2 activity readouts following acute activation of muscle β2-adrenergic or Gs signaling and during in vivo and ex vivo muscle contractions. Exercise increased phosphorylation of NDRG1 Thr346 in human soleus, gastrocnemius, and vastus lateralis muscle, without changing p-Akt Ser473, p-Akt Thr450, and p-mTOR Ser2481. In mouse muscle, stimulation of β2-adrenergic or Gs signaling and ex vivo contractions failed to increase p-NDRG1 Thr346, while in vivo contractions were sufficient to induce p-NDRG1 Thr346. In conclusion, the mTORC2 activity readout p-NDRG1 Thr346 is a novel exercise-responsive signaling protein in human skeletal muscle. Notably, contraction-induced p-NDRG1 Thr346 appears to require a systemic factor. Unlike exercise, and in contrast to published data obtained in cultured muscles cells, stimulation of β2-adrenergic signaling is not sufficient to trigger NDRG1 phosphorylation in mature mouse skeletal muscle.
    Keywords:  Exercise; Humans; Skeletal muscle; mTORC2; β-adrenergic signaling
    DOI:  https://doi.org/10.1152/ajpendo.00389.2021
  29. Front Genet. 2021 ;12 746101
    A Novel CLN6 Variant Associated With Juvenile Neuronal Ceroid Lipofuscinosis in Patients With Absence of Visual Loss as a Presenting Feature.
    Paschalis Nicolaou, George A Tanteles, Christina Votsi, Eleni Zamba-Papanicolaou, Savvas S Papacostas, Kyproula Christodoulou, Yiolanda-Panayiota Christou.
      The neuronal ceroid lipofuscinoses (NCLs), also known as Batten disease, are a group of autosomal recessive lysosomal storage disorders that are characterized by neurodegeneration, progressive cognitive decline, motor impairment, ataxia, loss of vision, seizures, and premature death. To date, pathogenic variants in more than 13 genes have been associated with NCLs. CLN6 encodes an endoplasmic reticulum non-glycosylated transmembrane protein, which is involved in lysosomal acidification. Mutations in CLN6 cause late-infantile juvenile NCL (JNCL) adult-onset NCL, and Kufs disease. Members from two available families with JNCL were clinically evaluated, and samples were collected from consenting individuals. The molecular investigation was performed by whole-exome sequencing, Sanger sequencing, and family segregation analysis. Furthermore, in silico prediction analysis and structural modeling of the identified CLN6 variants were performed. We report clinical and genetic findings of three patients from two Greek-Cypriot families (families 915 and 926) with JNCL. All patients were males, and the first symptoms appeared at the age of 6 years. The proband of family 926 presented with loss of motor abilities, ataxia, spasticity, seizure, and epilepsy. The proband of family 915 had ataxia, spasticity, dysarthria, dystonia, and intellectual disability. Both probands did not show initial signs of vision and/or hearing loss. Molecular analysis of family 926 revealed two CLN6 biallelic variants: the novel, de novo p.Tyr295Cys and the known p.Arg136His variants. In family 915, both patients were homozygous for the p.Arg136His CLN6 variant. Prediction analysis of the two CLN6 variants characterized them as probably damaging and disease-causing. Structural modeling of the variants predicted that they probably cause protein structural differentiation. In conclusion, we describe two unrelated Cypriot families with JNCL. Both families had variants in the CLN6 gene; however, they presented with slightly different symptoms, and notably none of the patients has loss of vision. In silico prediction and structural analyses indicate that both variants are most likely pathogenic.
    Keywords:  CNL6; batten disease; in silico prediction; lysosomal storage disorders; neuronal ceroid lipofuscinosis; next-generation sequencing
    DOI:  https://doi.org/10.3389/fgene.2021.746101
  30. Int J Mol Sci. 2021 Nov 28. pii: 12870. [Epub ahead of print]22(23):
    Acid Sphingomyelinase Deficiency: A Clinical and Immunological Perspective.
    Carolina Pinto, Diana Sousa, Vladimir Ghilas, Andrea Dardis, Maurizio Scarpa, Maria Fatima Macedo.
      Acid sphingomyelinase deficiency (ASMD) is a lysosomal storage disease caused by deficient activity of acid sphingomyelinase (ASM) enzyme, leading to the accumulation of varying degrees of sphingomyelin. Lipid storage leads to foam cell infiltration in tissues, and clinical features including hepatosplenomegaly, pulmonary insufficiency and in some cases central nervous system involvement. ASM enzyme replacement therapy is currently in clinical trial being the first treatment addressing the underlying pathology of the disease. Therefore, presently, it is critical to better comprehend ASMD to improve its diagnose and monitoring. Lung disease, including recurrent pulmonary infections, are common in ASMD patients. Along with lung disease, several immune system alterations have been described both in patients and in ASMD animal models, thus highlighting the role of ASM enzyme in the immune system. In this review, we summarized the pivotal roles of ASM in several immune system cells namely on macrophages, Natural Killer (NK) cells, NKT cells, B cells and T cells. In addition, an overview of diagnose, monitoring and treatment of ASMD is provided highlighting the new enzyme replacement therapy available.
    Keywords:  Niemann–Pick; acid sphingomyelinase deficiency; immune; lysosomal storage disease; sphingomyelinase
    DOI:  https://doi.org/10.3390/ijms222312870
  31. Neurobiol Dis. 2021 Dec 03. pii: S0969-9961(21)00325-9. [Epub ahead of print]162 105576
    The role of Alzheimer's disease risk genes in endolysosomal pathways.
    Marcell P Szabo, Swati Mishra, Allison Knupp, Jessica E Young.
      There is ample pathological and biological evidence for endo-lysosomal dysfunction in Alzheimer's disease (AD) and emerging genetic studies repeatedly implicate endo-lysosomal genes as associated with increased AD risk. The endo-lysosomal network (ELN) is essential for all cell types of the central nervous system (CNS), yet each unique cell type utilizes cellular trafficking differently (see Fig. 1). Challenges ahead involve defining the role of AD associated genes in the functionality of the endo-lysosomal network (ELN) and understanding how this impacts the cellular dysfunction that occurs in AD. This is critical to the development of new therapeutics that will impact, and potentially reverse, early disease phenotypes. Here we review some early evidence of ELN dysfunction in AD pathogenesis and discuss the role of selected AD-associated risk genes in this pathway. In particular, we review genes that have been replicated in multiple genome-wide association studies(Andrews et al., 2020; Jansen et al., 2019; Kunkle et al., 2019; Lambert et al., 2013; Marioni et al., 2018) and reviewed in(Andrews et al., 2020) that have defined roles in the endo-lysosomal network. These genes include SORL1, an AD risk gene harboring both rare and common variants associated with AD risk and a role in trafficking cargo, including APP, through the ELN; BIN1, a regulator of clathrin-mediated endocytosis whose expression correlates with Tau pathology; CD2AP, an AD risk gene with roles in endosome morphology and recycling; PICALM, a clathrin-binding protein that mediates trafficking between the trans-Golgi network and endosomes; and Ephrin Receptors, a family of receptor tyrosine kinases with AD associations and interactions with other AD risk genes. Finally, we will discuss how human cellular models can elucidate cell-type specific differences in ELN dysfunction in AD and aid in therapeutic development.
    Keywords:  AD risk genes; Endolysosomal network; Human cellular model
    DOI:  https://doi.org/10.1016/j.nbd.2021.105576
  32. Dis Model Mech. 2021 Dec 01. pii: dmm049152. [Epub ahead of print]14(12):
    Altered protein secretion in Batten disease.
    Robert J Huber.
      The neuronal ceroid lipofuscinoses (NCLs), collectively known as Batten disease, are a group of neurological diseases that affect all ages and ethnicities worldwide. There are 13 different subtypes of NCL, each caused by a mutation in a distinct gene. The NCLs are characterized by the accumulation of undigestible lipids and proteins in various cell types. This leads to progressive neurodegeneration and clinical symptoms including vision loss, progressive motor and cognitive decline, seizures, and premature death. These diseases have commonly been characterized by lysosomal defects leading to the accumulation of undigestible material but further research on the NCLs suggests that altered protein secretion may also play an important role. This has been strengthened by recent work in biomedical model organisms, including Dictyostelium discoideum, mice, and sheep. Research in D. discoideum has reported the extracellular localization of some NCL-related proteins and the effects of NCL-related gene loss on protein secretion during unicellular growth and multicellular development. Aberrant protein secretion has also been observed in mammalian models of NCL, which has allowed examination of patient-derived cerebrospinal fluid and urine for potential diagnostic and prognostic biomarkers. Accumulated evidence links seven of the 13 known NCL-related genes to protein secretion, suggesting that altered secretion is a common hallmark of multiple NCL subtypes. This Review highlights the impact of altered protein secretion in the NCLs, identifies potential biomarkers of interest and suggests that future work in this area can provide new therapeutic insight.
    Keywords:   Dictyostelium discoideum ; Batten disease; Cerebrospinal fluid; Model system; Neuronal ceroid lipofuscinosis; Secretion; Urine
    DOI:  https://doi.org/10.1242/dmm.049152
  33. J Cell Sci. 2021 Dec 01. pii: jcs259110. [Epub ahead of print]134(23):
    Cargo sorting at the trans-Golgi network at a glance.
    Charlotte Ford, Anup Parchure, Julia von Blume, Christopher G Burd.
      The Golgi functions principally in the biogenesis and trafficking of glycoproteins and lipids. It is compartmentalized into multiple flattened adherent membrane sacs termed cisternae, which each contain a distinct repertoire of resident proteins, principally enzymes that modify newly synthesized proteins and lipids sequentially as they traffic through the stack of Golgi cisternae. Upon reaching the final compartments of the Golgi, the trans cisterna and trans-Golgi network (TGN), processed glycoproteins and lipids are packaged into coated and non-coated transport carriers derived from the trans Golgi and TGN. The cargoes of clathrin-coated vesicles are chiefly residents of endo-lysosomal organelles, while uncoated carriers ferry cargo to the cell surface. There are outstanding questions regarding the mechanisms of protein and lipid sorting within the Golgi for export to different organelles. Nonetheless, conceptual advances have begun to define the key molecular features of cargo clients and the mechanisms underlying their sorting into distinct export pathways, which we have collated in this Cell Science at a Glance article and the accompanying poster.
    Keywords:  Calcium; Clathrin; Epithelial cells; Glycoprotein; Golgi; Lipids; Secretion
    DOI:  https://doi.org/10.1242/jcs.259110
  34. Nat Chem Biol. 2021 Dec 09.
    Dynamic eIF3a O-GlcNAcylation controls translation reinitiation during nutrient stress.
    Xin Erica Shu, Yuanhui Mao, Longfei Jia, Shu-Bing Qian.
      In eukaryotic cells, many messenger RNAs (mRNAs) possess upstream open reading frames (uORFs) in addition to the main coding region. After uORF translation, the ribosome could either recycle at the stop codon or resume scanning for downstream start codons in a process known as reinitiation. Accumulating evidence suggests that some initiation factors, including eukaryotic initiation factor 3 (eIF3), linger on the early elongating ribosome, forming an eIF3-80S complex. Very little is known about how eIF3 is carried along with the 80S during elongation and whether the eIF3-80S association is subject to regulation. Here, we report that eIF3a undergoes dynamic O-linked N-acetylglucosamine (O-GlcNAc) modification in response to nutrient starvation. Stress-induced de-O-GlcNAcylation promotes eIF3 retention on the elongating ribosome and facilitates activating transcription factor 4 (ATF4) reinitiation. Eliminating the modification site from eIF3a via CRISPR genome editing induces ATF4 reinitiation even under the nutrient-rich condition. Our findings illustrate a mechanism in balancing ribosome recycling and reinitiation, thereby linking the nutrient stress response and translational reprogramming.
    DOI:  https://doi.org/10.1038/s41589-021-00913-4
  35. Front Immunol. 2021 ;12 739452
    Dual Targeting by Inhibition of Phosphoinositide-3-Kinase and Mammalian Target of Rapamycin Attenuates the Neuroinflammatory Responses in Murine Hippocampal Cells and Seizures in C57BL/6 Mice.
    Preeti Vyas, Rajkumar Tulsawani, Divya Vohora.
      Emerging evidence suggests the association of seizures and inflammation; however, underlying cell signaling mechanisms are still not fully understood. Overactivation of phosphoinositide-3-kinases is associated with both neuroinflammation and seizures. Herein, we speculate the PI3K/Akt/mTOR pathway as a promising therapeutic target for neuroinflammation-mediated seizures and associated neurodegeneration. Firstly, we cultured HT22 cells for detection of the downstream cell signaling events activated in a lipopolysaccharide (LPS)-primed pilocarpine (PILO) model. We then evaluated the effects of 7-day treatment of buparlisib (PI3K inhibitor, 25 mg/kg p.o.), dactolisib (PI3K/mTOR inhibitor, 25 mg/kg p.o.), and rapamycin (mTORC1 inhibitor, 10 mg/kg p.o.) in an LPS-primed PILO model of seizures in C57BL/6 mice. LPS priming resulted in enhanced seizure severity and reduced latency. Buparlisib and dactolisib, but not rapamycin, prolonged latency to seizures and reduced neuronal loss, while all drugs attenuated seizure severity. Buparlisib and dactolisib further reduced cellular redox, mitochondrial membrane potential, cleaved caspase-3 and p53, nuclear integrity, and attenuated NF-κB, IL-1β, IL-6, TNF-α, and TGF-β1 and TGF-β2 signaling both in vitro and in vivo post-PILO and LPS+PILO inductions; however, rapamycin mitigated the same only in the PILO model. Both drugs protected against neuronal cell death demonstrating the contribution of this pathway in the seizure-induced neuronal pyknosis; however, rapamycin showed resistance in a combination model. Furthermore, LPS and PILO exposure enhanced pAkt/Akt and phospho-p70S6/total-p70S6 kinase activity, while buparlisib and dactolisib, but not rapamycin, could reduce it in a combination model. Partial rapamycin resistance was observed possibly due to the reactivation of the pathway by a functionally different complex of mTOR, i.e., mTORC2. Our study substantiated the plausible involvement of PI3K-mediated apoptotic and inflammatory pathways in LPS-primed PILO-induced seizures and provides evidence that its modulation constitutes an anti-inflammatory mechanism by which seizure inhibitory effects are observed. We showed dual inhibition by dactolisib as a promising approach. Targeting this pathway at two nodes at a time may provide new avenues for antiseizure therapies.
    Keywords:  PI3K/Akt/p-p70S6 pathway; cytokines; kinase inhibition ; lipopolysaccharide; mammalian target of rapamycin (mTOR); neuronal inflammation; phosphoinositide-3-kinase (PI3K); pilocarpine
    DOI:  https://doi.org/10.3389/fimmu.2021.739452
  36. EMBO J. 2021 Dec 09. e108713
    A viral protein disrupts vacuolar acidification to facilitate virus infection in plants.
    Meng Yang, Asigul Ismayil, Zhihao Jiang, Yan Wang, Xiyin Zheng, Liming Yan, Yiguo Hong, Dawei Li, Yule Liu.
      Vacuolar acidification is essential for vacuoles in diverse physiological functions. However, its role in plant defense, and whether and how pathogens affect vacuolar acidification to promote infection remain unknown. Here, we show that Barley stripe mosaic virus (BSMV) replicase γa, but not its mutant γaR569A , directly blocks acidification of vacuolar lumen and suppresses autophagic degradation to promote viral infection in plants. These were achieved via molecular interaction between γa and V-ATPase catalytic subunit B2 (VHA-B2), leading to disruption of the interaction between VHA-B2 and V-ATPase catalytic subunit E (VHA-E), which impairs the membrane localization of VHA-B2 and suppresses V-ATPase activity. Furthermore, a mutant virus BSMVR569A with the R569A point mutation possesses less viral pathogenicity. Interestingly, multiple viral infections block vacuolar acidification. These findings reveal that functional vacuolar acidification is required for plant antiviral defense and disruption of vacuolar acidification could be a general viral counter-defense strategy employed by multiple viruses.
    Keywords:   virus ; V-ATPase; autophagy; defense; vacuolar acidification
    DOI:  https://doi.org/10.15252/embj.2021108713
  37. Front Physiol. 2021 ;12 777050
    Pre-steady-state Kinetic Analysis of Amino Acid Transporter SLC6A14 Reveals Rapid Turnover Rate and Substrate Translocation.
    Yueyue Shi, Jiali Wang, Elias Ndaru, Christof Grewer.
      SLC6A14 (solute carrier family 6 member 14) is an amino acid transporter, driven by Na+ and Cl- co-transport, whose structure, function, and molecular and kinetic mechanism have not been well characterized. Its broad substrate selectivity, including neutral and cationic amino acids, differentiates it from other SLC6 family members, and its proposed involvement in nutrient transport in several cancers suggest that it could become an important drug target. In the present study, we investigated SLC6A14 function and its kinetic mechanism after expression in human embryonic kidney (HEK293) cells, including substrate specificity and voltage dependence under various ionic conditions. We applied rapid solution exchange, voltage jumps, and laser photolysis of caged alanine, allowing sub-millisecond temporal resolution, to study SLC6A14 steady state and pre-steady state kinetics. The results highlight the broad substrate specificity and suggest that extracellular chloride enhances substrate transport but is not required for transport. As in other SLC6 family members, Na+ binding to the substrate-free transporter (or conformational changes associated with it) is electrogenic and is likely rate limiting for transporter turnover. Transient current decaying with a time constant of <1ms is also observed after rapid amino acid application, both in forward transport and homoexchange modes, indicating a slightly electrogenic, but fast and not rate-limiting substrate translocation step. Our results, which are consistent with kinetic modeling, suggest rapid transporter turnover rate and substrate translocation with faster kinetics compared with other SLC6 family members. Together, these results provided novel information on the SLC6A14 transport cycle and mechanism, expanding our understanding of SLC6A14 function.
    Keywords:  ATB0,+; SLC6A14; electrophysiology; laser-photolysis; membrane transporter; molecular physiology; rapid kinetics
    DOI:  https://doi.org/10.3389/fphys.2021.777050
  38. Nat Commun. 2021 Dec 07. 12(1): 7113
    Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution.
    Ana Martinez-Val, Dorte B Bekker-Jensen, Sophia Steigerwald, Claire Koenig, Ole Østergaard, Adi Mehta, Trung Tran, Krzysztof Sikorski, Estefanía Torres-Vega, Ewa Kwasniewicz, Sólveig Hlín Brynjólfsdóttir, Lisa B Frankel, Rasmus Kjøbsted, Nicolai Krogh, Alicia Lundby, Simon Bekker-Jensen, Fridtjof Lund-Johansen, Jesper V Olsen.
      Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for eliciting a coordinated response to stimuli. Mass spectrometry-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of protein networks in cells, but involves laborious workflows that does not cover the phospho-proteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. We benchmark the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in vitro in HeLa cells and in vivo in mouse tissues. Finally, we investigate the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction. Proteomics data generated in this study can be explored through https://SpatialProteoDynamics.github.io .
    DOI:  https://doi.org/10.1038/s41467-021-27398-y
  39. Autophagy. 2021 Dec 08. 1-23
    Autophagy inhibition mediated by MCOLN1/TRPML1 suppresses cancer metastasis via regulating a ROS-driven TP53/p53 pathway.
    Yanhong Xing, Xiangqing Wei, Yucheng Liu, Meng-Meng Wang, Zhongheng Sui, Xinyan Wang, Wucheng Zhu, Mengmei Wu, Chen Lu, Yuan-Hui Fei, Yi Jiang, Yang Zhang, Yuqing Wang, Feng Guo, Jun-Li Cao, Jiansong Qi, Wuyang Wang.
      Compelling evidence has demonstrated that macroautophagy/autophagy plays an important role in regulating multiple steps of metastatic cascades; however, the precise role of autophagy in metastasis remains unclear. This study demonstrates that autophagy inhibition induced by MCOLN1/TRPML1 suppresses cancer metastasis by evoking the ROS-mediated TP53/p53 pathway. First, we found that MCOLN1-mediated autophagy inhibition not only profoundly inhibits both migration and invasion in malignant melanoma and glioma cell lines in vitro, but also suppresses melanoma metastasis in vivo. Second, our study reveals that autophagy inhibition induced by MCOLN1 leads to damaged mitochondria accumulation followed by large quantities of ROS release. Third, we demonstrate that the elevated ROS resulting from autophagy inhibition subsequently triggers TP53 activity, which in turn modulates expression of its downstream targets which are involved in a broad spectrum of the metastatic cascade to suppress metastasis including MMP members and TWIST. In summary, our findings have established a mechanism by which autophagy inhibition suppresses metastasis via the ROS-TP53 signaling pathway. More importantly, our study demonstrates that autophagy inhibition through stimulation of MCOLN1 could evidently be one of the therapeutic potentials for combating cancer metastasis.Abbreviations: 3-MA: 3-methyladenine; AA: amino acid; ATG5: autophagy related 5; ATG12: autophagy related 12; Baf-A1: bafilomycin A1; CCCP: carbonyl cyanide m-chlorophenylhydrazone; CQ: chloroquine; DMEM: Dulbecco's Modified Eagle Medium; EMT: epithelial-mesenchymal transition; FBS: fetal bovine serum; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HEK: human embryonic kidney; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MCOLN1/TRPML1: mucolipin TRP cation channel 1; MMP: matrix metallopeptidase; NC: negative control; NRK: normal rat kidney; PBS: phosphate-buffered saline; shRNA: short hairpin RNA; siRNA: short interfering RNA; SQSTM1/p62: sequestosome 1; ULK1: unc-51 like autophagy activating kinase 1.
    Keywords:  Autophagic arrest; MCOLN1; ROS; TP53; metastasis; mitochondria turnover
    DOI:  https://doi.org/10.1080/15548627.2021.2008752
  40. J Cell Sci. 2021 Dec 08. pii: jcs.259183. [Epub ahead of print]
    The Salmonella effector SifA initiates a kinesin-1 and kinesin-3 recruitment process mirroring that mediated by Arl8a/b.
    Ziyan Fang, Mathieu Fallet, Tomas Moest, Jean-Pierre Gorvel, Stéphane Méresse.
      When intracellular, pathogenic Salmonella reside in a membrane compartment composed of interconnected vacuoles and tubules, the formation of which depends on the translocation of bacterial effectors into the host cell. Cytoskeletons and their molecular motors are prime targets for these effectors. In this study, we show that the microtubule molecular motor KIF1Bß, a member of the kinesin-3 family, is a key element for the establishment of the Salmonella replication niche as its absence is detrimental to the stability of bacterial vacuoles and the formation of associated tubules. Kinesin-3 interacts with the Salmonella effector SifA but also with SKIP, a host protein complexed to SifA. The interaction with SifA is essential for the recruitment of kinesin-3 on Salmonella vacuoles while that with SKIP is incidental. In the non-infectious context, however, the interaction with SKIP is essential for the recruitment and activity of kinesin-3 on a part of lysosomes. Finally, our results show that in infected cells, the presence of SifA establishes a kinesin-1 and kinesin-3 recruitment pathway that is analogous to and functions independently of that mediated by the Arl8a/b GTPases.
    Keywords:   Salmonella ; Effector protein; Infection; Lysosome; Membrane trafficking; Molecular motor
    DOI:  https://doi.org/10.1242/jcs.259183
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