bims-lysosi Biomed News
on Lysosomes and signaling
Issue of 2021–03–28
47 papers selected by
Stephanie Fernandes, Max Planck Institute for Biology of Ageing
  1. LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation.
  2. TFEB-GDF15 axis protects against obesity and insulin resistance as a lysosomal stress response.
  3. PARsylated transcription factor EB (TFEB) regulates the expression of a subset of Wnt target genes by forming a complex with β-catenin-TCF/LEF1.
  4. Targeting Lysosomal Degradation Pathways: New Strategies and Techniques for Drug Discovery.
  5. Dysregulation of mitochondria-lysosome contacts by GBA1 dysfunction in dopaminergic neuronal models of Parkinson's disease.
  6. mTORC1 stimulates cell growth through SAM synthesis and m6A mRNA-dependent control of protein synthesis.
  7. mTORC1 promotes cell growth via m6A-dependent mRNA degradation.
  8. Synaptic Function and Dysfunction in Lysosomal Storage Diseases.
  9. Inhibition of GSK-3 ameliorates the pathogenesis of Huntington's disease.
  10. Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans.
  11. Cathepsin B and D deficiency in the mouse pancreas induces impaired autophagy and chronic pancreatitis.
  12. Imiquimod accelerated antitumor response by targeting lysosome adaptation in skin cancer cells.
  13. Degradation from the outside in: targeting extracellular and membrane proteins for degradation through the endolysosomal pathway.
  14. The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.
  15. Krabbe Disease: New Hope for an Old Disease.
  16. Human MC4R variants affect endocytosis, trafficking and dimerization revealing multiple cellular mechanisms involved in weight regulation.
  17. Autophagy-dependent survival is controlled with a unique regulatory network upon various cellular stress events.
  18. Lysosomal Stress Response (LSR): Physiological Importance and Pathological Relevance.
  19. WAVE2 suppresses mTOR activation to maintain T cell homeostasis and prevent autoimmunity.
  20. Akt-mTOR hypoactivity in bipolar disorder gives rise to cognitive impairments associated with altered neuronal structure and function.
  21. Light Stimuli and Circadian Clock Affect Neural Development in Drosophila melanogaster.
  22. Enhancing lifespan of budding yeast by pharmacological lowering of amino acid pools.
  23. Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control.
  24. Increased LRRK2 kinase activity alters neuronal autophagy by disrupting the axonal transport of autophagosomes.
  25. TSC1 Affects the Process of Renal Ischemia-Reperfusion Injury by Controlling Macrophage Polarization.
  26. mTOR-mediated calcium transients affect cardiac function in ex vivo ischemia-reperfusion injury.
  27. The Role of Mitophagy in the Regulation of Mitochondrial Energetic Status in Neurons.
  28. Golgi maturation-dependent glycoenzyme recycling controls glycosphingolipid biosynthesis and cell growth via GOLPH3.
  29. Mutant ASXL1 induces age-related expansion of phenotypic hematopoietic stem cells through activation of Akt/mTOR pathway.
  30. Elevated glucose represses lysosomal and mTOR-related genes in renal epithelial cells composed of progenitor CD133+ cells.
  31. Targeting Endosomal Recycling Pathways by Bacterial and Viral Pathogens.
  32. Paxbp1 controls a key checkpoint for cell growth and survival during early activation of quiescent muscle satellite cells.
  33. Structure, interdomain dynamics and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes.
  34. Precision control of mTORC1 is crucial for the maintenance and IL-13 responsiveness of alveolar macrophages.
  35. Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly.
  36. The S6k/4E-BP mediated growth promoting sub-pathway of insulin signalling cascade is essential to restrict pathogenesis of poly(Q) disorders in Drosophila.
  37. SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition.
  38. Target Reprogramming Lysosomes of CD8+ T Cells by a Mineralized Metal-Organic Framework for Cancer Immunotherapy.
  39. Essential requirement for JPT2 in NAADP-evoked Ca2+ signaling.
  40. Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs.
  41. Chemical Phosphoproteomics Sheds New Light on the Targets and Modes of Action of AKT Inhibitors.
  42. Host-commensal interaction promotes health and lifespan in Caenorhabditis elegans through the activation of HLH-30/TFEB-mediated autophagy.
  43. FGF21 facilitates autophagy in prostate cancer cells by inhibiting the PI3K-Akt-mTOR signaling pathway.
  44. Platelet autophagic machinery involved in thrombosis through a novel linkage of AMPK-MTOR to sphingolipid metabolism.
  45. Mitochondrial genotype alters the impact of rapamycin on the transcriptional response to nutrients in Drosophila.
  46. Balancing energy demand and production by mitochondrial trafficking of RHEB.
  47. Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.
  1. Nat Chem Biol. 2021 Mar 25.
    LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation.
    Green Ahn, Steven M Banik, Caitlyn L Miller, Nicholas M Riley, Jennifer R Cochran, Carolyn R Bertozzi.
      Selective protein degradation platforms have afforded new development opportunities for therapeutics and tools for biological inquiry. The first lysosome-targeting chimeras (LYTACs) targeted extracellular and membrane proteins for degradation by bridging a target protein to the cation-independent mannose-6-phosphate receptor (CI-M6PR). Here, we developed LYTACs that engage the asialoglycoprotein receptor (ASGPR), a liver-specific lysosome-targeting receptor, to degrade extracellular proteins in a cell-type-specific manner. We conjugated binders to a triantenerrary N-acetylgalactosamine (tri-GalNAc) motif that engages ASGPR to drive the downregulation of proteins. Degradation of epidermal growth factor receptor (EGFR) by GalNAc-LYTAC attenuated EGFR signaling compared to inhibition with an antibody. Furthermore, we demonstrated that a LYTAC consisting of a 3.4-kDa peptide binder linked to a tri-GalNAc ligand degrades integrins and reduces cancer cell proliferation. Degradation with a single tri-GalNAc ligand prompted site-specific conjugation on antibody scaffolds, which improved the pharmacokinetic profile of GalNAc-LYTACs in vivo. GalNAc-LYTACs thus represent an avenue for cell-type-restricted protein degradation.
    DOI:  https://doi.org/10.1038/s41589-021-00770-1
  2. Nat Metab. 2021 Mar;3(3): 410-427
    TFEB-GDF15 axis protects against obesity and insulin resistance as a lysosomal stress response.
    Jinyoung Kim, Seong Hun Kim, Hyereen Kang, Soyeon Lee, Shi-Young Park, Yoonil Cho, Yu-Mi Lim, Ji Woong Ahn, Young-Hwan Kim, Seungsoo Chung, Cheol Soo Choi, Yeon Jin Jang, Hye Soon Park, Yoonseok Heo, Kook Hwan Kim, Myung-Shik Lee.
      TFEB, a key regulator of lysosomal biogenesis and autophagy, is induced not only by nutritional deficiency but also by organelle stress. Here, we find that Tfeb and its downstream genes are upregulated together with lipofuscin accumulation in adipose tissue macrophages (ATMs) of obese mice or humans, suggestive of obesity-associated lysosomal dysfunction/stress in ATMs. Macrophage-specific TFEB-overexpressing mice display complete abrogation of diet-induced obesity, adipose tissue inflammation and insulin resistance, which is independent of autophagy, but dependent on TFEB-induced GDF15 expression. Palmitic acid induces Gdf15 expression through lysosomal Ca2+-mediated TFEB nuclear translocation in response to lysosomal stress. In contrast, mice fed a high-fat diet with macrophage-specific Tfeb deletion show aggravated adipose tissue inflammation and insulin resistance, accompanied by reduced GDF15 level. Finally, we observe activation of TFEB-GDF15 in ATMs of obese humans as a consequence of lysosomal stress. These findings highlight the importance of the TFEB-GDF15 axis as a lysosomal stress response in obesity or metabolic syndrome and as a promising therapeutic target for treatment of these conditions.
    DOI:  https://doi.org/10.1038/s42255-021-00368-w
  3. Cell Death Differ. 2021 Mar 22.
    PARsylated transcription factor EB (TFEB) regulates the expression of a subset of Wnt target genes by forming a complex with β-catenin-TCF/LEF1.
    Soyoung Kim, Gahyeon Song, Taebok Lee, Minseong Kim, Jeongrae Kim, Hyeryun Kwon, Jiyoung Kim, Wonyoung Jeong, Ukjin Lee, Chaebin Na, Sangwon Kang, Wantae Kim, Je Kyung Seong, Eek-Hoon Jho.
      Wnt signaling is mainly transduced by β-catenin via regulation of the β-catenin destruction complex containing Axin, APC, and GSK3β. Transcription factor EB (TFEB) is a well-known master regulator of autophagy and lysosomal biogenesis processes. TFEB's nuclear localization and transcriptional activity are also regulated by various upstream signals. In this study, we found that Wnt signaling induces the nuclear localization of TFEB and the expression of Wnt target genes is regulated by TFEB-β-catenin-TCF/LEF1 as well as β-catenin-TCF/LEF1 complexes. Our biochemical data revealed that TFEB is a part of the β-catenin destruction complex, and destabilization of the destruction complex by knockdown of either Axin or APC causes nuclear localization of TFEB. Interestingly, RNA-sequencing analysis revealed that about 27% of Wnt3a-induced genes were TFEB dependent. However, these "TFEB mediated Wnt target genes" were different from TFEB target genes involved in autophagy and lysosomal biogenesis processes. Mechanistically, we found that Tankyrase (TNKS) PARsylates TFEB with Wnt ON signaling, and the nuclear localized PARsylated TFEB forms a complex with β-catenin-TCF/LEF1 to induce the "TFEB mediated Wnt target genes". Finally, we found that in various types of cancer, the levels of TFEB mediated Wnt target genes exhibit strong correlations with the level of Axin2, which represents the activity of Wnt signaling. Overall, our data suggest that Wnt signaling induces the expression of a subset of genes that are distinct from previously known genes regulated by the β-catenin-TCF/LEF1 complex or TFEB, by forming a transcription factor complex consisting of PARsylated TFEB and β-catenin-TCF/LEF1.
    DOI:  https://doi.org/10.1038/s41418-021-00770-7
  4. J Med Chem. 2021 Mar 25.
    Targeting Lysosomal Degradation Pathways: New Strategies and Techniques for Drug Discovery.
    Junping Pei, Guan Wang, Lu Feng, Jifa Zhang, Tingting Jiang, Qiu Sun, Liang Ouyang.
      A series of tools for targeted protein degradation are inspiring scientists to develop new drugs with advantages over traditional small-molecule drugs. Among these tools, proteolysis-targeting chimeras (PROTACs) are most representative of the technology based on proteasomes. However, the proteasome has little degradation effect on certain macromolecular proteins or aggregates, extracellular proteins, and organelles, which limits the application of PROTACs. Additionally, lysosomes play an important role in protein degradation. Therefore, lysosome-induced protein degradation drugs can directly regulate protein levels in vivo, achieve the goal of treating diseases, and provide new strategies for drug discovery. Lysosome-based degradation technology has the potential for clinical translation. In this review, strategies targeting lysosomal pathways and lysosome-based degradation techniques are summarized. In addition, lysosome-based degrading drugs are described, and the advantages and challenges are listed. Our efforts will certainly promote the design, discovery, and clinical application of drugs associated with this technology.
    DOI:  https://doi.org/10.1021/acs.jmedchem.0c01689
  5. Nat Commun. 2021 03 22. 12(1): 1807
    Dysregulation of mitochondria-lysosome contacts by GBA1 dysfunction in dopaminergic neuronal models of Parkinson's disease.
    Soojin Kim, Yvette C Wong, Fanding Gao, Dimitri Krainc.
      Mitochondria-lysosome contacts are recently identified sites for mediating crosstalk between both organelles, but their role in normal and diseased human neurons remains unknown. In this study, we demonstrate that mitochondria-lysosome contacts can dynamically form in the soma, axons, and dendrites of human neurons, allowing for their bidirectional crosstalk. Parkinson's disease patient derived neurons harboring mutant GBA1 exhibited prolonged mitochondria-lysosome contacts due to defective modulation of the untethering protein TBC1D15, which mediates Rab7 GTP hydrolysis for contact untethering. This dysregulation was due to decreased GBA1 (β-glucocerebrosidase (GCase)) lysosomal enzyme activity in patient derived neurons, and could be rescued by increasing enzyme activity with a GCase modulator. These defects resulted in disrupted mitochondrial distribution and function, and could be further rescued by TBC1D15 in Parkinson's patient derived GBA1-linked neurons. Together, our work demonstrates a potential role of mitochondria-lysosome contacts as an upstream regulator of mitochondrial function and dynamics in midbrain dopaminergic neurons in GBA1-linked Parkinson's disease.
    DOI:  https://doi.org/10.1038/s41467-021-22113-3
  6. Mol Cell. 2021 Mar 17. pii: S1097-2765(21)00177-5. [Epub ahead of print]
    mTORC1 stimulates cell growth through SAM synthesis and m6A mRNA-dependent control of protein synthesis.
    Elodie Villa, Umakant Sahu, Brendan P O'Hara, Eunus S Ali, Kathryn A Helmin, John M Asara, Peng Gao, Benjamin D Singer, Issam Ben-Sahra.
      The mechanistic target of rapamycin complex 1 (mTORC1) regulates metabolism and cell growth in response to nutrient, growth, and oncogenic signals. We found that mTORC1 stimulates the synthesis of the major methyl donor, S-adenosylmethionine (SAM), through the control of methionine adenosyltransferase 2 alpha (MAT2A) expression. The transcription factor c-MYC, downstream of mTORC1, directly binds to intron 1 of MAT2A and promotes its expression. Furthermore, mTORC1 increases the protein abundance of Wilms' tumor 1-associating protein (WTAP), the positive regulatory subunit of the human N6-methyladenosine (m6A) RNA methyltransferase complex. Through the control of MAT2A and WTAP levels, mTORC1 signaling stimulates m6A RNA modification to promote protein synthesis and cell growth. A decline in intracellular SAM levels upon MAT2A inhibition decreases m6A RNA modification, protein synthesis rate, and tumor growth. Thus, mTORC1 adjusts m6A RNA modification through the control of SAM and WTAP levels to prime the translation machinery for anabolic cell growth.
    Keywords:  Cell growth; MAT2A; Methionine cycle; N(6)-methyladenosine; Protein Synthesis; RNA metabolism; S-adenosylmethionine; WTAP; mTOR; mTORC1
    DOI:  https://doi.org/10.1016/j.molcel.2021.03.009
  7. Mol Cell. 2021 Mar 19. pii: S1097-2765(21)00178-7. [Epub ahead of print]
    mTORC1 promotes cell growth via m6A-dependent mRNA degradation.
    Sungyun Cho, Gina Lee, Brian F Pickering, Cholsoon Jang, Jin H Park, Long He, Lavina Mathur, Seung-Soo Kim, Sunhee Jung, Hong-Wen Tang, Sebastien Monette, Joshua D Rabinowitz, Norbert Perrimon, Samie R Jaffrey, John Blenis.
      Dysregulated mTORC1 signaling alters a wide range of cellular processes, contributing to metabolic disorders and cancer. Defining the molecular details of downstream effectors is thus critical for uncovering selective therapeutic targets. We report that mTORC1 and its downstream kinase S6K enhance eIF4A/4B-mediated translation of Wilms' tumor 1-associated protein (WTAP), an adaptor for the N6-methyladenosine (m6A) RNA methyltransferase complex. This regulation is mediated by 5' UTR of WTAP mRNA that is targeted by eIF4A/4B. Single-nucleotide-resolution m6A mapping revealed that MAX dimerization protein 2 (MXD2) mRNA contains m6A, and increased m6A modification enhances its degradation. WTAP induces cMyc-MAX association by suppressing MXD2 expression, which promotes cMyc transcriptional activity and proliferation of mTORC1-activated cancer cells. These results elucidate a mechanism whereby mTORC1 stimulates oncogenic signaling via m6A RNA modification and illuminates the WTAP-MXD2-cMyc axis as a potential therapeutic target for mTORC1-driven cancers.
    Keywords:  MXD2; Protein translation; S6K1; WTAP; YTHDF readers; cMyc; eIF4A; m(6)A mRNA modification; mRNA stability; mTORC1
    DOI:  https://doi.org/10.1016/j.molcel.2021.03.010
  8. Front Cell Neurosci. 2021 ;15 619777
    Synaptic Function and Dysfunction in Lysosomal Storage Diseases.
    Rima Rebiai, Maria I Givogri, Swetha Gowrishankar, Stephania M Cologna, Simon T Alford, Ernesto R Bongarzone.
      Lysosomal storage diseases (LSDs) with neurological involvement are inherited genetic diseases of the metabolism characterized by lysosomal dysfunction and the accumulation of undegraded substrates altering glial and neuronal function. Often, patients with neurological manifestations present with damage to the gray and white matter and irreversible neuronal decline. The use of animal models of LSDs has greatly facilitated studying and identifying potential mechanisms of neuronal dysfunction, including alterations in availability and function of synaptic proteins, modifications of membrane structure, deficits in docking, exocytosis, recycling of synaptic vesicles, and inflammation-mediated remodeling of synapses. Although some extrapolations from findings in adult-onset conditions such as Alzheimer's disease or Parkinson's disease have been reported, the pathogenetic mechanisms underpinning cognitive deficits in LSDs are still largely unclear. Without being fully inclusive, the goal of this mini-review is to present a discussion on possible mechanisms leading to synaptic dysfunction in LSDs.
    Keywords:  GABA; LTD; LTP; cholesterol; glutamate receptors; lysosomes; sphingolipids; synapses
    DOI:  https://doi.org/10.3389/fncel.2021.619777
  9. Neurobiol Dis. 2021 Mar 19. pii: S0969-9961(21)00085-1. [Epub ahead of print] 105336
    Inhibition of GSK-3 ameliorates the pathogenesis of Huntington's disease.
    Ido Rippin, Katherina Bonder, Shirley Ben Joseph, Amar Sarsor, Lilach Vaks, Hagit Eldar-Finkelman.
      In Huntington's disease (HD), the mutant huntingtin (mHtt) accumulates as toxic aggregates in the striatum tissue, with deleterious effects on motor-coordination and cognitive functions. Reducing the levels of mHtt is therefore a promising therapeutic strategy. We have previously reported that GSK-3 is a negative regulator of the autophagy/lysosome pathway, which is responsible for intracellular degradation, and is critically important for maintaining neuronal vitality. Thus, we hypothesized that inhibition of GSK-3 may trigger mHtt clearance thereby reducing mHtt cytotoxicity and improving HD symptoms. Here, we demonstrate that depletion or suppression of autophagy results in a massive accumulation of mHtt aggregates. Accordingly, mHtt aggregates were localized in lysosomes, but, mostly mislocalized from lysosomes in the absence of functional autophagy. Overexpression of GSK-3, particularly the α isozyme, increased the number of mHtt aggregates, while silencing GSK-3α/β, or treatment with a selective GSK-3 inhibitor, L807mts, previously described by us, reduced the amounts of mHtt aggregates. This effect was mediated by increased autophagic and lysosomal activity. Treating R6/2 mouse model of HD with L807mts, reduced striatal mHtt aggregates and elevated autophagic and lysosomal markers. The L807mts treatment also reduced hyperglycemia and improved motor-coordination functions in these mice. In addition, L807mts restored the expression levels of Sirt1, a critical neuroprotective factor in the HD striatum, along with its targets BDNF, DRPP-32, and active Akt, all provide neurotrophic/pro-survival support and typically decline in the HD brain. Our results provide strong evidence for a role for GSK-3 in the regulation of mHtt dynamics, and demonstrate the benefits of GSK-3 inhibition in reducing mHtt toxicity, providing neuroprotective support, and improving HD symptoms.
    Keywords:  Autophagy; GSK-3; GSK-3 inhibitor; Huntington's diseases; L807mts; Lysosome; Mutant huntingtin; R6/2 mice; Sirt1
    DOI:  https://doi.org/10.1016/j.nbd.2021.105336
  10. Elife. 2021 Mar 22. pii: e61590. [Epub ahead of print]10
    Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans.
    Jamie L Courtland, Tyler Wa Bradshaw, Greg Waitt, Erik J Soderblom, Tricia Ho, Anna Rajab, Ricardo Vancini, Il Hwan Kim, Scott H Soderling.
      Mutation of the Wiskott-Aldrich syndrome protein and SCAR homology (WASH) complex subunit, SWIP, is implicated in human intellectual disability, but the cellular etiology of this association is unknown. We identify the neuronal WASH complex proteome, revealing a network of endosomal proteins. To uncover how dysfunction of endosomal SWIP leads to disease, we generate a mouse model of the human WASHC4c.3056C>G mutation. Quantitative spatial proteomics analysis of SWIPP1019R mouse brain reveals that this mutation destabilizes the WASH complex and uncovers significant perturbations in both endosomal and lysosomal pathways. Cellular and histological analyses confirm that SWIPP1019R results in endo-lysosomal disruption and uncover indicators of neurodegeneration. We find that SWIPP1019R not only impacts cognition, but also causes significant progressive motor deficits in mice. A retrospective analysis of SWIPP1019R patients reveals similar movement deficits in humans. Combined, these findings support the model that WASH complex destabilization, resulting from SWIPP1019R, drives cognitive and motor impairments via endo-lysosomal dysfunction in the brain.
    Keywords:  SWIP; WASH complex; cell biology; endosome; human; lysosome; motor impairment; mouse; neuroscience; proteomics
    DOI:  https://doi.org/10.7554/eLife.61590
  11. Sci Rep. 2021 Mar 23. 11(1): 6596
    Cathepsin B and D deficiency in the mouse pancreas induces impaired autophagy and chronic pancreatitis.
    Hideaki Iwama, Sally Mehanna, Mai Imasaka, Shinsuke Hashidume, Hiroshi Nishiura, Ken-Ichi Yamamura, Chigure Suzuki, Yasuo Uchiyama, Etsuro Hatano, Masaki Ohmuraya.
      The major lysosomal proteases, Cathepsin B (CTSB), Cathepsin D (CTSD) and Cathepsin L (CTSL), are implicated in autophagic activity. To investigate the role of each cathepsin in the exocrine pancreas, we generated mice in which the pancreas was specifically deficient in Ctsb, Ctsd and Ctsl. Each of these gene knockout (KO) and Ctsb;Ctsl and Ctsd;Ctsl double-knockout (DKO) mice were almost normal. However, we found cytoplasmic degeneration in the pancreatic acinar cells of Ctsb;Ctsd DKO mice, similar to autophagy related 5 (Atg5) KO mice. LC3 and p62 (autophagy markers) showed remarkable accumulation and the numbers of autophagosomes and autolysosomes were increased in the pancreatic acinar cells of Ctsb;Ctsd DKO mice. Moreover, these Ctsb;Ctsd DKO mice also developed chronic pancreatitis (CP). Thus, we conclude that both Ctsb and Ctsd deficiency caused impaired autophagy in the pancreatic acinar cells, and induced CP in mice.
    DOI:  https://doi.org/10.1038/s41598-021-85898-9
  12. J Invest Dermatol. 2021 Mar 17. pii: S0022-202X(21)01002-2. [Epub ahead of print]
    Imiquimod accelerated antitumor response by targeting lysosome adaptation in skin cancer cells.
    Shu-Hao Chang, Chun-Ying Wu, Kai-Cheng Chuang, Shi-Wei Huang, Zheng-Yi Li, Sin-Ting Wang, Zi-Lun Lai, Cheng-Chung Chang, Yi-Ju Chen, Tak-Wah Wong, Jun-Kai Kao, Jeng-Jer Shieh.
      Lysosomal adaptation is a cellular physiological process in which the number and function of lysosomes are regulated at the transcriptional and posttranscriptional levels in response to extracellular/intracellular cues or lysosomal damage. Imiquimod, a synthetic Toll-like receptor 7 ligand with hydrophobic and weak basic properties, exhibits both antitumor and antiviral activity against various skin malignancies as a clinical treatment. Interestingly, imiquimod has been suggested to be highly concentrated in the lysosomes of plasmacytoid DCs, indicating that imiquimod could modulate lysosome function after sequestration in the lysosome. Here, we found that imiquimod not only induced lysosomal membrane permeabilization and dysfunction but also increased lysosome biogenesis to achieve lysosomal adaptation in cancer cells. Imiquimod-induced ROS production but not lysosomal sequestration of imiquimod was the major cause of lysosomal adaptation. Moreover, imiquimod-induced lysosomal adaptation occurred through lysosomal Ca2+ release and activation of the calcineurin/TFEB axis to promote lysosome biogenesis. Finally, depletion of TFEB sensitized skin cancer cells to imiquimod-induced apoptosis in vitro and in vivo. In summary, disruption of lysosomal adaptation might represent a therapeutic strategy for synergistically enhancing the cytotoxicity of imiquimod in skin cancer cells.
    DOI:  https://doi.org/10.1016/j.jid.2021.01.034
  13. Cell Chem Biol. 2021 Mar 24. pii: S2451-9456(21)00109-4. [Epub ahead of print]
    Degradation from the outside in: targeting extracellular and membrane proteins for degradation through the endolysosomal pathway.
    Green Ahn, Steven M Banik, Carolyn R Bertozzi.
      Targeted protein degradation (TPD) is a promising strategy to remove deleterious proteins for therapeutic benefit and to probe biological pathways. The past two decades have witnessed a surge in the development of technologies that rely on intracellular machinery to degrade challenging cytosolic targets. However, these TPD platforms leave the majority of extracellular and membrane proteins untouched. To enable degradation of these classes of proteins, internalizing receptors can be co-opted to traffic extracellular proteins to the lysosome. Sweeping antibodies and Seldegs use Fc receptors in conjunction with engineered antibodies to degrade soluble proteins. Recently, lysosome-targeting chimeras (LYTACs) have emerged as a strategy to degrade both secreted and membrane-anchored targets. Together with other newcomer technologies, including antibody-based proteolysis-targeting chimeras, modalities that degrade extracellular proteins have promising translational potential. This perspective will give an overview of TPD platforms that degrade proteins via outside-in approaches and focus on the recent development of LYTACs.
    Keywords:  AbTACs; LYTACs; MoDE-As; Seldegs; Sweeping antibodies; extracellular and membrane protein degradation; lysosome; targeted protein degradation
    DOI:  https://doi.org/10.1016/j.chembiol.2021.02.024
  14. Nat Commun. 2021 Mar 26. 12(1): 1920
    The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer.
    Emily Golden, Rabab Rashwan, Eleanor A Woodward, Agustin Sgro, Edina Wang, Anabel Sorolla, Charlene Waryah, Wan Jun Tie, Elisabet Cuyàs, Magdalena Ratajska, Iwona Kardaś, Piotr Kozlowski, Elizabeth K M Johnstone, Heng B See, Ciara Duffy, Jeremy Parry, Kim A Lagerborg, Piotr Czapiewski, Javier A Menendez, Adam Gorczyński, Bartosz Wasag, Kevin D G Pfleger, Christina Curtis, Bum-Kyu Lee, Jonghwan Kim, Joseph Cursons, Nathan J Pavlos, Wojciech Biernat, Mohit Jain, Andrew J Woo, Andrew Redfern, Pilar Blancafort.
      Adipogenesis associated Mth938 domain containing (AAMDC) represents an uncharacterized oncogene amplified in aggressive estrogen receptor-positive breast cancers. We uncover that AAMDC regulates the expression of several metabolic enzymes involved in the one-carbon folate and methionine cycles, and lipid metabolism. We show that AAMDC controls PI3K-AKT-mTOR signaling, regulating the translation of ATF4 and MYC and modulating the transcriptional activity of AAMDC-dependent promoters. High AAMDC expression is associated with sensitization to dactolisib and everolimus, and these PI3K-mTOR inhibitors exhibit synergistic interactions with anti-estrogens in IntClust2 models. Ectopic AAMDC expression is sufficient to activate AKT signaling, resulting in estrogen-independent tumor growth. Thus, AAMDC-overexpressing tumors may be sensitive to PI3K-mTORC1 blockers in combination with anti-estrogens. Lastly, we provide evidence that AAMDC can interact with the RabGTPase-activating protein RabGAP1L, and that AAMDC, RabGAP1L, and Rab7a colocalize in endolysosomes. The discovery of the RabGAP1L-AAMDC assembly platform provides insights for the design of selective blockers to target malignancies having the AAMDC amplification.
    DOI:  https://doi.org/10.1038/s41467-021-22101-7
  15. Neurosci Lett. 2021 Mar 22. pii: S0304-3940(21)00219-6. [Epub ahead of print] 135841
    Krabbe Disease: New Hope for an Old Disease.
    Allison M Bradbury, Ernesto R Bongarzone, Mark S Sands.
      Krabbe disease (globoid cell leukodystrophy) is a lysosomal storage disease (LSD) characterized by progressive and profound demyelination. Infantile, juvenile and adult-onset forms of Krabbe disease have been described, with infantile being the most common. Children with an infantile-onset generally appear normal at birth but begin to miss developmental milestones by six months of age and die by two to four years of age. Krabbe disease is caused by a deficiency of the acid hydrolase galactosylceramidase (GALC) which is responsible for the degradation of galactosylceramides and sphingolipids, which are abundant in myelin membranes. The absence of GALC leads to the toxic accumulation of galactosylsphingosine (psychosine), a lysoderivative of galactosylceramides, in oligodendrocytes and Schwann cells resulting in demyelination of the central and peripheral nervous systems, respectively. Treatment strategies such as enzyme replacement, substrate reduction, enzyme chaperones, and gene therapy have shown promise in LSDs. Unfortunately, Krabbe disease has been relatively refractory to most single-therapy interventions. Although hematopoietic stem cell transplantation can alter the course of Krabbe disease and is the current standard-of-care, it simply slows the progression, even when initiated in pre-symptomatic children. However, the recent success of combinatorial therapeutic approaches in small animal models of Krabbe disease and the identification of new pathogenic mechanisms provide hope for the development of effective treatments for this devastating disease. This review provides a brief history of Krabbe disease and the evolution of single and combination therapeutic approaches and discusses new pathogenic mechanisms and how they might impact the development of more effective treatment strategies.
    Keywords:  Krabbe disease; gene therapy; globoid cell leukodystrophy; lysosomal storage disease
    DOI:  https://doi.org/10.1016/j.neulet.2021.135841
  16. Cell Rep. 2021 Mar 23. pii: S2211-1247(21)00176-5. [Epub ahead of print]34(12): 108862
    Human MC4R variants affect endocytosis, trafficking and dimerization revealing multiple cellular mechanisms involved in weight regulation.
    Bas Brouwers, Edson Mendes de Oliveira, Maria Marti-Solano, Fabiola B F Monteiro, Suli-Anne Laurin, Julia M Keogh, Elana Henning, Rebecca Bounds, Carole A Daly, Shane Houston, Vikram Ayinampudi, Natalia Wasiluk, David Clarke, Bianca Plouffe, Michel Bouvier, M Madan Babu, I Sadaf Farooqi, Jacek Mokrosiński.
      The Melanocortin-4 Receptor (MC4R) plays a pivotal role in energy homeostasis. We used human MC4R mutations associated with an increased or decreased risk of obesity to dissect mechanisms that regulate MC4R function. Most obesity-associated mutations impair trafficking to the plasma membrane (PM), whereas obesity-protecting mutations either accelerate recycling to the PM or decrease internalization, resulting in enhanced signaling. MC4R mutations that do not affect canonical Gαs protein-mediated signaling, previously considered to be non-pathogenic, nonetheless disrupt agonist-induced internalization, β-arrestin recruitment, and/or coupling to Gαs, establishing their causal role in severe obesity. Structural mapping reveals ligand-accessible sites by which MC4R couples to effectors and residues involved in the homodimerization of MC4R, which is disrupted by multiple obesity-associated mutations. Human genetic studies reveal that endocytosis, intracellular trafficking, and homodimerization regulate MC4R function to a level that is physiologically relevant, supporting the development of chaperones, agonists, and allosteric modulators of MC4R for weight loss therapy.
    Keywords:  GPCRs; Gα(s); MC4R; MSH; melanocortin; obesity; therapy; weight loss; β-arrestin
    DOI:  https://doi.org/10.1016/j.celrep.2021.108862
  17. Cell Death Dis. 2021 Mar 23. 12(4): 309
    Autophagy-dependent survival is controlled with a unique regulatory network upon various cellular stress events.
    Orsolya Kapuy, Marianna Holczer, Margita Márton, Tamás Korcsmáros.
      Although autophagy is a type of programmed cell death, it is also essential for cell survival upon tolerable level of various stress events. For the cell to respond adequately to an external and/or internal stimulus induced by cellular stress, autophagy must be controlled in a highly regulated manner. By using systems biology techniques, here we explore the dynamical features of autophagy induction. We propose that the switch-like characteristic of autophagy induction is achieved by a control network, containing essential feedback loops of four components, so-called autophagy inducer, autophagy controller, mTORC1 and autophagy executor, respectively. We show how an autophagy inducer is capable to turn on autophagy in a cellular stress-specific way. The autophagy controller acts as a molecular switch and not only promotes autophagy but also blocks the permanent hyperactivation of the process via downregulating the autophagy inducer. In this theoretical analysis, we explore in detail the properties of all four proposed controlling elements and their connections. Here we also prove that the kinetic features of this control network can be considered accurate in various stress processes (such as starvation, endoplasmic reticulum stress and oxidative stress), even if the exact components may be different. The robust response of the resulting control network is essential during cellular stress.
    DOI:  https://doi.org/10.1038/s41419-021-03599-7
  18. J Neuroimmune Pharmacol. 2021 Mar 22.
    Lysosomal Stress Response (LSR): Physiological Importance and Pathological Relevance.
    Koffi L Lakpa, Nabab Khan, Zahra Afghah, Xuesong Chen, Jonathan D Geiger.
      Extensive work has characterized endoplasmic reticulum (ER) and mitochondrial stress responses. In contrast, very little has been published about stress responses in lysosomes; subcellular acidic organelles that are physiologically important and are of pathological relevance. The greater lysosomal system is dynamic and is comprised of endosomes, lysosomes, multivesicular bodies, autophagosomes, and autophagolysosomes. They are important regulators of cellular physiology, they represent about 5% of the total cellular volume, they are heterogeneous in their sizes and distribution patterns, they are electron dense, and their subcellular positioning within cells varies in response to stimuli, insults and pH. These organelles are also integral to the pathogenesis of lysosomal storage diseases and it is increasingly recognized that lysosomes play important roles in the pathogenesis of such diverse conditions as neurodegenerative disorders and cancer. The purpose of this review is to focus attention on lysosomal stress responses (LSR), compare LSR with better characterized stress responses in ER and mitochondria, and form a framework for future characterizations of LSR. We synthesized data into the concept of LSR and present it here such that the definition of LSR can be modified as new knowledge is added and specific therapeutics are developed.
    Keywords:  Endoplasmic reticulum stress; Endosomes; Inter-organellar signaling; Lysosomes; Mitochondrial stress
    DOI:  https://doi.org/10.1007/s11481-021-09990-7
  19. Science. 2021 Mar 26. pii: eaaz4544. [Epub ahead of print]371(6536):
    WAVE2 suppresses mTOR activation to maintain T cell homeostasis and prevent autoimmunity.
    Ming Liu, Jinyi Zhang, Benjamin D Pinder, Qingquan Liu, Dingyan Wang, Hao Yao, Yubo Gao, Aras Toker, Jimin Gao, Alan Peterson, Jia Qu, Katherine A Siminovitch.
      Cytoskeletal regulatory protein dysfunction has been etiologically linked to inherited diseases associated with immunodeficiency and autoimmunity, but the mechanisms involved are incompletely understood. Here, we show that conditional Wave2 ablation in T cells causes severe autoimmunity associated with increased mammalian target of rapamycin (mTOR) activation and metabolic reprogramming that engender spontaneous activation and accelerated differentiation of peripheral T cells. These mice also manifest diminished antigen-specific T cell responses associated with increased inhibitory receptor expression, dysregulated mitochondrial function, and reduced cell survival upon activation. Mechanistically, WAVE2 directly bound mTOR and inhibited its activation by impeding mTOR interactions with RAPTOR (regulatory-associated protein of mTOR) and RICTOR (rapamycin-insensitive companion of mTOR). Both the T cell defects and immunodysregulatory disease were ameliorated by pharmacological mTOR inhibitors. Thus, WAVE2 restraint of mTOR activation is an absolute requirement for maintaining the T cell homeostasis supporting adaptive immune responses and preventing autoimmunity.
    DOI:  https://doi.org/10.1126/science.aaz4544
  20. Neuron. 2021 Mar 18. pii: S0896-6273(21)00156-2. [Epub ahead of print]
    Akt-mTOR hypoactivity in bipolar disorder gives rise to cognitive impairments associated with altered neuronal structure and function.
    Amanda M Vanderplow, Andrew L Eagle, Bailey A Kermath, Kathryn J Bjornson, Alfred J Robison, Michael E Cahill.
      The Akt family of kinases exerts many of its cellular effects via the activation of the mammalian target of rapamycin (mTOR) kinase through a series of intermediary proteins. Multiple lines of evidence have identified Akt-family kinases as candidate schizophrenia and bipolar disorder genes. Although dysfunction of the prefrontal cortex (PFC) is a key feature of both schizophrenia and bipolar disorder, no studies have comprehensively assessed potential alterations in Akt-mTOR pathway activity in the PFC of either disorder. Here, we examined the activity and expression profile of key proteins in the Akt-mTOR pathway in bipolar disorder and schizophrenia homogenates from two different PFC subregions. Our findings identify reduced Akt-mTOR PFC signaling in a subset of bipolar disorder subjects. Using a reverse-translational approach, we demonstrated that Akt hypofunction in the PFC is sufficient to give rise to key cognitive phenotypes that are paralleled by alterations in synaptic connectivity and function.
    Keywords:  akt; autophagy; bipolar disorder; cognition; dendritic spine; mTOR; memory; prefrontal cortex; synapse; ulk1
    DOI:  https://doi.org/10.1016/j.neuron.2021.03.008
  21. Front Cell Dev Biol. 2021 ;9 595754
    Light Stimuli and Circadian Clock Affect Neural Development in Drosophila melanogaster.
    Eleni Dapergola, Pamela Menegazzi, Thomas Raabe, Anna Hovhanyan.
      Endogenous clocks enable organisms to adapt cellular processes, physiology, and behavior to daily variation in environmental conditions. Metabolic processes in cyanobacteria to humans are under the influence of the circadian clock, and dysregulation of the circadian clock causes metabolic disorders. In mouse and Drosophila, the circadian clock influences translation of factors involved in ribosome biogenesis and synchronizes protein synthesis. Notably, nutrition signals are mediated by the insulin receptor/target of rapamycin (InR/TOR) pathways to regulate cellular metabolism and growth. However, the role of the circadian clock in Drosophila brain development and the potential impact of clock impairment on neural circuit formation and function is less understood. Here we demonstrate that changes in light stimuli or disruption of the molecular circadian clock cause a defect in neural stem cell growth and proliferation. Moreover, we show that disturbed cell growth and proliferation are accompanied by reduced nucleolar size indicative of impaired ribosomal biogenesis. Further, we define that light and clock independently affect the InR/TOR growth regulatory pathway due to the effect on regulators of protein biosynthesis. Altogether, these data suggest that alterations in InR/TOR signaling induced by changes in light conditions or disruption of the molecular clock have an impact on growth and proliferation properties of neural stem cells in the developing Drosophila brain.
    Keywords:  Drosophila; circadian clock; light stimuli; neuroblast growth; proliferation
    DOI:  https://doi.org/10.3389/fcell.2021.595754
  22. Aging (Albany NY). 2021 Mar 21. 13
    Enhancing lifespan of budding yeast by pharmacological lowering of amino acid pools.
    Nathaniel L Hepowit, Jessica K A Macedo, Lyndsay E A Young, Ke Liu, Ramon C Sun, Jason A MacGurn, Robert C Dickson.
      The increasing prevalence of age-related diseases and resulting healthcare insecurity and emotional burden require novel treatment approaches. Several promising strategies seek to limit nutrients and promote healthy aging. Unfortunately, the human desire to consume food means this strategy is not practical for most people but pharmacological approaches might be a viable alternative. We previously showed that myriocin, which impairs sphingolipid synthesis, increases lifespan in Saccharomyces cerevisiae by modulating signaling pathways including the target of rapamycin complex 1 (TORC1). Since TORC1 senses cellular amino acids, we analyzed amino acid pools and identified 17 that are lowered by myriocin treatment. Studying the methionine transporter, Mup1, we found that newly synthesized Mup1 traffics to the plasma membrane and is stable for several hours but is inactive in drug-treated cells. Activity can be restored by adding phytosphingosine to culture medium thereby bypassing drug inhibition, thus confirming a sphingolipid requirement for Mup1 activity. Importantly, genetic analysis of myriocin-induced longevity revealed a requirement for the Gtr1/2 (mammalian Rags) and Vps34-Pib2 amino acid sensing pathways upstream of TORC1, consistent with a mechanism of action involving decreased amino acid availability. These studies demonstrate the feasibility of pharmacologically inducing a state resembling amino acid restriction to promote healthy aging.
    Keywords:  amino acid transport; lifespan; longevity; nutrient restriction; sphingolipids
    DOI:  https://doi.org/10.18632/aging.202849
  23. Mol Cell. 2021 Mar 11. pii: S1097-2765(21)00167-2. [Epub ahead of print]
    Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control.
    Ladislav Dokládal, Michael Stumpe, Benjamin Pillet, Zehan Hu, Guillermo Miguel Garcia Osuna, Dieter Kressler, Jörn Dengjel, Claudio De Virgilio.
      The conserved Gcn2 protein kinase mediates cellular adaptations to amino acid limitation through translational control of gene expression that is exclusively executed by phosphorylation of the α-subunit of the eukaryotic translation initiation factor 2 (eIF2α). Using quantitative phosphoproteomics, however, we discovered that Gcn2 targets auxiliary effectors to modulate translation. Accordingly, Gcn2 also phosphorylates the β-subunit of the trimeric eIF2 G protein complex to promote its association with eIF5, which prevents spontaneous nucleotide exchange on eIF2 and thereby restricts the recycling of the initiator methionyl-tRNA-bound eIF2-GDP ternary complex in amino-acid-starved cells. This mechanism contributes to the inhibition of translation initiation in parallel to the sequestration of the nucleotide exchange factor eIF2B by phosphorylated eIF2α. Gcn2 further phosphorylates Gcn20 to antagonize, in an inhibitory feedback loop, the formation of the Gcn2-stimulatory Gcn1-Gcn20 complex. Thus, Gcn2 plays a substantially more intricate role in controlling translation initiation than hitherto appreciated.
    Keywords:  Gcn2; Gcn20; TORC1; amino acid starvation; eIF2; eIF5; eukaryotic initiation factor 2; eukaryotic initiation factor 5; general control nonderepressible 2; target of rapamycin complex 1; translation initiation
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.037
  24. Curr Biol. 2021 Mar 18. pii: S0960-9822(21)00305-5. [Epub ahead of print]
    Increased LRRK2 kinase activity alters neuronal autophagy by disrupting the axonal transport of autophagosomes.
    C Alexander Boecker, Juliet Goldsmith, Dan Dou, Gregory G Cajka, Erika L F Holzbaur.
      Parkinson's disease-causing mutations in the leucine-rich repeat kinase 2 (LRRK2) gene hyperactivate LRRK2 kinase activity and cause increased phosphorylation of Rab GTPases, important regulators of intracellular trafficking. We found that the most common LRRK2 mutation, LRRK2-G2019S, dramatically reduces the processivity of autophagosome transport in neurons in a kinase-dependent manner. This effect was consistent across an overexpression model, neurons from a G2019S knockin mouse, and human induced pluripotent stem cell (iPSC)-derived neurons gene edited to express the G2019S mutation, and the effect was reversed by genetic or pharmacological inhibition of LRRK2. Furthermore, LRRK2 hyperactivation induced by overexpression of Rab29, a known activator of LRRK2 kinase, disrupted autophagosome transport to a similar extent. Mechanistically, we found that hyperactive LRRK2 recruits the motor adaptor JNK-interacting protein 4 (JIP4) to the autophagosomal membrane, inducing abnormal activation of kinesin that we propose leads to an unproductive tug of war between anterograde and retrograde motors. Disruption of autophagosome transport correlated with a significant defect in autophagosome acidification, suggesting that the observed transport deficit impairs effective degradation of autophagosomal cargo in neurons. Our results robustly link increased LRRK2 kinase activity to defects in autophagosome transport and maturation, further implicating defective autophagy in the pathogenesis of Parkinson's disease.
    Keywords:  JIP4; LRRK2; Parkinson's disease; Rab29; autophagy; axonal transport
    DOI:  https://doi.org/10.1016/j.cub.2021.02.061
  25. Front Immunol. 2021 ;12 637335
    TSC1 Affects the Process of Renal Ischemia-Reperfusion Injury by Controlling Macrophage Polarization.
    Xiao Hu, Yanan Xu, Zhaoqi Zhang, Zuofu Tang, Jinhua Zhang, You Luo, Weiming Deng, Zhanwen Dong, Yong Zhao, Ning Na.
      Renal ischemia-reperfusion injury (IRI) contributes to acute kidney injury (AKI), increases morbidity and mortality, and is a significant risk factor for chronic kidney disease (CKD). Macrophage infiltration is a common feature after renal IRI, and infiltrating macrophages can be polarized into the following two distinct types: M1 macrophages, i.e., classically activated macrophages, which can not only inhibit infection but also accelerate renal injury, and M2 macrophages, i.e., alternatively activated macrophages, which have a repair phenotype that can promote wound healing and subsequent fibrosis. The role of TSC1, which is a negative regulator of mTOR signaling that regulates macrophage polarization in inflammation-linked diseases, has been well documented, but whether TSC1 contributes to macrophage polarization in the process of IRI is still unknown. Here, by using a mouse model of renal ischemia-reperfusion, we found that myeloid cell-specific TSC1 knockout mice (termed Lyz-TSC1 cKO mice) had higher serum creatinine levels, more severe histological damage, and greater proinflammatory cytokine production than wild-type (WT) mice during the early phase after renal ischemia-reperfusion. Furthermore, the Lyz-TSC1 cKO mice showed attenuated renal fibrosis during the repair phase of IRI with decreased levels of M2 markers on macrophages in the operated kidneys, which was further confirmed in a cell model of hypoxia-reoxygenation (H/R) in vitro. Mechanistically, by using RNA sequencing of sorted renal macrophages, we found that the expression of most M1-related genes was upregulated in the Lyz-TSC1 cKO group (Supplemental Table 1) during the early phase. However, C/EBPβ and CD206 expression was decreased during the repair phase compared to in the WT group. Overall, our findings demonstrate that the expression of TSC1 in macrophages contributes to the whole process of IRI but serves as an inflammation suppressor during the early phase and a fibrosis promoter during the repair phase.
    Keywords:  fibrosis; ischemia-reperfusion (IR); kidney; macrophage polarization; tuberous sclerosis complex 1 (TSC1)
    DOI:  https://doi.org/10.3389/fimmu.2021.637335
  26. Physiol Rep. 2021 Mar;9(6): e14807
    mTOR-mediated calcium transients affect cardiac function in ex vivo ischemia-reperfusion injury.
    Briana K Shimada, Naaiko Yorichika, Jason K Higa, Yuichi Baba, Motoi Kobayashi, Toshinori Aoyagi, Tomohiro Suhara, Takashi Matsui.
      The mechanistic target of rapamycin (mTOR) is a key mediator of energy metabolism, cell growth, and survival. While previous studies using transgenic mice with cardiac-specific overexpression of mTOR (mTOR-Tg) demonstrated the protective effects of cardiac mTOR against ischemia-reperfusion (I/R) injury in both ex vivo and in vivo models, the mechanisms underlying the role of cardiac mTOR in cardiac function following I/R injury are not well-understood. Torin1, a pharmacological inhibitor of mTOR complex (mTORC) 1 and mTORC2, significantly decreased functional recovery of LV developed pressure in ex vivo I/R models (p < 0.05). To confirm the role of mTOR complexes in I/R injury, we generated cardiac-specific mTOR-knockout (CKO) mice. In contrast to the effects of Torin1, CKO hearts recovered better after I/R injury than control hearts (p < 0.05). Interestingly, the CKO hearts had exhibited irregular contractions during the reperfusion phase. Calcium is a major factor in Excitation-Contraction (EC) coupling via Sarcoplasmic Reticulum (SR) calcium release. Calcium is also key in opening the mitochondrial permeability transition pore (mPTP) and cell death following I/R injury. Caffeine-induced SR calcium release in isolated CMs showed that total SR calcium content was lower in CKO than in control CMs. Western blotting showed that a significant amount of mTOR localizes to the SR/mitochondria and that GSK3-β phosphorylation, a key factor in SR calcium mobilization, was decreased. These findings suggest that cardiac mTOR located to the SR/mitochondria plays a vital role in EC coupling and cell survival in I/R injury.
    Keywords:  calcium; cardiomyocyte; ischemia-reperfusion; mTOR
    DOI:  https://doi.org/10.14814/phy2.14807
  27. Autophagy. 2021 Mar 23.
    The Role of Mitophagy in the Regulation of Mitochondrial Energetic Status in Neurons.
    Sinsuk Han, Mingyang Zhang, Yu Young Jeong, David Margolis, Qian Cai.
      Mitochondria are the main cellular energy powerhouses and supply most of the energy in the form of ATP to fuel essential neuronal functions through oxidative phosphorylation (OXPHOS). In Alzheimer disease (AD), metabolic and mitochondrial disruptions are an early feature preceding any histopathological and clinical manifestations. Mitochondrial malfunction is also linked to synaptic defects in early AD. Mitophagy serves as a key cellular quality control mechanism involving sequestration of damaged mitochondria within autophagosomes and their subsequent degradation in lysosomes. However, it remains largely unknown whether mitophagy is involved in the regulation of energy metabolism in neurons, and if so, whether metabolic deficiency in AD is attributed to mitophagy dysfunction. Here we reveal that mitophagy is broadly activated in metabolically enhanced neurons upon OXPHOS stimulation, which sustains high energetic activity by increasing mitochondrial turnover and hence facilitating mitochondrial maintenance. Unexpectedly, in AD-related mutant HsAPP Tg mouse brains, early stimulation of OXPHOS activity fails to correct energy deficits but exacerbates synapse loss as a consequence of mitophagy failure. Excitingly, lysosomal enhancement in AD neurons restores impaired metabolic function by promoting elimination of damaged mitochondria, protecting against synaptic damage in AD mouse brains. Taken together, we propose a new mechanism by which mitophagy controls bioenergetic status in neurons, furthering our understanding of the direct impact of mitophagy defects on AD-linked metabolic deficits and shedding light on the development of novel therapeutic strategies to treat AD by the early stimulation of mitochondrial metabolism combined with elevation of lysosomal proteolytic activity.
    Keywords:  Alzheimer; bioenergetics; energy metabolism; lysosomal proteolysis; metabolic deficiency; mitochondrial stress; mitophagosome; neuronal mitophagy; retrograde transport; synapse loss
    DOI:  https://doi.org/10.1080/15548627.2021.1907167
  28. EMBO J. 2021 Mar 22. e107238
    Golgi maturation-dependent glycoenzyme recycling controls glycosphingolipid biosynthesis and cell growth via GOLPH3.
    Riccardo Rizzo, Domenico Russo, Kazuo Kurokawa, Pranoy Sahu, Bernadette Lombardi, Domenico Supino, Mikhail A Zhukovsky, Anthony Vocat, Prathyush Pothukuchi, Vidya Kunnathully, Laura Capolupo, Gaelle Boncompain, Carlo Vitagliano, Federica Zito Marino, Gabriella Aquino, Daniela Montariello, Petra Henklein, Luigi Mandrich, Gerardo Botti, Henrik Clausen, Ulla Mandel, Toshiyuki Yamaji, Kentaro Hanada, Alfredo Budillon, Franck Perez, Seetharaman Parashuraman, Yusuf A Hannun, Akihiko Nakano, Daniela Corda, Giovanni D'Angelo, Alberto Luini.
      Glycosphingolipids are important components of the plasma membrane where they modulate the activities of membrane proteins including signalling receptors. Glycosphingolipid synthesis relies on competing reactions catalysed by Golgi-resident enzymes during the passage of substrates through the Golgi cisternae. The glycosphingolipid metabolic output is determined by the position and levels of the enzymes within the Golgi stack, but the mechanisms that coordinate the intra-Golgi localisation of the enzymes are poorly understood. Here, we show that a group of sequentially-acting enzymes operating at the branchpoint among glycosphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3. GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting as a component of the cisternal maturation mechanism. Through these effects, GOLPH3 controls the sub-Golgi localisation and the lysosomal degradation rate of specific enzymes. Increased GOLPH3 levels, as those observed in tumours, alter glycosphingolipid synthesis and plasma membrane composition thereby promoting mitogenic signalling and cell proliferation. These data have medical implications as they outline a novel oncogenic mechanism of action for GOLPH3 based on glycosphingolipid metabolism.
    Keywords:  GOLPH3; Golgi; Trafficking; cisternal maturation; mTOR
    DOI:  https://doi.org/10.15252/embj.2020107238
  29. Nat Commun. 2021 03 23. 12(1): 1826
    Mutant ASXL1 induces age-related expansion of phenotypic hematopoietic stem cells through activation of Akt/mTOR pathway.
    Takeshi Fujino, Susumu Goyama, Yuki Sugiura, Daichi Inoue, Shuhei Asada, Satoshi Yamasaki, Akiko Matsumoto, Kiyoshi Yamaguchi, Yumiko Isobe, Akiho Tsuchiya, Shiori Shikata, Naru Sato, Hironobu Morinaga, Tomofusa Fukuyama, Yosuke Tanaka, Tsuyoshi Fukushima, Reina Takeda, Keita Yamamoto, Hiroaki Honda, Emi K Nishimura, Yoichi Furukawa, Tatsuhiro Shibata, Omar Abdel-Wahab, Makoto Suematsu, Toshio Kitamura.
      Somatic mutations of ASXL1 are frequently detected in age-related clonal hematopoiesis (CH). However, how ASXL1 mutations drive CH remains elusive. Using knockin (KI) mice expressing a C-terminally truncated form of ASXL1-mutant (ASXL1-MT), we examined the influence of ASXL1-MT on physiological aging in hematopoietic stem cells (HSCs). HSCs expressing ASXL1-MT display competitive disadvantage after transplantation. Nevertheless, in genetic mosaic mouse model, they acquire clonal advantage during aging, recapitulating CH in humans. Mechanistically, ASXL1-MT cooperates with BAP1 to deubiquitinate and activate AKT. Overactive Akt/mTOR signaling induced by ASXL1-MT results in aberrant proliferation and dysfunction of HSCs associated with age-related accumulation of DNA damage. Treatment with an mTOR inhibitor rapamycin ameliorates aberrant expansion of the HSC compartment as well as dysregulated hematopoiesis in aged ASXL1-MT KI mice. Our findings suggest that ASXL1-MT provokes dysfunction of HSCs, whereas it confers clonal advantage on HSCs over time, leading to the development of CH.
    DOI:  https://doi.org/10.1038/s41467-021-22053-y
  30. PLoS One. 2021 ;16(3): e0248241
    Elevated glucose represses lysosomal and mTOR-related genes in renal epithelial cells composed of progenitor CD133+ cells.
    Swojani Shrestha, Sandeep Singhal, Donald A Sens, Seema Somji, Bethany A Davis, Rachel Guyer, Spencer Breen, Matthew Kalonick, Scott H Garrett.
      Hyperglycemia is one of the major health concern in many parts of the world. One of the serious complications of high glucose levels is diabetic nephropathy. The preliminary microarray study performed on primary human renal tubular epithelial (hRTE) cells exposed to high glucose levels showed a significant downregulation of mTOR as well as its associated genes as well as lysosomal genes. Based on this preliminary data, the expression of various lysosomal genes as well as mTOR and its associated genes were analyzed in hRTE cells exposed to 5.5, 7.5, 11 and 16 mM glucose. The results validated the microarray analysis, which showed a significant decrease in the mRNA as well as protein expression of the selected genes as the concentration of glucose increased. Co-localization of lysosomal marker, LAMP1 with mTOR showed lower expression of mTOR as the glucose concentration increased, suggesting decrease in mTOR activity. Although the mechanism by which glucose affects the regulation of lysosomal genes is not well known, our results suggest that high levels of glucose may lead to decrease in mTOR expression causing the cells to enter an anabolic state with subsequent downregulation of lysosomal genes.
    DOI:  https://doi.org/10.1371/journal.pone.0248241
  31. Front Cell Dev Biol. 2021 ;9 648024
    Targeting Endosomal Recycling Pathways by Bacterial and Viral Pathogens.
    Xin Yong, Lejiao Mao, Xiaofei Shen, Zhen Zhang, Daniel D Billadeau, Da Jia.
      Endosomes are essential cellular stations where endocytic and secretory trafficking routes converge. Proteins transiting at endosomes can be degraded via lysosome, or recycled to the plasma membrane, trans-Golgi network (TGN), or other cellular destinations. Pathways regulating endosomal recycling are tightly regulated in order to preserve organelle identity, to maintain lipid homeostasis, and to support other essential cellular functions. Recent studies have revealed that both pathogenic bacteria and viruses subvert host endosomal recycling pathways for their survival and replication. Several host factors that are frequently targeted by pathogens are being identified, including retromer, TBC1D5, SNX-BARs, and the WASH complex. In this review, we will focus on the recent advances in understanding how intracellular bacteria, human papillomavirus (HPV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijack host endosomal recycling pathways. This exciting work not only reveals distinct mechanisms employed by pathogens to manipulate host signaling pathways, but also deepens our understanding of the molecular intricacies regulating endosomal receptor trafficking.
    Keywords:  SARS-CoV-2; SNX; TBC1D5; WASH complex; endosomal recycling; human papillomavirus; pathogenic bacteria; retromer
    DOI:  https://doi.org/10.3389/fcell.2021.648024
  32. Proc Natl Acad Sci U S A. 2021 Mar 30. pii: e2021093118. [Epub ahead of print]118(13):
    Paxbp1 controls a key checkpoint for cell growth and survival during early activation of quiescent muscle satellite cells.
    Shaopu Zhou, Lifang Han, Mingxi Weng, Han Zhu, Youshan Heng, Gang Wang, Zeyu Shen, Xianwei Chen, Xinrong Fu, Mingjie Zhang, Zhenguo Wu.
      Adult mouse muscle satellite cells (MuSCs) are quiescent in uninjured muscles. Upon muscle injury, MuSCs exit quiescence, reenter the cell cycle to proliferate and self-renew, and then differentiate and fuse to drive muscle regeneration. However, it remains poorly understood how MuSCs transition from quiescence to the cycling state. Here, we report that Pax3 and Pax7 binding protein 1 (Paxbp1) controls a key checkpoint during this critical transition. Deletion of Paxbp1 in adult MuSCs prevented them from reentering the cell cycle upon injury, resulting in a total regeneration failure. Mechanistically, we found an abnormal elevation of reactive oxygen species (ROS) in Paxbp1-null MuSCs, which induced p53 activation and impaired mTORC1 signaling, leading to defective cell growth, apoptosis, and failure in S-phase reentry. Deliberate ROS reduction partially rescued the cell-cycle reentry defect in mutant MuSCs. Our study reveals that Paxbp1 regulates a late cell-growth checkpoint essential for quiescent MuSCs to reenter the cell cycle upon activation.
    Keywords:  Paxbp1; ROS; cell growth; muscle satellite cells; quiescence
    DOI:  https://doi.org/10.1073/pnas.2021093118
  33. J Biol Chem. 2021 Mar 18. pii: S0021-9258(21)00343-4. [Epub ahead of print] 100565
    Structure, interdomain dynamics and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes.
    Patrick Johé, Elmar Jaenicke, Hannes Neuweiler, Tanja Schirmeister, Christian Kersten, Ute A Hellmich.
      Rhodesain is the lysosomal cathepsin L-like cysteine protease of T. brucei rhodesiense, the causative agent of Human African Trypanosomiasis. The enzyme is essential for the proliferation and pathogenicity of the parasite as well as its ability to overcome the blood-brain barrier of the host. Lysosomal cathepsins are expressed as zymogens with an inactivating pro-domain that is cleaved under acidic conditions. A structure of the uncleaved maturation intermediate from a trypanosomal cathepsin L-like protease is currently not available. We thus established the heterologous expression of T. brucei rhodesiense pro-rhodesain in E. coli and determined its crystal structure. The trypanosomal pro-domain differs from non-parasitic pro-cathepsins by a unique, extended α-helix that blocks the active site and whose side-chain interactions resemble those of the antiprotozoal inhibitor K11777. Interdomain dynamics between pro- and core protease domain as observed by photoinduced electron transfer fluorescence correlation spectroscopy increase at low pH, where pro-rhodesain also undergoes autocleavage. Using the crystal structure, molecular dynamics simulations and mutagenesis, we identify a conserved interdomain salt bridge that prevents premature intramolecular cleavage at higher pH values and may thus present a control switch for the observed pH-sensitivity of pro-enzyme cleavage in (trypanosomal) CathL-like proteases.
    Keywords:  African Sleeping Sickness; Trypanosoma brucei; autoinhibition; crystal structure; cysteine protease; fluorescence correlation spectroscopy (FCS); molecular dynamics; pro-enzyme; rhodesain; zymogen
    DOI:  https://doi.org/10.1016/j.jbc.2021.100565
  34. Int Immunopharmacol. 2021 Mar 17. pii: S1567-5769(21)00188-0. [Epub ahead of print]95 107552
    Precision control of mTORC1 is crucial for the maintenance and IL-13 responsiveness of alveolar macrophages.
    Yanxiang Hu, Jing Wen, Bei Zhang, Hui Xiao.
      Alveolar macrophages (AMs) are the lung resident macrophages critically involved in pulmonary homeostasis and immune response. Recent researches have uncovered a diversity of regulators responsible for the development, maintenance, and function of AMs. Nevertheless, the molecular underpinnings that determine the developmental and functional specification of AMs remain incompletely understood. Here, we investigated the role of the TSC1-mTOR pathway in murine AMs by genetic ablating Tsc1 or mTor alleles through Cd11c-Cre or LysM-Cre. Flow cytometry analyses revealed a prominent decrease in AMs in Tsc1f/f-Cd11c-Cre and Tsc1f/f/-LysM-Cre mice. Moreover, a reduction in AMs was also noted in mTorf/f-Cd11c-Cre or Rptorf/f-Cd11c-Cre mice. Further evidence implicated that elevation in cell death, most likely aberrant apoptosis or/and necroptosis, might be attributable to disrupted AM homeostasis. Whereas a diversity of cytokines involved in AM homeostasis and function triggered mTOR activation, only the IL-13 signaling, particularly Jak1 and Stat3 activation, was affected by TSC1 in macrophages. Further, select genes induced by IL-13, including AM surface markers such as Pparg, Fabp4/5, Nfil3 and Car4, and M2 hallmarks such as Arg1, Fizz, Ym1 and Clec7a were fine-tuned by the TSC1-mTOR pathway. Therefore, our results demonstrated that the TSC1-mTOR pathway has a crucial role in the homeostasis and functional specification of AMs through integrating cytokine signaling with metabolic cues.
    Keywords:  Alveolar macrophage; Apoptosis; IL-13; Necroptosis; TSC1; mTOR
    DOI:  https://doi.org/10.1016/j.intimp.2021.107552
  35. Sci Adv. 2021 Mar;pii: eabf8598. [Epub ahead of print]7(13):
    Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly.
    Natalya Leneva, Oleksiy Kovtun, Dustin R Morado, John A G Briggs, David J Owen.
      Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes.
    DOI:  https://doi.org/10.1126/sciadv.abf8598
  36. Life Sci. 2021 Mar 18. pii: S0024-3205(21)00343-X. [Epub ahead of print]275 119358
    The S6k/4E-BP mediated growth promoting sub-pathway of insulin signalling cascade is essential to restrict pathogenesis of poly(Q) disorders in Drosophila.
    Shweta Tandon, Surajit Sarkar.
      Human neurodegenerative polyglutamine [poly(Q)] disorders, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA), are characterised by an abnormal expansion of CAG repeats in the affected gene. The mutated proteins misfold and aggregate to form inclusion bodies that sequester important factors involved in cellular transcription, growth, stress and autophagic response and other essential functions. The insulin signalling pathway has been demonstrated as a major modifier and a potential drug target to ameliorate the poly(Q) mediated neurotoxicity in various model systems. Insulin signalling cascade harbours several downstream sub-pathways, which are synergistically involved in discharging indispensable biological functions such as growth and proliferation, metabolism, autophagy, regulation of cell death pathways etc. Hence, it is difficult to conclude whether the mitigation of poly(Q) neurotoxicity is an accumulative outcome of the insulin cascade, or the result of a specific sub-pathway. For the first time, we report that the ligand binding domain of insulin receptor mediated downstream growth promoting sub-pathway plays the pivotal role in operating the rescue event. We show that the growth promoting activity of insulin cascade is essential to minimize the abundance of inclusion bodies, to restrict neurodegeneration, and to restore the cellular transcriptional balance. Subsequently, we noted the involvement of the mTOR/S6k/4E-BP candidates in mitigating poly(Q) mediated neurotoxicity. Due to the conserved cellular functioning of the insulin cascade across species, and availability of several growth promoting molecules, our results in Drosophila poly(Q) models indicate towards a possibility of designing novel therapeutic strategies to restrict the pathogenesis of devastating human poly(Q) disorders.
    Keywords:  Drosophila; Insulin pathway; Neurodegeneration; Poly(Q) disorders
    DOI:  https://doi.org/10.1016/j.lfs.2021.119358
  37. Nat Commun. 2021 03 25. 12(1): 1876
    SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition.
    Peter J Mullen, Gustavo Garcia, Arunima Purkayastha, Nedas Matulionis, Ernst W Schmid, Milica Momcilovic, Chandani Sen, Justin Langerman, Arunachalam Ramaiah, David B Shackelford, Robert Damoiseaux, Samuel W French, Kathrin Plath, Brigitte N Gomperts, Vaithilingaraja Arumugaswami, Heather R Christofk.
      Viruses hijack host cell metabolism to acquire the building blocks required for replication. Understanding how SARS-CoV-2 alters host cell metabolism may lead to potential treatments for COVID-19. Here we profile metabolic changes conferred by SARS-CoV-2 infection in kidney epithelial cells and lung air-liquid interface (ALI) cultures, and show that SARS-CoV-2 infection increases glucose carbon entry into the TCA cycle via increased pyruvate carboxylase expression. SARS-CoV-2 also reduces oxidative glutamine metabolism while maintaining reductive carboxylation. Consistent with these changes, SARS-CoV-2 infection increases the activity of mTORC1 in cell lines and lung ALI cultures. Lastly, we show evidence of mTORC1 activation in COVID-19 patient lung tissue, and that mTORC1 inhibitors reduce viral replication in kidney epithelial cells and lung ALI cultures. Our results suggest that targeting mTORC1 may be a feasible treatment strategy for COVID-19 patients, although further studies are required to determine the mechanism of inhibition and potential efficacy in patients.
    DOI:  https://doi.org/10.1038/s41467-021-22166-4
  38. Adv Mater. 2021 Mar 24. e2100616
    Target Reprogramming Lysosomes of CD8+ T Cells by a Mineralized Metal-Organic Framework for Cancer Immunotherapy.
    Qin Zhao, Zijian Gong, Zhihao Li, Jinyang Wang, Jinglun Zhang, Zifan Zhao, Peng Zhang, Shihang Zheng, Richard J Miron, Quan Yuan, Yufeng Zhang.
      T cell immunotherapy holds significant challenges in solid tumors, mainly due to the T cells' low activation and the decreased synthesis-release of therapeutic proteins, including perforin and granzyme B, which are present in lysosomes. In this study, a lysosome-targeting nanoparticle (LYS-NP) is developed by way of a mineralized metal-organic framework (MOF) coupled with a lysosome-targeting aptamer (CD63-aptamer) to enhance the antitumor effect of T cells. The MOF synthesized from Zn2+ and dimethylimidazole has good protein encapsulation and acid sensitivity, and is thus an ideal lysosomal delivery vector. Calcium carbonate (CaCO3 ) is used to induce MOF mineralization, improve the composite material's stability in encapsulating therapeutic protein, and provide calcium ions with synergistic effects. Before mineralization, perforin and granzyme B-T cell-needed therapeutic proteins for tumors-are preloaded with the MOF. Moreover, T cells are pretreated with processed tumor-specific antigens to activate or produce memory before reprogramming the lysosomes, facilitating the T cell receptor (TCR) for release of the therapeutic proteins. Using T cells recombined by LYS-NPs, a significant enhancement of breast cancer control is confirmed.
    Keywords:  adoptive T cells; cancer therapy; immunotherapy; lysosomes; metal-organic frameworks
    DOI:  https://doi.org/10.1002/adma.202100616
  39. Sci Signal. 2021 03 23. pii: eabd5605. [Epub ahead of print]14(675):
    Essential requirement for JPT2 in NAADP-evoked Ca2+ signaling.
    Gihan S Gunaratne, Eugen Brailoiu, Shijun He, Ellen M Unterwald, Sandip Patel, James T Slama, Timothy F Walseth, Jonathan S Marchant.
      Nicotinic acid adenine dinucleotide phosphate (NAADP) is a second messenger that releases Ca2+ from acidic organelles through the activation of two-pore channels (TPCs) to regulate endolysosomal trafficking events. NAADP action is mediated by NAADP-binding protein(s) of unknown identity that confer NAADP sensitivity to TPCs. Here, we used a "clickable" NAADP-based photoprobe to isolate human NAADP-binding proteins and identified Jupiter microtubule-associated homolog 2 (JPT2) as a TPC accessory protein required for endogenous NAADP-evoked Ca2+ signaling. JPT2 was also required for the translocation of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus through the endolysosomal system. Thus, JPT2 is a component of the NAADP receptor complex that is essential for TPC-dependent Ca2+ signaling and control of coronaviral entry.
    DOI:  https://doi.org/10.1126/scisignal.abd5605
  40. Elife. 2021 Mar 25. pii: e64283. [Epub ahead of print]10
    Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs.
    Swati Gaikwad, Fardin Ghobakhlou, David J Young, Jyothsna Visweswaraiah, Hongen Zhang, Alan G Hinnebusch.
      In eukaryotes, 43S preinitiation complex (PIC) formation is a rate-determining step of translation. Ribosome recycling following translation termination produces free 40S subunits for re-assembly of 43S PICs. Yeast mutants lacking orthologs of mammalian eIF2D (Tma64), and either MCT-1 (Tma20) or DENR (Tma22), are broadly impaired for 40S recycling; however, it was unknown whether this defect alters the translational efficiencies (TEs) of particular mRNAs. Here, we conducted ribosome profiling of a yeast tma64∆/tma20∆ double mutant and observed a marked reprogramming of translation, wherein the TEs of the most efficiently translated ('strong') mRNAs increase, while those of 'weak' mRNAs generally decline. Remarkably, similar reprogramming was seen on reducing 43S PIC assembly by inducing phosphorylation of eIF2α or by decreasing total 40S subunit levels by depleting Rps26. Our findings suggest that strong mRNAs outcompete weak mRNAs in response to 43S PIC limitation achieved in various ways, in accordance with previous mathematical modeling.
    Keywords:  S. cerevisiae; eIF2; genetics; genomics; initiation; recycling; ribosome; translation; yeast
    DOI:  https://doi.org/10.7554/eLife.64283
  41. ACS Chem Biol. 2021 Mar 23.
    Chemical Phosphoproteomics Sheds New Light on the Targets and Modes of Action of AKT Inhibitors.
    Svenja Wiechmann, Benjamin Ruprecht, Theresa Siekmann, Runsheng Zheng, Martin Frejno, Elena Kunold, Thomas Bajaj, Daniel P Zolg, Stephan A Sieber, Nils C Gassen, Bernhard Kuster.
      Due to its important roles in oncogenic signaling, AKT has been subjected to extensive drug discovery efforts leading to small molecule inhibitors investigated in advanced clinical trials. To better understand how these drugs exert their therapeutic effects at the molecular level, we combined chemoproteomic target affinity profiling using kinobeads and phosphoproteomics to analyze the five clinical AKT inhibitors AZD5363 (Capivasertib), GSK2110183 (Afuresertib), GSK690693, Ipatasertib, and MK-2206 in BT-474 breast cancer cells. Kinobead profiling identified between four and 29 nM targets for these compounds and showed that AKT1 and AKT2 were the only common targets. Similarly, measuring the response of the phosphoproteome to the same inhibitors identified ∼1700 regulated phosphorylation sites, 276 of which were perturbed by all five compounds. This analysis expanded the known AKT signaling network by 119 phosphoproteins that may represent direct or indirect targets of AKT. Within this new network, 41 regulated phosphorylation sites harbor the AKT substrate motif, and recombinant kinase assays validated 16 as novel AKT substrates. These included CEP170 and FAM83H, suggesting a regulatory function of AKT in mitosis and cytoskeleton organization. In addition, a specific phosphorylation pattern on the ULK1-FIP200-ATG13-VAPB complex was found to determine the active state of ULK1, leading to elevated autophagy in response to AKT inhibition.
    DOI:  https://doi.org/10.1021/acschembio.0c00872
  42. Aging (Albany NY). 2021 Mar 26. 13
    Host-commensal interaction promotes health and lifespan in Caenorhabditis elegans through the activation of HLH-30/TFEB-mediated autophagy.
    Miroslav Dinić, Marija Herholz, Uroš Kačarević, Dušan Radojević, Katarina Novović, Jelena Đokić, Aleksandra Trifunović, Nataša Golić.
      Gut homeostasis is maintained by the close interaction between commensal intestinal microbiota and the host, affecting the most complex physiological processes, such as aging. Some commensal bacteria with the potential to promote healthy aging arise as attractive candidates for the development of pro-longevity probiotics. Here, we showed that heat-inactivated human commensal Lactobacillus fermentum BGHV110 (BGHV110) extends the lifespan of Caenorhabditis elegans and improves age-related physiological features, including locomotor function and lipid metabolism. Mechanistically, we found that BGHV110 promotes HLH-30/TFEB-dependent autophagy to delay aging, as longevity assurance was completely abolished in the mutant lacking HLH-30, a major autophagy regulator in C. elegans. Moreover, we observed that BGHV110 partially decreased the content of lipid droplets in an HLH-30-dependent manner and, at the same time, slightly increased mitochondrial activity. In summary, this study demonstrates that specific factors from commensal bacteria can be used to exploit HLH-30/TFEB-mediated autophagy in order to promote longevity and fitness of the host.
    Keywords:  Caenorhabditis elegans; HLH-30; Lactobacillus fermentum; aging; autophagy
    DOI:  https://doi.org/10.18632/aging.202885
  43. Cell Death Dis. 2021 Mar 22. 12(4): 303
    FGF21 facilitates autophagy in prostate cancer cells by inhibiting the PI3K-Akt-mTOR signaling pathway.
    Han Dai, Wenjing Hu, Lianying Zhang, Feiyu Jiang, Xiongmin Mao, Gangyi Yang, Ling Li.
      Fibroblast growth factor 21 (FGF21) plays an important role in regulating glucose and lipid metabolism, but its role in cancer is less well-studied. We aimed to investigate the action of FGF21 in the development of prostate cancer (PCa). Herein, we found that FGF21 expression was markedly downregulated in PCa tissues and cell lines. FGF21 inhibited the proliferation and clone formation of LNCaP cells (a PCa cell line) and promoted apoptosis. FGF21 also inhibited PCa cell migration and invasiveness. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that FGF21 was related to autophagy and the phosphatidylinositol 3-kinase-Akt kinase-mammalian target of rapamycin (PI3K-Akt-mTOR) pathway. Mechanistically, FGF21 promoted autophagy in LNCaP cells by inhibiting the PI3K-Akt-mTOR-70S6K pathway. In addition, FGF21 inhibited PCa tumorigenesis in vivo in nude mice. Altogether, our findings show that FGF21 inhibits PCa cell proliferation and promoted apoptosis in PCa cells through facilitated autophagy. Therefore, FGF21 might be a potential novel target in PCa therapy.
    DOI:  https://doi.org/10.1038/s41419-021-03588-w
  44. Autophagy. 2021 Mar 22.
    Platelet autophagic machinery involved in thrombosis through a novel linkage of AMPK-MTOR to sphingolipid metabolism.
    Tzu-Yin Lee, Wan-Jung Lu, Chun A Changou, Yuan-Chin Hsiung, Nguyen T T Trang, Cheng-Yang Lee, Tzu-Hao Chang, Thanasekaran Jayakumar, Cheng-Ying Hsieh, Chih-Hao Yang, Chao-Chien Chang, Ray-Jade Chen, Joen-Rong Sheu, Kuan-Hung Lin.
      Basal macroautophagy/autophagy has recently been found in anucleate platelets. Platelet autophagy is involved in platelet activation and thrombus formation. However, the mechanism underlying autophagy in anucleate platelets require further clarification. Our data revealed that LC3-II formation and SQSTM1/p62 degradation were noted in H2O2-activated human platelets, which could be blocked by 3-methyladenine and bafilomycin A1, indicating that platelet activation may cause platelet autophagy. AMPK phosphorylation and MTOR dephosphorylation were also detected, and block of AMPK activity by the AMPK inhibitor dorsomorphin could reverse SQSTM1 degradation and LC3-II formation. Moreover, autophagosome formation was observed through transmission electron microscopy and deconvolution microscopy. These findings suggest that platelet autophagy was induced partly through the AMPK-MTOR pathway. In addition, increased LC3-II expression occurred only in H2O2-treated Atg5f/f platelets, but not in H2O2-treated atg5-/- platelets, providing further evidence that platelet autophagy occurs during platelet activation. atg5-/- platelets also exhibited a lower aggregation in response to agonists, and platelet-specific atg5-/- mice exhibited delayed thrombus formation in mesenteric microvessles and decreased mortality rate due to pulmonary thrombosis. Notably, metabolic analysis revealed that sphingolipid metabolism is involved in platelet activation, as evidenced by observed several altered metabolites, which could be reversed by dorsomorphin. Therefore, platelet autophagy and platelet activation are positively correlated, partly through the interconnected network of sphingolipid metabolism. In conclusion, this study for the first time demonstrated that AMPK-MTOR signaling could regulate platelet autophagy. A novel linkage between AMPK-MTOR and sphingolipid metabolism in anucleate platelet autophagy was also identified: platelet autophagy and platelet activation are positively correlated.
    Keywords:  AMPK; autophagy; hydrogen peroxide; platelets; sphingolipid metabolism
    DOI:  https://doi.org/10.1080/15548627.2021.1904495
  45. BMC Genomics. 2021 Mar 24. 22(1): 213
    Mitochondrial genotype alters the impact of rapamycin on the transcriptional response to nutrients in Drosophila.
    John C Santiago, Joan M Boylan, Faye A Lemieux, Philip A Gruppuso, Jennifer A Sanders, David M Rand.
       BACKGROUND: In addition to their well characterized role in cellular energy production, new evidence has revealed the involvement of mitochondria in diverse signaling pathways that regulate a broad array of cellular functions. The mitochondrial genome (mtDNA) encodes essential components of the oxidative phosphorylation (OXPHOS) pathway whose expression must be coordinated with the components transcribed from the nuclear genome. Mitochondrial dysfunction is associated with disorders including cancer and neurodegenerative diseases, yet the role of the complex interactions between the mitochondrial and nuclear genomes are poorly understood.
    RESULTS: Using a Drosophila model in which alternative mtDNAs are present on a common nuclear background, we studied the effects of this altered mitonuclear communication on the transcriptomic response to altered nutrient status. Adult flies with the 'native' and 'disrupted' genotypes were re-fed following brief starvation, with or without exposure to rapamycin, the cognate inhibitor of the nutrient-sensing target of rapamycin (TOR). RNAseq showed that alternative mtDNA genotypes affect the temporal transcriptional response to nutrients in a rapamycin-dependent manner. Pathways most greatly affected were OXPHOS, protein metabolism and fatty acid metabolism. A distinct set of testis-specific genes was also differentially regulated in the experiment.
    CONCLUSIONS: Many of the differentially expressed genes between alternative mitonuclear genotypes have no direct interaction with mtDNA gene products, suggesting that the mtDNA genotype contributes to retrograde signaling from mitochondria to the nucleus. The interaction of mitochondrial genotype (mtDNA) with rapamycin treatment identifies new links between mitochondria and the nutrient-sensing mTORC1 (mechanistic target of rapamycin complex 1) signaling pathway.
    Keywords:  Mitochondrial introgression; Mitonuclear genotype; Rapamycin; mTORC1
    DOI:  https://doi.org/10.1186/s12864-021-07516-2
  46. Dev Cell. 2021 Mar 22. pii: S1534-5807(21)00207-0. [Epub ahead of print]56(6): 721-722
    Balancing energy demand and production by mitochondrial trafficking of RHEB.
    Lawrence Kazak.
      In this issue of Developmental Cell,Yang et al. (2021) discover that, RHEB traffics to mitochondria to promote energy production by stimulating pyruvate dehydrogenase to convert pyruvate to acetyl-CoA.
    DOI:  https://doi.org/10.1016/j.devcel.2021.03.010
  47. Brain. 2021 Mar 25. pii: awaa459. [Epub ahead of print]
    Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.
    Leslie E Sanderson, Kristina Lanko, Maysoon Alsagob, Rawan Almass, Nada Al-Ahmadi, Maryam Najafi, Mohammad A Al-Muhaizea, Hamad Alzaidan, Hesham AlDhalaan, Elena Perenthaler, Herma C van der Linde, Anita Nikoncuk, Nikolas A Kühn, Dinu Antony, Tarek Mustafa Owaidah, Salmo Raskin, Luana Gabriela Dalla Rosa Vieira, Romulo Mombach, Najmeh Ahangari, Tainá Regina Damaceno Silveira, Najim Ameziane, Arndt Rolfs, Aljohara Alharbi, Raghda M Sabbagh, Khalid AlAhmadi, Bashayer Alawam, Hazem Ghebeh, Aljouhra AlHargan, Anoud A Albader, Faisal S Binhumaid, Ewa Goljan, Dorota Monies, Osama M Mustafa, Mazhor Aldosary, Albandary AlBakheet, Banan Alyounes, Faten Almutairi, Ali Al-Odaib, Durdane Bekar Aksoy, A Nazli Basak, Robin Palvadeau, Daniah Trabzuni, Jill A Rosenfeld, Ehsan Ghayoor Karimiani, Brian F Meyer, Bedri Karakas, Futwan Al-Mohanna, Stefan T Arold, Dilek Colak, Reza Maroofian, Henry Houlden, Aida M Bertoli-Avella, Miriam Schmidts, Tahsin Stefan Barakat, Tjakko J van Ham, Namik Kaya.
      Membrane trafficking is a complex, essential process in eukaryotic cells responsible for protein transport and processing. Deficiencies in vacuolar protein sorting (VPS) proteins, key regulators of trafficking, cause abnormal intracellular segregation of macromolecules and organelles and are linked to human disease. VPS proteins function as part of complexes such as the homotypic fusion and vacuole protein sorting (HOPS) tethering complex, composed of VPS11, VPS16, VPS18, VPS33A, VPS39 and VPS41. The HOPS-specific subunit VPS41 has been reported to promote viability of dopaminergic neurons in Parkinson's disease but to date has not been linked to human disease. Here, we describe five unrelated families with nine affected individuals, all carrying homozygous variants in VPS41 that we show impact protein function. All affected individuals presented with a progressive neurodevelopmental disorder consisting of cognitive impairment, cerebellar atrophy/hypoplasia, motor dysfunction with ataxia and dystonia, and nystagmus. Zebrafish disease modelling supports the involvement of VPS41 dysfunction in the disorder, indicating lysosomal dysregulation throughout the brain and providing support for cerebellar and microglial abnormalities when vps41 was mutated. This provides the first example of human disease linked to the HOPS-specific subunit VPS41 and suggests the importance of HOPS complex activity for cerebellar function.
    Keywords:   VPS41 ; cerebellar ataxia; membrane trafficking; neurodevelopmental disorder; zebrafish disease modelling
    DOI:  https://doi.org/10.1093/brain/awaa459
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