bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2023–05–21
eighty-two papers selected by
Viktor Korolchuk, Newcastle University
  1. Signal-Retaining Autophagy Indicator as a Quantitative Imaging Method for ER-Phagy.
  2. USP8 Down-Regulation Promotes Parkin-Independent Mitophagy in the Drosophila Brain and in Human Neurons.
  3. Role of Macroautophagy in Mammalian Male Reproductive Physiology.
  4. Role of autophagy pathway in Parkinson's disease and related Genetic Neurological disorders.
  5. Regulation of autophagy gene expression and its implications in cancer.
  6. The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy.
  7. Integrated proteomics identifies p62-dependent selective autophagy of the supramolecular vault complex.
  8. Unconventional initiation of PINK1/Parkin mitophagy by Optineurin.
  9. The Ragulator complex: delving its multifunctional impact on metabolism and beyond.
  10. Distinct Signaling Pathways for Autophagy-Driven Cell Death and Survival in Adult Hippocampal Neural Stem Cells.
  11. Role of microglia autophagy and mitophagy in age-related neurodegenerative diseases.
  12. Novel Insight into Functions of Transcription Factor EB (TFEB) in Alzheimer's Disease and Parkinson's Disease.
  13. Maintenance of cathepsin D-dependent autophagy-lysosomal function protects against cardiac ischemia/reperfusion injury.
  14. Hva22, a REEP family protein in fission yeast, promotes reticulophagy in collaboration with a receptor protein.
  15. Autophagy and Its Lineage-Specific Roles in the Hematopoietic System.
  16. RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome.
  17. Acrylamide interferes with autophagy and induces apoptosis in Neuro-2a cells by interfering with TFEB-regulated lysosomal function.
  18. Membrane Curvature: The Inseparable Companion of Autophagy.
  19. Autophagy in Cancer Progression and Therapeutics.
  20. The mTOR Signaling Pathway Interacts with the ER Stress Response and the Unfolded Protein Response in Cancer.
  21. Modulating autophagy to treat diseases: A revisited review on in silico methods.
  22. Identifying a selective inhibitor of autophagy that targets ATG12-ATG3 protein-protein interaction.
  23. Evaluating Autophagy Levels in Two Different Pancreatic Cell Models Using LC3 Immunofluorescence.
  24. Fyn Phosphorylates Transglutaminase 2 (Tgm2) and Modulates Autophagy and p53 Expression in the Development of Diabetic Kidney Disease.
  25. Editorial: Emerging mechanistic insights of selective and Nonselective Autophagy in liver and gut diseases and their treatment strategies in the era of COVID-19.
  26. Therapeutic potential of natural compounds from herbs and nutraceuticals in spinal cord injury: Regulation of the mTOR signaling pathway.
  27. Dichloroacetic acid and rapamycin synergistically inhibit tumor progression.
  28. SQSTM1/P62 promotes lysophagy via formation of liquid-like condensates maintained by HSP27.
  29. From jeopardy champion to drug discovery; semantic similarity artificial intelligence.
  30. Regulation of Autophagy via Carbohydrate and Lipid Metabolism in Cancer.
  31. CLEC16A-An Emerging Master Regulator of Autoimmunity and Neurodegeneration.
  32. Endomembrane remodeling in SARS-CoV-2 infection.
  33. AI-Predicted mTOR Inhibitor Reduces Cancer Cell Proliferation and Extends the Lifespan of C. elegans.
  34. Autoimmunity and Carcinogenesis: Their Relationship under the Umbrella of Autophagy.
  35. Autophagy and Breast Cancer: Connected in Growth, Progression, and Therapy.
  36. Arabidopsis AUTOPHAGY-RELATED2 is essential for ATG18a and ATG9 trafficking during autophagosome closure.
  37. Rab2 stimulates LC3 lipidation on secretory membranes by noncanonical autophagy.
  38. Cytoprotective autophagy as a pro-survival strategy in ART-resistant malaria parasites.
  39. β Cell and Autophagy: What Do We Know?
  40. Autophagic-Related Proteins in Brain Gliomas: Role, Mechanisms, and Targeting Agents.
  41. "Autophagic landscapes: on the paradox of survival through self-degradation" - A science-inspired exhibition.
  42. The RNA Demethylase ALKBH5 Maintains Endoplasmic Reticulum Homeostasis by Regulating UPR, Autophagy, and Mitochondrial Function.
  43. Mitochondrial quality control in abdominal aortic aneurysm: From molecular mechanisms to therapeutic strategies.
  44. Targeting VPS34 in autophagy: An update on pharmacological small-molecule compounds.
  45. Role of Autophagy in Ehrlichia-Induced Liver Injury.
  46. Sirtuins at the Crossroads between Mitochondrial Quality Control and Neurodegenerative Diseases: Structure, Regulation, Modifications, and Modulators.
  47. Knockout validation of LAMP2A antibodies for immunostaining in human cancer cells.
  48. Reciprocal interaction between mitochondrial fission and mitophagy in postoperative delayed neurocognitive recovery in aged rats.
  49. Autophagy and SARS-CoV-2-Old Players in New Games.
  50. Puerarin Prevents Cadmium-Induced Neuronal Injury by Alleviating Autophagic Dysfunction in Rat Cerebral Cortical Neurons.
  51. Microglia-specific knock-out of NF-κB/IKK2 increases the accumulation of misfolded α-synuclein through the inhibition of p62/sequestosome-1-dependent autophagy in the rotenone model of Parkinson's disease.
  52. Phosphorylated STYK1 restrains the inhibitory role of EGFR in autophagy initiation and EGFR-TKIs sensitivity.
  53. Liraglutide alleviates myocardial ischemia‒reperfusion injury in diabetic mice.
  54. Z-Disk-Associated Plectin (Isoform 1d): Spatial Arrangement, Interaction Partners, and Role in Filamin C Homeostasis.
  55. Enhanced Sestrin expression through Tanshinone 2A treatment improves PI3K-dependent inhibition of glioma growth.
  56. Beclin 1 regulates astrocyte phagocytosis and phagosomal recruitment of retromer.
  57. Senescence-related impairment of autophagy induces toxic intraneuronal amyloid-β accumulation in a mouse model of amyloid pathology.
  58. Role and mechanism of FOXG1-related epigenetic modifications in cisplatin-induced hair cell damage.
  59. A comprehensive review of the relationship between autophagy and sorafenib-resistance in hepatocellular carcinoma: ferroptosis is noteworthy.
  60. Mitochondrial dysfunction in aging.
  61. Autophagy in the pharmacological activities of celastrol (Review).
  62. Peroxisome proliferator-activated receptor γ activation ameliorates liver fibrosis-differential action of transcription factor EB and autophagy on hepatocytes and stellate cells.
  63. Autophagic Clearance of Lipid Droplets Alters Metabolic Phenotypes in a Genetic Obesity-Diabetes Mouse Model.
  64. SIRT3-mediated autophagy contributes to ferroptosis-induced anticancer by inducing the formation of BECN1-SLC7A11 complex.
  65. Preserved autophagy in cognitively intact non-demented individuals with Alzheimer's neuropathology.
  66. mTORC1-Dependent Protein and Parkinson's Disease: A Mendelian Randomization Study.
  67. Curcumin suppresses RANKL-induced osteoclast precursor autophagy in osteoclastogenesis by inhibiting RANK signaling and downstream JNK-BCL2-Beclin1 pathway.
  68. Butyrate dictates ferroptosis sensitivity through FFAR2-mTOR signaling.
  69. Autophagy exerts a protective role in cervical spinal cord injury by microglia inhibition through the NF-κB pathway.
  70. Bacterial extracellular vesicles induced oxidative stress and mitophagy through mTOR pathways in colon cancer cells, HT-29: Implications for bioactivity.
  71. Senolytic Flavonoids Enhance Type-I and Type-II Cell Death in Human Radioresistant Colon Cancer Cells through AMPK/MAPK Pathway.
  72. Reversing Dysdynamism to Interrupt Mitochondrial Degeneration in Amyotrophic Lateral Sclerosis.
  73. Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
  74. Ox-LDL aggravates contrast-induced injury of renal tubular epithelial cells.
  75. Not just protons: Chloride also activates lysosomal acidic hydrolases.
  76. Transcriptional Regulation of Autophagy-Related Genes by Sin3 Negatively Modulates Autophagy in Magnaporthe oryzae.
  77. Impaired lipophagy induced-microglial lipid droplets accumulation contributes to the buildup of TREM1 in diabetes-associated cognitive impairment.
  78. Obesity impairs cardiolipin-dependent mitophagy and therapeutic intercellular mitochondrial transfer ability of mesenchymal stem cells.
  79. The Role of Exercise in Maintaining Mitochondrial Proteostasis in Parkinson's Disease.
  80. The Small-Molecule Enhancers of Autophagy AUTEN-67 and -99 Delay Ageing in Drosophila Striated Muscle Cells.
  81. Protein Aggregates and Aggrephagy in Myopathies.
  82. Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription.
  1. Cells. 2023 04 11. pii: 1134. [Epub ahead of print]12(8):
    Signal-Retaining Autophagy Indicator as a Quantitative Imaging Method for ER-Phagy.
    Natalia Jimenez-Moreno, Carla Salomo-Coll, Laura C Murphy, Simon Wilkinson.
      Autophagy is an intracellular lysosomal degradation pathway by which cytoplasmic cargoes are removed to maintain cellular homeostasis. Monitoring autophagy flux is crucial to understand the autophagy process and its biological significance. However, assays to measure autophagy flux are either complex, low throughput or not sensitive enough for reliable quantitative results. Recently, ER-phagy has emerged as a physiologically relevant pathway to maintain ER homeostasis but the process is poorly understood, highlighting the need for tools to monitor ER-phagy flux. In this study, we validate the use of the signal-retaining autophagy indicator (SRAI), a fixable fluorescent probe recently generated and described to detect mitophagy, as a versatile, sensitive and convenient probe for monitoring ER-phagy. This includes the study of either general selective degradation of the endoplasmic reticulum (ER-phagy) or individual forms of ER-phagy involving specific cargo receptors (e.g., FAM134B, FAM134C, TEX264 and CCPG1). Crucially, we present a detailed protocol for the quantification of autophagic flux using automated microscopy and high throughput analysis. Overall, this probe provides a reliable and convenient tool for the measurement of ER-phagy.
    Keywords:  ER; ER-phagy; SRAI; autophagy; autophagy flux; fluorescent protein; lysosome; reporter
    DOI:  https://doi.org/10.3390/cells12081134
  2. Cells. 2023 04 13. pii: 1143. [Epub ahead of print]12(8):
    USP8 Down-Regulation Promotes Parkin-Independent Mitophagy in the Drosophila Brain and in Human Neurons.
    Sofia Mauri, Greta Bernardo, Aitor Martinez, Mariavittoria Favaro, Marta Trevisan, Gael Cobraiville, Marianne Fillet, Federico Caicci, Alexander J Whitworth, Elena Ziviani.
      Stress-induced mitophagy, a tightly regulated process that targets dysfunctional mitochondria for autophagy-dependent degradation, mainly relies on two proteins, PINK1 and Parkin, which genes are mutated in some forms of familiar Parkinson's Disease (PD). Upon mitochondrial damage, the protein kinase PINK1 accumulates on the organelle surface where it controls the recruitment of the E3-ubiquitin ligase Parkin. On mitochondria, Parkin ubiquitinates a subset of mitochondrial-resident proteins located on the outer mitochondrial membrane, leading to the recruitment of downstream cytosolic autophagic adaptors and subsequent autophagosome formation. Importantly, PINK1/Parkin-independent mitophagy pathways also exist that can be counteracted by specific deubiquitinating enzymes (DUBs). Down-regulation of these specific DUBs can presumably enhance basal mitophagy and be beneficial in models in which the accumulation of defective mitochondria is implicated. Among these DUBs, USP8 is an interesting target because of its role in the endosomal pathway and autophagy and its beneficial effects, when inhibited, in models of neurodegeneration. Based on this, we evaluated autophagy and mitophagy levels when USP8 activity is altered. We used genetic approaches in D. melanogaster to measure autophagy and mitophagy in vivo and complementary in vitro approaches to investigate the molecular pathway that regulates mitophagy via USP8. We found an inverse correlation between basal mitophagy and USP8 levels, in that down-regulation of USP8 correlates with increased Parkin-independent mitophagy. These results suggest the existence of a yet uncharacterized mitophagic pathway that is inhibited by USP8.
    Keywords:  DUBs; Parkin; USP8; autophagy; mitophagy
    DOI:  https://doi.org/10.3390/cells12081143
  3. Cells. 2023 05 05. pii: 1322. [Epub ahead of print]12(9):
    Role of Macroautophagy in Mammalian Male Reproductive Physiology.
    Doaa Kirat, Ahmed Mohamed Alahwany, Ahmed Hamed Arisha, Adel Abdelkhalek, Taku Miyasho.
      Physiologically, autophagy is an evolutionarily conserved and self-degradative process in cells. Autophagy carries out normal physiological roles throughout mammalian life. Accumulating evidence shows autophagy as a mechanism for cellular growth, development, differentiation, survival, and homeostasis. In male reproductive systems, normal spermatogenesis and steroidogenesis need a balance between degradation and energy supply to preserve cellular metabolic homeostasis. The main process of autophagy includes the formation and maturation of the phagophore, autophagosome, and autolysosome. Autophagy is controlled by a group of autophagy-related genes that form the core machinery of autophagy. Three types of autophagy mechanisms have been discovered in mammalian cells: macroautophagy, microautophagy, and chaperone-mediated autophagy. Autophagy is classified as non-selective or selective. Non-selective macroautophagy randomly engulfs the cytoplasmic components in autophagosomes that are degraded by lysosomal enzymes. While selective macroautophagy precisely identifies and degrades a specific element, current findings have shown the novel functional roles of autophagy in male reproduction. It has been recognized that dysfunction in the autophagy process can be associated with male infertility. Overall, this review provides an overview of the cellular and molecular basics of autophagy and summarizes the latest findings on the key role of autophagy in mammalian male reproductive physiology.
    Keywords:  Leydig cells; Sertoli cells; bulk autophagy; germ cells; selective autophagy; spermatogenesis; steroidogenesis; testis; testosterone
    DOI:  https://doi.org/10.3390/cells12091322
  4. J Mol Biol. 2023 May 12. pii: S0022-2836(23)00222-X. [Epub ahead of print] 168144
    Role of autophagy pathway in Parkinson's disease and related Genetic Neurological disorders.
    Christos Themistokleous, Enrico Bagnoli, Ramaa Parulekar, Miratul M K Muqit.
      The elucidation of the function of the PINK1 protein kinase and Parkin ubiquitin E3 ligase in the elimination of damaged mitochondria by autophagy (mitophagy) has provided unprecedented understanding of the mechanistic pathways underlying Parkinson's disease (PD). We provide a comprehensive overview of the general importance of autophagy in Parkinson's disease and related disorders of the central nervous system. This reveals a critical link between autophagy and neurodegenerative and neurodevelopmental disorders and suggests that strategies to modulate mitophagy may have greater relevance in the CNS beyond PD.
    Keywords:  PINK1; Parkin; Parkinson’s disease; autophagy; mitophagy
    DOI:  https://doi.org/10.1016/j.jmb.2023.168144
  5. J Cell Sci. 2023 May 15. pii: jcs260631. [Epub ahead of print]136(10):
    Regulation of autophagy gene expression and its implications in cancer.
    Shree Padma Metur, Yuchen Lei, Zhihai Zhang, Daniel J Klionsky.
      Autophagy is a catabolic cellular process that targets and eliminates superfluous cytoplasmic components via lysosomal degradation. This evolutionarily conserved process is tightly regulated at multiple levels as it is critical for the maintenance of homeostasis. Research in the past decade has established that dysregulation of autophagy plays a major role in various diseases, such as cancer and neurodegeneration. However, modulation of autophagy as a therapeutic strategy requires identification of key players that can fine tune the induction of autophagy without complete abrogation. In this Review, we summarize the recent discoveries on the mechanism of regulation of ATG (autophagy related) gene expression at the level of transcription, post transcription and translation. Furthermore, we briefly discuss the role of aberrant expression of ATG genes in the context of cancer.
    Keywords:  Post-translational modification; Transcription; Translation
    DOI:  https://doi.org/10.1242/jcs.260631
  6. Mol Cell. 2023 May 06. pii: S1097-2765(23)00316-7. [Epub ahead of print]
    The mitochondrial intermembrane space protein mitofissin drives mitochondrial fission required for mitophagy.
    Tomoyuki Fukuda, Kentaro Furukawa, Tatsuro Maruyama, Shun-Ichi Yamashita, Daisuke Noshiro, Chihong Song, Yuta Ogasawara, Kentaro Okuyama, Jahangir Md Alam, Manabu Hayatsu, Tetsu Saigusa, Keiichi Inoue, Kazuho Ikeda, Akira Takai, Lin Chen, Vikramjit Lahiri, Yasushi Okada, Shinsuke Shibata, Kazuyoshi Murata, Daniel J Klionsky, Nobuo N Noda, Tomotake Kanki.
      Mitophagy plays an important role in mitochondrial homeostasis by selective degradation of mitochondria. During mitophagy, mitochondria should be fragmented to allow engulfment within autophagosomes, whose capacity is exceeded by the typical mitochondria mass. However, the known mitochondrial fission factors, dynamin-related proteins Dnm1 in yeasts and DNM1L/Drp1 in mammals, are dispensable for mitophagy. Here, we identify Atg44 as a mitochondrial fission factor that is essential for mitophagy in yeasts, and we therefore term Atg44 and its orthologous proteins mitofissin. In mitofissin-deficient cells, a part of the mitochondria is recognized by the mitophagy machinery as cargo but cannot be enwrapped by the autophagosome precursor, the phagophore, due to a lack of mitochondrial fission. Furthermore, we show that mitofissin directly binds to lipid membranes and brings about lipid membrane fragility to facilitate membrane fission. Taken together, we propose that mitofissin acts directly on lipid membranes to drive mitochondrial fission required for mitophagy.
    Keywords:  Atg44; autophagy; crystal structure analysis; dynamin-related protein; high-speed atomic force microscopy; mitochondria; mitochondrial fission; mitofissin; mitophagy; yeast
    DOI:  https://doi.org/10.1016/j.molcel.2023.04.022
  7. Dev Cell. 2023 May 09. pii: S1534-5807(23)00191-0. [Epub ahead of print]
    Integrated proteomics identifies p62-dependent selective autophagy of the supramolecular vault complex.
    Reo Kurusu, Yuki Fujimoto, Hideaki Morishita, Daisuke Noshiro, Shuhei Takada, Koji Yamano, Hideaki Tanaka, Ritsuko Arai, Shun Kageyama, Tomoko Funakoshi, Satoko Komatsu-Hirota, Hikari Taka, Saiko Kazuno, Yoshiki Miura, Masato Koike, Toshifumi Wakai, Satoshi Waguri, Nobuo N Noda, Masaaki Komatsu.
      In addition to membranous organelles, autophagy selectively degrades biomolecular condensates, in particular p62/SQSTM1 bodies, to prevent diseases including cancer. Evidence is growing regarding the mechanisms by which autophagy degrades p62 bodies, but little is known about their constituents. Here, we established a fluorescence-activated-particle-sorting-based purification method for p62 bodies using human cell lines and determined their constituents by mass spectrometry. Combined with mass spectrometry of selective-autophagy-defective mouse tissues, we identified vault, a large supramolecular complex, as a cargo within p62 bodies. Mechanistically, major vault protein directly interacts with NBR1, a p62-interacting protein, to recruit vault into p62 bodies for efficient degradation. This process, named vault-phagy, regulates homeostatic vault levels in vivo, and its impairment may be associated with non-alcoholic-steatohepatitis-derived hepatocellular carcinoma. Our study provides an approach to identifying phase-separation-mediated selective autophagy cargoes, expanding our understanding of the role of phase separation in proteostasis.
    Keywords:  Mallory-Denk body; NBR1; fluorescence-activated particle sorting; hepatocellular carcinoma; liquid-liquid phase separation; non-alcoholic steatohepatitis; p62/SQSTM1; selective autophagy; vault; vault-phagy
    DOI:  https://doi.org/10.1016/j.devcel.2023.04.015
  8. Mol Cell. 2023 May 18. pii: S1097-2765(23)00292-7. [Epub ahead of print]83(10): 1693-1709.e9
    Unconventional initiation of PINK1/Parkin mitophagy by Optineurin.
    Thanh Ngoc Nguyen, Justyna Sawa-Makarska, Grace Khuu, Wai Kit Lam, Elias Adriaenssens, Dorotea Fracchiolla, Stephen Shoebridge, Daniel Bernklau, Benjamin Scott Padman, Marvin Skulsuppaisarn, Runa S J Lindblom, Sascha Martens, Michael Lazarou.
      Cargo sequestration is a fundamental step of selective autophagy in which cells generate a double-membrane structure termed an "autophagosome" on the surface of cargoes. NDP52, TAX1BP1, and p62 bind FIP200, which recruits the ULK1/2 complex to initiate autophagosome formation on cargoes. How OPTN initiates autophagosome formation during selective autophagy remains unknown despite its importance in neurodegeneration. Here, we uncover an unconventional path of PINK1/Parkin mitophagy initiation by OPTN that does not begin with FIP200 binding or require the ULK1/2 kinases. Using gene-edited cell lines and in vitro reconstitutions, we show that OPTN utilizes the kinase TBK1, which binds directly to the class III phosphatidylinositol 3-kinase complex I to initiate mitophagy. During NDP52 mitophagy initiation, TBK1 is functionally redundant with ULK1/2, classifying TBK1's role as a selective autophagy-initiating kinase. Overall, this work reveals that OPTN mitophagy initiation is mechanistically distinct and highlights the mechanistic plasticity of selective autophagy pathways.
    Keywords:  OPTN; PINK1; Parkin; TBK1; autophagosome; autophagy; selective autophagy
    DOI:  https://doi.org/10.1016/j.molcel.2023.04.021
  9. Inflamm Regen. 2023 May 12. 43(1): 28
    The Ragulator complex: delving its multifunctional impact on metabolism and beyond.
    Kohei Tsujimoto, Hyota Takamatsu, Atsushi Kumanogoh.
      Our understanding of lysosomes has undergone a significant transformation in recent years, from the view that they are static organelles primarily responsible for the disposal and recycling of cellular waste to their recognition as highly dynamic structures. Current research posits that lysosomes function as a signaling hub that integrates both extracellular and intracellular stimuli, thereby regulating cellular homeostasis. The dysregulation of lysosomal function has been linked to a wide range of diseases. Of note, lysosomes contribute to the activation of mammalian target of rapamycin complex 1 (mTORC1), a key regulator of cellular metabolism. The Ragulator complex, a protein complex anchored on the lysosomal membrane, was initially shown to tether the mTORC1 complex to lysosomes. Recent research has substantially expanded our understanding of the roles of the Ragulator complex in lysosomes, including roles in the regulation of metabolism, inflammation, cell death, cell migration, and the maintenance of homeostasis, via interactions with various proteins. This review summarizes our current knowledge on the diverse functions of the Ragulator complex, highlighting important protein interactions.
    Keywords:  Inflammation; LAMTOR; Lysosomes; The Ragulator complex; mTORC1
    DOI:  https://doi.org/10.1186/s41232-023-00278-2
  10. Int J Mol Sci. 2023 May 05. pii: 8289. [Epub ahead of print]24(9):
    Distinct Signaling Pathways for Autophagy-Driven Cell Death and Survival in Adult Hippocampal Neural Stem Cells.
    Seol-Hwa Jeong, Hyun-Kyu An, Shinwon Ha, Seong-Woon Yu.
      Autophagy is a cellular catabolic process that degrades and recycles cellular materials. Autophagy is considered to be beneficial to the cell and organism by preventing the accumulation of toxic protein aggregates, removing damaged organelles, and providing bioenergetic substrates that are necessary for survival. However, autophagy can also cause cell death depending on cellular contexts. Yet, little is known about the signaling pathways that differentially regulate the opposite outcomes of autophagy. We have previously reported that insulin withdrawal (IW) or corticosterone (CORT) induces autophagic cell death (ACD) in adult hippocampal neural stem (HCN) cells. On the other hand, metabolic stresses caused by 2-deoxy-D-glucose (2DG) and glucose-low (GL) induce autophagy without death in HCN cells. Rather, we found that 2DG-induced autophagy was cytoprotective. By comparing IW and CORT conditions with 2DG treatment, we revealed that ERK and JNK are involved with 2DG-induced protective autophagy, whereas GSK-3β regulates death-inducing autophagy. These data suggest that cell death and survival-promoting autophagy undergo differential regulation with distinct signaling pathways in HCN cells.
    Keywords:  ERK; GSK-3β; JNK; adult hippocampal neural stem cells; autophagic cell death; autophagy
    DOI:  https://doi.org/10.3390/ijms24098289
  11. Front Aging Neurosci. 2022 ;14 1100133
    Role of microglia autophagy and mitophagy in age-related neurodegenerative diseases.
    Mingkai Lin, Hongwen Yu, Qiuyan Xie, Zhiyun Xu, Pei Shang.
      Microglia, characterized by responding to damage, regulating the secretion of soluble inflammatory mediators, and engulfing specific segments in the central nervous system (CNS), function as key immune cells in the CNS. Emerging evidence suggests that microglia coordinate the inflammatory responses in CNS system and play a pivotal role in the pathogenesis of age-related neurodegenerative diseases (NDDs). Remarkably, microglia autophagy participates in the regulation of subcellular substances, which includes the degradation of misfolded proteins and other harmful constituents produced by neurons. Therefore, microglia autophagy regulates neuronal homeostasis maintenance and process of neuroinflammation. In this review, we aimed at highlighting the pivotal role of microglia autophagy in the pathogenesis of age-related NDDs. Besides the mechanistic process and the co-interaction between microglia autophagy and different kinds of NDDs, we also emphasized potential therapeutic agents and approaches that could be utilized at the onset and progression of these diseases through modulating microglia autophagy, including promising nanomedicines. Our review provides a valuable reference for subsequent studies focusing on treatments of neurodegenerative disorders. The exploration of microglia autophagy and the development of nanomedicines greatly enhances current understanding of NDDs.
    Keywords:  autophagy; microglia; nanomedicines; neurodegenerative diseases (NDDs); neuroinflammation
    DOI:  https://doi.org/10.3389/fnagi.2022.1100133
  12. Aging Dis. 2023 Jun 01. 14(3): 652-669
    Novel Insight into Functions of Transcription Factor EB (TFEB) in Alzheimer's Disease and Parkinson's Disease.
    Jing Yang, Wei Zhang, Shugeng Zhang, Ashok Iyaswamy, Jichao Sun, Jigang Wang, Chuanbin Yang.
      A key pathological feature of neurodegenerative diseases (NDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD) is the accumulation of aggregated and misfolded protein aggregates with limited effective therapeutic agents. TFEB (transcription factor EB), a key regulator of lysosomal biogenesis and autophagy, plays a pivotal role in the degradation of protein aggregates and has thus been regarded as a promising therapeutic target for these NDs. Here, we systematically summarize the molecular mechanisms and function of TFEB regulation. We then discuss the roles of TFEB and autophagy-lysosome pathways in major neurodegenerative diseases including AD and PD. Finally, we illustrate small molecule TFEB activators with protective roles in NDs animal models, which show great potential for being further developed into novel anti-neurodegenerative agents. Overall, targeting TFEB for enhancing lysosomal biogenesis and autophagy may represent a promising opportunity for the discovery of disease-modifying therapeutics for neurodegenerative disorders though more in-depth basic and clinical studies are required in the future.
    DOI:  https://doi.org/10.14336/AD.2022.0927
  13. Biochem Biophys Res Commun. 2023 Apr 28. pii: S0006-291X(23)00536-3. [Epub ahead of print]667 1-9
    Maintenance of cathepsin D-dependent autophagy-lysosomal function protects against cardiac ischemia/reperfusion injury.
    Qizhen Zhuang, Yang Zhang, Yanting Zhu, Lina He, Chunmin Kang, Peifeng Ke, Haibiao Lin, Yujuan Xiong, Xianzhang Huang.
      Cardiac ischemia/reperfusion(I/R) induced-cardiac vascular endothelial injury is an important pathological process that appears in the early stage of cardiac I/R injury. The autophagy-lysosomal pathway is essential for the maintenance of cellular homeostasis. However, in cardiac I/R injury, the role of the autophagy-lysosomal pathway is controversial. The present study aimed to use oxygen-glucose deprivation/oxygen-glucose resupply(OGD/OGR) in human coronary artery endothelial cells(HCAECs) with I/R injury to assess the role of the autophagy-lysosomal pathway in I/R-induced endothelial injury. The results revealed lysosomal dysfunction and impaired autophagic flux in endothelial cells exposed to OGD/OGR. Meanwhile, our data showed that the levels of cathepsin D(CTSD) decreased time-dependently. Knockdown of CTSD caused lysosomal dysfunction and impaired autophagic flux. Conversely, restoration of CTSD levels protected HCAECs against OGD/OGR induced-defects in autophagy-lysosomal function and cellular damage. Our findings indicated that I/R induced-impaired autophagic flux, rather than excessive autophagic initiation, mediates endothelial cells injury. The maintenance of autophagy-lysosomal function is critical to protect endothelial cells against I/R injury, and CTSD is a key regulator. Thus, strategies focused on restoring CTSD function are potentially novel treatments for cardiac reperfusion injury.
    Keywords:  Autophagy; Cathepsin D; Endothelial cells; Ischemia/reperfusion injury; Lysosome
    DOI:  https://doi.org/10.1016/j.bbrc.2023.04.105
  14. Autophagy. 2023 May 16.
    Hva22, a REEP family protein in fission yeast, promotes reticulophagy in collaboration with a receptor protein.
    Tomoyuki Fukuda, Tetsu Saigusa, Kentaro Furukawa, Keiichi Inoue, Shun-Ichi Yamashita, Tomotake Kanki.
      The endoplasmic reticulum (ER) undergoes selective autophagy called reticulophagy or ER-phagy. Multiple reticulon- and receptor expression enhancing protein (REEP)-like ER-shaping proteins, including budding yeast Atg40, serve as reticulophagy receptors that stabilize the phagophore on the ER by interacting with phagophore-conjugated Atg8. Additionally, they facilitate phagophore engulfment of the ER by remodeling ER morphology. We reveal that Hva22, a REEP family protein in fission yeast, promotes reticulophagy without Atg8-binding capacity. The role of Hva22 in reticulophagy can be replaced by expressing Atg40 independently of its Atg8-binding ability. Conversely, adding an Atg8-binding sequence to Hva22 enables it to substitute for Atg40 in budding yeast. Thus, the phagophore-stabilizing and ER-shaping activities, both of which Atg40 solely contains, are divided between two separate factors, receptors and Hva22, respectively, in fission yeast.
    Keywords:  Atg40; ER-phagy; ER-shaping; Hva22; REEP; autophagy; endoplasmic reticulum (ER); reticulon; reticulophagy; yeasts
    DOI:  https://doi.org/10.1080/15548627.2023.2214029
  15. Oxid Med Cell Longev. 2023 ;2023 8257217
    Autophagy and Its Lineage-Specific Roles in the Hematopoietic System.
    Kazi Md Mahmudul Hasan, Md Anwarul Haque.
      Autophagy is a dynamic process that regulates the selective and nonselective degradation of cytoplasmic components, such as damaged organelles and protein aggregates inside lysosomes to maintain tissue homeostasis. Different types of autophagy including macroautophagy, microautophagy, and chaperon-mediated autophagy (CMA) have been implicated in a variety of pathological conditions, such as cancer, aging, neurodegeneration, and developmental disorders. Furthermore, the molecular mechanism and biological functions of autophagy have been extensively studied in vertebrate hematopoiesis and human blood malignancies. In recent years, the hematopoietic lineage-specific roles of different autophagy-related (ATG) genes have gained more attention. The evolution of gene-editing technology and the easy access nature of hematopoietic stem cells (HSCs), hematopoietic progenitors, and precursor cells have facilitated the autophagy research to better understand how ATG genes function in the hematopoietic system. Taking advantage of the gene-editing platform, this review has summarized the roles of different ATGs at the hematopoietic cell level, their dysregulation, and pathological consequences throughout hematopoiesis.
    DOI:  https://doi.org/10.1155/2023/8257217
  16. Nat Commun. 2023 May 15. 14(1): 2775
    RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome.
    Irene Sambri, Marco Ferniani, Giulia Campostrini, Marialuisa Testa, Viviana Meraviglia, Mariana E G de Araujo, Ladislav Dokládal, Claudia Vilardo, Jlenia Monfregola, Nicolina Zampelli, Francesca Del Vecchio Blanco, Annalaura Torella, Carolina Ruosi, Simona Fecarotta, Giancarlo Parenti, Leopoldo Staiano, Milena Bellin, Lukas A Huber, Claudio De Virgilio, Francesco Trepiccione, Vincenzo Nigro, Andrea Ballabio.
      Heterozygous mutations in the gene encoding RagD GTPase were shown to cause a novel autosomal dominant condition characterized by kidney tubulopathy and cardiomyopathy. We previously demonstrated that RagD, and its paralogue RagC, mediate a non-canonical mTORC1 signaling pathway that inhibits the activity of TFEB and TFE3, transcription factors of the MiT/TFE family and master regulators of lysosomal biogenesis and autophagy. Here we show that RagD mutations causing kidney tubulopathy and cardiomyopathy are "auto- activating", even in the absence of Folliculin, the GAP responsible for RagC/D activation, and cause constitutive phosphorylation of TFEB and TFE3 by mTORC1, without affecting the phosphorylation of "canonical" mTORC1 substrates, such as S6K. By using HeLa and HK-2 cell lines, human induced pluripotent stem cell-derived cardiomyocytes and patient-derived primary fibroblasts, we show that RRAGD auto-activating mutations lead to inhibition of TFEB and TFE3 nuclear translocation and transcriptional activity, which impairs the response to lysosomal and mitochondrial injury. These data suggest that inhibition of MiT/TFE factors plays a key role in kidney tubulopathy and cardiomyopathy syndrome.
    DOI:  https://doi.org/10.1038/s41467-023-38428-2
  17. Food Chem Toxicol. 2023 May 10. pii: S0278-6915(23)00220-X. [Epub ahead of print]177 113818
    Acrylamide interferes with autophagy and induces apoptosis in Neuro-2a cells by interfering with TFEB-regulated lysosomal function.
    Pengcheng Pang, Xing Zhang, Jingping Yuan, Hong Yan, Dandan Yan.
      Acrylamide (ACR), a well-documented human neurotoxicant that is widely exists in starchy foods. More than 30% of human daily energy is provided by ACR-containing foods. Evidence indicated that ACR can induce apoptosis and inhibit autophagy, but the mechanisms are limited. Transcription Factor EB (TFEB) is a major transcriptional regulator of the autophagy-lysosomal biogenesis that regulates autophagy processes and cell degradation. Our study aimed to investigated the potential mechanisms of TFEB-regulated lysosomal function in ACR-caused autophagic flux inhibition and apoptosis in Neuro-2a cells. Our results found that ACR exposure inhibited the autophagic flux, as revealed by the elevated LC3-II/LC3-I and p62 levels and a notable increased autophagosomes. ACR exposure reduced the amounts of LAMP1 and mature cathepsin D and caused an accumulation of ubiquitinated proteins, which suggests lysosomal dysfunction. In addition, ACR increased cellular apoptosis via decreasing Bcl-2 expression, increasing Bax and cleaved caspase-3 expression, and raising the apoptotic rate. Interestingly, TFEB overexpression alleviated the ACR-induced lysosomal dysfunction, and then mitigated the autophagy flux inhibition and cellular apoptosis. On the other hand, TFEB knockdown exacerbated the ACR-induced lysosomal dysfunction, autophagy flux inhibition, and cellular apoptosis. These findings strongly suggested that TFEB- regulated lysosomal function is responsible for ACR-caused autophagic flux inhibition and apoptosis in Neuro-2a cells. The present study hopes to explore new sensitive indicators in the mechanism of ACR neurotoxicity and thus provide new targets for the prevention and treatment of ACR intoxication.
    Keywords:  Acrylamide; Apoptosis; Autophagy; Lysosomal function; Transcription factor EB
    DOI:  https://doi.org/10.1016/j.fct.2023.113818
  18. Cells. 2023 04 11. pii: 1132. [Epub ahead of print]12(8):
    Membrane Curvature: The Inseparable Companion of Autophagy.
    Lei Liu, Yu Tang, Zijuan Zhou, Yuan Huang, Rui Zhang, Hao Lyu, Shuai Xiao, Dong Guo, Declan William Ali, Marek Michalak, Xing-Zhen Chen, Cefan Zhou, Jingfeng Tang.
      Autophagy is a highly conserved recycling process of eukaryotic cells that degrades protein aggregates or damaged organelles with the participation of autophagy-related proteins. Membrane bending is a key step in autophagosome membrane formation and nucleation. A variety of autophagy-related proteins (ATGs) are needed to sense and generate membrane curvature, which then complete the membrane remodeling process. The Atg1 complex, Atg2-Atg18 complex, Vps34 complex, Atg12-Atg5 conjugation system, Atg8-phosphatidylethanolamine conjugation system, and transmembrane protein Atg9 promote the production of autophagosomal membranes directly or indirectly through their specific structures to alter membrane curvature. There are three common mechanisms to explain the change in membrane curvature. For example, the BAR domain of Bif-1 senses and tethers Atg9 vesicles to change the membrane curvature of the isolation membrane (IM), and the Atg9 vesicles are reported as a source of the IM in the autophagy process. The amphiphilic helix of Bif-1 inserts directly into the phospholipid bilayer, causing membrane asymmetry, and thus changing the membrane curvature of the IM. Atg2 forms a pathway for lipid transport from the endoplasmic reticulum to the IM, and this pathway also contributes to the formation of the IM. In this review, we introduce the phenomena and causes of membrane curvature changes in the process of macroautophagy, and the mechanisms of ATGs in membrane curvature and autophagosome membrane formation.
    Keywords:  Atg proteins; ER-phagy; autophagy; membrane curvature; nucleophagy; xenophagy
    DOI:  https://doi.org/10.3390/cells12081132
  19. Int J Mol Sci. 2023 Apr 28. pii: 7973. [Epub ahead of print]24(9):
    Autophagy in Cancer Progression and Therapeutics.
    Kamilla Kantserova, Ilya Ulasov.
      Autophagy is a catabolic process that is necessary for cellular homeostasis maintenance [...].
    DOI:  https://doi.org/10.3390/ijms24097973
  20. Cancer Res. 2023 May 17. pii: CAN-22-3032. [Epub ahead of print]
    The mTOR Signaling Pathway Interacts with the ER Stress Response and the Unfolded Protein Response in Cancer.
    Sahar Mafi, Elham Ahmadi, Eileen Meehan, Conner Chiari, Behzad Mansoori, Hossein Sadeghi, Sahar Milani, Morteza Jafarinia, Shahram Taeb, Bayan Mafakheri Bashmagh, Seyed Mohammad Ali Mansoorian, Mohammad Sadegh Soltani-Zangbar, Kepeng Wang, Davoud Rostamzadeh.
      The mTOR complex 1 (mTORC1) coordinates several important environmental and intracellular cues to control a variety of biological processes, such as cell growth, survival, autophagy, and metabolism in response to energy levels, growth signals, and nutrients. The endoplasmic reticulum (ER) is a crucial intracellular organelle that is essential for numerous cellular functions, including the synthesis, folding and modification of newly synthesized proteins, stress responsiveness, and maintainence of cellular homeostasis. mTOR-mediated upregulation of protein synthesis induces the accumulation of misfolded or unfolded proteins in the ER lumen which induces ER stress, leading to activation of the unfolded protein response (UPR) pathway. Reciprocally, ER stress regulates the PI3K/AKT/mTOR signaling pathway. Therefore, under pathological conditions, the crosstalk between the mTOR and UPR signaling pathways during cellular stress can critically affect cancer cell fate and may be involved in the pathogenesis and therapeutic outcome of cancer. Here, we discuss accumulating evidence showing the mechanism of action, interconnections, and molecular links between mTOR signaling and ER stress in tumorigenesis and highlight potential therapeutic implications for numerous cancers.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-3032
  21. J Adv Res. 2023 May 14. pii: S2090-1232(23)00140-6. [Epub ahead of print]
    Modulating autophagy to treat diseases: A revisited review on in silico methods.
    Lifeng Wu, Wenke Jin, Haiyang Yu, Bo Liu.
       BACKGROUND: Autophagy refers to the conserved cellular catabolic process relevant to lysosome activity and plays a vital role in maintaining the dynamic equilibrium of intracellular matter by degrading harmful and abnormally accumulated cellular components. Accumulating evidence has recently revealed that dysregulation of autophagy by genetic and exogenous interventions may disrupt cellular homeostasis in human diseases. In silico approaches as powerful aids to experiments have also been extensively reported to play their critical roles in the storage, prediction, and analysis of massive amounts of experimental data. Thus, modulating autophagy to treat diseases by in silico methods would be anticipated.
    AIM OF REVIEW: Here, we focus on summarizing the updated in silico approaches including databases, systems biology network approaches, omics-based analyses, mathematical models, and artificial intelligence (AI) methods that sought to modulate autophagy for potential therapeutic purposes, which will provide a new insight into more promising therapeutic strategies.
    KEY SCIENTIFIC CONCEPTS OF REVIEW: Autophagy-related databases are the data basis of the in silico method, storing a large amount of information about DNA, RNA, proteins, small molecules and diseases. The systems biology approach is a method to systematically study the interrelationships among biological processes including autophagy from a macroscopic perspective. Omics-based analyses are based on high-throughput data to analyze gene expression at different levels of biological processes involving autophagy. mathematical models are visualization methods to describe the dynamic process of autophagy, and its accuracy is related to the selection of parameters. AI methods use big data related to autophagy to predict autophagy targets, design targeted small molecules, and classify diverse human diseases for potential therapeutic applications.
    Keywords:  Artificial intelligence (AI); Autophagy; Database; Human disease; Mathematical model; Omics-based analysis; Systems biology approach; Therapeutic strategy
    DOI:  https://doi.org/10.1016/j.jare.2023.05.002
  22. Autophagy. 2023 Feb 22. 1-14
    Identifying a selective inhibitor of autophagy that targets ATG12-ATG3 protein-protein interaction.
    Gal Chaim Nuta, Yuval Gilad, Nadav Goldberg, Sara Meril, Marcela Bahlsen, Silvia Carvalho, Noga Kozer, Haim Barr, Yael Fridmann Sirkis, Kamil Hercík, Petra Břehová, Radim Nencka, Shani Bialik, Miriam Eisenstein, Adi Kimchi.
      Macroautophagy/autophagy is a catabolic process by which cytosolic content is engulfed, degraded and recycled. It has been implicated as a critical pathway in advanced stages of cancer, as it maintains tumor cell homeostasis and continuous growth by nourishing hypoxic or nutrient-starved tumors. Autophagy also supports alternative cellular trafficking pathways, providing a mechanism of non-canonical secretion of inflammatory cytokines. This opens a significant therapeutic opportunity for using autophagy inhibitors in cancer and acute inflammatory responses. Here we developed a high throughput compound screen to identify inhibitors of protein-protein interaction (PPI) in autophagy, based on the protein-fragment complementation assay (PCA). We chose to target the ATG12-ATG3 PPI, as this interaction is indispensable for autophagosome formation, and the analyzed structure of the interaction interface predicts that it may be amenable to inhibition by small molecules. We screened 41,161 compounds yielding 17 compounds that effectively inhibit the ATG12-ATG3 interaction in the PCA platform, and which were subsequently filtered by their ability to inhibit autophagosome formation in viable cells. We describe a lead compound (#189) that inhibited GFP-fused MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) puncta formation in cells with IC50 value corresponding to 9.3 μM. This compound displayed a selective inhibitory effect on the growth of autophagy addicted tumor cells and inhibited secretion of IL1B/IL-1β (interleukin 1 beta) by macrophage-like cells. Compound 189 has the potential to be developed into a therapeutic drug and its discovery documents the power of targeting PPIs for acquiring specific and selective compound inhibitors of autophagy.Abbreviations: ANOVA: analysis of variance; ATG: autophagy related; CQ: chloroquine; GFP: green fluorescent protein; GLuc: Gaussia Luciferase; HEK: human embryonic kidney; IL1B: interleukin 1 beta; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; PCA: protein-fragment complementation assay; PDAC: pancreatic ductal adenocarcinoma; PMA: phorbol 12-myristate 13-acetate; PPI: protein-protein interaction. VCL: vinculin.
    Keywords:  Autophagy inhibition; LC3B; cancer; drug screen; pancreatic cancer; protein-fragment complementation assay; small molecules
    DOI:  https://doi.org/10.1080/15548627.2023.2178159
  23. J Vis Exp. 2023 Apr 28.
    Evaluating Autophagy Levels in Two Different Pancreatic Cell Models Using LC3 Immunofluorescence.
    Felipe J Renna, Malena Herrera Lopez, Maria Manifava, Nicholas T Ktistakis, Maria I Vaccaro.
      Autophagy is a specialized catabolic process that selectively degrades cytoplasmic components, including proteins and damaged organelles. Autophagy allows cells to physiologically respond to stress stimuli and, thus, maintain cellular homeostasis. Cancer cells might modulate their autophagy levels to adapt to adverse conditions such as hypoxia, nutrient deficiency, or damage caused by chemotherapy. Ductal pancreatic adenocarcinoma is one of the deadliest types of cancer. Pancreatic cancer cells have high autophagy activity due to the transcriptional upregulation and post-translational activation of autophagy proteins. Here, the PANC-1 cell line was used as a model of pancreatic human cancer cells, and the AR42J pancreatic acinar cell line was used as a physiological model of highly differentiated mammalian cells. This study used the immunofluorescence of microtubule-associated protein light chain 3 (LC3) as an indicator of the status of autophagy activation. LC3 is an autophagy protein that, in basal conditions, shows a diffuse pattern of distribution in the cytoplasm (known as LC3-I in this condition). Autophagy induction triggers the conjugation of LC3 to phosphatidylethanolamine on the surface of newly formed autophagosomes to form LC3-II, a membrane-bound protein that aids in the formation and expansion of autophagosomes. To quantify the number of labeled autophagic structures, the open-source software FIJI was utilized with the aid of the "3D Objects Counter" tool. The measure of the autophagic levels both in physiological conditions and in cancer cells allows us to study the modulation of autophagy under diverse conditions such as hypoxia, chemotherapy treatment, or the knockdown of certain proteins.
    DOI:  https://doi.org/10.3791/65005
  24. Cells. 2023 04 20. pii: 1197. [Epub ahead of print]12(8):
    Fyn Phosphorylates Transglutaminase 2 (Tgm2) and Modulates Autophagy and p53 Expression in the Development of Diabetic Kidney Disease.
    Ryota Uehara, Eijiro Yamada, Shuichi Okada, Claire C Bastie, Akito Maeshima, Hidekazu Ikeuchi, Kazuhiko Horiguchi, Masanobu Yamada.
      Autophagy is involved in the development of diabetic kidney disease (DKD), the leading cause of end-stage renal disease. The Fyn tyrosine kinase (Fyn) suppresses autophagy in the muscle. However, its role in kidney autophagic processes is unclear. Here, we examined the role of Fyn kinase in autophagy in proximal renal tubules both in vivo and in vitro. Phospho-proteomic analysis revealed that transglutaminase 2 (Tgm2), a protein involved in the degradation of p53 in the autophagosome, is phosphorylated on tyrosine 369 (Y369) by Fyn. Interestingly, we found that Fyn-dependent phosphorylation of Tgm2 regulates autophagy in proximal renal tubules in vitro, and that p53 expression is decreased upon autophagy in Tgm2-knockdown proximal renal tubule cell models. Using streptozocin (STZ)-induced hyperglycemic mice, we confirmed that Fyn regulated autophagy and mediated p53 expression via Tgm2. Taken together, these data provide a molecular basis for the role of the Fyn-Tgm2-p53 axis in the development of DKD.
    Keywords:  autophagy; diabetic; end-stage renal disease; hyperglycemia; kidney
    DOI:  https://doi.org/10.3390/cells12081197
  25. Front Pharmacol. 2023 ;14 1206291
    Editorial: Emerging mechanistic insights of selective and Nonselective Autophagy in liver and gut diseases and their treatment strategies in the era of COVID-19.
    Md Abdul Alim Al-Bari, Manoj B Menon, Nabil Eid.
      
    Keywords:  COVID-19; autophagy; lipophagy; liver diseases; mitophagy; xenophagy
    DOI:  https://doi.org/10.3389/fphar.2023.1206291
  26. Biomed Pharmacother. 2023 May 17. pii: S0753-3322(23)00695-9. [Epub ahead of print]163 114905
    Therapeutic potential of natural compounds from herbs and nutraceuticals in spinal cord injury: Regulation of the mTOR signaling pathway.
    Yan Du, Xue Cai.
      Spinal cord injury (SCI) is a disease in which the spinal cord is subjected to various external forces that cause it to burst, shift, or, in severe cases, injure the spinal tissue, resulting in nerve injury. SCI includes not only acute primary injury but also delayed and persistent spinal tissue injury (i.e., secondary injury). The pathological changes post-SCI are complex, and effective clinical treatment strategies are lacking. The mammalian target of rapamycin (mTOR) coordinates the growth and metabolism of eukaryotic cells in response to various nutrients and growth factors. The mTOR signaling pathway has multiple roles in the pathogenesis of SCI. There is evidence for the beneficial effects of natural compounds and nutraceuticals that regulate the mTOR signaling pathways in a variety of diseases. Therefore, the effects of natural compounds on the pathogenesis of SCI were evaluated by a comprehensive review using electronic databases, such as PubMed, Web of Science, Scopus, and Medline, combined with our expertise in neuropathology. In particular, we reviewed the pathogenesis of SCI, including the importance of secondary nerve injury after the primary mechanical injury, the roles of the mTOR signaling pathways, and the beneficial effects and mechanisms of natural compounds that regulate the mTOR signaling pathway on pathological changes post-SCI, including effects on inflammation, neuronal apoptosis, autophagy, nerve regeneration, and other pathways. This recent research highlights the value of natural compounds in regulating the mTOR pathway, providing a basis for developing novel therapeutic strategies for SCI.
    Keywords:  Apoptosis; Autophagy; MTOR signaling pathways; Natural compounds; Spinal cord injury
    DOI:  https://doi.org/10.1016/j.biopha.2023.114905
  27. J Zhejiang Univ Sci B. 2023 May 15. pii: 1673-1581(2023)05-0397-09. [Epub ahead of print]24(5): 397-405
    Dichloroacetic acid and rapamycin synergistically inhibit tumor progression.
    Huan Chen, Kunming Liang, Cong Hou, Hai-Long Piao.
      Mammalian target of rapamycin (mTOR) controls cellular anabolism, and mTOR signaling is hyperactive in most cancer cells. As a result, inhibition of mTOR signaling benefits cancer patients. Rapamycin is a US Food and Drug Administration (FDA)-approved drug, a specific mTOR complex 1 (mTORC1) inhibitor, for the treatment of several different types of cancer. However, rapamycin is reported to inhibit cancer growth rather than induce apoptosis. Pyruvate dehydrogenase complex (PDHc) is the gatekeeper for mitochondrial pyruvate oxidation. PDHc inactivation has been observed in a number of cancer cells, and this alteration protects cancer cells from senescence and nicotinamide adenine dinucleotide (NAD+‍) exhaustion. In this paper, we describe our finding that rapamycin treatment promotes pyruvate dehydrogenase E1 subunit alpha 1 (PDHA1) phosphorylation and leads to PDHc inactivation dependent on mTOR signaling inhibition in cells. This inactivation reduces the sensitivity of cancer cells' response to rapamycin. As a result, rebooting PDHc activity with dichloroacetic acid (DCA), a pyruvate dehydrogenase kinase (PDK) inhibitor, promotes cancer cells' susceptibility to rapamycin treatment in vitro and in vivo.
    Keywords:  Dichloroacetic acid (DCA); Mammalian target of rapamycin (mTOR); Pyruvate dehydrogenase E1 subunit alpha 1 (PDHA1); Rapamycin
    DOI:  https://doi.org/10.1631/jzus.B2200356
  28. Autophagy. 2023 May 16. 1-2
    SQSTM1/P62 promotes lysophagy via formation of liquid-like condensates maintained by HSP27.
    Elizabeth R Gallagher, Erika L F Holzbaur.
       ABBREVIATIONS: SQSTM1/p62: Sequestosome-1; HSP27: Heat shock protein 27; LLPS: liquid-liquid phase separation; iPSC: induced pluripotent stem cell; PB1: Phox and Bem1p; FRAP: fluorescence recovery after photo-bleaching; ATG: autophagy-related; ALS: amyotrophic lateral sclerosis.
    Keywords:  HSP27; Lysosomes; Sqstm1/P62; lysophagy; neurodegeneration; phase separation
    DOI:  https://doi.org/10.1080/15548627.2023.2210943
  29. Autophagy. 2023 May 14. 1-3
    From jeopardy champion to drug discovery; semantic similarity artificial intelligence.
    Natalia Moskal, G Angus McQuibban.
      We have employed artificial intelligence to streamline the small molecule drug screening pipeline and identified the cholesterol-reducing compound probucol in the process. Probucol augmented mitophagy and prevented loss of dopaminergic neurons in flies and zebrafish challenged with mitochondrial toxins. Further dissection of the mechanism of action led to the identification of ABCA1, the target of probucol, as a mitophagy modulator. Probucol treatment regulates lipid droplet dynamics during mitophagy and ABCA1 is required for these effects. Here we will summarize the combination of in silico and cell-based screening that led us to identify and characterize probucol as a compound that enhances mitophagy and include thoughts about future directions for the topics explored in our study.Abbreviations: ABCA1: ATP binding cassette transporter protein 1; ATP: Adenosine tri-phosphate; CCCP: carbonyl cyanide m-chlorophenylhydrazone; DsRed: Discosoma red; FDA: Food and drug administration; GFP: Green fluorescent protein; LAMP: lysosome-associated membrane glycoproteins; LD: Lipid droplet; PD: Parkinson's disease; PINK: PTEN-induced kinase.
    Keywords:  Artificial intelligence; Parkinson disease; drug repurposing; drug screening; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2023.2210995
  30. Cancers (Basel). 2023 Apr 07. pii: 2195. [Epub ahead of print]15(8):
    Regulation of Autophagy via Carbohydrate and Lipid Metabolism in Cancer.
    Javad Alizadeh, Mahboubeh Kavoosi, Navjit Singh, Shahrokh Lorzadeh, Amir Ravandi, Biniam Kidane, Naseer Ahmed, Fatima Mraiche, Michael R Mowat, Saeid Ghavami.
      Metabolic changes are an important component of tumor cell progression. Tumor cells adapt to environmental stresses via changes to carbohydrate and lipid metabolism. Autophagy, a physiological process in mammalian cells that digests damaged organelles and misfolded proteins via lysosomal degradation, is closely associated with metabolism in mammalian cells, acting as a meter of cellular ATP levels. In this review, we discuss the changes in glycolytic and lipid biosynthetic pathways in mammalian cells and their impact on carcinogenesis via the autophagy pathway. In addition, we discuss the impact of these metabolic pathways on autophagy in lung cancer.
    Keywords:  Bcl2 family protein; Warburg effect; ceramide metabolism; glycolysis; mitophagy; non-small cell lung carcinoma
    DOI:  https://doi.org/10.3390/cancers15082195
  31. Int J Mol Sci. 2023 May 04. pii: 8224. [Epub ahead of print]24(9):
    CLEC16A-An Emerging Master Regulator of Autoimmunity and Neurodegeneration.
    Rahul Pandey, Marina Bakay, Hakon Hakonarson.
      CLEC16A is emerging as an important genetic risk factor for several autoimmune disorders and for Parkinson disease (PD), opening new avenues for translational research and therapeutic development. While the exact role of CLEC16A in health and disease is still being elucidated, the gene plays a critical role in the regulation of autophagy, mitophagy, endocytosis, intracellular trafficking, immune function, and in biological processes such as insulin secretion and others that are important to cellular homeostasis. As shown in both human and animal modeling studies, CLEC16A hypofunction predisposes to both autoinflammatory phenotype and neurodegeneration. While the two are clearly related, further functional studies are needed to fully understand the mechanisms involved for optimized therapeutic interventions. Based on recent data, mitophagy-inducing drugs may be warranted, and such therapy should be tested in clinical trials as these drugs would tackle the underlying pathogenic mechanism (s) and could treat or prevent symptoms of autoimmunity and neurodegeneration in individuals with CLEC16A risk variants. Accordingly, interventions directed at reversing the dysregulated mitophagy and the consequences of loss of function of CLEC16A without activating other detrimental cellular pathways could present an effective therapy. This review presents the emerging role of CLEC16A in health and disease and provides an update on the disease processes that are attributed to variants located in the CLEC16A gene, which are responsible for autoimmune disorders and neurodegeneration with emphasis on how this information is being translated into practical and effective applications in the clinic.
    Keywords:  C-type lectin-like domain family 16A (CLEC16A) gene; CLEC16A; Parkinson’s disease (PD); autoimmunity; autophagy; genome-wide association studies (GWAS); mitophagy; neurodegeneration; suppressor of cytokine signaling 1 (SOCS1); susceptibility loci; type 1 diabetes (T1D)
    DOI:  https://doi.org/10.3390/ijms24098224
  32. Cell Insight. 2022 Jun;1(3): 100031
    Endomembrane remodeling in SARS-CoV-2 infection.
    Di Chen, Yan G Zhao, Hong Zhang.
      During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the viral proteins intimately interact with host factors to remodel the endomembrane system at various steps of the viral lifecycle. The entry of SARS-CoV-2 can be mediated by endocytosis-mediated internalization. Virus-containing endosomes then fuse with lysosomes, in which the viral S protein is cleaved to trigger membrane fusion. Double-membrane vesicles generated from the ER serve as platforms for viral replication and transcription. Virions are assembled at the ER-Golgi intermediate compartment and released through the secretory pathway and/or lysosome-mediated exocytosis. In this review, we will focus on how SARS-CoV-2 viral proteins collaborate with host factors to remodel the endomembrane system for viral entry, replication, assembly and egress. We will also describe how viral proteins hijack the host cell surveillance system-the autophagic degradation pathway-to evade destruction and benefit virus production. Finally, potential antiviral therapies targeting the host cell endomembrane system will be discussed.
    Keywords:  Autophagy; Coronavirus; DMV; Endocytosis; SARS-CoV-2
    DOI:  https://doi.org/10.1016/j.cellin.2022.100031
  33. Int J Mol Sci. 2023 Apr 25. pii: 7850. [Epub ahead of print]24(9):
    AI-Predicted mTOR Inhibitor Reduces Cancer Cell Proliferation and Extends the Lifespan of C. elegans.
    Tinka Vidovic, Alexander Dakhovnik, Oleksii Hrabovskyi, Michael R MacArthur, Collin Y Ewald.
      The mechanistic target of rapamycin (mTOR) kinase is one of the top drug targets for promoting health and lifespan extension. Besides rapamycin, only a few other mTOR inhibitors have been developed and shown to be capable of slowing aging. We used machine learning to predict novel small molecules targeting mTOR. We selected one small molecule, TKA001, based on in silico predictions of a high on-target probability, low toxicity, favorable physicochemical properties, and preferable ADMET profile. We modeled TKA001 binding in silico by molecular docking and molecular dynamics. TKA001 potently inhibits both TOR complex 1 and 2 signaling in vitro. Furthermore, TKA001 inhibits human cancer cell proliferation in vitro and extends the lifespan of Caenorhabditis elegans, suggesting that TKA001 is able to slow aging in vivo.
    Keywords:  AI drug discovery; C. elegans; cancer; longevity; mTOR; rapalog
    DOI:  https://doi.org/10.3390/ijms24097850
  34. Biomedicines. 2023 Apr 08. pii: 1130. [Epub ahead of print]11(4):
    Autoimmunity and Carcinogenesis: Their Relationship under the Umbrella of Autophagy.
    Györgyi Műzes, Ferenc Sipos.
      The immune system and autophagy share a functional relationship. Both innate and adaptive immune responses involve autophagy and, depending on the disease's origin and pathophysiology, it may have a detrimental or positive role on autoimmune disorders. As a "double-edged sword" in tumors, autophagy can either facilitate or impede tumor growth. The autophagy regulatory network that influences tumor progression and treatment resistance is dependent on cell and tissue types and tumor stages. The connection between autoimmunity and carcinogenesis has not been sufficiently explored in past studies. As a crucial mechanism between the two phenomena, autophagy may play a substantial role, though the specifics remain unclear. Several autophagy modifiers have demonstrated beneficial effects in models of autoimmune disease, emphasizing their therapeutic potential as treatments for autoimmune disorders. The function of autophagy in the tumor microenvironment and immune cells is the subject of intensive study. The objective of this review is to investigate the role of autophagy in the simultaneous genesis of autoimmunity and malignancy, shedding light on both sides of the issue. We believe our work will assist in the organization of current understanding in the field and promote additional research on this urgent and crucial topic.
    Keywords:  autoimmune disorders; autoimmunity; autophagy; carcinogenesis; immune system; treatment; tumor; tumor microenvironment
    DOI:  https://doi.org/10.3390/biomedicines11041130
  35. Cells. 2023 04 14. pii: 1156. [Epub ahead of print]12(8):
    Autophagy and Breast Cancer: Connected in Growth, Progression, and Therapy.
    Qitong Wu, Dipali Sharma.
      Despite an increase in the incidence of breast cancer worldwide, overall prognosis has been consistently improving owing to the development of multiple targeted therapies and novel combination regimens including endocrine therapies, aromatase inhibitors, Her2-targeted therapies, and cdk4/6 inhibitors. Immunotherapy is also being actively examined for some breast cancer subtypes. This overall positive outlook is marred by the development of resistance or reduced efficacy of the drug combinations, but the underlying mechanisms are somewhat unclear. It is interesting to note that cancer cells quickly adapt and evade most therapies by activating autophagy, a catabolic process designed to recycle damaged cellular components and provide energy. In this review, we discuss the role of autophagy and autophagy-associated proteins in breast cancer growth, drug sensitivity, tumor dormancy, stemness, and recurrence. We further explore how autophagy intersects and reduces the efficacy of endocrine therapies, targeted therapies, radiotherapy, chemotherapies as well as immunotherapy via modulating various intermediate proteins, miRs, and lncRNAs. Lastly, the potential application of autophagy inhibitors and bioactive molecules to improve the anticancer effects of drugs by circumventing the cytoprotective autophagy is discussed.
    Keywords:  autophagy; autophagy inhibitors; breast cancer; chemotherapy; stemness; tamoxifen; trastuzumab; tumor dormancy
    DOI:  https://doi.org/10.3390/cells12081156
  36. Plant Physiol. 2023 May 17. pii: kiad287. [Epub ahead of print]
    Arabidopsis AUTOPHAGY-RELATED2 is essential for ATG18a and ATG9 trafficking during autophagosome closure.
    Mengqian Luo, Kai Ching Law, Yilin He, Ka Kit Chung, Muk Kuen Po, Lanlan Feng, Kin Pan Chung, Caiji Gao, Xiaohong Zhuang, Liwen Jiang.
      As a fundamental metabolic pathway, autophagy plays important roles in plant growth and development, particularly under stress conditions. A set of autophagy-related (ATG) proteins is recruited for the formation of a double-membrane autophagosome. Among them, the essential roles of ATG2, ATG18, and ATG9 have been well established in plant autophagy via genetic analysis; however, the underlying molecular mechanism for ATG2 in plant autophagosome formation remains poorly understood. In this study, we focused on the specific role of ATG2 in the trafficking of ATG18a and ATG9 during autophagy in Arabidopsis (Arabidopsis thaliana). Under normal conditions, YFP-ATG18a proteins are partially localized on late endosomes and translocated to ATG8e-labeled autophagosomes upon autophagic induction. Real-time imaging analysis revealed sequential recruitment of ATG18a on the phagophore membrane, showing that ATG18a specifically decorated the closing edges and finally disassociated from the completed autophagosome. However, in the absence of ATG2, most of the YFP-ATG18a proteins are arrested on autophagosomal membranes. Ultrastructural and 3D tomography analysis showed that unclosed autophagosome structures are accumulated in the atg2 mutant, displaying direct connections with the endoplasmic reticulum (ER) membrane and vesicular structures. Dynamic analysis of ATG9 vesicles suggested that ATG2 depletion also affects the association between ATG9 vesicles and the autophagosomal membrane. Furthermore, using interaction and recruitment analysis, we mapped the interaction relationship between ATG2 and ATG18a, implying a possible role of ATG18a in recruiting ATG2 and ATG9 to the membrane. Our findings unveil a specific role of ATG2 in coordinating ATG18a and ATG9 trafficking to mediate autophagosome closure in Arabidopsis.
    Keywords:  ATG18a; ATG2; ATG9; Arabidopsis; autophagosome biogenesis; endosomes
    DOI:  https://doi.org/10.1093/plphys/kiad287
  37. Exp Cell Res. 2023 May 16. pii: S0014-4827(23)00182-9. [Epub ahead of print] 113635
    Rab2 stimulates LC3 lipidation on secretory membranes by noncanonical autophagy.
    Ellen J Tisdale, Cristina R Artalejo.
      The Golgi complex is a highly dynamic organelle that regulates various cellular activities and yet maintains a distinct structure. Multiple proteins participate in Golgi structure/organization including the small GTPase Rab2. Rab2 is found on the cis/medial Golgi compartments and the endoplasmic reticulum-Golgi intermediate compartment. Interestingly, Rab2 gene amplification occurs in a wide range of human cancers and Golgi morphological alterations are associated with cellular transformation. To learn how Rab2 'gain of function' influences the structure/activity of membrane compartments in the early secretory pathway that may contribute to oncogenesis, NRK cells were transfected with Rab2B cDNA. We found that Rab2B overexpression had a dramatic effect on the morphology of pre- and early Golgi compartments that resulted in a decreased transport rate of VSV-G in the early secretory pathway. We monitored the cells for the autophagic marker protein LC3 based on the findings that depressed membrane trafficking affects homeostasis. Morphological and biochemical studies confirmed that Rab2 ectopic expression stimulated LC3-lipidation on Rab2-containing membranes that was dependent on GAPDH and utilized a non-canonical LC3-conjugation mechanism that is nondegradative. Golgi structural alterations are associated with changes in Golgi-associated signalling pathways. Indeed, Rab2 overexpressing cells had elevated Src activity. We propose that increased Rab2 expression facilitates cis Golgi structural changes that are maintained and tolerated by the cell due to LC3 tagging, and subsequent membrane remodeling triggers Golgi associated signaling pathways that may contribute to oncogenesis.
    Keywords:  ERGIC; GAPDH; LC3; Noncanonical autophagy; Rab2; V-ATPase
    DOI:  https://doi.org/10.1016/j.yexcr.2023.113635
  38. Cell Death Discov. 2023 May 13. 9(1): 160
    Cytoprotective autophagy as a pro-survival strategy in ART-resistant malaria parasites.
    Deepika Kannan, Nishant Joshi, Sonal Gupta, Soumya Pati, Souvik Bhattacharjee, Gordon Langsley, Shailja Singh.
      Despite several initiatives to subside the global malaria burden, the spread of artemisinin-resistant parasites poses a big threat to malaria elimination. Mutations in PfKelch13 are predictive of ART resistance, whose underpinning molecular mechanism remains obscure. Recently, endocytosis and stress response pathways such as the ubiquitin-proteasome machinery have been linked to artemisinin resistance. With Plasmodium, however, ambiguity persists regarding a role in ART resistance for another cellular stress defence mechanism called autophagy. Therefore, we investigated whether, in the absence of ART treatment, basal autophagy is augmented in PfK13-R539T mutant ART-resistant parasites and analyzed whether PfK13-R539T endowed mutant parasites with an ability to utilize autophagy as a pro-survival strategy. We report that in the absence of any ART treatment, PfK13-R539T mutant parasites exhibit increased basal autophagy compared to PfK13-WT parasites and respond aggressively through changes in autophagic flux. A clear cytoprotective role of autophagy in parasite resistance mechanism is evident by the observation that a suppression of PI3-Kinase (PI3K) activity (a master autophagy regulator) rendered difficulty in the survival of PfK13-R539T ART-resistant parasites. In conclusion, we now show that higher PI3P levels reported for mutant PfKelch13 backgrounds led to increased basal autophagy that acts as a pro-survival response to ART treatment. Our results highlight PfPI3K as a druggable target with the potential to re-sensitize ART-resistant parasites and identify autophagy as a pro-survival function that modulates ART-resistant parasite growth.
    DOI:  https://doi.org/10.1038/s41420-023-01401-5
  39. Biomolecules. 2023 Apr 04. pii: 649. [Epub ahead of print]13(4):
    β Cell and Autophagy: What Do We Know?
    Hamid-Reza Mohammadi-Motlagh, Mona Sadeghalvad, Niloofar Yavari, Rosita Primavera, Setareh Soltani, Shashank Chetty, Abantika Ganguly, Shobha Regmi, Tina Fløyel, Simranjeet Kaur, Aashiq H Mirza, Avnesh S Thakor, Flemming Pociot, Reza Yarani.
      Pancreatic β cells are central to glycemic regulation through insulin production. Studies show autophagy as an essential process in β cell function and fate. Autophagy is a catabolic cellular process that regulates cell homeostasis by recycling surplus or damaged cell components. Impaired autophagy results in β cell loss of function and apoptosis and, as a result, diabetes initiation and progress. It has been shown that in response to endoplasmic reticulum stress, inflammation, and high metabolic demands, autophagy affects β cell function, insulin synthesis, and secretion. This review highlights recent evidence regarding how autophagy can affect β cells' fate in the pathogenesis of diabetes. Furthermore, we discuss the role of important intrinsic and extrinsic autophagy modulators, which can lead to β cell failure.
    Keywords:  autophagy; autophagy modulators; insulin homeostasis; type 1 diabetes; type 2 diabetes; β cell
    DOI:  https://doi.org/10.3390/biom13040649
  40. Cancers (Basel). 2023 May 05. pii: 2622. [Epub ahead of print]15(9):
    Autophagic-Related Proteins in Brain Gliomas: Role, Mechanisms, and Targeting Agents.
    Cristina Pizzimenti, Vincenzo Fiorentino, Mariausilia Franchina, Maurizio Martini, Giuseppe Giuffrè, Maria Lentini, Nicola Silvestris, Martina Di Pietro, Guido Fadda, Giovanni Tuccari, Antonio Ieni.
      The present review focuses on the phenomenon of autophagy, a catabolic cellular process, which allows for the recycling of damaged organelles, macromolecules, and misfolded proteins. The different steps able to activate autophagy start with the formation of the autophagosome, mainly controlled by the action of several autophagy-related proteins. It is remarkable that autophagy may exert a double role as a tumour promoter and a tumour suppressor. Herein, we analyse the molecular mechanisms as well as the regulatory pathways of autophagy, mainly addressing their involvement in human astrocytic neoplasms. Moreover, the relationships between autophagy, the tumour immune microenvironment, and glioma stem cells are discussed. Finally, an excursus concerning autophagy-targeting agents is included in the present review in order to obtain additional information for the better treatment and management of therapy-resistant patients.
    Keywords:  autophagy; autophagy-related proteins; glioblastomas; gliomas; prognosis; treatment
    DOI:  https://doi.org/10.3390/cancers15092622
  41. Autophagy. 2023 May 16.
    "Autophagic landscapes: on the paradox of survival through self-degradation" - A science-inspired exhibition.
    Ayelen Valko, Dorotea Fracchiolla.
      The Complexity Science Hub Vienna is hosting an autophagy-based art exhibition that shows the artwork by Ayelen Valko and Dorotea Fracchiolla, two artists who are also scientists engaged in autophagy research. This exhibition, called "Autophagic landscapes: on the paradox of survival through self-degradation"-which will be open to the general public from January to May 2023-proposes a visual journey from entire organisms towards the interior of a single cell. The core ideas represented in the exhibited artworks are the molecular mechanisms and vesicular dynamics of autophagy-two phenomena that have been feeding the imagination of the two artists, inspiring the creation of art that depicts intriguing subcellular landscapes. Although the microscale bears very valuable aesthetic features, it is not a common subject in art. Correcting this is the main aim of this exhibition and of the two artists.
    Keywords:  -; art; autophagy; exhibition; science communication
    DOI:  https://doi.org/10.1080/15548627.2023.2214031
  42. Cells. 2023 04 29. pii: 1283. [Epub ahead of print]12(9):
    The RNA Demethylase ALKBH5 Maintains Endoplasmic Reticulum Homeostasis by Regulating UPR, Autophagy, and Mitochondrial Function.
    Panneerdoss Subbarayalu, Pooja Yadav, Santosh Timilsina, Daisy Medina, Kunal Baxi, Robert Hromas, Ratna K Vadlamudi, Yidong Chen, Patrick Sung, Manjeet K Rao.
      Eukaryotic cells maintain cellular fitness by employing well-coordinated and evolutionarily conserved processes that negotiate stress induced by internal or external environments. These processes include the unfolded protein response, autophagy, endoplasmic reticulum-associated degradation (ERAD) of unfolded proteins and altered mitochondrial functions that together constitute the ER stress response. Here, we show that the RNA demethylase ALKBH5 regulates the crosstalk among these processes to maintain normal ER function. We demonstrate that ALKBH5 regulates ER homeostasis by controlling the expression of ER lipid raft associated 1 (ERLIN1), which binds to the activated inositol 1, 4, 5,-triphosphate receptor and facilitates its degradation via ERAD to maintain the calcium flux between the ER and mitochondria. Using functional studies and electron microscopy, we show that ALKBH5-ERLIN-IP3R-dependent calcium signaling modulates the activity of AMP kinase, and consequently, mitochondrial biogenesis. Thus, these findings reveal that ALKBH5 serves an important role in maintaining ER homeostasis and cellular fitness.
    Keywords:  ALKBH5; ER homeostasis; ERLIN1; autophagy; m6A; mitochondria; unfolded protein response
    DOI:  https://doi.org/10.3390/cells12091283
  43. FASEB J. 2023 06;37(6): e22969
    Mitochondrial quality control in abdominal aortic aneurysm: From molecular mechanisms to therapeutic strategies.
    Ding Wang, Longyuan Jia, Chengdong Zhao, Huitao Wang, Zhengnan Dai, Yuchen Jing, Bo Jiang, Shijie Xin.
      Mitochondria are the energy supply sites of cells and are crucial for eukaryotic life. Mitochondrial dysfunction is involved in the pathogenesis of abdominal aortic aneurysm (AAA). Multiple mitochondrial quality control (MQC) mechanisms, including mitochondrial DNA repair, biogenesis, antioxidant defense, dynamics, and autophagy, play vital roles in maintaining mitochondrial homeostasis under physiological and pathological conditions. Abnormalities in these mechanisms may induce mitochondrial damage and dysfunction leading to cell death and tissue remodeling. Recently, many clues suggest that dysregulation of MQC is closely related to the pathogenesis of AAA. Therefore, specific interventions targeting MQC mechanisms to maintain and restore mitochondrial function have become promising therapeutic methods for the prevention and treatment of AAA.
    Keywords:  abdominal aortic aneurysm; mitochondrial quality control; molecular mechanisms; therapeutic strategies
    DOI:  https://doi.org/10.1096/fj.202202158RR
  44. Eur J Med Chem. 2023 May 06. pii: S0223-5234(23)00433-6. [Epub ahead of print]256 115467
    Targeting VPS34 in autophagy: An update on pharmacological small-molecule compounds.
    Yuan Liu, Qilin Yang, Siwei Chen, Zixiang Li, Leilei Fu.
      VPS34 is well-known to be the unique member of the class III phosphoinositide 3-kinase (PI3K) family, forming VPS34 complex 1 and complex 2, which are involved in several key physiological processes. Of note, VPS34 complex 1 is an important node of autophagosome generation, which controls T cell metabolism and maintains cellular homeostasis through the autophagic pathway. And, VPS34 complex 2 is involved in endocytosis as well as vesicular transport, and is closely related to neurotransmission, antigen presentation and brain development. Due to the two important biological functions of VPS34, its dysregulation can lead to the development of cardiovascular disease, cancer, neurological disorders, and many types of human diseases by altering normal human physiology. Thus, in this review, we not only summarize the molecular structure and function of VPS34, but demonstrate the relationships between VPS34 and human diseases. Moreover, we further discuss the current small molecule inhibitors targeting VPS34 based upon the structure and function of VPS34, which may provide an insight into the future targeted drug development.
    Keywords:  Autophagy; Drug development; Human disease; Small-molecule compound; VPS34
    DOI:  https://doi.org/10.1016/j.ejmech.2023.115467
  45. Cells. 2023 05 07. pii: 1334. [Epub ahead of print]12(9):
    Role of Autophagy in Ehrlichia-Induced Liver Injury.
    Aditya Kumar Sharma, Nahed Ismail.
      Autophagy is a cellular process that involves the cell breakdown and recycling of cellular components, such as old, damaged, or abnormal proteins, for important cellular functions including development, immune function, stress, and starvation [...].
    DOI:  https://doi.org/10.3390/cells12091334
  46. Aging Dis. 2023 Jun 01. 14(3): 794-824
    Sirtuins at the Crossroads between Mitochondrial Quality Control and Neurodegenerative Diseases: Structure, Regulation, Modifications, and Modulators.
    Hui Xu, Yi-Yang Liu, Lin-Seng Li, You-Shuo Liu.
      Sirtuins (SIRT1-SIRT7), a family of nicotinamide adenine dinucleotide (NAD+)-dependent enzymes, are key regulators of life span and metabolism. In addition to acting as deacetylates, some sirtuins have the properties of deacylase, decrotonylase, adenosine diphosphate (ADP)-ribosyltransferase, lipoamidase, desuccinylase, demalonylase, deglutarylase, and demyristolyase. Mitochondrial dysfunction occurs early on and acts causally in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Sirtuins are implicated in the regulation of mitochondrial quality control, which is highly associated with the pathogenesis of neurodegenerative diseases. There is growing evidence indicating that sirtuins are promising and well-documented molecular targets for the treatment of mitochondrial dysfunction and neurodegenerative disorders by regulating mitochondrial quality control, including mitochondrial biogenesis, mitophagy, mitochondrial fission/fusion dynamics, and mitochondrial unfolded protein responses (mtUPR). Therefore, elucidation of the molecular etiology of sirtuin-mediated mitochondrial quality control points to new prospects for the treatment of neurodegenerative diseases. However, the mechanisms underlying sirtuin-mediated mitochondrial quality control remain obscure. In this review, we update and summarize the current understanding of the structure, function, and regulation of sirtuins with an emphasis on the cumulative and putative effects of sirtuins on mitochondrial biology and neurodegenerative diseases, particularly their roles in mitochondrial quality control. In addition, we outline the potential therapeutic applications for neurodegenerative diseases of targeting sirtuin-mediated mitochondrial quality control through exercise training, calorie restriction, and sirtuin modulators in neurodegenerative diseases.
    DOI:  https://doi.org/10.14336/AD.2022.1123
  47. Autophagy. 2023 May 16. 1-3
    Knockout validation of LAMP2A antibodies for immunostaining in human cancer cells.
    Xun Zhou, Vera Shirokova, Vitaliy O Kaminskyy, Eva Berenger, Elena Kochetkova, Erik Norberg, Maria Genander, Helin Vakifahmetoglu-Norberg.
      LAMP2A is the rate-limiting factor of chaperone-mediated autophagy (CMA), a unique selective protein degradative pathway. To date LAMP2A antibodies are not knockout (KO)-validated in human cells. We have recently generated human isoform-specific LAMP2A KO cells, and here we assessed the specificity of select commercial LAMP2A antibodies on wild-type and LAMP2A KO human cancer cells. While all tested antibodies were suitable for immunoblotting, the anti-LAMP2A antibody (ab18528) is likely to exhibit an off-target reactivity in immunostaining approaches using human cancer cells, and alternative antibodies, which seem more appropriate, are available.
    Keywords:  Antibody; CRISPR-Cas9; LAMP2A; cancer; chaperone-mediated autophagy; immunofluorescence
    DOI:  https://doi.org/10.1080/15548627.2023.2213515
  48. CNS Neurosci Ther. 2023 May 19.
    Reciprocal interaction between mitochondrial fission and mitophagy in postoperative delayed neurocognitive recovery in aged rats.
    Yitong Li, Yue Li, Lei Chen, Yi Li, Kaixi Liu, Jingshu Hong, Qian Wang, Ning Kang, Yanan Song, Xinning Mi, Yi Yuan, Dengyang Han, Taotao Liu, Ning Yang, Xiangyang Guo, Zhengqian Li.
       INTRODUCTION: Emerging evidence suggests that mitochondrial dysfunction plays a crucial role in the pathogenesis of postoperative delayed neurocognitive recovery (dNCR). Mitochondria exist in a dynamic equilibrium that involves fission and fusion to regulate morphology and maintains normal cell function via the removal of damaged mitochondria through mitophagy. Nonetheless, the relationship between mitochondrial morphology and mitophagy, and how they influence mitochondrial function in the development of postoperative dNCR, remains poorly understood. Here, we observed morphological alterations of mitochondria and mitophagy activity in hippocampal neurons and assessed the involvement of their interaction in dNCR following general anesthesia and surgical stress in aged rats.
    METHODS: Firstly, we evaluated the spatial learning and memory ability of the aged rats after anesthesia/surgery. Hippocampal mitochondrial function and mitochondrial morphology were detected. Afterwards, mitochondrial fission was inhibited by Mdivi-1 and siDrp1 in vivo and in vitro separately. We then detected mitophagy and mitochondrial function. Finally, we used rapamycin to activate mitophagy and observed mitochondrial morphology and mitochondrial function.
    RESULTS: Surgery impaired hippocampal-dependent spatial learning and memory ability and caused mitochondrial dysfunction. It also increased mitochondrial fission and inhibited mitophagy in hippocampal neurons. Mdivi-1 improved mitophagy and learning and memory ability of aged rats by inhibiting mitochondrial fission. Knocking down Drp1 by siDrp1 also improved mitophagy and mitochondrial function. Meanwhile, rapamycin inhibited excessive mitochondrial fission and improved mitochondrial function.
    CONCLUSION: Surgery simultaneously increases mitochondrial fission and inhibits mitophagy activity. Mechanistically, mitochondrial fission/fusion and mitophagy activity interact reciprocally with each other and are both involved in postoperative dNCR. These mitochondrial events after surgical stress may provide novel targets and modalities for therapeutic intervention in postoperative dNCR.
    Keywords:  aged rats; delayed neurocognitive recovery; mitochondrial dysfunction; mitochondrial fission; mitophagy
    DOI:  https://doi.org/10.1111/cns.14261
  49. Int J Mol Sci. 2023 Apr 23. pii: 7734. [Epub ahead of print]24(9):
    Autophagy and SARS-CoV-2-Old Players in New Games.
    Tsvetomira Ivanova, Yuliia Mariienko, Nikolay Mehterov, Maria Kazakova, Yordan Sbirkov, Krassimira Todorova, Soren Hayrabedyan, Victoria Sarafian.
      At present it is well-defined that autophagy is a fundamental process essential for cell life but its pro-viral and anti-viral role has been stated out with the COVID pandemic. However, viruses in turn have evolved diverse adaptive strategies to cope with autophagy driven host defense, either by blocking or hijacking the autophagy machinery for their own benefit. The mechanisms underlying autophagy modulation are presented in the current review which summarizes the accumulated knowledge on the crosstalk between autophagy and viral infections, with a particular emphasizes on SARS-CoV-2. The different types of autophagy related to infections and their molecular mechanisms are focused in the context of inflammation. In particular, SARS-CoV-2 entry, replication and disease pathogenesis are discussed. Models to study autophagy and to formulate novel treatment approaches and pharmacological modulation to fight COVID-19 are debated. The SARS-CoV-2-autophagy interplay is presented, revealing the complex dynamics and the molecular machinery of autophagy. The new molecular targets and strategies to treat COVID-19 effectively are envisaged. In conclusion, our finding underline the importance of development new treatment strategies and pharmacological modulation of autophagy to fight COVID-19.
    Keywords:  SARS-CoV-2; autophagy; treatment strategies
    DOI:  https://doi.org/10.3390/ijms24097734
  50. Int J Mol Sci. 2023 May 05. pii: 8328. [Epub ahead of print]24(9):
    Puerarin Prevents Cadmium-Induced Neuronal Injury by Alleviating Autophagic Dysfunction in Rat Cerebral Cortical Neurons.
    Li Wang, Tao Wang, Shuangquan Wen, Ruilong Song, Hui Zou, Jianhong Gu, Xuezhong Liu, Jianchun Bian, Zongping Liu, Yan Yuan.
      Autophagic dysfunction is one of the main mechanisms of cadmium (Cd)-induced neurotoxicity. Puerarin (Pue) is a natural antioxidant extracted from the medicinal and edible homologous plant Pueraria lobata. Studies have shown that Pue has neuroprotective effects in a variety of brain injuries, including Cd-induced neuronal injury. However, the role of Pue in the regulation of autophagy to alleviate Cd-induced injury in rat cerebral cortical neurons remains unclear. This study aimed to elucidate the protective mechanism of Pue in alleviating Cd-induced injury in rat cerebral cortical neurons by targeting autophagy. Our results showed that Pue alleviated Cd-induced injury in rat cerebral cortical neurons in vitro and in vivo. Pue activates autophagy and alleviates Cd-induced autophagic blockade in rat cerebral cortical neurons. Further studies have shown that Pue alleviates the Cd-induced inhibition of autophagosome-lysosome fusion, as well as the inhibition of lysosomal degradation. The specific mechanism is related to Pue alleviating the inhibition of Cd on the expression levels of the key proteins Rab7, VPS41, and SNAP29, which regulate autophagosome-lysosome fusion, as well as the lysosome-related proteins LAMP2, CTSB, and CTSD. In summary, these results indicate that Pue alleviates Cd-induced autophagic dysfunction in rat cerebral cortical neurons by alleviating autophagosome-lysosome fusion dysfunction and lysosomal degradation dysfunction, thereby alleviating Cd-induced neuronal injury.
    Keywords:  autophagic dysfunction; cadmium; puerarin; rat cerebral cortical neurons
    DOI:  https://doi.org/10.3390/ijms24098328
  51. Glia. 2023 May 18.
    Microglia-specific knock-out of NF-κB/IKK2 increases the accumulation of misfolded α-synuclein through the inhibition of p62/sequestosome-1-dependent autophagy in the rotenone model of Parkinson's disease.
    Savannah M Rocha, Kelly S Kirkley, Debotri Chatterjee, Tawfik A Aboellail, Richard J Smeyne, Ronald B Tjalkens.
      Parkinson's disease (PD) is the most common neurodegenerative movement disorder worldwide, with a greater prevalence in men than women. The etiology of PD is largely unknown, although environmental exposures and neuroinflammation are linked to protein misfolding and disease progression. Activated microglia are known to promote neuroinflammation in PD, but how environmental agents interact with specific innate immune signaling pathways in microglia to stimulate conversion to a neurotoxic phenotype is not well understood. To determine how nuclear factor kappa B (NF-κB) signaling dynamics in microglia modulate neuroinflammation and dopaminergic neurodegeneration, we generated mice deficient in NF-κB activation in microglia (CX3CR1-Cre::IKK2fl/fl ) and exposed them to 2.5 mg/kg/day of rotenone for 14 days, followed by a 14-day post-lesioning incubation period. We postulated that inhibition of NF-κB signaling in microglia would reduce overall inflammatory injury in lesioned mice. Subsequent analysis indicated decreased expression of the NF-κB-regulated autophagy gene, sequestosome 1 (p62), in microglia, which is required for targeting ubiquitinated α-synuclein (α-syn) for lysosomal degradation. Knock-out animals had increased accumulation of misfolded α-syn within microglia, despite an overall reduction in neurodegeneration. Interestingly, this occurred more prominently in males. These data suggest that microglia play key biological roles in the degradation and clearance of misfolded α-syn and this process works in concert with the innate immune response associated with neuroinflammation. Importantly, the accumulation of misfolded α-syn protein aggregates alone did not increase neurodegeneration following exposure to rotenone but required the NF-κB-dependent inflammatory response in microglia.
    Keywords:  autophagy; microglia; neurodegeneration; neuroinflammation; α-synuclein
    DOI:  https://doi.org/10.1002/glia.24385
  52. Cell Insight. 2022 Aug;1(4): 100045
    Phosphorylated STYK1 restrains the inhibitory role of EGFR in autophagy initiation and EGFR-TKIs sensitivity.
    Cefan Zhou, Xueying Dong, Ming Wang, Xuehong Qian, Miao Hu, Kai Liang, Yanyan Liang, Rui Zhang, Yuan Huang, Hao Lyu, Shuai Xiao, Yongfei Tang, Declan William Ali, Marek Michalak, Xing-Zhen Chen, Jingfeng Tang.
      Epidermal growth factor receptor (EGFR) plays critical roles in cell proliferation and tumorigenesis. Autophagy has emerged as a potential mechanism involved in the acquired resistance to anti-EGFR treatments, however, the molecular mechanisms has not been fully addressed. In this study, we identified EGFR interacts with STYK1, a positive autophagy regulator, in EGFR kinase activity dependent manner. We found that EGFR phosphorylates STYK1 at Y356 site and STYK1 inhibits activated EGFR mediated Beclin1 tyrosine phosphorylation and interaction between Bcl2 and Beclin1, thus enhances PtdIns3K-C1 complex assembly and autophagy initiation. We also demonstrated that STYK1 depletion increased the sensitivity of NSCLC cells to EGFR-TKIs in vitro and in vivo. Moreover, EGFR-TKIs induced activation of AMPK phosphorylates STYK1 at S304 site. STYK1 S304 collaborated with Y356 phosphorylation to enhance the EGFR-STYK1 interaction and reverse the inhibitory effects of EGFR to autophagy flux. Collectively, these data revealed new roles and cross-talk between STYK1 and EGFR in autophagy regulation and EGFR-TKIs sensitivity in NSCLC.
    Keywords:  Autophagy initiation; EGFR; NSCLC; Resistance; STYK1
    DOI:  https://doi.org/10.1016/j.cellin.2022.100045
  53. Mol Cell Endocrinol. 2023 May 10. pii: S0303-7207(23)00105-3. [Epub ahead of print] 111954
    Liraglutide alleviates myocardial ischemia‒reperfusion injury in diabetic mice.
    Binbin Fang, Fen Liu, Xiaolin Yu, Junyi Luo, Xuehe Zhang, Tong Zhang, Jixin Zhang, Yining Yang, Xiaomei Li.
      Diabetic patients are prone to acute myocardial infarction. Although reperfusion therapy can preserve the viability of the myocardium, it also causes fatal ischemia‒reperfusion injury. Diabetes can exacerbate myocardial ischemia‒reperfusion injury, but the mechanism is unclear. We aimed to characterize the effects of liraglutide on the prevention of ischemia‒reperfusion injury and inadequate autophagy. Liraglutide reduced the myocardial infarction area and improved cardiac function in diabetic mice. We further demonstrated that liraglutide mediated these protective effects by activating AMPK/mTOR-mediated autophagy. Liraglutide markedly increased p-AMPK levels and the LC3 II/LC3 I ratio and reduced p-mTOR levels and p62 expression. Pharmacological inhibition of mTOR increased cell viability and autophagy levels in high glucose and H/R-treated H9C2 cells. Overall, our study reveals that liraglutide acts upstream of the AMPK/mTOR pathway to effectively counteract high glucose- and H/R-induced cell dysfunction by activating AMPK/mTOR-dependent autophagy, providing a basis for the clinical prevention and treatment of ischemia‒reperfusion in diabetes.
    Keywords:  AMPK/mTOR signaling pathway; Autophagy; Diabetes mellitus; Ischemia‒reperfusion injury; Liraglutide
    DOI:  https://doi.org/10.1016/j.mce.2023.111954
  54. Cells. 2023 04 26. pii: 1259. [Epub ahead of print]12(9):
    Z-Disk-Associated Plectin (Isoform 1d): Spatial Arrangement, Interaction Partners, and Role in Filamin C Homeostasis.
    Lilli Winter, Ilona Staszewska-Daca, Stefan Zittrich, Fatiha Elhamine, Michaela M Zrelski, Katy Schmidt, Irmgard Fischer, Christian Jüngst, Astrid Schauss, Wolfgang H Goldmann, Robert Stehle, Gerhard Wiche.
      Plectin, a highly versatile cytolinker protein, is crucial for myofiber integrity and function. Accordingly, mutations in the human gene (PLEC) cause several rare diseases, denoted as plectinopathies, with most of them associated with progressive muscle weakness. Of several plectin isoforms expressed in skeletal muscle and the heart, P1d is the only isoform expressed exclusively in these tissues. Using high-resolution stimulated emission depletion (STED) microscopy, here we show that plectin is located within the gaps between individual α-actinin-positive Z-disks, recruiting and bridging them to desmin intermediate filaments (Ifs). Loss of plectin in myofibril bundles led to a complete loss of desmin Ifs. Loss of Z-disk-associated plectin isoform P1d led to disorganization of muscle fibers and slower relaxation of myofibrils upon mechanical strain, in line with an observed inhomogeneity of muscle ultrastructure. In addition to binding to α-actinin and thereby providing structural support, P1d forms a scaffolding platform for the chaperone-assisted selective autophagy machinery (CASA) by directly interacting with HSC70 and synpo2. In isoform-specific knockout (P1d-KO) mouse muscle and mechanically stretched plectin-deficient myoblasts, we found high levels of undigested filamin C, a bona fide substrate of CASA. Similarly, subjecting P1d-KO mice to forced swim tests led to accumulation of filamin C aggregates in myofibers, highlighting a specific role of P1d in tension-induced proteolysis activated upon high loads of physical exercise and muscle contraction.
    Keywords:  chaperone-assisted selective autophagy; cytolinker; desmin intermediate filaments; myofibril; plectin; skeletal muscle
    DOI:  https://doi.org/10.3390/cells12091259
  55. Cell Death Discov. 2023 May 19. 9(1): 172
    Enhanced Sestrin expression through Tanshinone 2A treatment improves PI3K-dependent inhibition of glioma growth.
    Judith Schaf, Sonia Shinhmar, Qingyu Zeng, Olivier E Pardo, Philip Beesley, Nelofer Syed, Robin S B Williams.
      Glioblastomas are a highly aggressive cancer type which respond poorly to current pharmaceutical treatments, thus novel therapeutic approaches need to be investigated. One such approach involves the use of the bioactive natural product Tanshinone IIA (T2A) derived from the Chinese herb Danshen, where mechanistic insight for this anti-cancer agent is needed to validate its use. Here, we employ a tractable model system, Dictyostelium discoideum, to provide this insight. T2A potently inhibits cellular proliferation of Dictyostelium, suggesting molecular targets in this model. We show that T2A rapidly reduces phosphoinositide 3 kinase (PI3K) and protein kinase B (PKB) activity, but surprisingly, the downstream complex mechanistic target of rapamycin complex 1 (mTORC1) is only inhibited following chronic treatment. Investigating regulators of mTORC1, including PKB, tuberous sclerosis complex (TSC), and AMP-activated protein kinase (AMPK), suggests these enzymes were not responsible for this effect, implicating an additional molecular mechanism of T2A. We identify this mechanism as the increased expression of sestrin, a negative regulator of mTORC1. We further show that combinatory treatment using a PI3K inhibitor and T2A gives rise to a synergistic inhibition of cell proliferation. We then translate our findings to human and mouse-derived glioblastoma cell lines, where both a PI3K inhibitor (Paxalisib) and T2A reduces glioblastoma proliferation in monolayer cultures and in spheroid expansion, with combinatory treatment significantly enhancing this effect. Thus, we propose a new approach for cancer treatment, including glioblastomas, through combinatory treatment with PI3K inhibitors and T2A.
    DOI:  https://doi.org/10.1038/s41420-023-01462-6
  56. Tissue Cell. 2023 Apr 28. pii: S0040-8166(23)00088-5. [Epub ahead of print]82 102100
    Beclin 1 regulates astrocyte phagocytosis and phagosomal recruitment of retromer.
    Evelyn G Lemus Silva, Yuberki Delgadillo, Robin E White, Kurt M Lucin.
      Phagocytosis plays an important role in maintaining brain homeostasis and when impaired can result in the accumulation of unwanted cellular material. While microglia are traditionally considered the phagocytes of the brain, astrocytes are also capable of phagocytosis and are the most numerous cells in the brain. In Alzheimer's disease (AD), astrocytes can be found surrounding β-amyloid (Aβ) plaques yet they seem unable to eliminate these deposits, suggesting phagocytosis may be impaired in AD. Mechanisms that might diminish astrocyte phagocytosis in AD are currently unclear. Here, we demonstrate that the autophagy protein beclin 1, which is reduced in AD, plays a role in regulating astrocyte phagocytosis. Specifically, we show that reducing beclin 1 in C6 astrocytes impairs the phagocytosis of latex beads, reduces retromer levels, and impairs retromer recruitment to the phagosomal membrane. Furthermore, we show that these beclin 1-mediated changes are accompanied by reduced expression of the phagocytic receptor Scavenger Receptor Class B type I (SR-BI). Collectively, these findings suggest a critical role for the protein beclin 1 in both receptor trafficking and receptor-mediated phagocytosis in astrocytes. Moreover, these findings provide insight into mechanisms by which astrocytes may become impaired in AD.
    Keywords:  Astrocytes; Beclin 1; Phagocytosis; Retromer; SR-B1
    DOI:  https://doi.org/10.1016/j.tice.2023.102100
  57. Acta Neuropathol Commun. 2023 May 17. 11(1): 82
    Senescence-related impairment of autophagy induces toxic intraneuronal amyloid-β accumulation in a mouse model of amyloid pathology.
    Nuria Suelves, Shirine Saleki, Tasha Ibrahim, Debora Palomares, Sebastiaan Moonen, Marta J Koper, Céline Vrancx, Devkee M Vadukul, Nicolas Papadopoulos, Nikenza Viceconte, Eloïse Claude, Rik Vandenberghe, Christine A F von Arnim, Stefan N Constantinescu, Dietmar Rudolf Thal, Anabelle Decottignies, Pascal Kienlen-Campard.
      Aging is the main risk factor for Alzheimer's disease (AD) and other neurodegenerative pathologies, but the molecular and cellular changes underlying pathological aging of the nervous system are poorly understood. AD pathology seems to correlate with the appearance of cells that become senescent due to the progressive accumulation of cellular insults causing DNA damage. Senescence has also been shown to reduce the autophagic flux, a mechanism involved in clearing damaged proteins from the cell, and such impairment has been linked to AD pathogenesis. In this study, we investigated the role of cellular senescence on AD pathology by crossing a mouse model of AD-like amyloid-β (Aβ) pathology (5xFAD) with a mouse model of senescence that is genetically deficient for the RNA component of the telomerase (Terc-/-). We studied changes in amyloid pathology, neurodegeneration, and the autophagy process in brain tissue samples and primary cultures derived from these mice by complementary biochemical and immunostaining approaches. Postmortem human brain samples were also processed to evaluate autophagy defects in AD patients. Our results show that accelerated senescence produces an early accumulation of intraneuronal Aβ in the subiculum and cortical layer V of 5xFAD mice. This correlates with a reduction in amyloid plaques and Aβ levels in connecting brain regions at a later disease stage. Neuronal loss was specifically observed in brain regions presenting intraneuronal Aβ and was linked to telomere attrition. Our results indicate that senescence affects intraneuronal Aβ accumulation by impairing autophagy function and that early autophagy defects can be found in the brains of AD patients. Together, these findings demonstrate the instrumental role of senescence in intraneuronal Aβ accumulation, which represents a key event in AD pathophysiology, and emphasize the correlation between the initial stages of amyloid pathology and defects in the autophagy flux.
    Keywords:  Alzheimer’s disease; Autophagy; Cellular senescence; Intraneuronal Aβ; Telomere shortening
    DOI:  https://doi.org/10.1186/s40478-023-01578-x
  58. Front Mol Neurosci. 2023 ;16 1064579
    Role and mechanism of FOXG1-related epigenetic modifications in cisplatin-induced hair cell damage.
    Yu-Rong Mu, Sheng-Yu Zou, Ming Li, Yan-Yan Ding, Xiang Huang, Zu-Hong He, Wei-Jia Kong.
      Cisplatin is widely used in clinical tumor chemotherapy but has severe ototoxic side effects, including tinnitus and hearing damage. This study aimed to determine the molecular mechanism underlying cisplatin-induced ototoxicity. In this study, we used CBA/CaJ mice to establish an ototoxicity model of cisplatin-induced hair cell loss, and our results showed that cisplatin treatment could reduce FOXG1 expression and autophagy levels. Additionally, H3K9me2 levels increased in cochlear hair cells after cisplatin administration. Reduced FOXG1 expression caused decreased microRNA (miRNA) expression and autophagy levels, leading to reactive oxygen species (ROS) accumulation and cochlear hair cell death. Inhibiting miRNA expression decreased the autophagy levels of OC-1 cells and significantly increased cellular ROS levels and the apoptosis ratio in vitro. In vitro, overexpression of FOXG1 and its target miRNAs could rescue the cisplatin-induced decrease in autophagy, thereby reducing apoptosis. BIX01294 is an inhibitor of G9a, the enzyme in charge of H3K9me2, and can reduce hair cell damage and rescue the hearing loss caused by cisplatin in vivo. This study demonstrates that FOXG1-related epigenetics plays a role in cisplatin-induced ototoxicity through the autophagy pathway, providing new ideas and intervention targets for treating ototoxicity.
    Keywords:  FOXG1; autophagy; cisplatin; epigenetics; hair cells; ototoxicity
    DOI:  https://doi.org/10.3389/fnmol.2023.1064579
  59. Front Cell Dev Biol. 2023 ;11 1156383
    A comprehensive review of the relationship between autophagy and sorafenib-resistance in hepatocellular carcinoma: ferroptosis is noteworthy.
    Kangnan Zhang, Qinghui Zhang, Rongrong Jia, Shihao Xiang, Ling Xu.
      Patients with hepatocellular carcinoma (HCC) bear a heavy burden of disease and economic burden but have fewer treatment options. Sorafenib, a multi-kinase inhibitor, is the only approved drug that can be used to limit the progression of inoperable or distant metastatic HCC. However, enhanced autophagy and other molecular mechanisms after sorafenib exposure further induce drug resistance in HCC patients. Sorafenib-associated autophagy also generates a series of biomarkers, which may represent that autophagy is a critical section of sorafenib-resistance in HCC. Furthermore, many classic signaling pathways have been found to be involved in sorafenib-associated autophagy, including the HIF/mTOR signaling pathway, endoplasmic reticulum stress, and sphingolipid signaling, among others. In turn, autophagy also provokes autophagic activity in components of the tumor microenvironment, including tumor cells and stem cells, further impacting sorafenib-resistance in HCC through a special autophagic cell death process called ferroptosis. In this review, we summarized the latest research progress and molecular mechanisms of sorafenib-resistance-associated autophagy in detail, providing new insights and ideas for unraveling the dilemma of sorafenib-resistance in HCC.
    Keywords:  autophagy; cell; ferroptosis; hepatocellular carcinoma; sorafenib-resistant
    DOI:  https://doi.org/10.3389/fcell.2023.1156383
  60. Ageing Res Rev. 2023 May 15. pii: S1568-1637(23)00114-9. [Epub ahead of print] 101955
    Mitochondrial dysfunction in aging.
    Ying Guo, Teng Guan, Kashfia Shafiq, Qiang Yu, Xin Jiao, Donghui Na, Meiyu Li, Guohui Zhang, Jiming Kong.
      Aging is a complex process that features a functional decline in many organelles. Although mitochondrial dysfunction is suggested as one of the determining factors of aging, the role of mitochondrial quality control (MQC) in aging is still poorly understood. A growing body of evidence points out that reactive oxygen species (ROS) stimulates mitochondrial dynamic changes and accelerates the accumulation of oxidized by-products through mitochondrial proteases and mitochondrial unfolded protein response (UPRmt). Mitochondrial-derived vesicles (MDVs) are the first line of MQC to dispose of oxidized derivatives. Besides, mitophagy helps remove partially damaged mitochondria to ensure that mitochondria are healthy and functional. Although abundant interventions on MQC have been explored, over-activation or inhibition of any type of MQC may even accelerate abnormal energy metabolism and mitochondrial dysfunction-induced senescence. This review summarizes mechanisms essential for maintaining mitochondrial homeostasis and emphasizes that imbalanced MQC may accelerate cellular senescence and aging. Thus, appropriate interventions on MQC may delay the aging process and extend lifespan.
    Keywords:  Aging; mitochondrial dysfunction; mitochondrial quality control; reactive oxygen species
    DOI:  https://doi.org/10.1016/j.arr.2023.101955
  61. Exp Ther Med. 2023 Jun;25(6): 268
    Autophagy in the pharmacological activities of celastrol (Review).
    Caixia Zhang, Weiyan Wang, Chenhui Du, Huifang Li, Kun Zhou, Zhihua Luan, Yinxia Chang, Shan Liu, Yanming Wei.
      Celastrol, a natural compound extracted from the traditional Chinese medicinal herb Tripterygium wilfordii Hook F, possesses broad-spectrum pharmacological properties. Autophagy is an evolutionarily conserved catabolic process through which cytoplasmic cargo is delivered to the lysosomes for degradation. Autophagy dysregulation contributes to multiple pathological processes. Therefore, targeting autophagic activity is a promising therapy for various diseases, as well as a drug-development strategy. According to previous studies, autophagy is specifically targeted and may be altered in response to celastrol treatment, highlighting that autophagy modulation is an important mechanism underlying the therapeutic efficacy of celastrol for the treatment of various diseases. The present study summarizes the currently available information regarding the role of autophagy in the effect of celastrol to exert anti-tumor, anti-inflammatory, immunomodulatory, neuroprotective, anti-atherosclerosis, anti-pulmonary fibrosis and anti-macular degeneration activities. The diverse signaling pathways involved are also analyzed to provide insight into the mechanisms of action of celastrol and thereby pave the way for establishing celastrol as an efficacious autophagy modulator in clinical practice.
    Keywords:  anti-atherosclerosis; anti-inflammatory; anti-macular degeneration; anti-pulmonary fibrosis; anti-tumor; autophagy; celastrol; immunomodulatory; neuroprotective
    DOI:  https://doi.org/10.3892/etm.2023.11967
  62. Hepatol Commun. 2023 Jun 01. pii: e0154. [Epub ahead of print]7(6):
    Peroxisome proliferator-activated receptor γ activation ameliorates liver fibrosis-differential action of transcription factor EB and autophagy on hepatocytes and stellate cells.
    Yunjin J Yum, Jin Yoo, Kyuhoon Bang, Ji Eun Jun, In-Kyung Jeong, Kyu Jeung Ahn, Ho Yeon Chung, You-Cheol Hwang.
       BACKGROUND: Peroxisome proliferator-activated receptor γ (PPARγ) activation suppresses HSC activation and liver fibrosis. Moreover, autophagy is implicated in hepatic lipid metabolism. Here, we determined whether PPARγ activation ameliorates HSC activation by downregulating transcription factor EB (TFEB)-mediated autophagy.
    METHODS AND RESULTS: Atg7 or Tfeb knockdown in human HSC line LX-2 cells downregulated the expression of fibrogenic markers including α smooth muscle actin, glial fibrillary acidic protein, and collagen type 1. Conversely, Atg7 or Tfeb overexpression upregulated fibrogenic marker expression. Rosiglitazone (RGZ)-mediated PPARγ activation and/or overexpression in LX-2 cells and primary HSCs decreased autophagy, as indicated by LC3B conversion, total and nuclear-TFEB contents, mRFP-LC3 and BODIPY 493/503 colocalization, and GFP-LC3 and LysoTracker colocalization. RGZ treatment decreased liver fat content, liver enzyme levels, and fibrogenic marker expression in high-fat high-cholesterol diet-fed mice. Electron microscopy showed that RGZ treatment restored the high-fat high-cholesterol diet-mediated lipid droplet decrease and autophagic vesicle induction in primary HSCs and liver tissues. However, TFEB overexpression in LX-2 cells offset the aforementioned effects of RGZ on autophagic flux, lipid droplets, and fibrogenic marker expression.
    CONCLUSIONS: Activation of PPARγ with RGZ ameliorated liver fibrosis and downregulation of TFEB and autophagy in HSCs may be important for the antifibrotic effects of PPARγ activation.
    DOI:  https://doi.org/10.1097/HC9.0000000000000154
  63. Phenomics. 2023 Apr;3(2): 119-129
    Autophagic Clearance of Lipid Droplets Alters Metabolic Phenotypes in a Genetic Obesity-Diabetes Mouse Model.
    Ningxie Chen, Boxun Lu, Yuhua Fu.
      Lipid droplets (LDs) are intracellular organelles that store neutral lipids, and their aberrant accumulation is associated with many diseases including metabolic disorders such as obesity and diabetes. Meanwhile, the potential pathological contributions of LDs in these diseases are unclear, likely due to a lack of chemical biology tools to clear LDs. We recently developed LD-clearance small molecule compounds, Lipid Droplets·AuTophagy TEthering Compounds (LD·ATTECs), that are able to induce autophagic clearance of LDs in cells and in the liver of db/db (C57BL/6J Leprdb/Leprdb) mouse model, which is a widely used genetic model for obesity-diabetes. Meanwhile, the potential effects on the metabolic phenotype remain to be elucidated. Here, using the metabolic cage assay and the blood glucose assay, we performed phenotypic characterization of the effects of the autophagic degradation of LDs by LD·ATTECs in the db/db mouse model. The study reveals that LD·ATTECs increased the oxygen uptake of mice and the release of carbon dioxide, enhanced the heat production of animals, partially enhanced the exercise during the dark phase, decreased the blood glucose level and improved insulin sensitivity. Collectively, the study characterized the metabolic phenotypes induced by LD·ATTECs in an obesity-diabetes mouse model, revealing novel functional impacts of autophagic clearance of LDs and providing insights into LD biology and obesity-diabetes pathogenesis from the phenotypic perspective.
    Keywords:  Autophagy; LD·ATTECs; Lipid droplets; Metabolic cages; Obesity–diabetes; Targeted degradation
    DOI:  https://doi.org/10.1007/s43657-022-00080-z
  64. Biochem Pharmacol. 2023 May 15. pii: S0006-2952(23)00183-1. [Epub ahead of print] 115592
    SIRT3-mediated autophagy contributes to ferroptosis-induced anticancer by inducing the formation of BECN1-SLC7A11 complex.
    Ping Huang, Han Zhao, Xiafang Pan, Jinying Li, Wentian Pan, Hua Dai, Jia Wang, Chunhua Xia, Fanglan Liu.
      Ferroptosis is an autophagy-dependent cell death associated with iron accumulation and lipid peroxidation, which plays a crucial part in anticancer activity. Sirtuin 3 (SIRT3) positively regulates autophagy by phosphorylation of activated protein kinase (AMPK). However, whether SIRT3-mediated autophagy can inhibit the cystine/glutamate antiporter (system Xc-) activity by inducing the formation of a BECN1-SLC7A11 complex and consequently promote induction of ferroptosis is unknown. Using both in vitro and in vivo models, we revealed that combination treatment with erastin and TGF-β1 decreased the expression of epithelial-mesenchymal transition-related markers and inhibited the invasion and metastasis of breast cancer. Furthermore, TGF-β1 promoted erastin-induced ferroptosis-related indicators in MCF-7 cells and tumor-bearing nude mouse models. Interestingly, the expression of SIRT3, p-AMPK, and autophagy-related markers were significantly elevated after co-treatment with erastin and TGF-β1, suggesting that combination treatment of erastin and TGF-β1 mediated autophagy by the SIRT3/AMPK signaling pathway. In addition, erastin-induced BECN1-SLC7A11 complexes were more abundant after co-treatment with TGF-β1. This effect was inhibited by the autophagy inhibitor 3-methyladenine or siSIRT3, further revealing that combination treatment of erastin and TGF-β1 mediated autophagy-dependent ferroptosis by inducing the formation of BECN1-SLC7A11 complexes. Our results agreed with the concept that BECN1 directly binds to SLC7A11 to inhibit system Xc- activity. In summary, our studies confirmed that SIRT3-mediated autophagy is conducive to ferroptosis-mediated anticancer activity by inducing the formation of BECN1-SLC7A11 complexes, which is a potential therapeutic approach for treating breast cancer.
    Keywords:  Ferroptosis; SIRT3; autophagy; breast cancer; tumor metastasis
    DOI:  https://doi.org/10.1016/j.bcp.2023.115592
  65. Alzheimers Dement. 2023 May 16.
    Preserved autophagy in cognitively intact non-demented individuals with Alzheimer's neuropathology.
    Batbayar Tumurbaatar, Anna Fracassi, Pietro Scaduto, Jutatip Guptarak, Randall Woltjer, Daniel Jupiter, Giulio Taglialatela.
       INTRODUCTION: Growing evidence supports that dysfunctional autophagy, the major cell mechanism responsible for removing protein aggregates and a route of clearance for Tau in healthy neurons, is a major finding in demented Alzheimer's disease (AD) patients. However, the association of autophagy with maintenance of cognitive integrity in resilient individuals who have AD neuropathology but remain non-demented (NDAN) has not been evaluated.
    METHODS: Using post mortem brain samples from age-matched healthy control, AD, and NDAN subjects, we evaluated autophagy in relation to Tau pathology using Western blot, immunofluorescence and RNA-seq.
    RESULTS: Compared to AD patients, NDAN subjects had preserved autophagy and reduced tauopathy. Furthermore, expression of autophagy genes and AD-related proteins were significantly associated in NDAN compared to AD and control subjects.
    DISCUSSION: Our results suggest preserved autophagy is a protective mechanism that maintains cognitive integrity in NDAN individuals. This novel observation supports the potential of autophagy-inducing strategies in AD therapeutics.
    HIGHLIGHTS: NDAN subjects have preserved autophagic protein levels comparable with control subjects. Compared to control subjects, NDAN subjects have significantly reduced Tau oligomers and PHF Tau phosphorylation at synapses that negatively correlate with autophagy markers. Transcription of autophagy genes strongly associates with AD-related proteins in NDAN donors.
    Keywords:  Alzheimer's disease; Tau; autophagy; resilience
    DOI:  https://doi.org/10.1002/alz.13074
  66. Brain Sci. 2023 Mar 24. pii: 536. [Epub ahead of print]13(4):
    mTORC1-Dependent Protein and Parkinson's Disease: A Mendelian Randomization Study.
    Cheng Tan, Jianzhong Ai, Ye Zhu.
       BACKGROUND: The mTOR pathway is crucial in controlling the growth, differentiation, and survival of neurons, and its pharmacological targeting has promising potential as a treatment for Parkinson's disease. However, the function of mTORC1 downstream proteins, such as RPS6K, EIF4EBP, EIF-4E, EIF-4G, and EIF4A, in PD development remains unclear.
    METHODS: We performed a Mendelian randomization study to evaluate the causal relationship between mTORC1 downstream proteins and Parkinson's disease. We utilized various MR methods, including inverse-variance-weighted, weighted median, MR-Egger, MR-PRESSO, and MR-RAPS, and conducted sensitivity analyses to identify potential pleiotropy and heterogeneity.
    RESULTS: The genetic proxy EIF4EBP was found to be inversely related to PD risk (OR = 0.79, 95% CI = 0.67-0.92, p = 0.003), with the results from WM, MR-PRESSO, and MR-RAPS being consistent. The plasma protein levels of EIF4G were also observed to show a suggestive protective effect on PD (OR = 0.85, 95% CI = 0.75-0.97, p = 0.014). No clear causal effect was found for the genetically predicted RP-S6K, EIF-4E, and EIF-4A on PD risk. Sensitivity analyses showed no significant imbalanced pleiotropy or heterogeneity, indicating that the MR estimates were robust and independent.
    CONCLUSION: Our unbiased MR study highlights the protective role of serum EIF4EBP levels in PD, suggesting that the pharmacological activation of EIF4EBP activity could be a promising treatment option for PD.
    Keywords:  EIF4EBP; EIF4G; Mendelian randomization; Parkinson’s disease; mTORC1-dependent protein
    DOI:  https://doi.org/10.3390/brainsci13040536
  67. Biomed J. 2023 May 11. pii: S2319-4170(23)00042-2. [Epub ahead of print] 100605
    Curcumin suppresses RANKL-induced osteoclast precursor autophagy in osteoclastogenesis by inhibiting RANK signaling and downstream JNK-BCL2-Beclin1 pathway.
    Dianshan Ke, Haoying Xu, Junyong Han, Hanhao Dai, Xinwen Wang, Jun Luo, Yunlong Yu, Jie Xu.
       BACKGROUND: Curcumin ameliorates bone loss by inhibiting osteoclastogenesis. Curcumin inhibits RANKL-promoted autophagy in osteoclast precursors (OCPs), which mediates its anti-osteoclastogenic effect. But the role of RANKL signaling in curcumin-regulated OCP autophagy is unknown. This study aimed to explore the relationship between curcumin, RANKL signaling, and OCP autophagy during osteoclastogenesis.
    METHODS: We investigated the role of curcumin in RANKL-related molecular signaling in OCPs, and identified the significance of RANK-TRAF6 signaling in curcumin-treated osteoclastogenesis and OCP autophagy using flow sorting and lentiviral transduction. Tg-hRANKL mice were used to observe the in vivo effects of curcumin on RANKL-regulated bone loss, osteoclastogenesis, and OCP autophagy. The significance of JNK-BCL2-Beclin1 pathway in curcumin-regulated OCP autophagy with RANKL was explored via rescue assays and BCL2 phosphorylation detection.
    RESULTS: Curcumin inhibited RANKL-related molecular signaling in OCPs, and repressed osteoclast differentiation and autophagy in sorted RANK+ OCPs but did not affect those of RANK- OCPs. Curcumin-inhibited osteoclast differentiation and OCP autophagy were recovered by TRAF6 overexpression. But curcumin lost these effects under TRAF6 knockdown. Furthermore, curcumin prevented the decrease in bone mass and the increase in trabecular osteoclast formation and autophagy in RANK+ OCPs in Tg-hRANKL mice. Additionally, curcumin-inhibited OCP autophagy with RANKL was reversed by JNK activator anisomycin and TAT-Beclin1 overexpressing Beclin1. Curcumin inhibited BCL2 phosphorylation at Ser70 and enhanced protein interaction between BCL2 and Beclin1 in OCPs.
    CONCLUSIONS: Curcumin suppresses RANKL-promoted OCP autophagy by inhibiting signaling pathway downstream of RANKL, contributing to its anti-osteoclastogenic effect. Moreover, JNK-BCL2-Beclin1 pathway plays an important role in curcumin-regulated OCP autophagy.
    Keywords:  Autophagy; BCL2; Beclin1; Curcumin; Osteoclast; RANKL
    DOI:  https://doi.org/10.1016/j.bj.2023.100605
  68. Cell Death Dis. 2023 Apr 25. 14(4): 292
    Butyrate dictates ferroptosis sensitivity through FFAR2-mTOR signaling.
    GuoYan Wang, SenLin Qin, Lei Chen, HuiJun Geng, YiNing Zheng, Chao Xia, JunHu Yao, Lu Deng.
      Evidence shows that short-chain fatty acids (SCFAs) play an important role in health maintenance and disease development. In particular, butyrate is known to induce apoptosis and autophagy. However, it remains largely unclear whether butyrate can regulate cell ferroptosis, and the mechanism by which has not been studied. In this study, we found that RAS-selective lethal compound 3 (RSL3)- and erastin-induced cell ferroptosis were enhanced by sodium butyrate (NaB). With regard to the underlying mechanism, our results showed that NaB promoted ferroptosis by inducing lipid ROS production via downregulating the expression of solute carrier family 7 member 11 (SLC7A11) and glutathione peroxidase 4 (GPX4). Moreover, the FFAR2-AKT-NRF2 axis and FFAR2-mTORC1 axis accounts for the NaB-mediated downregulation of SLC7A11 and GPX4, respectively, in a cAMP-PKA-dependent manner. Functionally, we found that NaB can inhibit tumor growth and the inhibitory effect could be eliminated by administrating MHY1485 (mTORC1 activator) and Ferr-1 (ferroptosis inhibitor). Altogether, in vivo results suggest that NaB treatment is correlated to the mTOR-dependent ferroptosis and consequent tumor growth through xenografts and colitis-associated colorectal tumorigenesis, implicating the potential clinical applications of NaB for future colorectal cancer treatments. Based on all these findings, we have proposed a regulatory mechanism via which butyrate inhibits the mTOR pathway to control ferroptosis and consequent tumorigenesis.
    DOI:  https://doi.org/10.1038/s41419-023-05778-0
  69. Folia Morphol (Warsz). 2023 May 15.
    Autophagy exerts a protective role in cervical spinal cord injury by microglia inhibition through the NF-κB pathway.
    Baicheng Yang, Xinming Yang.
      Spinal cord injury (SCI) is a serious trauma to the central nervous system. M1/M2 microglial polarization as well as the following neuroinflammatory response are crucial factors in SCI. Autophagy plays an important role in SCI, but its neuroprotective or neurodegenerative role remains controversial. Here, we majorly probed the property of autophagy in SCI and uncover the regulatory relationship between autophagy and microglial polarization in SCI. In our study, the BBB score was declined in SCI. The cervical contusion SCI stimulated a sustaining neuropathic pain-linked phenotype characterized by thermal hyperalgesia as well as mechanical allodynia. It was revealed the structural damage to the spinal cord in SCI. Besides, the expression of microglia markers as well as inflammatory factor were promoted in SCI. Cervical contusion SCI induced autophagy inhibition and NF-κB activation in mice. More importantly, enhanced autophagy induced by rapamycin (RAP) suppressed the NF-κB pathway and alleviated cervical contusion SCI-induced neurological function damage in mice. Additionally, RAP promoted microglia M2 polarization and improved microglia-mediated inflammatory response. In conclusion, our study demonstrated that autophagy played a protective role in cervical SCI by promoting microglia polarization toward M2 through the NF-κB pathway. Our study may provide a novel sight for SCI treatment.
    Keywords:  NF-κB; autophagy; microglia activation; spinal cord injury
    DOI:  https://doi.org/10.5603/FM.a2023.0036
  70. Biochim Biophys Acta Mol Cell Res. 2023 May 10. pii: S0167-4889(23)00058-7. [Epub ahead of print] 119486
    Bacterial extracellular vesicles induced oxidative stress and mitophagy through mTOR pathways in colon cancer cells, HT-29: Implications for bioactivity.
    Thorria R Marzoog, Majid S Jabir, Sumayah Ibraheem, Sabrean F Jawad, Sawsan S Hamzah, Ghassan M Sulaiman, Hamdoon A Mohammed, Riaz A Khan.
      Bacterial-extracellular-vesicles (BEVs) derived from Escherichia coli, strain-A5922, were used as a therapeutic tool to treat colon cancer cells, HT-29. BEVs induced oxidative stress, and observed mitochondrial autophagy, known as mitophagy, were crucial in initiation of treatment. The mitophagy, induced by the BEVs in HT-29 cells, produced adenocarcinomic cytotoxicity, and stopped the cells growth. The trigger for mitophagy, and an increase in productions of reactive oxygen species led to cellular oxidative stress, that eventually led to cells death. A reduction in the mitochondrial membrane potential, and an increase in the PINK1 expressions confirmed the oxidative stress involvements. The BEVs triggered cytotoxicity, and mitophagy in the HT-29 carcinoid cells, channelized through the Akt/mTOR pathways connecting the cellular oxidative stress, effectively played its part to cause cells death. These findings substantiated the BEVs' potential as a plausible tool for treating, and possibly preventing the colorectal cancer.
    Keywords:  Anticancer; Autophagy; BEVs; Bacterial extracellular vesicles; Cancer cell-line; Cytotoxicity; E. coli; HT-29 cells; Mitophagy; OIMVs; OMVs; Outer inner membrane vesicles; Outer membrane vesicles; Oxidation; Oxidative stress; ROS; Reactive oxygen species; Strain A 5922
    DOI:  https://doi.org/10.1016/j.bbamcr.2023.119486
  71. Cancers (Basel). 2023 May 08. pii: 2660. [Epub ahead of print]15(9):
    Senolytic Flavonoids Enhance Type-I and Type-II Cell Death in Human Radioresistant Colon Cancer Cells through AMPK/MAPK Pathway.
    Maria Russo, Stefania Moccia, Diomira Luongo, Gian Luigi Russo.
      Resistance to cancer therapies remains a clinical challenge and an unsolved problem. In a previous study, we characterized a new colon cancer cell line, namely HT500, derived from human HT29 cells and resistant to clinically relevant levels of ionizing radiation (IR). Here, we explored the effects of two natural flavonoids, quercetin (Q) and fisetin (F), well-known senolytic agents that inhibit genotoxic stress by selectively removing senescent cells. We hypothesized that the biochemical mechanisms responsible for the radiosensitising effects of these natural senolytics could intercept multiple biochemical pathways of signal transduction correlated to cell death resistance. Radioresistant HT500 cells modulate autophagic flux differently than HT29 cells and secrete pro-inflammatory cytokines (IL-8), commonly associated with senescence-related secretory phenotypes (SASP). Q and F inhibit PI3K/AKT and ERK pathways, which promote p16INK4 stability and resistance to apoptosis, but they also activate AMPK and ULK kinases in response to autophagic stress at an early stage. In summary, the combination of natural senolytics and IR activates two forms of cell death: apoptosis correlated to the inhibition of ERKs and lethal autophagy dependent on AMPK kinase. Our study confirms that senescence and autophagy partially overlap, share common modulatory pathways, and reveal how senolytic flavonoids can play an important role in these processes.
    Keywords:  AMPK; ERKs kinases; SASP; autophagy; natural senolytics; radioresistance
    DOI:  https://doi.org/10.3390/cancers15092660
  72. Cells. 2023 04 19. pii: 1188. [Epub ahead of print]12(8):
    Reversing Dysdynamism to Interrupt Mitochondrial Degeneration in Amyotrophic Lateral Sclerosis.
    Gerald W Dorn.
      Amyotrophic lateral sclerosis is one of several chronic neurodegenerative conditions in which mitochondrial abnormalities are posited to contribute to disease progression. Therapeutic options targeting mitochondria include enhancing metabolism, suppressing reactive oxygen production and disrupting mitochondria-mediated programmed cell death pathways. Herein is reviewed mechanistic evidence supporting a meaningful pathophysiological role for the constellation of abnormal mitochondrial fusion, fission and transport, collectively designated mitochondrial dysdynamism, in ALS. Following this is a discussion on preclinical studies in ALS mice that seemingly validate the idea that normalizing mitochondrial dynamism can delay ALS by interrupting a vicious cycle of mitochondrial degeneration, leading to neuronal die-back and death. Finally, the relative benefits of suppressing mitochondrial fusion vs. enhancing mitochondrial fusion in ALS are speculated upon, and the paper concludes with the prediction that the two approaches could be additive or synergistic, although a side-by-side comparative trial may be challenging to perform.
    Keywords:  mitochondrial fission; mitochondrial fusion; mitochondrial transport; mitophagy
    DOI:  https://doi.org/10.3390/cells12081188
  73. Int J Mol Sci. 2023 Apr 24. pii: 7786. [Epub ahead of print]24(9):
    Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
    Xiao-Min Li, Jun-Hao Wen, Ze-Sen Feng, Yun-Shan Wu, Dong-Yi Li, Shan Liang, Dan Wu, Hong-Luan Wu, Shang-Mei Li, Zhen-Nan Ye, Chen Yang, Lin Sun, Ji-Xin Tang, Hua-Feng Liu.
      Transcription factors can affect autophagy activity by promoting or inhibiting the expression of autophagic and lysosomal genes. As a member of the zinc finger family DNA-binding proteins, ZKSCAN3 has been reported to function as a transcriptional repressor of autophagy, silencing of which can induce autophagy and promote lysosomal biogenesis in cancer cells. However, studies in Zkscan3 knockout mice showed that the deficiency of ZKSCAN3 did not induce autophagy or increase lysosomal biogenesis. In order to further explore the role of ZKSCAN3 in the transcriptional regulation of autophagic genes in human cancer and non-cancer cells, we generated ZKSCAN3 knockout HK-2 (non-cancer) and Hela (cancer) cells via the CRISPR/Cas9 system and analyzed the differences in gene expression between ZKSCAN3 deleted cells and non-deleted cells through fluorescence quantitative PCR, western blot and transcriptome sequencing, with special attention to the differences in expression of autophagic and lysosomal genes. We found that ZKSCAN3 may be a cancer-related gene involved in cancer progression, but not an essential transcriptional repressor of autophagic or lysosomal genes, as the lacking of ZKSCAN3 cannot significantly promote the expression of autophagic and lysosomal genes.
    Keywords:  CRISPR/Cas9; ZKSCAN3; autophagy; lysosomal biogenesis; senescence; transcriptome sequencing
    DOI:  https://doi.org/10.3390/ijms24097786
  74. J Biochem Mol Toxicol. 2023 Apr 26. e23379
    Ox-LDL aggravates contrast-induced injury of renal tubular epithelial cells.
    Dingwei Yang, Xueyan Yang, Sha Chen, Meiling Lv, Jin Tan, Dingping Yang.
      Hypercholesterolemia can aggravate contrast-induced acute kidney injury, and the exacerbation of renal tubular epithelial cell (RTEC) injury is a major cause. However, the exact mechanisms remain obscure. Mitophagy, a type of autophagy, selectively eliminates damaged mitochondria and reduces mitochondrial oxidative stress, which is strongly implicated in cell homeostasis and acute kidney injury. Oxidized low-density lipoprotein (Ox-LDL) is accumulated in hypercholesterolemia and has a cytotoxic effect. This study aimed to determine whether and how ox-LDL exacerbates contrast-induced injury in RTECs and to further explore whether PINK1/Parkin-dependent mitophagy is involved in this process. Iohexol and ox-LDL were used alone or in combination to treat HK-2 cells. Rapamycin pretreatment was utilized to enhance mitophagy. Cell viability, apoptosis, mitochondrial membrane potential (MMP) and mitochondrial reactive oxygen species (mtROS) were detected by cell counting kit-8, TUNEL staining, JC-1 kit and MitoSOX fluorescence, respectively. The expression of mitophagy-related proteins (including PINK1, Parkin, and so on) and cleaved caspase-3 was confirmed by western blot. Colocalization of MitoTracker-labeled mitochondria and LysoTracker-labeled lysosomes was observed by fluorescence microscopy to evaluate mitophagy. The results of our study showed that ox-LDL aggravated MMP decline, mtROS release and apoptosis in iohexol-treated HK-2 cells, accompanied by a further increased autophagy level. Enhancement of PINK1/Parkin-dependent mitophagy by rapamycin alleviated apoptosis and mitochondrial injury in HK-2 cells in response to iohexol under ox-LDL condition. Therefore, our findings indicate that ox-LDL aggravates contrast-induced injury of RTECs by increasing mitochondrial damage and mitochondrial oxidative stress, which may be associated with the relative insufficiency of PINK1/Parkin-dependent mitophagy.
    Keywords:  CI-AKI; mitochondrial damage; mitophagy; ox-LDL; oxidative stress
    DOI:  https://doi.org/10.1002/jbt.23379
  75. J Cell Biol. 2023 Jun 05. pii: e202305007. [Epub ahead of print]222(6):
    Not just protons: Chloride also activates lysosomal acidic hydrolases.
    Xinghua Feng, Siyu Liu, Haoxing Xu.
      Lysosomal hydrolases require an acidic lumen for their optimal activities. In this issue, two independent groups (Wu et al. 2023. J. Cell Biol.https://doi.org/10.1083/jcb.202208155; Zhang et al. 2023. J. Cell. Biol.https://doi.org/10.1083/jcb.202210063) report that hydrolase activation also requires high intralysosomal Cl-, which is established by the lysosomal Cl-/H+ exchanger ClC-7.
    DOI:  https://doi.org/10.1083/jcb.202305007
  76. Microbiol Spectr. 2023 May 16. e0017123
    Transcriptional Regulation of Autophagy-Related Genes by Sin3 Negatively Modulates Autophagy in Magnaporthe oryzae.
    Zhongling Wu, Huanbin Shi, Yuan Li, Fei Yan, Ziyue Sun, Chuyu Lin, Mengting Xu, Fucheng Lin, Yanjun Kou, Zeng Tao.
      Autophagy is a conserved degradation and recycling pathway in eukaryotes and is important for their normal growth and development. An appropriate status of autophagy is crucial for organisms which is tightly regulated both temporally and continuously. Transcriptional regulation of autophagy-related genes (ATGs) is an important layer in autophagy regulation. However, the transcriptional regulators and their mechanisms are still unclear, especially in fungal pathogens. Here, we identified Sin3, a component of the histone deacetylase complex, as a transcriptional repressor of ATGs and negative regulator of autophagy induction in the rice fungal pathogen Magnaporthe oryzae. A loss of SIN3 resulted in upregulated expression of ATGs and promoted autophagy with an increased number of autophagosomes under normal growth conditions. Furthermore, we found that Sin3 negatively regulated the transcription of ATG1, ATG13, and ATG17 through direct occupancy and changed levels of histone acetylation. Under nutrient-deficient conditions, the transcription of SIN3 was downregulated, and the reduced occupancy of Sin3 from those ATGs resulted in histone hyperacetylation and activated their transcription and in turn promoted autophagy. Thus, our study uncovers a new mechanism of Sin3 in modulating autophagy through transcriptional regulation. IMPORTANCE Autophagy is an evolutionarily conserved metabolic process and is required for the growth and pathogenicity of phytopathogenic fungi. The transcriptional regulators and precise mechanisms of regulating autophagy, as well as whether the induction or repression of ATGs is associated with autophagy level, are still poorly understood in M. oryzae. In this study, we revealed that Sin3 acts as a transcriptional repressor of ATGs to negatively regulate autophagy level in M. oryzae. Under the nutrient-rich conditions, Sin3 inhibits autophagy with a basal level through directly repressing the transcription of ATG1-ATG13-ATG17. Upon nutrient-deficient treatment, the transcriptional level of SIN3 would decrease and dissociation of Sin3 from those ATGs associates with histone hyperacetylation and activates their transcriptional expression and in turn contributes to autophagy induction. Our findings are important as we uncover a new mechanism of Sin3 for the first time to negatively modulate autophagy at the transcriptional level in M. oryzae.
    Keywords:  ATG8; fungal pathogen; histone deacetylation; rice blast; transcriptional regulation
    DOI:  https://doi.org/10.1128/spectrum.00171-23
  77. Autophagy. 2023 May 19. 1-18
    Impaired lipophagy induced-microglial lipid droplets accumulation contributes to the buildup of TREM1 in diabetes-associated cognitive impairment.
    Qing Li, Yujing Zhao, Hongyan Guo, Qiao Li, Chaoying Yan, Yansong Li, Shuxuan He, Nan Wang, Qiang Wang.
      Neuroinflammation caused by microglial activation and consequent neurological impairment are prominent features of diabetes-associated cognitive impairment (DACI). Microglial lipophagy, a significant fraction of autophagy contributing to lipid homeostasis and inflammation, had mostly been ignored in DACI. Microglial lipid droplets (LDs) accumulation is a characteristic of aging, however, little is known about the pathological role of microglial lipophagy and LDs in DACI. Therefore, we hypothesized that microglial lipophagy could be an Achilles's heel exploitable to develop effective strategies for DACI therapy. Here, starting with characterization of microglial accumulation of LDs in leptin receptor-deficient (db/db) mice and in high-fat diet and STZ (HFD/STZ) induced T2DM mice, as well as in high-glucose (HG)-treated mice BV2, human HMC3 and primary mice microglia, we revealed that HG-dampened lipophagy was responsible for LDs accumulation in microglia. Mechanistically, accumulated LDs colocalized with the microglial specific inflammatory amplifier TREM1 (triggering receptor expressed on myeloid cells 1), resulting in the buildup of microglial TREM1, which in turn aggravates HG-induced lipophagy damage and subsequently promoted HG-induced neuroinflammatory cascades via NLRP3 (NLR family pyrin domain containing 3) inflammasome. Moreover, pharmacological blockade of TREM1 with LP17 in db/db mice and HFD/STZ mice inhibited accumulation of LDs and TREM1, reduced hippocampal neuronal inflammatory damage, and consequently improved cognitive functions. Taken together, these findings uncover a previously unappreciated mechanism of impaired lipophagy-induced TREM1 accumulation in microglia and neuroinflammation in DACI, suggesting its translational potential as an attractive therapeutic target for delaying diabetes-associated cognitive decline.Abbreviations: ACTB: beta actin; AIF1/IBA1: allograft inflammatory factor 1; ALB: albumin; ARG1: arginase 1; ATG3: autophagy related 3; Baf: bafilomycin A1; BECN1: beclin 1, autophagy related; BW: body weight; CNS: central nervous system; Co-IP: co-immunoprecipitation; DACI: diabetes-associated cognitive impairment; DAPI: 4',6-diamidino-2-phenylindole; DGs: dentate gyrus; DLG4/PSD95: discs large MAGUK scaffold protein 4; DMEM: Dulbecco's modified Eagle's medium; DSST: digit symbol substitution test; EDTA: ethylenedinitrilotetraacetic acid; ELISA: enzyme linked immunosorbent assay; GFAP: glial fibrillary acidic protein; HFD: high-fat diet; HG: high glucose; IFNG/IFN-γ: interferon gamma; IL1B/IL-1β: interleukin 1 beta; IL4: interleukin 4; IL6: interleukin 6; IL10: interleukin 10; LDs: lipid droplets; LPS: lipopolysaccharide; MAP2: microtubule associated protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MWM: morris water maze; NFKB/NF-κB: nuclear factor of kappa light polypeptide gene enhancer in B cells; NLRP3: NLR family pyrin domain containing 3; NOS2/iNOS: nitric oxide synthase 2, inducible; NOR: novel object recognition; OA: oleic acid; PA: palmitic acid; PBS: phosphate-buffered saline; PFA: paraformaldehyde; PLIN2: perilipin 2; PLIN3: perilipin 3; PS: penicillin-streptomycin solution; RAPA: rapamycin; RBFOX3/NeuN: RNA binding protein, fox-1 homolog (C. elegans) 3; RELA/p65: RELA proto-oncogene, NF-kB subunit; ROS: reactive oxygen species; RT: room temperature; RT-qPCR: Reverse transcription quantitative real-time polymerase chain reaction; STZ: streptozotocin; SQSTM1/p62: sequestosome 1; SYK: spleen asociated tyrosine kinase; SYP: synaptophysin; T2DM: type 2 diabetes mellitus; TNF/TNF-α: tumor necrosis factor; TREM1: triggering receptor expressed on myeloid cells 1; TUNEL: terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling.
    Keywords:  TREM1; hippocampus; lipid droplets; lipophagy; neuroinflammation; type 2 diabetes mellitus
    DOI:  https://doi.org/10.1080/15548627.2023.2213984
  78. Cell Death Dis. 2023 05 13. 14(5): 324
    Obesity impairs cardiolipin-dependent mitophagy and therapeutic intercellular mitochondrial transfer ability of mesenchymal stem cells.
    Shakti Sagar, Md Imam Faizan, Nisha Chaudhary, Vandana Singh, Praveen Singh, Atish Gheware, Khushboo Sharma, Iqbal Azmi, Vijay Pal Singh, Gaurav Kharya, Ulaganathan Mabalirajan, Anurag Agrawal, Tanveer Ahmad, Soumya Sinha Roy.
      Mesenchymal stem cell (MSC) transplantation alleviates metabolic defects in diseased recipient cells by intercellular mitochondrial transport (IMT). However, the effect of host metabolic conditions on IMT and thereby on the therapeutic efficacy of MSCs has largely remained unexplored. Here we found impaired mitophagy, and reduced IMT in MSCs derived from high-fat diet (HFD)-induced obese mouse (MSC-Ob). MSC-Ob failed to sequester their damaged mitochondria into LC3-dependent autophagosomes due to decrease in mitochondrial cardiolipin content, which we propose as a putative mitophagy receptor for LC3 in MSCs. Functionally, MSC-Ob exhibited diminished potential to rescue mitochondrial dysfunction and cell death in stress-induced airway epithelial cells. Pharmacological modulation of MSCs enhanced cardiolipin-dependent mitophagy and restored their IMT ability to airway epithelial cells. Therapeutically, these modulated MSCs attenuated features of allergic airway inflammation (AAI) in two independent mouse models by restoring healthy IMT. However, unmodulated MSC-Ob failed to do so. Notably, in human (h)MSCs, induced metabolic stress associated impaired cardiolipin-dependent mitophagy was restored upon pharmacological modulation. In summary, we have provided the first comprehensive molecular understanding of impaired mitophagy in obese-derived MSCs and highlight the importance of pharmacological modulation of these cells for therapeutic intervention. A MSCs obtained from (HFD)-induced obese mice (MSC-Ob) show underlying mitochondrial dysfunction with a concomitant decrease in cardiolipin content. These changes prevent LC3-cardiolipin interaction, thereby reducing dysfunctional mitochondria sequestration into LC3-autophagosomes and thus impaired mitophagy. The impaired mitophagy is associated with reduced intercellular mitochondrial transport (IMT) via tunneling nanotubes (TNTs) between MSC-Ob and epithelial cells in co-culture or in vivo. B Pyrroloquinoline quinone (PQQ) modulation in MSC-Ob restores mitochondrial health, cardiolipin content, and thereby sequestration of depolarized mitochondria into the autophagosomes to alleviate impaired mitophagy. Concomitantly, MSC-Ob shows restoration of mitochondrial health upon PQQ treatment (MSC-ObPQQ). During co-culture with epithelial cells or transplantation in vivo into the mice lungs, MSC-ObPQQ restores IMT and prevents epithelial cell death. C Upon transplantation in two independent allergic airway inflammatory mouse models, MSC-Ob failed to rescue the airway inflammation, hyperactivity, metabolic changes in epithelial cells. D PQQ modulated MSCs restored these metabolic defects and restored lung physiology and airway remodeling parameters.
    DOI:  https://doi.org/10.1038/s41419-023-05810-3
  79. Int J Mol Sci. 2023 Apr 28. pii: 7994. [Epub ahead of print]24(9):
    The Role of Exercise in Maintaining Mitochondrial Proteostasis in Parkinson's Disease.
    Jingwen Li, Yanli Xu, Tingting Liu, Yuxiang Xu, Xiantao Zhao, Jianshe Wei.
      Parkinson's disease (PD) is the second most common rapidly progressive neurodegenerative disease and has serious health and socio-economic consequences. Mitochondrial dysfunction is closely related to the onset and progression of PD, and the use of mitochondria as a target for PD therapy has been gaining traction in terms of both recognition and application. The disruption of mitochondrial proteostasis in the brain tissue of PD patients leads to mitochondrial dysfunction, which manifests as mitochondrial unfolded protein response, mitophagy, and mitochondrial oxidative phosphorylation. Physical exercise is important for the maintenance of human health, and has the great advantage of being a non-pharmacological therapy that is non-toxic, low-cost, and universally applicable. In this review, we investigate the relationships between exercise, mitochondrial proteostasis, and PD and explore the role and mechanisms of mitochondrial proteostasis in delaying PD through exercise.
    Keywords:  Parkinson’s disease; exercise; mitochondria; mitochondrial proteostasis; neurodegenerative disease
    DOI:  https://doi.org/10.3390/ijms24097994
  80. Int J Mol Sci. 2023 Apr 30. pii: 8100. [Epub ahead of print]24(9):
    The Small-Molecule Enhancers of Autophagy AUTEN-67 and -99 Delay Ageing in Drosophila Striated Muscle Cells.
    Marcell Komlós, Janka Szinyákovics, Gergő Falcsik, Tímea Sigmond, Bálint Jezsó, Tibor Vellai, Tibor Kovács.
      Autophagy (cellular self-degradation) plays a major role in maintaining the functional integrity (homeostasis) of essentially all eukaryotic cells. During the process, superfluous and damaged cellular constituents are delivered into the lysosomal compartment for enzymatic degradation. In humans, age-related defects in autophagy have been linked to the incidence of various age-associated degenerative pathologies (e.g., cancer, neurodegenerative diseases, diabetes, tissue atrophy and fibrosis, and immune deficiency) and accelerated ageing. Muscle mass decreases at detectable levels already in middle-aged patients, and this change can increase up to 30-50% at age 80. AUTEN-67 and -99, two small-molecule enhancers of autophagy with cytoprotective and anti-ageing effects have been previously identified and initially characterized. These compounds can increase the life span in wild-type and neurodegenerative model strains of the fruit fly Drosophila melanogaster. Adult flies were treated with these AUTEN molecules via feeding. Fluorescence and electron microscopy and Western blotting were used to assess the level of autophagy and cellular senescence. Flying tests were used to measure the locomotor ability of the treated animals at different ages. In the current study, the effects of AUTEN-67 and -99 were observed on striated muscle cells using the Drosophila indirect flight muscle (IFM) as a model. The two molecules were capable of inducing autophagy in IFM cells, thereby lowering the accumulation of protein aggregates and damaged mitochondria, both characterizing muscle ageing. Furthermore, the two molecules significantly improved the flying ability of treated animals. AUTEN-67 and -99 decrease the rate at which striated muscle cells age. These results may have a significant medical relevance that could be further examined in mammalian models.
    Keywords:  AUTEN-67; AUTEN-99; Drosophila; EDTP; MTMR14; ageing; autophagy induction; muscle ageing
    DOI:  https://doi.org/10.3390/ijms24098100
  81. Int J Mol Sci. 2023 May 08. pii: 8456. [Epub ahead of print]24(9):
    Protein Aggregates and Aggrephagy in Myopathies.
    Sara Gibertini, Alessandra Ruggieri, Marta Cheli, Lorenzo Maggi.
      A number of muscular disorders are hallmarked by the aggregation of misfolded proteins within muscle fibers. A specialized form of macroautophagy, termed aggrephagy, is designated to remove and degrade protein aggregates. This review aims to summarize what has been studied so far about the direct involvement of aggrephagy and the activation of the key players, among others, p62, NBR1, Alfy, Tollip, Optineurin, TAX1BP1 and CCT2 in muscular diseases. In the first part of the review, we describe the aggrephagy pathway with the involved proteins; then, we illustrate the muscular disorder histologically characterized by protein aggregates, highlighting the role of aggrephagy pathway abnormalities in these muscular disorders.
    Keywords:  aggrephagy; aggresome; muscle disorders; protein aggregates; protein quality control (PQC)
    DOI:  https://doi.org/10.3390/ijms24098456
  82. Nat Commun. 2023 May 18. 14(1): 2855
    Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription.
    Ália Dos Santos, Daniel E Rollins, Yukti Hari-Gupta, Hannah McArthur, Mingxue Du, Sabrina Yong Zi Ru, Kseniia Pidlisna, Ane Stranger, Faeeza Lorgat, Danielle Lambert, Ian Brown, Kevin Howland, Jesse Aaron, Lin Wang, Peter J I Ellis, Teng-Leong Chew, Marisa Martin-Fernandez, Alice L B Pyne, Christopher P Toseland.
      NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.
    DOI:  https://doi.org/10.1038/s41467-023-38572-9
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