bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2024–07–21
47 papers selected by
Viktor Korolchuk, Newcastle University
  1. Ccr4-Not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy.
  2. The Spectrum of "TFEopathies" - Flipping the mTOR Switch in Renal Tumorigenesis.
  3. Functional Analysis of Genes in Mycobacterium tuberculosis Action Against Autophagosome-Lysosome Fusion.
  4. Phosphorylation of GCN2 by mTOR confers adaptation to conditions of hyper-mTOR activation under stress.
  5. Truncated tau interferes with the autophagy and endolysosomal pathway and results in lipid accumulation.
  6. An E3 ligase and autophagy adaptor regulates tau proteostasis through nested phase separation.
  7. Autophagy as a Therapeutic Target in Breast Tumors: The Cancer stem cell perspective.
  8. Key considerations for investigating and interpreting autophagy in skeletal muscle.
  9. Lassa virus Z protein hijacks the autophagy machinery for efficient transportation by interrupting CCT2-mediated cytoskeleton network formation.
  10. Human fibroblasts from sporadic Alzheimer's disease (AD) patients show mitochondrial alterations and lysosome dysfunction.
  11. Autophagy regulates age-related delayed jawbone regeneration and decreased osteoblast osteogenesis by degrading FABP3.
  12. TAX1BP1 and FIP200 orchestrate non-canonical autophagy of p62 aggregates for mouse neural stem cell maintenance.
  13. TgATG9 is required for autophagosome biogenesis and maintenance of chronic infection in Toxoplasma gondii.
  14. Exacerbation of atherosclerosis by STX17 knockdown: Unravelling the role of autophagy and inflammation.
  15. Mitophagy-related regulated cell death: molecular mechanisms and disease implications.
  16. Quantification of Autophagosomes in Human Fibroblasts Using Cyto-ID® Staining and Cytation Imaging.
  17. Increased regional activity of a pro-autophagy pathway in schizophrenia as a contributor to sex differences in the disease pathology.
  18. MEC-12/alpha tubulin regulates mitochondrial distribution and mitophagy during oxidative stress in C. elegans.
  19. NLRP3-mediated autophagy dysfunction links gut microbiota dysbiosis to tau pathology in chronic sleep deprivation.
  20. Tau phosphorylation suppresses oxidative stress-induced mitophagy via FKBP8 receptor modulation.
  21. A novel fluorescence-activated cell sorting (FACS)-based screening identified ATG14, the gene required for pexophagy in the methylotrophic yeast.
  22. Activation of macroautophagy and chaperone-mediated autophagy in human skeletal muscle by high-intensity exercise in normoxia and hypoxia and after recovery with or without post-exercise ischemia.
  23. Cytoplasmic vacuolization and ectopic formation of perineuronal nets are characteristic pathologies of cytomegalic neurons in tuberous sclerosis.
  24. The erlin1/erlin2 complex binds to and stabilizes phosphatidylinositol 3-phosphate and regulates autophagy.
  25. The autophagy adaptor TRIAD3A promotes tau fibrillation by nested phase separation.
  26. The actin binding protein profilin 1 localizes inside mitochondria and is critical for their function.
  27. Phytochemicals targeting mitophagy: Therapeutic opportunities and prospects for treating Alzheimer's disease.
  28. Sestrin2 in POMC Neurons Modulates Energy Balance and Obesity Related Metabolic Disorders via mTOR Signaling.
  29. Impaired autophagy-mediated macrophage polarization contributes to age-related hyposalivation.
  30. mTOR inhibition by AZD2014 alleviates BCR::ABL1 independent imatinib resistance through enhancing autophagy in CML resistant cells.
  31. Proteostasis in health and disease: a conversation with Professor Rick Morimoto.
  32. Integrated RNA sequencing and biochemical studies reveal endoplasmic reticulum stress and autophagy dysregulation contribute to Tri (2-Ethylhexyl) phosphate (TEHP)-induced cell injury in Sertoli cells.
  33. Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function.
  34. Chemical genetic screens reveal defective lysosomal trafficking as synthetic lethal with NF1 loss.
  35. Fission yeast Pib2 localizes to vacuolar membranes and regulates TOR complex 1 through evolutionarily conserved domains.
  36. Ischemic Stroke and Autophagy: The Roles of Long Non-Coding RNAs.
  37. Dysfunctional mitochondria elicit bioenergetic decline in the aged heart.
  38. Mapping the landscape: A bibliometric perspective on autophagy in spinal cord injury.
  39. Amino acid deprivation in cancer cells with compensatory autophagy induction increases sensitivity to autophagy inhibitors.
  40. An MITF- and mTOR-dependent FLCN pathway suppresses TFE3-driven metastasis in melanoma.
  41. Structure-Based Design and Discovery of a Potent and Cell-Active LC3A/B Covalent Inhibitor.
  42. MiR-200b-3p elevates 5-FU sensitivity in cholangiocarcinoma cells via autophagy inhibition by targeting KLF4.
  43. FNIP1: A key regulator of mitochondrial function.
  44. Sulfiredoxin-1 promotes the growth of hepatocellular carcinoma by inhibiting TFEB-mediated autophagy and lysosome biogenesis.
  45. Role of vaccinia virus growth factor in stimulating the mTORC1-CAD axis of the de novo pyrimidine pathway under different nutritional cues.
  46. Metformin induces ZFP36 by mTORC1 inhibition in cervical cancer-derived cell lines.
  47. Regulation of and challenges in targeting NAD+ metabolism.
  1. J Biol Chem. 2024 Jul 16. pii: S0021-9258(24)02083-0. [Epub ahead of print] 107582
    Ccr4-Not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy.
    Daniel L Johnson, Ravinder Kumar, David Kakhniashvili, Lawrence M Pfeffer, R Nicholas Laribee.
      The Ccr4-Not complex contains the poorly understood Not4 ubiquitin ligase that functions in transcription, mRNA decay, translation, proteostasis, and endolysosomal nutrient signaling. To gain further insight into the in vivo functions of the ligase, we performed quantitative proteomics in Saccharomyces cerevisiae using yeast cells lacking Not4, or cells overexpressing wild-type Not4 or an inactive Not4 mutant. Herein, we provide evidence that balanced Not4 activity maintains ribosomal protein (RP) homeostasis independent of changes to RP mRNA or known Not4 ribosomal substrates. Intriguingly, we also find that Not4 loss activates 40S ribosomal autophagy independently of canonical Atg7-dependent macroautophagy, indicating that microautophagy is responsible. We previously demonstrated that Ccr4-Not stimulates target of rapamycin complex 1 (TORC1) signaling, which activates RP expression and inhibits autophagy, by maintaining vacuole V-ATPase H+ pump activity. Importantly, combining Not4 deficient cells with a mutant that blocks vacuole H+ export fully restores RP expression and increases 40S RP autophagy efficiency. In contrast, restoring TORC1 activity alone fails to rescue either process, indicating that Not4 loss disrupts additional endolysosomal functions that regulate RP expression and 40S autophagy. Analysis of the Not4 regulated proteome reveals increases in endolysosomal and autophagy-related factors that functionally interact with Not4 to control RP expression and affect 40S autophagy. Collectively, our data indicate that balanced Ccr4-Not ubiquitin ligase signaling maintains RP homeostasis and inhibits 40S autophagy via the ligase's emerging role as an endolysosomal regulator.
    Keywords:  Ccr4-Not; autophagy; lysosome; microautophagy; ribosome; ubiquitin ligase
    DOI:  https://doi.org/10.1016/j.jbc.2024.107582
  2. Physiology (Bethesda). 2024 Jul 16.
    The Spectrum of "TFEopathies" - Flipping the mTOR Switch in Renal Tumorigenesis.
    Nicola Alesi, Kaushal Asrani, Tamara L Lotan, Elizabeth P Henske.
      The Mammalian Target of Rapamycin Complex 1 (mTORC1) is a serine threonine kinase that couples nutrient and growth factor signaling to the cellular control of metabolism and plays a fundamental role in aberrant proliferation in cancer. mTORC1 has previously been considered an "on/off" switch, capable of phosphorylating the entire pool of its substrates when activated. However recent studies have indicated that mTORC1 may be active towards its canonical substrates, 4EBP1 and S6K, involved in mRNA translation and protein synthesis, and inactive towards TFEB and TFE3, transcription factors involved in the regulation of lysosome biogenesis, in several pathological contexts. Among these conditions are Birt Hogg Dube (BHD) and recently, Tuberous Sclerosis Complex (TSC). Furthermore, TFEB and TFE3 hyperactivation in these syndromes, and in translocation Renal Cell Carcinomas (tRCC), drives mTORC1 activity towards the canonical substrates, through the transcriptional activation of the Rag GTPases, thereby positioning TFEB and TFE3 upstream of mTORC1 activity towards 4EBP1 and S6K. The expanding importance of TFEB and TFE3 in the pathogenesis of these renal diseases warrants a novel clinical grouping that we term "TFEopathies". Currently, there no therapeutic options directly targeting TFEB and TFE3, which represents a challenging and critically required avenue for cancer research.
    Keywords:  Kidney TFEopathies; TFE3; TFEB; TSC; mTORC1
    DOI:  https://doi.org/10.1152/physiol.00026.2024
  3. Indian J Microbiol. 2024 Jun;64(2): 367-375
    Functional Analysis of Genes in Mycobacterium tuberculosis Action Against Autophagosome-Lysosome Fusion.
    Karthikeyan Sundaram, Leela Kagithakara Vajravelu.
      Tuberculosis is a lethal disease that is one of the world's top ten death-associated infections in humans; Mycobacterium tuberculosis causes tuberculosis, and this bacterium is linked to the lysis of autophagolysosomal fusion action, a self-defense mechanism of its own. Thus, Cytoplasmic bacilli are sequestered by autophagy and transported to lysosomes to be inactivated to destroy intracellular bacteria. Besides this, a macrophage can limit intracellular Mycobacterium by using a type of autophagy, selective autophagy, a cell that marks undesirable ubiquitin existence in cytosolic cargo, acting as a "eat me" sensor in conjunction with cellular homeostasis. Mycobacterium tuberculosis genes of the PE_PGRS protein family inhibit autophagy, increase mycobacterial survival, and lead to latent tuberculosis infection associated with miRNAs. In addition, the family of autophagy-regulated (ATG) gene members are involved in autophagy and controls the initiation, expansion, maturation, and fusion of autophagosomes with lysosomes, among other signaling events that control autophagy flux and reduce inflammatory responses and forward to promote cellular proliferation. In line with the formation of caseous necrosis in macrophages by Mycobacterium tuberculosis and their action on the lysis of autophagosome fusion, it leads to latent tuberculosis infection. Therefore, we aimed to comprehensively analyses the autophagy and self-defense mechanism of Mycobacterium tuberculosis, which is to be gratified future research on novel therapeutic tools and diagnostic markers against tuberculosis.
    Keywords:  Autophagy; Lysosome; Mycobacterium tuberculosis; Pathogenesis; Tuberculosis
    DOI:  https://doi.org/10.1007/s12088-024-01227-4
  4. J Biol Chem. 2024 Jul 14. pii: S0021-9258(24)02076-3. [Epub ahead of print] 107575
    Phosphorylation of GCN2 by mTOR confers adaptation to conditions of hyper-mTOR activation under stress.
    Odai Darawshi, Olaya Yassin, Miri Shmuel, Ronald C Wek, S Jalil Mahdizadeh, Leif A Eriksson, Maria Hatzoglou, Boaz Tirosh.
      Adaptation to shortage in free amino acids (AA) is mediated by two pathways, the integrated stress response (ISR) and the mechanistic target of rapamycin (mTOR). In response to reduced levels, primarily of leucine or arginine, mTOR in its complex 1 configuration (mTORC1) is suppressed leading to a decrease in translation initiation and elongation. The eIF2α kinase general control nonderepressible 2 (GCN2) is activated by uncharged tRNAs, leading to induction of the ISR in response to a broader range of AA shortage. ISR confers a reduced translation initiation, while promoting the selective synthesis of stress proteins, such as ATF4. To efficiently adapt to AA starvation, the two pathways are cross-regulated at multiple levels. Here we identified a new mechanism of ISR/mTORC1 crosstalk that optimizes survival under AA starvation, when mTORC1 is forced to remain active. mTORC1 activation during acute AA shortage, augmented ATF4 expression in a GCN2-dependent manner. Under these conditions, enhanced GCN2 activity was not dependent on tRNA sensing, inferring a different activation mechanism. We identified a labile physical interaction between GCN2 and mTOR that results in a phosphorylation of GCN2 on serine 230 by mTOR, which promotes GCN2 activity. When examined under prolonged AA starvation, GCN2 phosphorylation by mTOR promoted survival. Our data unveils an adaptive mechanism to AA starvation, when mTORC1 evades inhibition.
    DOI:  https://doi.org/10.1016/j.jbc.2024.107575
  5. Cell Mol Life Sci. 2024 Jul 15. 81(1): 304
    Truncated tau interferes with the autophagy and endolysosomal pathway and results in lipid accumulation.
    Saskia J Pollack, Dina Dakkak, Tong Guo, George Chennell, Patricia Gomez-Suaga, Wendy Noble, Maria Jimenez-Sanchez, Diane P Hanger.
      The autophagy-lysosomal pathway plays a critical role in the clearance of tau protein aggregates that deposit in the brain in tauopathies, and defects in this system are associated with disease pathogenesis. Here, we report that expression of Tau35, a tauopathy-associated carboxy-terminal fragment of tau, leads to lipid accumulation in cell lines and primary cortical neurons. Our findings suggest that this is likely due to a deleterious block of autophagic clearance and lysosomal degradative capacity by Tau35. Notably, upon induction of autophagy by Torin 1, Tau35 inhibited nuclear translocation of transcription factor EB (TFEB), a key regulator of lysosomal biogenesis. Both cell lines and primary cortical neurons expressing Tau35 also exhibited changes in endosomal protein expression. These findings implicate autophagic and endolysosomal dysfunction as key pathological mechanisms through which disease-associated tau fragments could lead to the development and progression of tauopathy.
    Keywords:  Alzheimer’s disease; Autophagy; Dementia; Endosomes; Lysosomes; TFEB; Tau
    DOI:  https://doi.org/10.1007/s00018-024-05337-6
  6. Nat Cell Biol. 2024 Jul 19.
    An E3 ligase and autophagy adaptor regulates tau proteostasis through nested phase separation.
      
    DOI:  https://doi.org/10.1038/s41556-024-01466-z
  7. Autophagy Rep. 2024 Dec 31. pii: 27694127.2024.2358648. [Epub ahead of print]3(1):
    Autophagy as a Therapeutic Target in Breast Tumors: The Cancer stem cell perspective.
    Sana Raza, Jawed Akhtar Siddiqui, Anubhav Srivastava, Naibedya Chattopadhyay, Rohit Anthony Sinha, Bandana Chakravarti.
      Breast cancer is a heterogeneous disease, with a subpopulation of tumor cells known as breast cancer stem cells (BCSCs) with self-renewal and differentiation abilities that play a critical role in tumor initiation, progression, and therapy resistance. The tumor microenvironment (TME) is a complex area where diverse cancer cells reside creating a highly interactive environment with secreted factors, and the extracellular matrix. Autophagy, a cellular self-digestion process, influences dynamic cellular processes in the tumor TME integrating diverse signals that regulate tumor development and heterogeneity. Autophagy acts as a double-edged sword in the breast TME, with both tumor-promoting and tumor-suppressing roles. Autophagy promotes breast tumorigenesis by regulating tumor cell survival, migration and invasion, metabolic reprogramming, and epithelial-mesenchymal transition (EMT). BCSCs harness autophagy to maintain stemness properties, evade immune surveillance, and resist therapeutic interventions. Conversely, excessive, or dysregulated autophagy may lead to BCSC differentiation or cell death, offering a potential avenue for therapeutic exploration. The molecular mechanisms that regulate autophagy in BCSCs including the mammalian target of rapamycin (mTOR), AMPK, and Beclin-1 signaling pathways may be potential targets for pharmacological intervention in breast cancer. This review provides a comprehensive overview of the relationship between autophagy and BCSCs, highlighting recent advancements in our understanding of their interplay. We also discuss the current state of autophagy-targeting agents and their preclinical and clinical development in BCSCs.
    Keywords:  Autophagy; Breast Cancer; Breast Cancer stem cells; Metabolism; Tumor microenvironment
    DOI:  https://doi.org/10.1080/27694127.2024.2358648
  8. Autophagy. 2024 Jul 15. 1-12
    Key considerations for investigating and interpreting autophagy in skeletal muscle.
    Fasih A Rahman, Brittany L Baechler, Joe Quadrilatero.
      Skeletal muscle plays a crucial role in generating force to facilitate movement. Skeletal muscle is a heterogenous tissue composed of diverse fibers with distinct contractile and metabolic profiles. The intricate classification of skeletal muscle fibers exists on a continuum ranging from type I (slow-twitch, oxidative) to type II (fast-twitch, glycolytic). The heterogenous distribution and characteristics of fibers within and between skeletal muscles profoundly influences cellular signaling; however, this has not been broadly discussed as it relates to macroautophagy/autophagy. The growing interest in skeletal muscle autophagy research underscores the necessity of comprehending the interplay between autophagic responses among skeletal muscles and fibers with different contractile properties, metabolic profiles, and other related signaling processes. We recommend approaching the interpretation of autophagy findings with careful consideration for two key reasons: 1) the distinct behaviors and responses of different skeletal muscles or fibers to various perturbations, and 2) the potential impact of alterations in skeletal muscle fiber type or metabolic profile on observed autophagic outcomes. This review provides an overview of the autophagic profile and response in skeletal muscles/fibers of different types and metabolic profiles. Further, this review discusses autophagic findings in various conditions and diseases that may differentially affect skeletal muscle. Finally, we provide key points of consideration to better enable researchers to fine-tune the design and interpretation of skeletal muscle autophagy experiments.Abbreviation: AKT1: AKT serine/threonine kinase 1; AMPK: AMP-activated protein kinase; ATG: autophagy related; ATG4: autophagy related 4 cysteine peptidase; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG12: autophagy related 12; BECN1: beclin 1; BNIP3: BCL2 interacting protein 3; CKD: chronic kidney disease; COPD: chronic obstructive pulmonary disease; CS: citrate synthase; DIA: diaphragm; EDL: extensor digitorum longus; FOXO3/FOXO3A: forkhead box O3; GAS; gastrocnemius; GP: gastrocnemius-plantaris complex; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAPK: mitogen-activated protein kinase; MYH: myosin heavy chain; PINK1: PTEN induced kinase 1; PLANT: plantaris; PRKN: parkin RBR E3 ubiquitin protein ligase; QUAD: quadriceps; RA: rectus abdominis; RG: red gastrocnemius; RQ: red quadriceps; SOL: soleus; SQSTM1: sequestosome 1; TA: tibialis anterior; WG: white gastrocnemius; WQ: white quadriceps; WVL: white vastus lateralis; VL: vastus lateralis; ULK1: unc-51 like autophagy activating kinase 1.
    Keywords:  Contraction; fiber type; metabolic; mitochondria; mitophagy; skeletal muscle
    DOI:  https://doi.org/10.1080/15548627.2024.2373676
  9. Autophagy. 2024 Jul 20. 1-18
    Lassa virus Z protein hijacks the autophagy machinery for efficient transportation by interrupting CCT2-mediated cytoskeleton network formation.
    Yueming Yuan, An Fang, Mai Zhang, Ming Zhou, Zhen F Fu, Ling Zhao.
      The Lassa virus (LASV) is a widely recognized virulent pathogen that frequently results in lethal viral hemorrhagic fever (VHF). Earlier research has indicated that macroautophagy/autophagy plays a role in LASV replication, but, the precise mechanism is unknown. In this present study, we show that LASV matrix protein (LASV-Z) is essential for blocking intracellular autophagic flux. LASV-Z hinders actin and tubulin folding by interacting with CCT2, a component of the chaperonin-containing T-complexes (TRiC). When the cytoskeleton is disrupted, lysosomal enzyme transit is hampered. In addition, cytoskeleton disruption inhibits the merge of autophagosomes with lysosomes, resulting in autophagosome accumulation that promotes the budding of LASV virus-like particles (VLPs). Inhibition of LASV-Z-induced autophagosome accumulation blocks the LASV VLP budding process. Furthermore, it is found that glutamine at position 29 and tyrosine at position 48 on LASV-Z are important in interacting with CCT2. When these two sites are mutated, LASV-mut interacts with CCT2 less efficiently and can no longer inhibit the autophagic flux. These findings demonstrate a novel strategy for LASV-Z to hijack the host autophagy machinery to accomplish effective transportation.Abbreviation: 3-MA: 3-methyladenine; ATG5: autophagy related 5; ATG7: autophagy related 7; Baf-A1: bafilomycin A1; CCT2: chaperonin containing TCP1 subunit 2; co-IP: co-immunoprecipitation; CTSD: cathepsin D; DAPI: 4',6-diamidino-2'-phenylindole; DMSO: dimethyl sulfoxide; EGFR: epidermal growth factor receptor; GFP: green fluorescent protein; hpi: hours post-infection; hpt: hours post-transfection; LAMP1: lysosomal-associated membrane protein 1; LASV: lassa virus; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; mCherry: red fluorescent protein; PM: plasma membrane; SQSTM1/p62: sequestosome 1; STX6: syntaxin 6; VLP: virus-like particle; TEM: transmission electron microscopy; TRiC: chaperonin-containing T-complex; WB: western blotting; μm: micrometer; μM: micromole.
    Keywords:  Autophagosome; CCT2; cytoskeleton; lassa virus; matrix protein; virus-like particle
    DOI:  https://doi.org/10.1080/15548627.2024.2379099
  10. Free Radic Biol Med. 2024 Jul 14. pii: S0891-5849(24)00559-8. [Epub ahead of print]222 569-578
    Human fibroblasts from sporadic Alzheimer's disease (AD) patients show mitochondrial alterations and lysosome dysfunction.
    Yuan Li, Zhiquan Li, Emanuela Grillo, Claus Desler, Claudia Navarro, Vilhelm A Bohr, Laura Berliocchi, Lene Juel Rasmussen.
      Mitophagy is a mechanism that maintains mitochondrial integrity and homeostasis and is thought to promote longevity and reduce the risk of age-related neurodegenerative diseases, including Alzheimer's disease (AD). Here, we investigate the abundance of mitochondrial reactive oxygen species (ROS), mitochondrial function, and mitophagy in primary fibroblasts from patients with sporadic AD (sAD) and normal healthy controls. The results show increased levels of mitochondrial ROS, changes in mitochondrial morphology, altered bioenergetic properties, and defects in autophagy, mitophagy, and lysosome-mediated degradation pathways in sAD fibroblasts relative to control fibroblasts. Interestingly, lysosome abundance and the staining of lysosomal markers remained high, while the capacity of lysosome-dependent degradation was lower in sAD fibroblasts than in controls fibroblasts. Nicotinamide riboside supplementation decreased mitochondrial ROS, while capacity for lysosomal degradation remained unchanged in sAD fibroblasts relative to healthy control fibroblasts. These findings provide insight into molecular mechanisms involving the dysregulation of lysosome and autophagy/mitophagy pathways that may contribute significantly to clinical signs and pathological features of sAD.
    Keywords:  Alzheimer's disease; Autophagy; Lysosome; Mitochondria; Mitophagy; Oxidative stress
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2024.07.013
  11. FASEB J. 2024 Jul 31. 38(14): e23824
    Autophagy regulates age-related delayed jawbone regeneration and decreased osteoblast osteogenesis by degrading FABP3.
    Yifan Xu, Bin Sun, Haicheng Wang, Yuyi Cai, Danna Chu, Rongkai Cao, Zuolin Wang.
      The regenerative ability of limb bones after injury decreases during aging, but whether a similar phenomenon occurs in jawbones and whether autophagy plays a role in this process remain unclear. Through retrospective analysis of clinical data and studies on a mouse model of jawbone defects, we confirmed the presence of delayed or impaired bone regeneration in the jawbones of old individuals and mice. Subsequently, osteoblasts (OBs) derived from mouse jawbones were isolated, showing reduced osteogenesis in senescent osteoblasts (S-OBs). We observed a reduction in autophagy within both aged jawbones and S-OBs. Additionally, pharmacological inhibition of autophagy in normal OBs (N-OBs) led to cell aging and decreased osteogenesis, while autophagic activation reversed the aging phenotype of S-OBs. The activator rapamycin (RAPA) increased the autophagy level and bone regeneration in aged jawbones. Finally, we found that fatty acid-binding protein 3 (FABP3) was degraded by autolysosomes through its interaction with sequestosome 1 (P62/SQSTM1). Autophagy inhibition within senescent jawbones and S-OBs led to the excessive accumulation of FABP3, and FABP3 knockdown partially rescued the decreased osteogenesis in S-OBs and alleviated age-related compromised jawbone regeneration. In summary, we confirmed that autophagy inhibition plays an important role in delaying bone regeneration in aging jawbones. Autophagic activation or FABP3 knockdown can partially rescue the osteogenesis of S-OBs and the regeneration of aging jawbones, providing insight into jawbone aging.
    Keywords:  aging; autophagy; bone regeneration; jaw; osteoblasts
    DOI:  https://doi.org/10.1096/fj.202400549RR
  12. Zool Res. 2024 07 18. pii: 2095-8137(2024)04-0937-14. [Epub ahead of print]45(4): 937-950
    TAX1BP1 and FIP200 orchestrate non-canonical autophagy of p62 aggregates for mouse neural stem cell maintenance.
    Yi-Fu Zhu, Rong-Hua Yu, Shuai Zhou, Pei-Pei Tang, Rui Zhang, Yu-Xin Wu, Ran Xu, Jia-Ming Wei, Ying-Ying Wang, Jia-Li Zhang, Meng-Ke Li, Xiao-Jing Shi, Yu-Wei Zhang, Guang-Zhi Liu, Rick F Thorne, Xu Dong Zhang, Mian Wu, Song Chen.
      Autophagy plays a pivotal role in diverse biological processes, including the maintenance and differentiation of neural stem cells (NSCs). Interestingly, while complete deletion of Fip200 severely impairs NSC maintenance and differentiation, inhibiting canonical autophagy via deletion of core genes, such as Atg5, Atg16l1, and Atg7, or blockade of canonical interactions between FIP200 and ATG13 (designated as FIP200-4A mutant or FIP200 KI) does not produce comparable detrimental effects. This highlights the likely critical involvement of the non-canonical functions of FIP200, the mechanisms of which have remained elusive. Here, utilizing genetic mouse models, we demonstrated that FIP200 mediates non-canonical autophagic degradation of p62/sequestome1, primarily via TAX1BP1 in NSCs. Conditional deletion of Tax1bp1 in fip200 hGFAP conditional knock-in (cKI) mice led to NSC deficiency, resembling the fip200 hGFAP conditional knockout (cKO) mouse phenotype. Notably, reintroducing wild-type TAX1BP1 not only restored the maintenance of NSCs derived from tax1bp1-knockout fip200 hGFAP cKI mice but also led to a marked reduction in p62 aggregate accumulation. Conversely, a TAX1BP1 mutant incapable of binding to FIP200 or NBR1/p62 failed to achieve this restoration. Furthermore, conditional deletion of Tax1bp1 in fip200 hGFAP cKO mice exacerbated NSC deficiency and p62 aggregate accumulation compared to fip200 hGFAP cKO mice. Collectively, these findings illustrate the essential role of the FIP200-TAX1BP1 axis in mediating the non-canonical autophagic degradation of p62 aggregates towards NSC maintenance and function, presenting novel therapeutic targets for neurodegenerative diseases.
    Keywords:  Aggregates; FIP200; Neural stem cell; Non-canonical autophagy; TAX1BP1; p62
    DOI:  https://doi.org/10.24272/j.issn.2095-8137.2024.021
  13. bioRxiv. 2024 Jul 09. pii: 2024.07.08.602581. [Epub ahead of print]
    TgATG9 is required for autophagosome biogenesis and maintenance of chronic infection in Toxoplasma gondii.
    Pariyamon Thaprawat, Zhihai Zhang, Eric C Rentchler, Fengrong Wang, Shreya Chalasani, Christopher J Giuliano, Sebastian Lourido, Manlio Di Cristina, Daniel J Klionsky, Vern B Carruthers.
      Toxoplasma gondii is a ubiquitous protozoan parasite that can reside long-term within hosts as intracellular tissue cysts comprised of chronic stage bradyzoites. To perturb chronic infection requires a better understanding of the cellular processes that mediate parasite persistence. Macroautophagy/autophagy is a catabolic and homeostatic pathway that is required for T. gondii chronic infection, although the molecular details of this process remain poorly understood. A key step in autophagy is the initial formation of the phagophore that sequesters cytoplasmic components and matures into a double-membraned autophagosome for delivery of the cargo to a cell's digestive organelle for degradative recycling. While T. gondii appears to have a reduced repertoire of autophagy proteins, it possesses a putative phospholipid scramblase, TgATG9. Through structural modeling and complementation assays, we show herein that TgATG9 can partially rescue bulk autophagy in atg9Δ yeast. We demonstrated the importance of TgATG9 for proper autophagosome dynamics at the subcellular level using three-dimensional live cell lattice light sheet microscopy. Conditional knockdown of TgATG9 in T. gondii after bradyzoite differentiation resulted in markedly reduced parasite viability. Together, our findings provide insights into the molecular dynamics of autophagosome biogenesis within an early-branching eukaryote and pinpoint the indispensable role of autophagy in maintaining T. gondii chronic infection.
    DOI:  https://doi.org/10.1101/2024.07.08.602581
  14. J Cell Mol Med. 2024 May;28(10): e18402
    Exacerbation of atherosclerosis by STX17 knockdown: Unravelling the role of autophagy and inflammation.
    Xinyue Cui, Bo Wang, Dongjian Han, Mengdie Cheng, Peiyu Yuan, Pengchong Du, Yachen Hou, Chang Su, Junnan Tang, Jinying Zhang.
      Syntaxin 17 (STX17) has been identified as a crucial factor in mediating the fusion of autophagosomes and lysosomes. However, its specific involvement in the context of atherosclerosis (AS) remains unclear. This study sought to elucidate the role and mechanistic contributions of STX17 in the initiation and progression of AS. Utilizing both in vivo and in vitro AS model systems, we employed ApoE knockout (KO) mice subjected to a high-fat diet and human umbilical vein endothelial cells (HUVECs) treated with oxidized low-density lipoprotein (ox-LDL) to assess STX17 expression. To investigate underlying mechanisms, we employed shRNA-STX17 lentivirus to knock down STX17 expression, followed by evaluating autophagy and inflammation in HUVECs. In both in vivo and in vitro AS models, STX17 expression was significantly upregulated. Knockdown of STX17 exacerbated HUVEC damage, both with and without ox-LDL treatment. Additionally, we observed that STX17 knockdown impaired autophagosome degradation, impeded autophagy flux and also resulted in the accumulation of dysfunctional lysosomes in HUVECs. Moreover, STX17 knockdown intensified the inflammatory response following ox-LDL treatment in HUVECs. Further mechanistic exploration revealed an association between STX17 and STING; reducing STX17 expression increased STING levels. Further knockdown of STING enhanced autophagy flux. In summary, our findings suggest that STX17 knockdown worsens AS by impeding autophagy flux and amplifying the inflammatory response. Additionally, the interaction between STX17 and STING may play a crucial role in STX17-mediated autophagy.
    Keywords:  STING; atherosclerosis; autophagy; inflammation; syntaxin 17
    DOI:  https://doi.org/10.1111/jcmm.18402
  15. Cell Death Dis. 2024 Jul 16. 15(7): 505
    Mitophagy-related regulated cell death: molecular mechanisms and disease implications.
    Molin Yang, Xiang Wei, Xin Yi, Ding-Sheng Jiang.
      During oxidative phosphorylation, mitochondria continuously produce reactive oxygen species (ROS), and untimely ROS clearance can subject mitochondria to oxidative stress, ultimately resulting in mitochondrial damage. Mitophagy is essential for maintaining cellular mitochondrial quality control and homeostasis, with activation involving both ubiquitin-dependent and ubiquitin-independent pathways. Over the past decade, numerous studies have indicated that different forms of regulated cell death (RCD) are connected with mitophagy. These diverse forms of RCD have been shown to be regulated by mitophagy and are implicated in the pathogenesis of a variety of diseases, such as tumors, degenerative diseases, and ischemia‒reperfusion injury (IRI). Importantly, targeting mitophagy to regulate RCD has shown excellent therapeutic potential in preclinical trials, and is expected to be an effective strategy for the treatment of related diseases. Here, we present a summary of the role of mitophagy in different forms of RCD, with a focus on potential molecular mechanisms by which mitophagy regulates RCD. We also discuss the implications of mitophagy-related RCD in the context of various diseases.
    DOI:  https://doi.org/10.1038/s41419-024-06804-5
  16. Bio Protoc. 2024 Jul 05. 14(13): e5025
    Quantification of Autophagosomes in Human Fibroblasts Using Cyto-ID® Staining and Cytation Imaging.
    Barbara Hochecker, Katja C Matt, Alica L Meßmer, Melanie M Scherer, Jörg Bergemann.
      As an essential process for the maintenance of cellular homeostasis and function, autophagy is responsible for the lysosome-mediated degradation of damaged proteins and organelles; therefore, dysregulation of autophagy in humans can lead to a variety of diseases. The link between impaired autophagy and disease highlights the need to investigate possible interventions to address dysregulations. One possible intervention is hyperthermia, which is described in this protocol. To investigate these interventions, a method for absolute quantification of autophagosomal compartments is required that allows comparison of autophagosomal activity under different conditions. Existing methods such as western blotting and immunohistochemistry for analysing the location and relative abundance of intracellular proteins associated with autophagy, or transmission electron microscopy (TEM), which are either very time-consuming, expensive, or both, are less suitable for this purpose. The method described in this protocol allows the absolute quantification of autophagosomes per cell in human fibroblasts using the CYTO-ID® Autophagy Detection Kit after heat therapy compared to a control. The Cyto-ID® assay is based on the use of a specific dye that selectively stains autophagic compartments, combined with an additional Hoechst 33342 dye for nuclear staining. The subsequent recognition of these stained compartments by the Cytation Imager enables the software to determine the number of autophagosomes per nucleus in living cells. Additionally, this absolute quantification uses an image-based method, and the protocol is easy to use and not time-consuming. Furthermore, the method is not only suitable for heat therapy but can also be adapted to any other desired therapy or substance. Key features • Absolute quantification of autophagic compartments in living cells. • Optimised protocol for the determination of autophagy in primary human skin fibroblasts. • Allows the testing of active substances and treatments concerning autophagy. • Imaging-based method for the determination of autophagy.
    Keywords:  Absolute quantification; Autophagy; Hyperthermia; Imaging-based method; Primary human skin fibroblasts
    DOI:  https://doi.org/10.21769/BioProtoc.5025
  17. Cell Rep Med. 2024 Jul 16. pii: S2666-3791(24)00366-5. [Epub ahead of print]5(7): 101652
    Increased regional activity of a pro-autophagy pathway in schizophrenia as a contributor to sex differences in the disease pathology.
    Kathryn J Bjornson, Amanda M Vanderplow, Aishwarya I Bhasker, Michael E Cahill.
      Based on recent genome-wide association studies, it is theorized that altered regulation of autophagy contributes to the pathophysiology of schizophrenia and bipolar disorder. As activity of autophagy-regulatory pathways is controlled by discrete phosphorylation sites on the relevant proteins, phospho-protein profiling is one of the few approaches available for enabling a quantitative assessment of autophagic activity in the brain. Despite this, a comprehensive phospho-protein assessment in the brains of schizophrenia and bipolar disorder subjects is currently lacking. Using this direction, our broad screening identifies an increase in AMP-activated protein kinase (AMPK)-mediated phospho-activation of the pro-autophagy protein beclin-1 solely in the prefrontal cortex of female, but not male, schizophrenia subjects. Using a reverse translational approach, we surprisingly find that this increase in beclin-1 activity facilitates synapse formation and enhances cognition. These findings are interpreted in the context of human studies demonstrating that female schizophrenia subjects have a lower susceptibility to cognitive dysfunction than males.
    DOI:  https://doi.org/10.1016/j.xcrm.2024.101652
  18. MicroPubl Biol. 2024 ;2024
    MEC-12/alpha tubulin regulates mitochondrial distribution and mitophagy during oxidative stress in C. elegans.
    Fivos Borbolis, Myrsini Kteniadaki, Konstantinos Palikaras.
      Mitophagy, the selective removal of dysfunctional mitochondria, is pivotal for the maintenance of neuronal function and survival. MEC-12/α-tubulin contributes to neuronal physiology through the regulation of microtubule assembly, intracellular transport and mitochondrial distribution. However, its role in mitochondrial dynamics and mitophagy remains obscure. Here, we demonstrate that MEC-12 influences mitochondrial morphology under basal conditions and regulates the axonal mitochondrial population. Impairment of MEC-12 results in compromised axonal mitophagy under both basal conditions and oxidative stress. Our results uncover the critical role of MEC-12/α-tubulin for maintaining a healthy mitochondrial population in axons and highlight the complex interplay between microtubules, mitophagy and neuronal health.
    DOI:  https://doi.org/10.17912/micropub.biology.001232
  19. Zool Res. 2024 Jul 18. pii: 2095-8137(2024)04-0857-18. [Epub ahead of print]45(4): 857-874
    NLRP3-mediated autophagy dysfunction links gut microbiota dysbiosis to tau pathology in chronic sleep deprivation.
    Na Zhao, Xiu Chen, Qiu-Gu Chen, Xue-Ting Liu, Fan Geng, Meng-Meng Zhu, Fu-Ling Yan, Zhi-Jun Zhang, Qing-Guo Ren.
      Emerging evidence indicates that sleep deprivation (SD) can lead to Alzheimer's disease (AD)-related pathological changes and cognitive decline. However, the underlying mechanisms remain obscure. In the present study, we identified the existence of a microbiota-gut-brain axis in cognitive deficits resulting from chronic SD and revealed a potential pathway by which gut microbiota affects cognitive functioning in chronic SD. Our findings demonstrated that chronic SD in mice not only led to cognitive decline but also induced gut microbiota dysbiosis, elevated NLRP3 inflammasome expression, GSK-3β activation, autophagy dysfunction, and tau hyperphosphorylation in the hippocampus. Colonization with the "SD microbiota" replicated the pathological and behavioral abnormalities observed in chronic sleep-deprived mice. Remarkably, both the deletion of NLRP3 in NLRP3 -/- mice and specific knockdown of NLRP3 in the hippocampus restored autophagic flux, suppressed tau hyperphosphorylation, and ameliorated cognitive deficits induced by chronic SD, while GSK-3β activity was not regulated by the NLRP3 inflammasome in chronic SD. Notably, deletion of NLRP3 reversed NLRP3 inflammasome activation, autophagy deficits, and tau hyperphosphorylation induced by GSK-3β activation in primary hippocampal neurons, suggesting that GSK-3β, as a regulator of NLRP3-mediated autophagy dysfunction, plays a significant role in promoting tau hyperphosphorylation. Thus, gut microbiota dysbiosis was identified as a contributor to chronic SD-induced tau pathology via NLRP3-mediated autophagy dysfunction, ultimately leading to cognitive deficits. Overall, these findings highlight GSK-3β as a regulator of NLRP3-mediated autophagy dysfunction, playing a critical role in promoting tau hyperphosphorylation.
    Keywords:  Autophagy; Chronic sleep deprivation; GSK-3β; Microbiota-gut-brain axis; NLRP3 inflammasome; Tau pathology
    DOI:  https://doi.org/10.24272/j.issn.2095-8137.2024.085
  20. bioRxiv. 2024 Jul 09. pii: 2024.07.05.602170. [Epub ahead of print]
    Tau phosphorylation suppresses oxidative stress-induced mitophagy via FKBP8 receptor modulation.
    Michael O Isei, Meredith Crockett, Emily Chen, Joel Rodwell-Bullock, Trae Caroll, Peter A Girardi, Keith Nehrke, Gail Vw Johnson.
      Neurodegenerative diseases are often characterized by mitochondrial dysfunction. In Alzheimer's disease, abnormal tau phosphorylation disrupts mitophagy, a quality control process through which damaged organelles are selectively removed from the mitochondrial network. The precise mechanism through which this occurs remains unclear. Previously, we showed that tau which has been mutated at Thr-231 to glutamic acid to mimic an Alzheimer's-relevant phospho-epitope expressed early in disease selectively inhibits oxidative stress-induced mitophagy in C. elegans . Here, we use immortalized mouse hippocampal neuronal cell lines to extend that result into mammalian cells. Specifically, we show that phosphomimetic tau at Ser-396/404 (EC) or Thr-231/Ser-235 (EM) partly inhibits mitophagy induction by paraquat, a potent inducer of mitochondrial oxidative stress. Moreover, a combination of immunologic and biochemical approaches demonstrates that the levels of the mitophagy receptor FKBP8, significantly decrease in response to paraquat in cells expressing EC or EM tau mutants, but not in cells expressing wildtype tau. In contrast, paraquat treatment results in a decrease in the levels of the mitophagy receptors FUNDC1 and BNIP3 in the presence of both wildtype tau and the tau mutants. Interestingly, FKBP8 is normally trafficked to the endoplasmic reticulum during oxidative stress induced mitophagy, and our results support a model where this trafficking is impacted by disease-relevant tau, perhaps through a direct interaction. We provide new insights into the molecular mechanisms underlying tau pathology in Alzheimer's disease and highlight FKBP8 receptor as a potential target for mitigating mitochondrial dysfunction in neurodegenerative diseases.
    DOI:  https://doi.org/10.1101/2024.07.05.602170
  21. FEMS Yeast Res. 2024 Jul 18. pii: foae022. [Epub ahead of print]
    A novel fluorescence-activated cell sorting (FACS)-based screening identified ATG14, the gene required for pexophagy in the methylotrophic yeast.
    Kosuke Shiraishi, Yumi Arima, Motoharu Nakamura, Takumi Nakatsuji, Masahide Oku, Yasuyoshi Sakai.
      Pexophagy is a type of autophagy that selectively degrades peroxisomes and can be classified as either macropexophagy or micropexophagy. During macropexophagy, individual peroxisomes are sequestered by pexophagosomes and transported to the vacuole for degradation, while in micropexophagy, peroxisomes are directly engulfed by the septated vacuole. To date, some autophagy-related genes (ATGs) required for pexophagy have been identified through plate-based assays performed primarily under micropexophagy-induced conditions. Here, we developed a novel high-throughput screening system using fluorescence-activated cell sorting (FACS) to identify genes required for macropexophagy. Using this system, we discovered KpATG14, a gene that could not be identified previously in the methylotrophic yeast Komagataella phaffii due to technical limitations. Microscopic and immunoblot analyses found that KpAtg14 was required for both macropexophagy and micropexophagy. We also revealed that KpAtg14 was necessary for recruitment of the downstream factor KpAtg5 at the pre-autophagosomal structure (PAS), and consequently, for bulk autophagy. We anticipate our assay to be used to identify novel genes that are exclusively required for macropexophagy, leading to better understanding of the physiological significance of the existing two types of autophagic degradation pathways for peroxisomes.
    Keywords:  Atg14; FACS; autophagy; methylotrophic yeast; pexophagy
    DOI:  https://doi.org/10.1093/femsyr/foae022
  22. Free Radic Biol Med. 2024 Jul 13. pii: S0891-5849(24)00558-6. [Epub ahead of print]
    Activation of macroautophagy and chaperone-mediated autophagy in human skeletal muscle by high-intensity exercise in normoxia and hypoxia and after recovery with or without post-exercise ischemia.
    Miriam Martinez-Canton, Victor Galvan-Alvarez, Angel Gallego-Selles, Miriam Gelabert-Rebato, Eduardo Garcia-Gonzalez, Juan Jose Gonzalez-Henriquez, Marcos Martin-Rincon, Jose Al Calbet.
      Autophagy is essential for the adaptive response to exercise and physiological skeletal muscle functionality. However, the mechanisms leading to the activation of macroautophagy and chaperone-mediated autophagy in human skeletal muscle in response to high-intensity exercise remain elusive. Our findings demonstrate that macroautophagy and chaperone-mediated autophagy are stimulated by high-intensity exercise in normoxia (PIO2: 143 mmHg) and severe acute hypoxia (PIO2: 73 mmHg) in healthy humans. High-intensity exercise induces macroautophagy initiation through AMPKα phosphorylation, which phosphorylates and activates ULK1. ULK1 phosphorylates BECN1 at Ser15, eliciting the dissociation of BECN1-BCL2 crucial for phagophore formation. Besides, high-intensity exercise elevates the LC3B-II:LC3B-I ratio, reduces total SQSTM1/p62 levels, and induces p-Ser349 SQSTM1/p62 phosphorylation, suggesting heightened autophagosome degradation. PHAF1/MYTHO, a novel macroautophagy biomarker, is highly upregulated in response to high-intensity exercise. The latter is accompanied by elevated LAMP2A expression, indicating chaperone-mediated autophagy activation despite post-exercise HSPA8/HSC70 downregulation. Despite increased glycolytic metabolism, severe acute hypoxia does not exacerbate the autophagy signaling response. Signaling changes revert within 1 minute of recovery with free circulation, while the application of immediate post-exercise ischemia impedes recovery. Our study concludes that macroautophagy and chaperone-mediated autophagy pathways are strongly activated by high-intensity exercise, regardless of PO2, and that oxygenation is necessary to revert these signals to pre-exercise values. PHAF1/MYTHO emerges as a pivotal exercise-responsive autophagy marker positively associated with the LC3B-II:LC3B-I ratio.
    Keywords:  Autophagy; biopsies; exercise; fatigue; hypoxia; ischemia; signaling
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2024.07.012
  23. J Neuropathol Exp Neurol. 2024 Jul 18. pii: nlae079. [Epub ahead of print]
    Cytoplasmic vacuolization and ectopic formation of perineuronal nets are characteristic pathologies of cytomegalic neurons in tuberous sclerosis.
    Alexander A Sosunov, Guy McKhann Ii, Guomei Tang, James E Goldman.
      Cytomegalic neurons, characterized by increased size and a hyperactive mechanistic target of rapamycin complex 1 (mTORC1), are pathognomonic for tuberous sclerosis complex (TSC). To model these neurons, we recently generated a murine Tsc1 conditional knockout model in which Tsc1 deletion in late embryonic radial glia results in neuronal hypertrophy of a subset of isocortical pyramidal neurons. In the current study, we compared the cellular pathology of these cytomegalic neurons to those of the enlarged neurons in human cortical tubers. Neurons from the mice showed unique features, such as cytoplasmic vacuoles associated with Golgi complexes and the ectopic formation of perineuronal nets (PNNs), a feature of inhibitory neurons, rarely present in excitatory cortical neurons. The membranes of these vacuoles were enriched for the plasma membrane proteins CD44, KCC2, and Na+/K+ ATPase, suggesting deficits in Golgi membrane trafficking. These aberrant features in the mouse appeared only after the onset of seizures, probably due to the prolonged seizure activity in the context of constitutive mTORC1 activation. Similar PNNs and cytoplasmic vacuoles were present in the cytomegalic neurons of human cortical tubers. Our findings reveal novel pathological features of Golgi complexes and PNNs in the cytomegalic neurons in TSC.
    Keywords:  ATPase; CD44; Golgi complex; KCC2; Na+/K+; cytomegalic neurons; perineuronal nets; tuberous sclerosis
    DOI:  https://doi.org/10.1093/jnen/nlae079
  24. Biochem Biophys Res Commun. 2024 Jul 14. pii: S0006-291X(24)00933-1. [Epub ahead of print]731 150397
    The erlin1/erlin2 complex binds to and stabilizes phosphatidylinositol 3-phosphate and regulates autophagy.
    Fanghui Hua, Caden G Bonzerato, Katherine R Keller, Dandan Guo, Juntao Luo, Richard J H Wojcikiewicz.
      The erlin1/erlin2 (E1/E2) complex is an endoplasmic reticulum membrane-located assemblage of the proteins erlin1 and erlin2. Here, we demonstrate direct and selective binding of phosphatidylinositol 3-phosphate (PI(3)P) to recombinant erlins and that disruption or deletion of the E1/E2 complex reduces HeLa cell PI(3)P levels by ∼50 %. This reduction correlated with a decrease in autophagic flux, with no effect on the endocytic pathway, and was not due to reduced VPS34 kinase activity, which is critical for maintaining steady-state PI(3)P levels. Pharmacological inhibition of VPS34 and suppression of PI(3)P levels caused a similar reduction in autophagic flux. Overall, these data indicate that by binding to PI(3)P, the E1/E2 complex plays an important role in maintaining the steady-state levels of PI(3)P and, thus, sustains some key PI(3)P-dependent processes, e.g., autophagy.
    Keywords:  Autophagy; Endocytosis; Erlin complex; Lipid metabolism; Phosphatidylinositol 3-phosphate
    DOI:  https://doi.org/10.1016/j.bbrc.2024.150397
  25. Nat Cell Biol. 2024 Jul 15.
    The autophagy adaptor TRIAD3A promotes tau fibrillation by nested phase separation.
    Jiechao Zhou, Yang 'an Chuang, Javier Redding-Ochoa, Rongzhen Zhang, Alexander J Platero, Alexander H Barrett, Juan C Troncoso, Paul F Worley, Wenchi Zhang.
      Multiple neurodegenerative diseases are characterized by aberrant proteinaceous accumulations of tau. Here, we report a RING-in-between-RING-type E3 ligase, TRIAD3A, that functions as an autophagy adaptor for tau. TRIAD3A(RNF216) is an essential gene with mutations causing age-progressive neurodegeneration. Our studies reveal that TRIAD3A E3 ligase catalyses mixed K11/K63 polyubiquitin chains and self-assembles into liquid-liquid phase separated (LLPS) droplets. Tau is ubiquitinated and accumulates within TRIAD3A LLPS droplets and, via LC3 interacting regions, targets tau for autophagic degradation. Unexpectedly, tau sequestered within TRIAD3A droplets rapidly converts to fibrillar aggregates without the transitional liquid phase of tau. In vivo studies show that TRIAD3A decreases the accumulation of phosphorylated tau in a tauopathy mouse model, and a disease-associated mutation of TRIAD3A increases accumulation of phosphorylated tau, exacerbates gliosis and increases pathological tau spreading. In human Alzheimer disease brain, TRIAD3A co-localizes with tau amyloid in multiple histological forms, suggesting a role in tau proteostasis. TRIAD3A is an autophagic adaptor that utilizes E3 ligase and LLPS as a mechanism to capture cargo and appears especially relevant to neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41556-024-01461-4
  26. EMBO Rep. 2024 Jul 18.
    The actin binding protein profilin 1 localizes inside mitochondria and is critical for their function.
    Tracy-Ann Read, Bruno A Cisterna, Kristen Skruber, Samah Ahmadieh, Tatiana M Liu, Josefine A Vitriol, Yang Shi, Joseph B Black, Mitchell T Butler, Halli L Lindamood, Austin Eyt Lefebvre, Alena Cherezova, Daria V Ilatovskaya, James E Bear, Neal L Weintraub, Eric A Vitriol.
      The monomer-binding protein profilin 1 (PFN1) plays a crucial role in actin polymerization. However, mutations in PFN1 are also linked to hereditary amyotrophic lateral sclerosis, resulting in a broad range of cellular pathologies which cannot be explained by its primary function as a cytosolic actin assembly factor. This implies that there are important, undiscovered roles for PFN1 in cellular physiology. Here we screened knockout cells for novel phenotypes associated with PFN1 loss of function and discovered that mitophagy was significantly upregulated. Indeed, despite successful autophagosome formation, fusion with the lysosome, and activation of additional mitochondrial quality control pathways, PFN1 knockout cells accumulate depolarized, dysmorphic mitochondria with altered metabolic properties. Surprisingly, we also discovered that PFN1 is present inside mitochondria and provide evidence that mitochondrial defects associated with PFN1 loss are not caused by reduced actin polymerization in the cytosol. These findings suggest a previously unrecognized role for PFN1 in maintaining mitochondrial integrity and highlight new pathogenic mechanisms that can result from PFN1 dysregulation.
    Keywords:  Actin; Mitochondria; Mitochondrial-derived Vesicles; Mitophagy; Profilin
    DOI:  https://doi.org/10.1038/s44319-024-00209-3
  27. Biomed Pharmacother. 2024 Jul 13. pii: S0753-3322(24)01028-X. [Epub ahead of print]177 117144
    Phytochemicals targeting mitophagy: Therapeutic opportunities and prospects for treating Alzheimer's disease.
    Jing Yang, He Zhao, Shengtao Qu.
      Alzheimer's disease (AD) is a prevalent neurodegenerative disorder and the leading cause of age-related cognitive decline. Recent studies have established a close relationship between mitophagy and the pathogenesis of AD. Various phytochemicals have shown promising therapeutic effects in mitigating the onset and progression of AD. This review offers a comprehensive overview of the typical features of mitophagy and the underlying mechanisms leading to its occurrence in AD, highlighting its significance in the disease's pathogenesis and progression. Additionally, we examine the therapeutic mechanisms of synthetic drugs that induce mitophagy in AD. Finally, we summarize recent advances in research on phytochemicals that regulate mitophagy in the treatment of AD, potentially guiding the development of new anti-AD drugs.
    Keywords:  Alzheimer’s disease; Autophagy; Mitophagy; Phytochemicals; Therapy
    DOI:  https://doi.org/10.1016/j.biopha.2024.117144
  28. J Nutr Biochem. 2024 Jul 16. pii: S0955-2863(24)00136-0. [Epub ahead of print] 109703
    Sestrin2 in POMC Neurons Modulates Energy Balance and Obesity Related Metabolic Disorders via mTOR Signaling.
    Huiling Hu, Xiaoxia Lu, Yuqing He, Jing Li, Shoujie Wang, Zhijun Luo, Ying Wang, Jie Wei, Hao Huang, Chaohui Duan, Nannan Sun.
      Sestrin2 is a highly conserved protein that can be induced under various stress conditions. Researches have revealed that the signaling pathway of the mammalian target of rapamycin (mTOR) is essential in modulating both glucose and lipid metabolism. However, the precise involvement of Sestrin2 in the hypothalamus, particularly in pro-opiomelanocortin (POMC) neurons, in control of energy homeostasis remains uncertain. In this study, we aimed to investigate the functional role of Sestrin2 in hypothalamic POMC neurons in regulation of energy balance, as well as revealing the underlying mechanisms. Therefore, Cre-dependent AAV virus encoding or silencing Sestrin2 was injected into the hypothalamic ARC of Pomc-cre transgenic mice. The results demonstrated that Sestrin2 overexpression in POMC neurons ameliorated high-fat diet (HFD)-induced obesity and increased energy expenditure. Conversely, Sestrin2 deficiency in POMC neurons predisposed mice to HFD induced obesity. Additionally, the thermogenesis of brown adipose tissue and lipolysis of inguinal white adipose tissue were both enhanced by the increased sympathetic nerve innervation in Sestrin2 overexpressed mice. Further exploration revealed that Sestrin2 overexpression inhibited the mTOR signaling pathway in hypothalamic POMC neurons, which may account for the alleviation of systematic metabolic disturbance induced by HFD in these mice. Collectively, our findings demonstrate that Sestrin2 in POMC neurons plays a pivotal role in maintaining energy balance in a context of HFD-induced obesity by inhibiting the mTOR pathway, providing new insights into how hypothalamic neurons respond to nutritional signals to protect against obesity-associated metabolic dysfunction.
    Keywords:  Energy Balance; Metabolic Disorders; POMC; Sestrin2; mTOR
    DOI:  https://doi.org/10.1016/j.jnutbio.2024.109703
  29. Cell Prolif. 2024 Jul 14. e13714
    Impaired autophagy-mediated macrophage polarization contributes to age-related hyposalivation.
    Zhili Xin, Rongyao Xu, Yangjiele Dong, Shenghao Jin, Xiao Ge, Xin Shen, Songsong Guo, Yu Fu, Ping Zhang, Hongbing Jiang.
      Age-related dysfunction of salivary glands (SGs) leading to xerostomia or dry mouth is typically associated with increased dental caries and difficulties in mastication, deglutition or speech. Inflammaging-induced hyposalivation plays a significant role in aged SGs; however, the mechanisms by which ageing shapes the inflammatory microenvironment of SGs remain unclear. Here, we show that reduced salivary secretion flow rate in aged human and mice SGs is associated with impaired autophagy and increased M1 polarization of macrophages. Our study reveals the crucial roles of SIRT6 in regulating macrophage autophagy and polarization through the PI3K/AKT/mTOR pathway, as demonstrated by generating two conditional knock out mice. Furthermore, triptolide (TP) effectively rejuvenates macrophage autophagy and polarization via targeting this pathway. We also design a local delivery of TP-loaded apoptotic extracellular vesicles (ApoEVs) to improve age-related SGs dysfunction therapeutically. Collectively, our findings uncover a previously unknown link between SIRT6-regulated autophagy and macrophage polarization in age-mediated hyposalivation, while our locally therapeutic strategy exhibits potential preventive effects for age-related hyposalivation.
    DOI:  https://doi.org/10.1111/cpr.13714
  30. Am J Cancer Res. 2024 ;14(6): 2770-2789
    mTOR inhibition by AZD2014 alleviates BCR::ABL1 independent imatinib resistance through enhancing autophagy in CML resistant cells.
    Wei He, Suotian Liu, Wei Wei, Run Qin, Jinfeng Tan, Jie Tang, Zhenglan Huang, Miao Gao.
      Chronic myeloid leukemia (CML) is a common hematopoietic malignancy in adults. Great progress has been made in CML therapy with imatinib. However, resistance to imatinib may occur during treatment. BCR::ABL1 dependent imatinib resistance has been well resolved with more potent tyrosine kinase inhibitors, but BCR::ABL1 independent resistance still remains to be resolved. This study is devoted to find novel targets for BCR::ABL1 independent imatinib-resistant patients. It is reported BCR::ABL1 independent resistance is mainly related to the activation of alternative survival pathway, and mTOR is an important regulator for cell growth especially in tumor cells. Hence, we explored the role of mTOR in BCR::ABL1 independent resistance, the possibility of mTOR to be a therapeutic target for imatinib resistant patients and the related mechanism. We found mTOR was upregulated in imatinib-resistant cells. mTOR inhibition by AZD2014 led to growth inhibition and synergized with imatinib in apoptosis induction in K562/G01. AZD2014 exerted its anti-leukemia effect through enhancing autophagy. mTOR signal pathway is poorly inhibited by imatinib and AZD2014 shows little effect on BCR::ABL1 signal pathway, which indicates that mTOR is involved in imatinib resistance via a BCR::ABL1 independent manner. Taken together, mTOR represents a potential target to overcome BCR::ABL1 independent imatinib resistance.
    Keywords:  AZD2014; autophagy; chronic myeloid leukemia; imatinib resistance; mTOR
    DOI:  https://doi.org/10.62347/RWLJ3990
  31. Autophagy. 2024 Jul 15.
    Proteostasis in health and disease: a conversation with Professor Rick Morimoto.
    Richard I Morimoto, Nicholas T Ktistakis.
      Professor Richard (Rick) Morimoto is the Bill and Gayle Cook Professor of Biology and Director of the Rice Institute for Biomedical Research at Northwestern University. He has made foundational contributions to our understanding of how cells respond to various stresses, and the role played in those responses by chaperones. Working across a variety of experimental models, from C. elegans to human neuronal cells, he has identified a number of important molecular components that sense and respond to stress, and he has dissected how stress alters cellular and organismal physiology. Together with colleagues, Professor Morimoto has coined the term "proteostasis" to signify the homeostatic control of protein expression and function, and in recent years he has been one of the leaders of a consortium trying to understand proteostasis in healthy and disease states. I took the opportunity to talk with Professor Morimoto about proteostasis in general, the aims of the consortium, and how autophagy is playing an important role in their research effort.
    Keywords:  Autophagy; Disclosure statement: the authors declare no competing interests; chemical tools; consortium; proteostasis
    DOI:  https://doi.org/10.1080/15548627.2024.2377051
  32. Environ Pollut. 2024 Jul 17. pii: S0269-7491(24)01250-8. [Epub ahead of print] 124536
    Integrated RNA sequencing and biochemical studies reveal endoplasmic reticulum stress and autophagy dysregulation contribute to Tri (2-Ethylhexyl) phosphate (TEHP)-induced cell injury in Sertoli cells.
    Pengchen Chen, Yali Song, Li Tang, Zhuolin Qiu, Junhui Chen, Siyu Xia, Ashok Iyaswamy, Jing Cai, Yan Sun, Chuanbin Yang, Jigang Wang.
      Tri (2-Ethylhexyl) phosphate (TEHP), widely used as a fire retardant and plasticizer, has been commonly found in the environment. Its potential health-related risks, especially reproductive toxicity, have aroused concern. However, the potential cellular mechanisms remain unexplored. In this study, we aimed to investigate the molecular mechanisms underlying TEHP-caused cell damage in Sertoli cells, which play a crucial role in supporting spermatogenesis. Our findings indicate that TEHP induces apoptosis in 15P-1 mouse Sertoli cells. Subsequently, we conducted RNA sequencing analyses, which suggested that ER stress, autophagy, and MAPK-related pathways may participate in TEHP-induced cytotoxicity. Furthermore, we demonstrated that TEHP triggers ER stress, activates p38 MAPK, and inhibits autophagy flux. Then, we showed that the inhibition of ER stress or p38 MAPK activation attenuates TEHP-induced apoptosis, while the inhibition of autophagy flux is responsible for TEHP-induced apoptosis. These results collectively reveal that TEHP induces ER stress, activates p38, and inhibits autophagy flux, ultimately leading to apoptosis in Sertoli cells. These shed light on the molecular mechanisms underlying TEHP-associated testicular toxicity.
    Keywords:  Sertoli cell; Tri (2-Ethylhexyl) phosphate; autophagy dysregulation; endoplasmic reticulum stress; reproductive toxicity
    DOI:  https://doi.org/10.1016/j.envpol.2024.124536
  33. bioRxiv. 2024 Jul 12. pii: 2024.07.10.602886. [Epub ahead of print]
    Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function.
    Masroor Ahmad Paddar, Fulong Wang, Einar S Trosdal, Emily Hendrix, Yi He, Michelle Salemi, Michal Mudd, Jingyue Jia, Thabata L A Duque, Ruheena Javed, Brett Phinney, Vojo Deretic.
      ATG5 is one of the core autophagy proteins with additional functions such as noncanonical membrane atg8ylation, which among a growing number of biological outputs includes control of tuberculosis in animal models. Here we show that ATG5 associates with retromer's core components VPS26, VPS29 and VPS35 and modulates retromer function. Knockout of ATG5 blocked trafficking of a key glucose transporter sorted by the retromer, GLUT1, to the plasma membrane. Knockouts of other genes essential for membrane atg8ylation, of which ATG5 is a component, affected GLUT1 sorting, indicating that membrane atg8ylation as a process affects retromer function and endosomal sorting. The contribution of membrane atg8ylation to retromer function in GLUT1 sorting was independent of canonical autophagy. These findings expand the scope of membrane atg8ylation to specific sorting processes in the cell dependent on the retromer and its known interactors.
    DOI:  https://doi.org/10.1101/2024.07.10.602886
  34. J Cell Sci. 2024 Jul 17. pii: jcs.262343. [Epub ahead of print]
    Chemical genetic screens reveal defective lysosomal trafficking as synthetic lethal with NF1 loss.
    Stephanie J Bouley, Andrew V Grassetti, Robert J Allaway, Matthew D Wood, Helen W Hou, India R Burdon Dasbach, William Seibel, Jimmy Wu, Scott A Gerber, Konstantin H Dragnev, James A Walker, Yolanda Sanchez.
      Neurofibromatosis type 1, a genetic disorder caused by germline mutations in NF1, predisposes patients to the development of tumors, including cutaneous and plexiform neurofibromas (CNs and PNs), optic gliomas, astrocytomas, juvenile myelomonocytic leukemia, high-grade gliomas, and malignant peripheral nerve sheath tumors (MPNSTs), which are chemotherapy- and radiation-resistant sarcomas with poor survival. Loss of NF1 also occurs in sporadic tumors such as glioblastoma (GBM), melanoma, breast, ovarian, and lung cancers. We performed a high-throughput screen for compounds that were synthetic lethal with NF1 loss, which identified several leads, including the small molecule Y102. Treatment of cells with Y102 perturbed autophagy, mitophagy, and lysosome positioning in NF1-deficient cells. A dual proteomics approach identified the BORC complex, which is required for lysosome positioning and trafficking, as a potential target of Y102. Knockdown of a BORC complex subunit using siRNA recapitulated the phenotypes observed with Y102 treatment. Our findings demonstrate that the BORC complex may be a promising therapeutic target for NF1-deficient tumors.
    Keywords:  NF1; RAS; synthetic lethal; mitochondria; lysosomes; BORC
    DOI:  https://doi.org/10.1242/jcs.262343
  35. FEBS Lett. 2024 Jul 15.
    Fission yeast Pib2 localizes to vacuolar membranes and regulates TOR complex 1 through evolutionarily conserved domains.
    Yuichi Morozumi, Yumi Hayashi, Cuong Minh Chu, Fajar Sofyantoro, Yutaka Akikusa, Tomoyuki Fukuda, Kazuhiro Shiozaki.
      TOR complex 1 (TORC1) is a multi-protein kinase complex that coordinates cellular growth with environmental cues. Recent studies have identified Pib2 as a critical activator of TORC1 in budding yeast. Here, we show that loss of Pib2 causes severe growth defects in fission yeast cells, particularly when basal TORC1 activity is diminished by hypomorphic mutations in tor2, the gene encoding the catalytic subunit of TORC1. Consistently, TORC1 activity is significantly compromised in the tor2 hypomorphic mutants lacking Pib2. Moreover, as in budding yeast, fission yeast Pib2 localizes to vacuolar membranes via its FYVE domain, with its tail motif indispensable for TORC1 activation. These results strongly suggest that Pib2-mediated positive regulation of TORC1 is evolutionarily conserved between the two yeast species.
    Keywords:  Pib2; TOR complex 1; fission yeast; vacuolar membrane
    DOI:  https://doi.org/10.1002/1873-3468.14980
  36. Curr Neuropharmacol. 2024 Jul 04.
    Ischemic Stroke and Autophagy: The Roles of Long Non-Coding RNAs.
    Longqiang Ouyang, Wenyan Xia, Ameen Abdulhasan Al-Alwany, Reena Gupta, Ibrokhim Sapaev, Sami G Almalki, Saud Almawash, Rand Ali Ziyad, Ahmed Hussien Alawadi, Ali Alsalamy.
      Ischemic stroke is a significant cause of morbidity and mortality worldwide. Autophagy, a process of intracellular degradation, has been shown to play a crucial role in the pathogenesis of ischemic stroke. Long non-coding RNAs (lncRNAs) have emerged as essential regulators of autophagy in various diseases, including ischemic stroke. Recent studies have identified several lncRNAs that modulate autophagy in ischemic stroke, including MALAT1, MIAT, SNHG12, H19, AC136007. 2, C2dat2, MEG3, KCNQ1OT1, SNHG3, and RMRP. These lncRNAs regulate autophagy by interacting with key proteins involved in the autophagic process, such as Beclin-1, ATG7, and LC3. Understanding the role of lncRNAs in regulating autophagy in ischemic stroke may provide new insights into the pathogenesis of this disease and identify potential therapeutic targets for its treatment.
    Keywords:  Ischemic stroke; autophagy; long non-coding RNAs; pathogenesis; treatment
    DOI:  https://doi.org/10.2174/1570159X22666240704123701
  37. J Cardiovasc Aging. 2024 Apr;pii: 13. [Epub ahead of print]4(2):
    Dysfunctional mitochondria elicit bioenergetic decline in the aged heart.
    Pasquale Mone, Esther Densu Agyapong, Giampaolo Morciano, Stanislovas S Jankauskas, Antonio De Luca, Fahimeh Varzideh, Paolo Pinton, Gaetano Santulli.
      Aging represents a complex biological progression affecting the entire body, marked by a gradual decline in tissue function, rendering organs more susceptible to stress and diseases. The human heart holds significant importance in this context, as its aging process poses life-threatening risks. It entails macroscopic morphological shifts and biochemical changes that collectively contribute to diminished cardiac function. Among the numerous pivotal factors in aging, mitochondria play a critical role, intersecting with various molecular pathways and housing several aging-related agents. In this comprehensive review, we provide an updated overview of the functional role of mitochondria in cardiac aging.
    Keywords:  Autophagy; RAAS; ROS; cardiac aging; fibrosis; mitochondria; mitophagy; neurohormonal systems; oxidative stress; sympathetic nervous system
    DOI:  https://doi.org/10.20517/jca.2023.50
  38. Medicine (Baltimore). 2024 Jul 19. 103(29): e38954
    Mapping the landscape: A bibliometric perspective on autophagy in spinal cord injury.
    Fei Wang, Songou Zhang, Yangjun Xu, Wei He, Xiang Wang, Zhongwei He, Jinxiang Shang, Zhang Zhenyu.
       BACKGROUND: Spinal cord injury (SCI) is a severe condition that often leads to persistent damage of nerve cells and motor dysfunction. Autophagy is an intracellular system that regulates the recycling and degradation of proteins and lipids, primarily through lysosomal-dependent organelle degradation. Numerous publications have highlighted the involvement of autophagy in the secondary injury of SCI. Therefore, gaining a comprehensive understanding of autophagy research is crucial for designing effective therapies for SCI.
    METHODS: Dates were obtained from Web of Science, including articles and article reviews published from its inception to October 2023. VOSviewer, Citespace, and SCImago were used to visualized analysis. Bibliometric analysis was conducted using the Web of Science data, focusing on various categories such as publications, authors, journals, countries, organizations, and keywords. This analysis was aimed to summarize the knowledge map of autophagy and SCI.
    RESULTS: From 2009 to 2023, the number of annual publications in this field exhibited wave-like growth, with the highest number of publications recorded in 2020 (44 publications). Our analysis identified Mei Xifan as the most prolific author, while Kanno H emerged as the most influential author based on co-citations. Neuroscience Letters was found to have published the largest number of papers in this field. China was the most productive country, contributing 232 publications, and Wenzhou Medical University was the most active organization, publishing 39 papers.
    CONCLUSION: We demonstrated a comprehensive overview of the relationship between autophagy and SCI utilizing bibliometric tools. This article could help to enhance the understanding of the field about autophagy and SCI, foster collaboration among researchers and organizations, and identify potential therapeutic targets for treatment.
    DOI:  https://doi.org/10.1097/MD.0000000000038954
  39. Mol Cell Oncol. 2024 ;11(1): 2377404
    Amino acid deprivation in cancer cells with compensatory autophagy induction increases sensitivity to autophagy inhibitors.
    Takahito Fukui, Manami Yabumoto, Misuzu Nishida, Shiori Hirokawa, Riho Sato, Taichi Kurisu, Miyu Nakai, Md Abul Hassan, Koji Kishimoto.
      Inhibition of autophagy is an important strategy in cancer therapy. However, prolonged inhibition of certain autophagies in established cancer cells may increase therapeutic resistance, though the underlying mechanisms of its induction and enhancement remain unclear. This study sought to elucidate the mechanisms of therapeutic resistance through repeated autophagy inhibition and amino acid deprivation (AD) in an in vitro model of in vivo chronic nutrient deprivation associated with cancer cell treatment. In the human cervical cancer cell line HeLa and human breast cancer cell line MCF-7, initial extracellular AD induced the immediate expression of endosomal microautophagy (eMI). However, repeated inhibition of eMI with U18666A and extracellular AD induced macroautophagy (MA) to compensate for reduced eMI, simultaneously decreasing cytotoxicity. Here, hyperphosphorylated JNK was transformed into a hypophosphorylated state, suggesting conversion of the cell death signal to a survival signal. In a nutrient medium, cell death could not be induced by MA inhibition. However, since LAT1 inhibitors induce intracellular AD, combining them with MA and eMI inhibitors successfully promoted cell death in resistant cells. Our study identified a novel therapeuic approach for promoting cell death and addressing therapeutic resistance in cancers under autophagy-inhibitor treatment.
    Keywords:  Amino acid deprivation; amino acid transporter; autophagy; cancer; chemoresistance
    DOI:  https://doi.org/10.1080/23723556.2024.2377404
  40. bioRxiv. 2024 Jul 12. pii: 2024.07.11.603140. [Epub ahead of print]
    An MITF- and mTOR-dependent FLCN pathway suppresses TFE3-driven metastasis in melanoma.
    Jeremy Chang, Katelyn R Campbell-Hanson, Marion Vanneste, Julius Yevdash, Nicholas I Bartschat, Jiang Jiarui, Ardith Bhinu, Annika Helverson, Michael Henry, Eirikur Steingrimsson, Ronald J Weigel, Robert Cornell, Colin Kenny.
      Cancer cells have remarkable plasticity allowing them to acquire many biological states. Melanoma cells have the ability to switch from a proliferative melanocytic state to an invasive mesenchymal state and back again resulting in intratumoral heterogeneity. While microphthalmia-associated transcription factor (MITF) promotes the melanocytic phenotype, it is unclear what transcription factors drive the mesenchymal phenotype, and what mechanisms regulate the switch from the proliferative state to the mesenchymal state. We show that nuclear localization of the MITF paralog TFE3 correlates positively with metastatic potential in melanoma cell lines and tumors, and that deletion of TFE3 in MITF-low melanoma cell lines eliminates migration and metastatic ability. Further, we find that MITF suppresses the mesenchymal phenotype by activating expression of FNIP2, which encodes a component of an mTORC1-stimulated pathway promoting cytoplasmic retention and lysosomal degradation of TFE3. These findings point to the mTOR pathway and TFE3 as key regulators of melanoma plasticity.
    DOI:  https://doi.org/10.1101/2024.07.11.603140
  41. J Med Chem. 2024 Jul 15.
    Structure-Based Design and Discovery of a Potent and Cell-Active LC3A/B Covalent Inhibitor.
    Zhenfei Zhou, Siqi Huang, Shijie Fan, Xueyuan Li, Chengyu Wang, Wanlin Yu, Daohai Du, Yuanyuan Zhang, Kaixian Chen, Wei Fu, Cheng Luo.
      Autophagy is a highly conserved cellular homeostasis maintenance mechanism in eukaryotes. Microtubule-associated protein light chain 3 (LC3) plays a crucial role in autophagy. It has multiple pairs of protein-protein interactions (PPIs) with other proteins, and these PPIs have an effect on the regulation of autophagosome formation and the recruitment of autophagic substrates. In our previous work, a small molecule covalent inhibitor DC-LC3in-D5 which could inhibit LC3A/B PPIs was identified, but a detailed study of structure-activity relationships (SARs) was lacking. Herein, a new molecule LC3in-C42 was discovered utilizing the hybridization of advantageous fragments, whose potency (IC50 = 7.6 nM) had been greatly improved compared with that of DC-LC3in-D5. LC3in-C42 inhibits autophagy at the cellular level and its efficacy far exceeds that of DC-LC3in-D5. Thus far, LC3in-C42 stands as the most potent LC3A/B small molecule inhibitor. LC3in-C42 could serve as a powerful tool for LC3A/B protein and autophagy research.
    DOI:  https://doi.org/10.1021/acs.jmedchem.4c00898
  42. Noncoding RNA Res. 2024 Dec;9(4): 1098-1110
    MiR-200b-3p elevates 5-FU sensitivity in cholangiocarcinoma cells via autophagy inhibition by targeting KLF4.
    Feng Peng, Ruizhi He, Yuhui Liu, Yu Xie, Guangbing Xiong, Xu Li, Min Wang, Chunle Zhao, Hang Zhang, Simiao Xu, Renyi Qin.
      Cholangiocarcinoma is one of the most lethal human cancers, and chemotherapy failure is a major cause of recurrence and poor prognosis. We previously demonstrated that miR-200 family members are downregulated in clinical samples of cholangiocarcinoma and inhibit cholangiocarcinoma tumorigenesis and metastasis. However, the role of differentially expressed miR-200b-3p in 5-fluorouracil chemosensitivity remains unclear. Here, we examined how miR-200b-3p modulates 5-fluorouracil chemosensitivity in cholangiocarcinoma. We observed that miR-200b-3p was associated with 5-fluorouracil sensitivity in cholangiocarcinoma and increased 5-fluorouracil-induced mitochondrial apoptosis in cholangiocarcinoma cells. Mechanistically, miR-200b-3p suppressed autophagy in cholangiocarcinoma cells to mediate 5-fluorouracil sensitivity. Further, we identified KLF4 as an essential target of miR-200b-3p in cholangiocarcinoma. Notably, the miR-200b-3p/KLF4/autophagy pathway augmented the chemosensitivity of cholangiocarcinoma cells to 5-fluorouracil. Our findings underscore the key role of miR-200b-3p in chemosensitivity to 5-fluorouracil and highlight the miR-200b-3p/KLF4/autophagy axis as a potential therapeutic target for cholangiocarcinoma.
    Keywords:  Autophagy; Chemosensitivity; Cholangiocarcinoma; KLF4; miR-200b-3p
    DOI:  https://doi.org/10.1016/j.ncrna.2024.06.004
  43. Biomed Pharmacother. 2024 Jul 15. pii: S0753-3322(24)01030-8. [Epub ahead of print]177 117146
    FNIP1: A key regulator of mitochondrial function.
    Feng Zeng, Jiaying Cao, Wentao Li, Yanhong Zhou, Xia Yuan.
      Folliculin interacting protein 1 (FNIP1), a novel folliculin interacting protein 1, is a key regulatory factor for mitochondrial function. FNIP1 mainly responds to energy signal transduction through physical interactions with 5'-AMP activated protein kinase (AMPK). Simultaneously, it affects the transcription of mitochondria-associated genes by regulating the lysosomal localization of mechanistic target of rapamycin kinase (mTORC1). This article takes FNIP1 as the core and first introduces its involvement in the development of B cells and invariant natural killer T (iNKT) cells, muscle fiber type conversion, and the thermogenic remodeling of adipocytes by regulating mitochondrial function. In addition we discuss the detailed impact of upstream regulatory factors of FNIP1 on its function. Finally, the impact of FNIP1 on the prognosis and treatment of clinically related metabolic diseases is summarized, aiming to provide a new theoretical basis and treatment plans for the diagnosis and treatment of such diseases.
    Keywords:  AMPK; FNIP1; Metabolism; Mitochondria; mTORC1
    DOI:  https://doi.org/10.1016/j.biopha.2024.117146
  44. Exp Cell Res. 2024 Jul 17. pii: S0014-4827(24)00260-X. [Epub ahead of print] 114169
    Sulfiredoxin-1 promotes the growth of hepatocellular carcinoma by inhibiting TFEB-mediated autophagy and lysosome biogenesis.
    Qianwen Rao, Mengzhou Guo, Jialei Sun, Biwei Yang, Xin Cao, Jinglin Xia.
      Advanced hepatocellular carcinoma (HCC) patients have poor prognosis. As an endogenous antioxidant enzyme involved in a variety of bioprocesses, sulfiredoxin-1 (SRXN1) plays an irreplaceable role in promoting the development of tumors. However, the role and working mechanism of SRXN1 in HCC remain unclear. In this study, we confirmed that SRXN1 promoted the cell proliferation of HCC at genetic and pharmacological level, respectively. Transcriptome sequencing analysis revealed SRXN1 knockdown had a significant effect on the expression of lysosome biogenesis related genes. Further experiments validated that lysosome biogenesis and autophagic flux were enhanced after SRXN1 inhibition and reduced as SRXN1 overexpression. Mechanism study revealed that ROS accumulation induced TFEB nuclear translocation, followed by increased autophagy. Following this rationale, the combination of SRXN1 inhibitor and sorafenib demonstrated noticeable synergistic antitumor effect through the boost of ROS both in vivo and in vitro. Taken together, SRXN1 could be a potential therapeutic target for HCC therapy.
    Keywords:  HCC; ROS; SRXN1; TFEB; autophagy
    DOI:  https://doi.org/10.1016/j.yexcr.2024.114169
  45. bioRxiv. 2024 Jul 02. pii: 2024.07.02.601567. [Epub ahead of print]
    Role of vaccinia virus growth factor in stimulating the mTORC1-CAD axis of the de novo pyrimidine pathway under different nutritional cues.
    Lara Dsouza, Anil Pant, Blake Pope, Zhilong Yang.
      Vaccinia virus (VACV), the prototype poxvirus, actively reprograms host cell metabolism upon infection. However, the nature and molecular mechanisms remain largely elusive. Given the diverse nutritional exposures of cells in different physiological contexts, it is essential to understand how VACV may alter various metabolic pathways in different nutritional conditions. In this study, we established the importance of de novo pyrimidine biosynthesis in VACV infection. We elucidated the significance of vaccinia growth factor (VGF), a viral early protein and a homolog of cellular epidermal growth factor, in enabling VACV to phosphorylate the key enzyme CAD of the de novo pyrimidine pathway at serine 1859, a site known to positively regulate CAD activity. While nutrient-poor conditions typically inhibit mTORC1 activation, VACV activates CAD via mTORC1-S6K1 signaling axis, in conditions where glutamine and asparagine are absent. However, unlike its cellular homolog, epidermal growth factor (EGF), VGF peptide alone in the absence of VACV infection has minimal ability to activate CAD, suggestive of the involvement of other viral factor(s) and differential functions to EGF acquired during poxvirus evolution. Our research provides a foundation for understanding the regulation of a significant metabolic pathway, namely, de novo pyrimidine synthesis during VACV infection, shedding new light on viral regulation under distinct nutritional environments. This study not only has the potential to contribute to the advancement of antiviral treatments but also improve the development of VACV as an oncolytic agent and vaccine vector.
    Importance: Our research provides new insights into how VACV alters the mTORC1-CAD signaling axis under different nutritional cues. The identification of how VACV regulates a major enzyme, CAD, within the de novo pyrimidine synthesis pathway, establishes a molecular mechanism for determining how VACV reshapes this essential pathway, necessary for facilitating efficient VACV replication. We further emphasize that, despite nutrient-poor conditions, which typically inhibit mTORC1 activation, VACV can stimulate mTORC1. We identify its early growth factor, VGF, as an important factor for this stimulation of mTORC1 and its downstream effector CAD, revealing a new mechanism for how VACV sustains mTORC1-CAD axis activation under these nutrient deficient conditions. This work provides fresh insights into the molecular mechanisms of mTORC1-CAD regulation, which has the potential to be utilized to enhance VACV as an oncolytic tool, vaccine vector and aid in the development of antiviral drugs.
    DOI:  https://doi.org/10.1101/2024.07.02.601567
  46. BMC Cancer. 2024 Jul 18. 24(1): 853
    Metformin induces ZFP36 by mTORC1 inhibition in cervical cancer-derived cell lines.
    Karen Griselda De la Cruz-López, Eduardo Alvarado-Ortiz, Heriberto A Valencia-González, Fredy Omar Beltrán-Anaya, José María Zamora-Fuentes, Alfredo Hidalgo-Miranda, Elizabeth Ortiz-Sánchez, Jesús Espinal-Enríquez, Alejandro García-Carrancá.
       BACKGROUND: Metformin, a widely prescribed antidiabetic drug, has shown several promising effects for cancer treatment. These effects have been shown to be mediated by dual modulation of the AMPK-mTORC1 axis, where AMPK acts upstream of mTORC1 to decrease its activity. Nevertheless, alternative pathways have been recently discovered suggesting that metformin can act through of different targets regulation.
    METHODS: We performed a transcriptome screening analysis using HeLa xenograft tumors generated in NOD-SCID mice treated with or without metformin to examine genes regulated by metformin. Western Blot analysis, Immunohistochemical staining, and RT-qPCR were used to confirm alterations in gene expression. The TNMplot and GEPIA2 platform were used for in silico analysis of genes found up-regulated by metformin, in cervical cancer patients. We performed an AMPK knock-down using AMPK-targeted siRNAs and mTOR inhibition with rapamycin to investigate the molecular mechanisms underlying the effect of metformin in cervical cancer cell lines.
    RESULTS: We shown that metformin decreases tumor growth and increased the expression of a group of antitumoral genes involved in DNA-binding transcription activator activity, hormonal response, and Dcp1-Dcp2 mRNA-decapping complex. We demonstrated that ZFP36 could act as a new molecular target increased by metformin. mTORC1 inhibition using rapamycin induces ZFP36 expression, which could suggest that metformin increases ZFP36 expression and requires mTORC1 inhibition for such effect. Surprisingly, in HeLa cells AMPK inhibition did not affect ZFP36 expression, suggesting that additional signal transducers related to suppressing mTORC1 activity, could be involved.
    CONCLUSIONS: These results highlight the importance of ZFP36 activation in response to metformin treatment involving mTORC1 inhibition.
    Keywords:  AMPK-independent; Metformin; ZFP36; mTORC1
    DOI:  https://doi.org/10.1186/s12885-024-12555-5
  47. Nat Rev Mol Cell Biol. 2024 Jul 18.
    Regulation of and challenges in targeting NAD+ metabolism.
    Marie E Migaud, Mathias Ziegler, Joseph A Baur.
      Nicotinamide adenine dinucleotide, in its oxidized (NAD+) and reduced (NADH) forms, is a reduction-oxidation (redox) co-factor and substrate for signalling enzymes that have essential roles in metabolism. The recognition that NAD+ levels fall in response to stress and can be readily replenished through supplementation has fostered great interest in the potential benefits of increasing or restoring NAD+ levels in humans to prevent or delay diseases and degenerative processes. However, much about the biology of NAD+ and related molecules remains poorly understood. In this Review, we discuss the current knowledge of NAD+ metabolism, including limitations of, assumptions about and unappreciated factors that might influence the success or contribute to risks of NAD+ supplementation. We highlight several ongoing controversies in the field, and discuss the role of the microbiome in modulating the availability of NAD+ precursors such as nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), the presence of multiple cellular compartments that have distinct pools of NAD+ and NADH, and non-canonical NAD+ and NADH degradation pathways. We conclude that a substantial investment in understanding the fundamental biology of NAD+, its detection and its metabolites in specific cells and cellular compartments is needed to support current translational efforts to safely boost NAD+ levels in humans.
    DOI:  https://doi.org/10.1038/s41580-024-00752-w
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