bims-lysosi Biomed News
on Lysosomes and signaling
Issue of 2020‒07‒12
twenty-nine papers selected by
Stephanie Fernandes
Max Planck Institute for Biology of Ageing


  1. Sci Adv. 2020 Jun;6(26): eaaz9805
    Higuchi-Sanabria R, Shen K, Kelet N, Frankino PA, Durieux J, Bar-Ziv R, Sing CN, Garcia EJ, Homentcovschi S, Sanchez M, Wu R, Tronnes SU, Joe L, Webster B, Ahilon-Jeronimo A, Monshietehadi S, Dallarda S, Pender C, Pon LA, Zoncu R, Dillin A.
      Recent work has highlighted the fact that lysosomes are a critical signaling hub of metabolic processes, providing fundamental building blocks crucial for anabolic functions. How lysosomal functions affect other cellular compartments is not fully understood. Here, we find that lysosomal recycling of the amino acids lysine and arginine is essential for proper ER quality control through the UPRER. Specifically, loss of the lysine and arginine amino acid transporter LAAT-1 results in increased sensitivity to proteotoxic stress in the ER and decreased animal physiology. We find that these LAAT-1-dependent effects are linked to glycine metabolism and transport and that the loss of function of the glycine transporter SKAT-1 also increases sensitivity to ER stress. Direct lysine and arginine supplementation, or glycine supplementation alone, can ameliorate increased ER stress sensitivity found in laat-1 mutants. These data implicate a crucial role in recycling lysine, arginine, and glycine in communication between the lysosome and ER.
    DOI:  https://doi.org/10.1126/sciadv.aaz9805
  2. EMBO Rep. 2020 Jul 09. e49898
    Zhang J, Andersen JP, Sun H, Liu X, Sonenberg N, Nie J, Shi Y.
      Nutrient sensing by the mTOR complex 1 (mTORC1) requires its translocation to the lysosomal membrane. Upon amino acids removal, mTORC1 becomes cytosolic and inactive, yet its precise subcellular localization and the mechanism of inhibition remain elusive. Here, we identified Aster-C as a negative regulator of mTORC1 signaling. Aster-C earmarked a special rough ER subdomain where it sequestered mTOR together with the GATOR2 complex to prevent mTORC1 activation during nutrient starvation. Amino acids stimulated rapid disassociation of mTORC1 from Aster-C concurrently with assembly of COP I vesicles which escorted mTORC1 to the lysosomal membrane. Consequently, ablation of Aster-C led to spontaneous activation of mTORC1 and dissociation of TSC2 from lysosomes, whereas inhibition of COP I vesicle biogenesis or actin dynamics prevented mTORC1 activation. Together, these findings identified Aster-C as a missing link between lysosomal trafficking and mTORC1 activation by revealing an unexpected role of COP I vesicles in mTORC1 signaling.
    Keywords:  ARF1; COP I; GRAMD1C; lysosomes; mTORC1
    DOI:  https://doi.org/10.15252/embr.201949898
  3. Trends Biochem Sci. 2020 Jul 02. pii: S0968-0004(20)30151-1. [Epub ahead of print]
    Zhao Q, Gao SM, Wang MC.
      Lysosomes transcend the role of degradation stations, acting as key nodes for interorganelle crosstalk and signal transduction. Lysosomes communicate with the nucleus through physical proximity and functional interaction. In response to external and internal stimuli, lysosomes actively adjust their distribution between peripheral and perinuclear regions and modulate lysosome-nucleus signaling pathways; in turn, the nucleus fine-tunes lysosomal biogenesis and functions through transcriptional controls. Changes in coordination between these two essential organelles are associated with metabolic disorders, neurodegenerative diseases, and aging. In this review, we address recent advances in lysosome-nucleus communication by multi-tiered regulatory mechanisms and discuss how these regulations couple metabolic inputs with organellar motility, cellular signaling, and transcriptional network.
    Keywords:  lysosomal adaptation; lysosomal metabolites; lysosome positioning; lysosome-to-nucleus signaling; transcription factors
    DOI:  https://doi.org/10.1016/j.tibs.2020.06.004
  4. EMBO J. 2020 Jul 09. e104494
    Herbst S, Campbell P, Harvey J, Bernard EM, Papayannopoulos V, Wood NW, Morris HR, Gutierrez MG.
      Cells respond to endolysosome damage by either repairing the damage or targeting damaged endolysosomes for degradation via lysophagy. However, the signals regulating the decision for repair or lysophagy are poorly characterised. Here, we show that the Parkinson's disease (PD)-related kinase LRRK2 is activated in macrophages by pathogen- or sterile-induced endomembrane damage. LRRK2 recruits the Rab GTPase Rab8A to damaged endolysosomes as well as the ESCRT-III component CHMP4B, thereby favouring ESCRT-mediated repair. Conversely, in the absence of LRRK2 and Rab8A, damaged endolysosomes are targeted to lysophagy. These observations are recapitulated in macrophages from PD patients where pathogenic LRRK2 gain-of-function mutations result in the accumulation of endolysosomes which are positive for the membrane damage marker Galectin-3. Altogether, this work indicates that LRRK2 regulates endolysosomal homeostasis by controlling the balance between membrane repair and organelle replacement, uncovering an unexpected function for LRRK2, and providing a new link between membrane damage and PD.
    Keywords:  LRRK2; Parkinson's disease; endolysosomal damage; lysosomes; tuberculosis
    DOI:  https://doi.org/10.15252/embj.2020104494
  5. J Biol Chem. 2020 Jul 09. pii: jbc.RA119.012346. [Epub ahead of print]
    Manandhar SP, Siddiqah IM, Cocca SM, Gharakhanian E.
      Membrane fusion/fission is a highly dynamic and conserved process that responds to intra- and extracellular signals. While the molecular machineries involved in membrane fusion/fission have been dissected, regulation of membrane dynamics remains poorly understood. The lysosomal vacuole of budding yeast (Saccharomyces cerevisiae) has served as a seminal model in studies of membrane dynamics. We have previously established that yeast ENV7 encodes an ortholog of STK16-related kinases that localizes to the vacuolar membrane and down-regulates vacuolar membrane fusion. Additionally, we have previously reported that Env7 phosphorylation in vivo is dependent on YCK3, a gene that encodes a vacuolar membrane casein kinase I (CKI) homolog that non-redundantly functions in fusion regulation. Here, we report that Env7 physically interacts with and is directly phosphorylated by Yck3. We also establish that Env7 vacuole fusion/fission regulation and vacuolar localization are mediated through its Yck3-dependent phosphorylation. Through extensive site-directed mutagenesis, we map phosphorylation to the Env7 C terminus and confirm that Ser-331 is a primary and preferred phosphorylation site. Phospho-deficient Env7 mutants were defective in negative regulation of membrane fusion, increasing the number of prominent vacuoles, whereas a phospho-mimetic substitution at Ser-331 increased the number of fragmented vacuoles. Bioinformatics approaches confirmed that Env7 Ser-331 is within a motif that is highly conserved in STK16-related kinases and that it also anchors an SXXS CKI phosphorylation motif (328SRFS331). This study represents the first report on the regulatory mechanism of an STK16 related kinase. It also points to regulation of vacuolar membrane dynamics via a novel Yck3-Env7 kinase cascade.
    Keywords:  CK1 YCK3; ENV7; LYSOSOMAL VACUOLE; REGULATION OF MEMBRANE DYNAMICS; Saccharomyces cerevisiae; VACUOLAR MEMBRANE DYNAMICS; lysosome; membrane fusion; protein phosphorylation; serine/threonine protein kinase; subcellular organelle; vacuole
    DOI:  https://doi.org/10.1074/jbc.RA119.012346
  6. J Am Soc Nephrol. 2020 Jul 08. pii: ASN.2019090960. [Epub ahead of print]
    Sachs W, Sachs M, Krüger E, Zielinski S, Kretz O, Huber TB, Baranowsky A, Westermann LM, Voltolini Velho R, Ludwig NF, Yorgan TA, Di Lorenzo G, Kollmann K, Braulke T, Schwartz IV, Schinke T, Danyukova T, Pohl S, Meyer-Schwesinger C.
      BACKGROUND: The mechanisms balancing proteostasis in glomerular cells are unknown. Mucolipidosis (ML) II and III are rare lysosomal storage disorders associated with mutations of the Golgi-resident GlcNAc-1-phosphotransferase, which generates mannose 6-phosphate residues on lysosomal enzymes. Without this modification, lysosomal enzymes are missorted to the extracellular space, which results in lysosomal dysfunction of many cell types. Patients with MLII present with severe skeletal abnormalities, multisystemic symptoms, and early death; the clinical course in MLIII is less progressive. Despite dysfunction of a major degradative pathway, renal and glomerular involvement is rarely reported, suggesting organ-specific compensatory mechanisms.METHODS: MLII mice were generated and compared with an established MLIII model to investigate the balance of protein synthesis and degradation, which reflects glomerular integrity. Proteinuria was assessed in patients. High-resolution confocal microscopy and functional assays identified proteins to deduce compensatory modes of balancing proteostasis.
    RESULTS: Patients with MLII but not MLIII exhibited microalbuminuria. MLII mice showed lysosomal enzyme missorting and several skeletal alterations, indicating that they are a useful model. In glomeruli, both MLII and MLIII mice exhibited reduced levels of lysosomal enzymes and enlarged lysosomes with abnormal storage material. Nevertheless, neither model had detectable morphologic or functional glomerular alterations. The models rebalance proteostasis in two ways: MLII mice downregulate protein translation and increase the integrated stress response, whereas MLIII mice upregulate the proteasome system in their glomeruli. Both MLII and MLIII downregulate the protein complex mTORC1 (mammalian target of rapamycin complex 1) signaling, which decreases protein synthesis.
    CONCLUSIONS: Severe lysosomal dysfunction leads to microalbuminuria in some patients with mucolipidosis. Mouse models indicate distinct compensatory pathways that balance proteostasis in MLII and MLIII.
    Keywords:  glomerular disease; integrated stress response; lysosomal storage disorder; mucolipidosis; osteopenia; proteotoxic stress
    DOI:  https://doi.org/10.1681/ASN.2019090960
  7. ACS Omega. 2020 Jun 30. 5(25): 15476-15486
    Elimam H, El-Say KM, Cybulsky AV, Khalil H.
      Fluvastatin (FLV) is a statin family member that may play a role in modulating a variety of medical disorders such as atherosclerosis and breast cancer. The present study addresses the ability of FLV to modulate the cellular immune response and provides a new nanosized FLV formula (self-nanoemulsifying delivery system, SNED) potentially more effective for suppression of breast cancer development. We monitored autophagic machinery through the expression of microtubule-associated protein 1A/1B-light chain 3 (LC3I/II). Lysosomal activity upon treatment was evaluated by mRNA and protein expression of lysosomal-associated membrane protein 1 (LAMP-1). Mitogen-activated protein kinase (MAPK) signaling and its association with proinflammatory cytokine secretion were assessed in treated cells. Autophagosome formation was significantly increased in cells that were pretreated with FLV-SNED in comparison to FLV-treated cells. Activation of autophagy was accompanied with arrest of LAMP-1 expression, which correlates with lysosomal activity. Simultaneously, both FLV and FLV-SNED activated MAPK signaling and modified interleukin-6 and tumor necrosis factor-α levels in treated cells. These findings indicate that FLV reduces cell viability via depletion of lysosomal activities along with accumulation of autophagosomes leading to disturbance of autophagosome-lysosomal fusion in treated cells. Furthermore, our data reveal the effectiveness of both FLV agents in the modulation of proinflammatory cytokine secretion from treated cells via regulation of MAPK signaling cascades and indicate that FLV-SNED is more efficient than FLV. This study provides new insights into how FLV regulates breast cancer cell viability via modulation of AMPK-mTOR and ERK-mTOR signaling, and through autophagosome formation accompanied by lysosomal degradation.
    DOI:  https://doi.org/10.1021/acsomega.0c01618
  8. Cell Chem Biol. 2020 Jun 30. pii: S2451-9456(20)30234-8. [Epub ahead of print]
    Wang Y, Zhang L, Wei Y, Huang W, Li L, Wu AA, Dastur A, Greninger P, Bray WM, Zhang CS, Li M, Lian W, Hu Z, Wang X, Liu G, Yao L, Guh JH, Chen L, Wang HR, Zhou D, Lin SC, Xu Q, Shen Y, Zhang J, Jurica MS, Benes CH, Deng X.
      Multidrug resistance (MDR) in cancer remains a major challenge for the success of chemotherapy. Natural products have been a rich source for the discovery of drugs against MDR cancers. Here, we applied high-throughput cytotoxicity screening of an in-house natural product library against MDR SGC7901/VCR cells and identified that the cyclodepsipeptide verucopeptin demonstrated notable antitumor potency. Cytological profiling combined with click chemistry-based proteomics revealed that ATP6V1G directly interacted with verucopeptin. ATP6V1G, a subunit of the vacuolar H+-ATPase (v-ATPase) that has not been previously targeted, was essential for SGC7901/VCR cell growth. Verucopeptin exhibited strong inhibition of both v-ATPase activity and mTORC1 signaling, leading to substantial pharmacological efficacy against SGC7901/VCR cell proliferation and tumor growth in vivo. Our results demonstrate that targeting v-ATPase via its V1G subunit constitutes a unique approach for modulating v-ATPase and mTORC1 signaling with great potential for the development of therapeutics against MDR cancers.
    Keywords:  V-ATPase; mTORC1 pathway; natural product; target identification
    DOI:  https://doi.org/10.1016/j.chembiol.2020.06.011
  9. Arterioscler Thromb Vasc Biol. 2020 Jul 09. ATVBAHA120314053
    Ni H, Xu S, Chen H, Dai Q.
      OBJECTIVE: Increased CTSS (cathepsin S) has been reported to play a critical role in atherosclerosis progression. Both CTSS synthesis and secretion are essential for exerting its functions. However, the underlying mechanisms contributing to CTSS synthesis and secretion in atherosclerosis remain unclear. Approach and Results: In this study, we showed that nicotine activated autophagy and upregulated CTSS expression in vascular smooth muscle cells and in atherosclerotic plaques. Western blotting and immunofluorescent staining showed that nicotine inhibited the mTORC1 activity, promoted the nuclear translocation of TFEB (transcription factor EB), and upregulated the expression of CTSS. Chromatin immunoprecipitation-qualificative polymerase chain reaction, electrophoretic mobility shift assay, and luciferase reporter assay further demonstrated that TFEB directly bound to the CTSS promoter. mTORC1 inhibition by nicotine or rapamycin promoted lysosomal exocytosis and CTSS secretion. Live cell assays and IP-mass spectrometry identified that the interactions involving Rab10 and mTORC1 control CTSS secretion. Nicotine promoted vascular smooth muscle cell migration by upregulating CTSS, and CTSS inhibition suppressed nicotine-induced atherosclerosis in vivo.CONCLUSIONS: We concluded that nicotine mediates CTSS synthesis and secretion through regulating the autophagy-lysosomal machinery, which offers a potential therapeutic target for atherosclerosis treatment.
    Keywords:  atherosclerosis; autophagy; ion channels; nicotine; staining and labeling
    DOI:  https://doi.org/10.1161/ATVBAHA.120.314053
  10. Alzheimers Res Ther. 2020 Jul 06. 12(1): 80
    Suire CN, Abdul-Hay SO, Sahara T, Kang D, Brizuela MK, Saftig P, Dickson DW, Rosenberry TL, Leissring MA.
      BACKGROUND: Cathepsin D (CatD) is a lysosomal protease that degrades both the amyloid β-protein (Aβ) and the microtubule-associated protein, tau, and has been genetically linked to late-onset Alzheimer disease (AD). Here, we sought to examine the consequences of genetic deletion of CatD on Aβ proteostasis in vivo and to more completely characterize the degradation of Aβ42 and Aβ40 by CatD.METHODS: We quantified Aβ degradation rates and levels of endogenous Aβ42 and Aβ40 in the brains of CatD-null (CatD-KO), heterozygous null (CatD-HET), and wild-type (WT) control mice. CatD-KO mice die by ~ 4 weeks of age, so tissues from younger mice, as well as embryonic neuronal cultures, were investigated. Enzymological assays and surface plasmon resonance were employed to quantify the kinetic parameters (KM, kcat) of CatD-mediated degradation of monomeric human Aβ42 vs. Aβ40, and the degradation of aggregated Aβ42 species was also characterized. Competitive inhibition assays were used to interrogate the relative inhibition of full-length human and mouse Aβ42 and Aβ40, as well as corresponding p3 fragments.
    RESULTS: Genetic deletion of CatD resulted in 3- to 4-fold increases in insoluble, endogenous cerebral Aβ42 and Aβ40, exceeding the increases produced by deletion of an insulin-degrading enzyme, neprilysin or both, together with readily detectable intralysosomal deposits of endogenous Aβ42-all by 3 weeks of age. Quite significantly, CatD-KO mice exhibited ~ 30% increases in Aβ42/40 ratios, comparable to those induced by presenilin mutations. Mechanistically, the perturbed Aβ42/40 ratios were attributable to pronounced differences in the kinetics of degradation of Aβ42 vis-à-vis Aβ40. Specifically, Aβ42 shows a low-nanomolar affinity for CatD, along with an exceptionally slow turnover rate that, together, renders Aβ42 a highly potent competitive inhibitor of CatD. Notably, the marked differences in the processing of Aβ42 vs. Aβ40 also extend to p3 fragments ending at positions 42 vs. 40.
    CONCLUSIONS: Our findings identify CatD as the principal intracellular Aβ-degrading protease identified to date, one that regulates Aβ42/40 ratios via differential degradation of Aβ42 vs. Aβ40. The finding that Aβ42 is a potent competitive inhibitor of CatD suggests a possible mechanistic link between elevations in Aβ42 and downstream pathological sequelae in AD.
    Keywords:  Alzheimer disease; Amyloid-β protein; Cathepsin D; Lysosomes; Proteostasis
    DOI:  https://doi.org/10.1186/s13195-020-00649-8
  11. iScience. 2020 Jun 20. pii: S2589-0042(20)30487-9. [Epub ahead of print]23(7): 101300
    Beck WHJ, Kim D, Das J, Yu H, Smolka MB, Mao Y.
      Legionella pneumophila is an intracellular pathogen that requires nutrients from the host for its replication. It has been shown that replicating L. pneumophila prefers amino acids as main sources of carbon and energy. The homeostasis of amino acids in eukaryotic cells is regulated by the transcription factor EB (TFEB), which translocates into the nucleus and activates genes for autophagy and lysosomal biogenesis. Here we show that the Legionella effector SetA causes a robust nuclear translocation of TFEB when exogenously expressed in mammalian cells and that the translocation is dependent on the glucosyltransferase activity of SetA. We further show that SetA directly glucosylates TFEB at multiple sites. Our findings of TFEB glucosylation by SetA may suggest an alternative strategy for exploiting host nutrients in addition to the control of host mTORC1 signaling by L. pneumophila. Our results provide further insight into the molecular mechanism of the delicate TFEB nuclear shuttling.
    Keywords:  Microbiology; Molecular Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101300
  12. Nanoscale Res Lett. 2020 Jul 08. 15(1): 143
    Pang C, Song C, Li Y, Wang Q, Zhu X, Wu J, Tian Y, Fan H, Hu J, Li C, Wang B, Li X, Liu W, Fan L.
      Acidic pH of lysosomes is closely related to autophagy; thus, well known of the precise lysosomes, pH changes will give more information on the autophagy process and status. So far, however, only pH changes in a relatively broad range could be indicated, the exact lysosomes pH detection has never arrived. In our study, we established an endo/lysosome pH indicator based on the self-decomposable SiO2 nanoparticle system with specific synthesis parameters. The central concentrated methylene blue (MB) in the central-hollow structural nanoparticles presented sensitive release as a function of pH values from pH 4.0-4.8, which is exactly the pH range of lysosomes. The linear correlation of the optical density (OD) values and the pH values has been built up, which has been used for the detection of lysosomes pH in 6 different cell lines. Moreover, by this system, we succeeded in precisely detecting the pH average changes of lysosomes before and after black mesoporous silicon (BPSi) NP endocytosis, clarifying the mechanism of the autophagy termination after BPSi endocytosis. So, the self-decomposable nanoparticle-based luminal pH indicator may provide a new methodology and strategy to know better of the lysosome pH, then indicate more details on the autophagy process or other important signaling about metabolisms.
    Keywords:  Autophagy; BPSi; Lysosome pH indicator; MB@SiO2
    DOI:  https://doi.org/10.1186/s11671-020-03367-0
  13. EBioMedicine. 2020 Jul 06. pii: S2352-3964(20)30251-6. [Epub ahead of print] 102876
    Baumer Y, Dey AK, Gutierrez-Huerta CA, Khalil NO, Sekine Y, Sanda GE, Zhuang J, Saxena A, Stempinski E, Elnabawi YA, Dagur PK, Ng Q, Teague HL, Keel A, Rodante JA, Boisvert WA, Tsoi LC, Gudjonsson JE, Bleck CKE, Chen MY, Bluemke DA, Gelfand JM, Schwartz DM, Kruth HS, Powell-Wiley TM, Playford MP, Mehta NN.
      BACKGROUND: Inflammation plays an important role in the development of cardiovascular disease (CVD). Patients with chronic inflammatory diseases have high levels of inflammatory and early fatal myocardial infarction due to early, unstable coronary plaques. Cholesterol crystals (CC) play a key role in atherogenesis. However, the underlying mechanisms of endothelial cell (EC)-derived CC formation are not well understood in chronic inflammation.METHODS: We utilized a combination of a mouse psoriasis model (K14-Rac1V12 mouse model) and human psoriasis patients to study the effect of inflammatory cytokines on CC formation in ECs. Lysosomal pH, alterations in lipid load and inflammatory proteins were evaluated as potential mechanisms linking inflammatory cytokines to CC formation. Coronary CT angiography was performed (n = 224) to characterize potential IFNγ and TNFα synergism on vascular diseases in vivo.
    FINDINGS: We detected CC presence in the aorta of K14-Rac1V12 mice on chow diet. IFNγ and TNFα were found to synergistically increase LDL-induced CC formation by almost 2-fold. There was an increase in lysosomal pH accompanied by a 28% loss in pH-dependent lysosomal signal and altered vATPaseV1E1 expression patterns. In parallel, we found that LDL+IFNγ/TNFα treatments increased free cholesterol content within EC and led to a decrease in SOAT-1 expression, an enzyme critically involved cholesterol homeostasis. Finally, the product of IFNγ and TNFα positively associated with early non-calcified coronary burden in patients with psoriasis (n = 224; β = 0.28, p < 0.001).
    INTERPRETATION: Our results provide evidence that IFNγ and TNFα accelerate CC formation in endothelial cells in part by altering lysosomal pH and free cholesterol load. These changes promote early atherogenesis and contribute to understanding the burden of CVD in psoriasis.
    FUNDING: Funding was provided by the Intramural Research Program at NIH (NNM) and the National Psoriasis Foundation (NNM and YB).
    Keywords:  Atherosclerosis; Cholesterol crystals; Endothelium; Inflammation; Lipid metabolism; Lysosomal function; Psoriasis
    DOI:  https://doi.org/10.1016/j.ebiom.2020.102876
  14. Cancers (Basel). 2020 Jul 04. pii: E1790. [Epub ahead of print]12(7):
    Cash TP, Alcalá S, Rico-Ferreira MDR, Hernández-Encinas E, García J, Albarrán MI, Valle S, Muñoz J, Martínez-González S, Blanco-Aparicio C, Pastor J, Serrano M, Sainz B.
      Despite significant efforts to improve pancreatic ductal adenocarcinoma (PDAC) clinical outcomes, overall survival remains dismal. The poor response to current therapies is partly due to the existence of pancreatic cancer stem cells (PaCSCs), which are efficient drivers of PDAC tumorigenesis, metastasis and relapse. To find new therapeutic agents that could efficiently kill PaCSCs, we screened a chemical library of 680 compounds for candidate small molecules with anti-CSC activity, and identified two compounds of a specific chemical series with potent activity in vitro and in vivo against patient-derived xenograft (PDX) cultures. The anti-CSC mechanism of action of this specific chemical series was found to rely on induction of lysosomal membrane permeabilization (LMP), which is likely associated with the increased lysosomal mass observed in PaCSCs. Using the well characterized LMP-inducer siramesine as a tool molecule, we show elimination of the PaCSC population in mice implanted with tumors from two PDX models. Collectively, our approach identified lysosomal disruption as a promising anti-CSC therapeutic strategy for PDAC.
    Keywords:  cancer stem cells; compound library; lysosomal membrane permeabilization; pancreatic ductal adenocarcinoma; patient-derived xenografts
    DOI:  https://doi.org/10.3390/cancers12071790
  15. J Neurosci. 2020 Jul 08. pii: JN-RM-0951-20. [Epub ahead of print]
    Reed CB, Frick LR, Weaver A, Sidoli M, Schlant E, Feltri ML, Wrabetz L.
      In the PNS, myelination occurs postnatally when Schwann cells (SCs) contact axons. Axonal factors, such as Neuregulin-1 Type III, trigger promyelinating signals that upregulate myelin genes. Neuregulin-1 Type III has been proposed to activate calcineurin signaling in immature SCs to initiate differentiation and myelination. However, little is known about the role of calcineurin in promyelinating SCs after birth. By creating an SC conditional KO of calcineurin B (CnBscko), we assessed the effects of CnB ablation on peripheral myelination after birth in both male and female mice. Surprisingly, CnBscko mice have minimal myelination defects, no alteration of myelin thickness, and normal KROX20 expression. In contrast, we did find a unique role for calcineurin in SCs after nerve injury. Following nerve crush, CnBscko mice have slower degeneration of myelin compared with WT mice. Furthermore, absence of CnB in primary SCs delays clearance of myelin debris. SCs clear myelin via autophagy and recent literature has demonstrated that calcineurin can regulate autophagy via dephosphorylation of transcription factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy. We demonstrate that loss of CnB reduces autophagic flux in primary SCs, indicating a possible mechanism for impaired myelin clearance. In addition, ablation of CnB impairs TFEB translocation to the nucleus 3 d after crush, suggesting that calcineurin may regulate autophagy in SCs via TFEB activation. Together, our data indicate that calcineurin is not essential for myelination but has a novel role in myelin clearance after injury.Significance Statement:Our data offer a novel mechanism for activation of autophagy after peripheral nerve injury. Efficient clearance of myelin after injury by Schwann cells is important for axonal regrowth and remyelination, which is one reason why the PNS is significantly better at recovery compared with the CNS. Improved understanding of myelin clearance allows for the identification of pathways that are potentially accessible to increase myelin clearance and improve remyelination and recovery. Finally, this paper clarifies the role of calcineurin in Schwann cells and myelination.
    DOI:  https://doi.org/10.1523/JNEUROSCI.0951-20.2020
  16. J Hum Genet. 2020 Jul 10.
    Pasumarthi D, Gupta N, Sheth J, Jain SJMN, Rungsung I, Kabra M, Ranganath P, Aggarwal S, Phadke SR, Girisha KM, Shukla A, Datar C, Verma IC, Puri RD, Bhavsar R, Mistry M, Sankar VH, Gowrishankar K, Agrawal D, Nair M, Danda S, Soni JP, Dalal A.
      Mucolipidosis (ML) (OMIM 607840 & 607838) is a rare autosomal recessive inherited disorder that occurs due to the deficiency of golgi enzyme uridine diphosphate (UDP)- N-acetylglucosamine-1-phosphotransferase (GlcNAc-phosphotransferase) responsible for tagging mannose-6-phosphate for proper trafficking of lysosomal enzymes to lysosomes. Variants in GlcNAc-phosphotransferase (GNPTAB (α, β subunits) and GNPTG (γ subunits) are known to result in impaired targeting of lysosomal enzymes leading to Mucolipidosis (ML) Type II or Type III. We analyzed 69 Indian families of MLII/III for clinical features and molecular spectrum and performed in silico analysis for novel variants. We identified 38 pathogenic variants in GNPTAB and 5 pathogenic variants in GNPTG genes including missense, frame shift, deletion, duplication and splice site variations. A total of 26 novel variants were identified in GNPTAB and 4 in GNPTG gene. In silico studies using mutation prediction software like SIFT, Polyphen2 and protein structure analysis further confirmed the pathogenic nature of the novel sequence variants detected in our study. Except for a common variant c.3503_3504delTC in early onset MLII, we could not establish any other significant genotype and phenotype correlation. This is one of the largest studies reported till date on Mucolipidosis II/III in order to identify mutation spectrum and any recurrent mutations specific to the Indian ethnic population. The mutational spectrum information in Indian patients will be useful in better genetic counselling, carrier detection and prenatal diagnosis for patients with ML II/III.
    DOI:  https://doi.org/10.1038/s10038-020-0797-8
  17. Front Cell Dev Biol. 2020 ;8 464
    Nicolas V, Lievin-Le Moal V.
      Autophagy is a catabolic recycling process by which a cell degrades its own constituents to contribute to cell homeostasis or survival. We report that the small trafficking inhibitor Retro-2 impairs microtubule-dependent vacuolar trafficking in autophagy. Retro-2 induced autophagy and promoted the dramatic cytoplasmic accumulation of large autophagosomes. Moreover, Retro-2 decreased the spreading of autophagosomes within the cytoplasm of nutrient-starved cells. In addition, Retro-2 abolished autolysosomes formation. We show that these effects arise from hitherto unsuspected disassembly activity of the small molecule on the cellular microtubule network, which is known to act as a key regulator of vacuolar trafficking of the autophagy pathway.
    Keywords:  autolysosome; autophagosome; autophagy; microtubules; nutrient starvation; trafficking inhibitor Retro-2; vacuolar trafficking
    DOI:  https://doi.org/10.3389/fcell.2020.00464
  18. Diabetes. 2020 Jul 08. pii: db190699. [Epub ahead of print]
    Zhang L, Li X, Zhang N, Yang X, Hou T, Fu W, Yuan F, Wang L, Wen H, Tian Y, Zhang H, Lu X, Zhu WG.
      Endosomes help activate the hepatic insulin-evoked Akt signaling pathway, but the underlying regulatory mechanisms are unclear. Previous studies have suggested that the endosome located protein WD Repeat and FYVE Domain Containing 2 (WDFY2) might be involved in metabolic disorders, such as diabetes. Here, we generated Wdfy2 knockout (KO) mice and assessed the metabolic consequences. These KO mice exhibited systemic insulin resistance, with increased gluconeogenesis and suppressed glycogen accumulation in the liver. Mechanistically, we found that the insulin-stimulated activation of Akt2 and its substrates FoxO1 and GSK-3β, is attenuated in the Wdfy2 KO liver and H2.35 hepatocytes, suggesting that WDFY2 acts as an important regulator of hepatic Akt2 signaling. We further found that WDFY2 interacts with the insulin receptor (INSR) via its WD1-4 domain and localizes the INSR to endosomes after insulin stimulation. This process ensures that the downstream insulin receptor substrates 1 and 2 (IRS1/2) can be recruited to the endosomal INSR. IRS1/2-INSR binding promotes IRS1/2 phosphorylation and subsequent activation, initiating downstream Akt2 signaling in the liver. Interestingly, adeno-associated viral WDFY2 delivery ameliorated metabolic defects in db/db mice. These findings demonstrate that WDFY2 activates insulin-evoked Akt2 signaling by controlling endosomal localization of the insulin receptor and IRS1/2 in hepatocytes. This pathway might constitute a new potential target for diabetes prevention and/or treatment.
    DOI:  https://doi.org/10.2337/db19-0699
  19. Cell Death Dis. 2020 Jul 08. 11(7): 513
    Feng Y, Zhong X, Tang TT, Wang C, Wang LT, Li ZL, Ni HF, Wang B, Wu M, Liu D, Liu H, Tang RN, Liu BC, Lv LL.
      Exosomes are increasingly recognized as vehicles of intercellular communication. However, the role of exosome in maintaining cellular homeostasis under stress conditions remained unclear. Here we show that Rab27a expression was upregulated exclusively in tubular epithelial cells (TECs) during proteinuria nephropathy established by adriamycin (ADR) injection and 5/6 nephrectomy as well as in chronic kidney disease patients, leading to the increased secretion of exosomes carrying albumin. The active exosome production promoted tubule injury and inflammation in neighboring and the producing cells. Interferon regulatory factor 1 (IRF-1) was found as the transcription factor contributed to the upregulation of Rab27a. Albumin could be detected in exosome fraction and co-localized with exosome marker CD63 indicating the secretion of albumin into extracellular space by exosomes. Interestingly, inhibition of exosome release accelerated albumin degradation which reversed tubule injury with albumin overload, while lysosome suppression augmented exosome secretion and tubule inflammation. Our findings revealed that IRF-1/Rab27a mediated exosome secretion constituted a coordinated approach to lysosome degradation for albumin handling, which lead to the augment of albumin toxicity as a maladaptive response to maintain cell homeostasis. The findings may suggest a novel therapeutic strategy for proteinuric kidney disease by targeting exosome secretion.
    DOI:  https://doi.org/10.1038/s41419-020-2709-4
  20. Antibodies (Basel). 2020 Jul 02. pii: E29. [Epub ahead of print]9(3):
    Charrin S, Palmulli R, Billard M, Clay D, Boucheix C, Van Niel G, Rubinstein E.
      CD63, a member of the tetraspanin superfamily, is used as a marker of late endosomes and lysosome-related organelles, as well as a marker of exosomes. Here, we selected rare isotype variants of TS63 by sorting hybridoma cells on the basis of their high expression of surface immunoglobulins of the IgG2a and IgG2b subclass. Pure populations of cells secreting IgG2a and IgG2b variants of TS63 (referred to as TS63a and TS63b) were obtained using two rounds of cell sorting and one limited dilution cloning step. We validate that these new TS63 variants are suitable for co-labeling with mAb of the IgG1 subclass directed to other molecules, using anti mouse subclass antibodies, and for the labeling of exosomes through direct binding to protein A-coated gold particles. These mAbs will be useful to study the intracellular localization of various proteins and facilitate electron microscopy analysis of CD63 localization.
    Keywords:  CD63; exosomes; isotype switch; late endosomes
    DOI:  https://doi.org/10.3390/antib9030029
  21. Autophagy. 2020 Jul 05. 1-21
    Sanchez-Garrido J, Shenoy AR.
      Nutrients not only act as building blocks but also as signaling molecules. Nutrient-availability promotes cell growth and proliferation and suppresses catabolic processes, such as macroautophagy/autophagy. These effects are mediated by checkpoint kinases such as MTOR (mechanistic target of rapamycin kinase), which is activated by amino acids and growth factors, and AMP-activated protein kinase (AMPK), which is activated by low levels of glucose or ATP. These kinases have wide-ranging activities that can be co-opted by immune cells upon exposure to danger signals, cytokines or pathogens. Here, we discuss recent insight into the regulation and repurposing of nutrient-sensing responses by the innate immune system during infection. Moreover, we examine how natural mutations and pathogen-mediated interventions can alter the balance between anabolic and autophagic pathways leading to a breakdown in tissue homeostasis and/or host defense.ABBREVIATIONS: AKT1/PKB: AKT serine/threonine kinase 1; ATG: autophagy related; BECN1: beclin 1; CGAS: cyclic GMP-AMP synthase; EIF2AK4/GCN2: eukaryotic translation initiation factor 2 alpha kinase 4; ER: endoplasmic reticulum; FFAR: free fatty acid receptor; GABARAP: GABA type A receptor-associated protein; IFN: interferon; IL: interleukin; LAP: LC3-associated phagocytosis; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK: mitogen-activated protein kinase; MTOR: mechanistic target of rapamycin kinase; NLR: NOD (nucleotide-binding oligomerization domain) and leucine-rich repeat containing proteins; PI3K, phosphoinositide 3-kinase; PRR: pattern-recognition receptor; PtdIns3K: phosphatidylinositol 3-kinase; RALB: RAS like proto-oncogene B; RHEB: Ras homolog, MTORC1 binding; RIPK1: receptor interacting serine/threonine kinase 1; RRAG: Ras related GTP binding; SQSTM1/p62: sequestosome 1; STING1/TMEM173: stimulator of interferon response cGAMP interactor 1; STK11/LKB1: serine/threonine kinase 11; TBK1: TANK binding kinase 1; TLR: toll like receptor; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; TRIM: tripartite motif protein; ULK1: unc-51 like autophagy activating kinase 1; V-ATPase: vacuolar-type H+-proton-translocating ATPase.
    Keywords:  AMPK; LC3-associated phagocytosis; MTOR; immunity; microbial pathogenesis; unconventional secretion
    DOI:  https://doi.org/10.1080/15548627.2020.1783119
  22. Exp Eye Res. 2020 Jul 02. pii: S0014-4835(20)30389-4. [Epub ahead of print] 108131
    Losiewicz MK, Elghazi L, Fingar DC, Rajala RVS, Lentz SI, Fort PE, Abcouwer SF, Gardner TW.
      The retina is one of the most metabolically active tissues, yet the processes that control retinal metabolism remains poorly understood. The mTOR complex (mTORC) that drives protein and lipid biogenesis and autophagy has been studied extensively in regards to retinal development and responses to optic nerve injury but the processes that regulate homeostasis in the adult retina have not been determined. We previously demonstrated that normal adult retina has high rates of protein synthesis compared to skeletal muscle, associated with high levels of mechanistic target of rapamycin (mTOR), a kinase that forms multi-subunit complexes that sense and integrate diverse environmental cues to control cell and tissue physiology. This study was undertaken to: 1) quantify expression of mTOR complex 1 (mTORC1)- and mTORC2-specific partner proteins in normal adult rat retina, brain and liver; and 2) to localize these components in normal human, rat, and mouse retinas. Immunoblotting and immunoprecipitation studies revealed greater expression of raptor (exclusive to mTORC1) and rictor (exclusive for mTORC2) in normal rat retina relative to liver or brain, as well as the activating mTORC components, pSIN1 and pPRAS40. By contrast, liver exhibits greater amounts of the mTORC inhibitor, DEPTOR. Immunolocalization studies for all three species showed that mTOR, raptor, and rictor, as well as most other known components of mTORC1 and mTORC2, were primarily localized in the inner retina with mTORC1 primarily in retinal ganglion cells (RGCs) and mTORC2 primarily in glial cells. In addition, phosphorylated ribosomal protein S6, a direct target of the mTORC1 substrate ribosomal protein S6 kinase beta-1 (S6K1), was readily detectable in RGCs, indicating active mTORC1 signaling, and was preserved in human donor eyes. Collectively, this study demonstrates that the inner retina expresses high levels of mTORC1 and mTORC2 and possesses active mTORC1 signaling that may provide cell- and tissue-specific regulation of homeostatic activity. These findings help to define the physiology of the inner retina, which is key for understanding the pathophysiology of optic neuropathies, glaucoma and diabetic retinopathy.
    Keywords:  Protein synthesis; Raptor; Retina; Retinal ganglion cells; Rictor; mTORC
    DOI:  https://doi.org/10.1016/j.exer.2020.108131
  23. Cell Struct Funct. 2020 ;45(2): 93-105
    Ito S, Nada S, Yamazaki D, Kimura T, Kajiwara K, Miki H, Okada M.
      Mechanistic target of rapamycin complex 1 (mTORC1) plays a pivotal role in controlling cell growth and metabolism in response to nutrients and growth factors. The activity of mTORC1 is dually regulated by amino acids and growth factor signaling, and amino acid-dependent mTORC1 activity is regulated by mTORC1 interaction with the Ragulator-Rag GTPase complex, which is localized to the surface of lysosomes via a membrane-anchored protein, p18/Lamtor1. However, the physiological function of p18-Ragulator-dependent mTORC1 signaling remains elusive. The present study evaluated the function of p18-mediated mTORC1 signaling in the intestinal epithelia using p18 conditional knockout mice. In p18 knockout colonic crypts, mTORC1 was delocalized from lysosomes, and in vivo mTORC1 activity was markedly decreased. Histologically, p18 knockout crypts exhibited significantly increased proliferating cells and dramatically decreased mucin-producing goblet cells, while overall crypt architecture and enteroendocrine cell differentiation were unaffected. Furthermore, p18 knockout crypts normally expressed transcription factors implicated in crypt differentiation, such as Cdx2 and Klf4, indicating that p18 ablation did not affect the genetic program of cell differentiation. Analysis of colon crypt organoid cultures revealed that both p18 ablation and rapamycin treatment robustly suppressed development of mucin-producing goblet cells. Hence, p18-mediated mTORC1 signaling could promote the anabolic metabolism required for robust mucin production in goblet cells to protect the intestinal epithelia from various external stressors.Key words: mTORC1, p18/lamtor1, intestinal epithelium, goblet cells, mucin.
    Keywords:  goblet cells; intestinal epithelium; mTORC1; mucin; p18/lamtor1
    DOI:  https://doi.org/10.1247/csf.20018
  24. Acta Pharm Sin B. 2020 Jun;10(6): 1004-1019
    Lu Z, Shi X, Gong F, Li S, Wang Y, Ren Y, Zhang M, Yu B, Li Y, Zhao W, Zhang J, Hou G.
      Dysregulation of mTORC1/mTORC2 pathway is observed in many cancers and mTORC1 inhibitors have been used clinically in many tumor types; however, the mechanism of mTORC2 in tumorigenesis is still obscure. Here, we mainly explored the potential role of mTORC2 in esophageal squamous cell carcinoma (ESCC) and its effects on the sensitivity of cells to mTOR inhibitors. We demonstrated that RICTOR, the key factor of mTORC2, and p-AKT (Ser473) were excessively activated in ESCC and their overexpression is related to lymph node metastasis and the tumor-node-metastasis (TNM) phase of ESCC patients. Furthermore, we found that mTORC1/ mTORC2 inhibitor PP242 exhibited more efficacious anti-proliferative effect on ESCC cells than mTORC1 inhibitor RAD001 due to RAD001-triggered feedback activation of AKT signal. Another, we demonstrated that down-regulating expression of RICTOR in ECa109 and EC9706 cells inhibited proliferation and migration as well as induced cell cycle arrest and apoptosis. Noteworthy, knocking-down stably RICTOR significantly suppresses RAD001-induced feedback activation of AKT/PRAS40 signaling, and enhances inhibition efficacy of PP242 on the phosphorylation of AKT and PRAS40, thus potentiates the antitumor effect of RAD001 and PP242 both in vitro and in vivo. Our findings highlight that selective targeting mTORC2 could be a promising therapeutic strategy for future treatment of ESCC.
    Keywords:  4EBP-1, E binding protein-1; AKT; AKT, protein kinase B (PKB); ESCC, esophageal squamous cell carcinoma; Esophageal squamous cell carcinoma; FDA, U.S. Food and Drug Administration; H&E staining, hematoxylin and eosin staining; IC50, half maximal inhibitory concentration; PI3K, phosphatidylinositol 3 kinase; RAD001; RICTOR; RICTOR, rapamycin-insensitive companion of mTOR; TNM, tumor-node-metastasis; TUNEL, terminal deoxynucleotidyl transferase dUTP nick end labeling; mTOR, mammalian target of rapamycin; mTORC1, mTOR complex 1; mTORC2, mTOR complex 2; p70S6K, p70 ribosomal S6 kinase-1; pp242; rapalogs, rapamycin and its analogs
    DOI:  https://doi.org/10.1016/j.apsb.2020.01.010
  25. J Biol Chem. 2020 Jul 07. pii: jbc.REV119.007624. [Epub ahead of print]
    Wang YP, Li JT, Qu J, Yin M, Lei QY.
      Metabolites are not only substrates in metabolic reactions, but also signaling molecules controlling a wide range of cellular processes. Discovery of the oncometabolite 2-hydroxyglutarate (2HG) provides an important link between metabolic dysfunction and cancer, unveiling the signaling function of metabolites in regulating epigenetic and epitranscriptomic modifications, genome integrity, and signal transduction. It is now known that cancer cells sense and remodel their metabolic network to support biogenesis, caused by or resulting in the dysregulation of various metabolites. Cancer cells can sense alterations in metabolic intermediates to better coordinate multiple biological processes and enhance cell metabolism. Recent studies have demonstrated that metabolite signaling is involved in the regulation of malignant transformation, cell proliferation, epithelial-to-mesenchymal transition (EMT), differentiation blockade, and cancer stemness. Additionally, intercellular metabolite signaling modulates inflammatory response and immunosurveillance in the tumor microenvironment. Here, we review recent advances in cancer-associated metabolite signaling. An in-depth understanding of metabolite signaling will provide new opportunities for the development of therapeutic interventions that target cancer.
    Keywords:  Metabolite; Sensing; Signaling; cancer; metabolic disease; metabolic regulation; metabolomics; oncometabolite; signaling
    DOI:  https://doi.org/10.1074/jbc.REV119.007624
  26. Dev Cell. 2020 Jul 02. pii: S1534-5807(20)30501-3. [Epub ahead of print]
    Brunkard JO.
      Target of rapamycin (TOR) is a protein kinase that coordinates metabolism with nutrient and energy availability in eukaryotes. TOR and its primary interactors, RAPTOR and LST8, have been remarkably evolutionarily static since they arose in the unicellular last common ancestor of plants, fungi, and animals, but the upstream regulatory mechanisms and downstream effectors of TOR signaling have evolved considerable diversity in these separate lineages. Here, I focus on the roles of exaptation and adaptation in the evolution of novel signaling axes in the TOR network in multicellular eukaryotes, concentrating especially on amino acid sensing, cell-cell signaling, and cell differentiation.
    Keywords:  PIKKs; evolution; exaptation; mTOR; metabolism; multicellularity; nutrient sensing; plasmodesmata; ribosome biogenesis; target of rapamycin
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.022
  27. Clin Exp Ophthalmol. 2020 Jul 08.
    Yao A, van Wijngaarden P.
      The mechanistic target of rapamycin (mTOR) signalling network plays a key role in growth and development, autophagy, metabolism, inflammation as well as ageing, and it is therefore important in ocular health and disease. mTOR dysregulation has been identified in a range of conditions, including age-related macular degeneration, diabetic retinopathy, retinitis pigmentosa, traumatic optic neuropathy and glaucoma. Experimental modulation of the pathway has contributed to the understanding of these diseases and offers the potential for new avenues of therapy. This review discusses the mTOR pathway and its role in health and in diseases of the retina and optic nerve. This article is protected by copyright. All rights reserved.
    Keywords:  Metabolism; Optic nerve; Retina; mTOR
    DOI:  https://doi.org/10.1111/ceo.13819
  28. Int J Mol Sci. 2020 Jun 25. pii: E4507. [Epub ahead of print]21(12):
    Shorning BY, Dass MS, Smalley MJ, Pearson HB.
      Oncogenic activation of the phosphatidylinositol-3-kinase (PI3K), protein kinase B (PKB/AKT), and mammalian target of rapamycin (mTOR) pathway is a frequent event in prostate cancer that facilitates tumor formation, disease progression and therapeutic resistance. Recent discoveries indicate that the complex crosstalk between the PI3K-AKT-mTOR pathway and multiple interacting cell signaling cascades can further promote prostate cancer progression and influence the sensitivity of prostate cancer cells to PI3K-AKT-mTOR-targeted therapies being explored in the clinic, as well as standard treatment approaches such as androgen-deprivation therapy (ADT). However, the full extent of the PI3K-AKT-mTOR signaling network during prostate tumorigenesis, invasive progression and disease recurrence remains to be determined. In this review, we outline the emerging diversity of the genetic alterations that lead to activated PI3K-AKT-mTOR signaling in prostate cancer, and discuss new mechanistic insights into the interplay between the PI3K-AKT-mTOR pathway and several key interacting oncogenic signaling cascades that can cooperate to facilitate prostate cancer growth and drug-resistance, specifically the androgen receptor (AR), mitogen-activated protein kinase (MAPK), and WNT signaling cascades. Ultimately, deepening our understanding of the broader PI3K-AKT-mTOR signaling network is crucial to aid patient stratification for PI3K-AKT-mTOR pathway-directed therapies, and to discover new therapeutic approaches for prostate cancer that improve patient outcome.
    Keywords:  AKT; AR; MAPK; PI3K; WNT; castration-resistant prostate cancer (CRPC); mTOR; prostate cancer; therapeutic resistance
    DOI:  https://doi.org/10.3390/ijms21124507
  29. Genes (Basel). 2020 Jul 02. pii: E738. [Epub ahead of print]11(7):
    Qian J, Su S, Liu P.
      The mTOR signaling controls essential biological functions including proliferation, growth, metabolism, autophagy, ageing, and others. Hyperactivation of mTOR signaling leads to a plethora of human disorders; thus, mTOR is an attractive drug target. The discovery of mTOR signaling started from isolation of rapamycin in 1975 and cloning of TOR genes in 1993. In the past 27 years, numerous research groups have contributed significantly to advancing our understanding of mTOR signaling and mTOR biology. Notably, a variety of experimental approaches have been employed in these studies to identify key mTOR pathway members that shape up the mTOR signaling we know today. Technique development drives mTOR research, while canonical biochemical and yeast genetics lay the foundation for mTOR studies. Here in this review, we summarize major experimental approaches used in the past in delineating mTOR signaling, including biochemical immunoprecipitation approaches, genetic approaches, immunofluorescence microscopic approaches, hypothesis-driven studies, protein sequence or motif search driven approaches, and bioinformatic approaches. We hope that revisiting these distinct types of experimental approaches will provide a blueprint for major techniques driving mTOR research. More importantly, we hope that thinking and reasonings behind these experimental designs will inspire future mTOR research as well as studies of other protein kinases beyond mTOR.
    Keywords:  biochemical approach; bioinformatic approach; experimental approach; genetic approach; hypothesis-driven; immunofluorescence; mTOR; protein motif search
    DOI:  https://doi.org/10.3390/genes11070738