bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020‒11‒15
thirty-one papers selected by
Viktor Korolchuk
Newcastle University


  1. iScience. 2020 Nov 20. 23(11): 101691
    Contreras PS, Tapia PJ, González-Hódar L, Peluso I, Soldati C, Napolitano G, Matarese M, Heras ML, Valls C, Martinez A, Balboa E, Castro J, Leal N, Platt FM, Sobota A, Winter D, Klein AD, Medina DL, Ballabio A, Alvarez AR, Zanlungo S.
      The transcription factor EB (TFEB) has emerged as a master regulator of lysosomal biogenesis, exocytosis, and autophagy, promoting the clearance of substrates stored in cells. c-Abl is a tyrosine kinase that participates in cellular signaling in physiological and pathophysiological conditions. In this study, we explored the connection between c-Abl and TFEB. Here, we show that under pharmacological and genetic c-Abl inhibition, TFEB translocates into the nucleus promoting the expression of its target genes independently of its well-known regulator, mammalian target of rapamycin complex 1. Active c-Abl induces TFEB phosphorylation on tyrosine and the inhibition of this kinase promotes lysosomal biogenesis, autophagy, and exocytosis. c-Abl inhibition in Niemann-Pick type C (NPC) models, a neurodegenerative disease characterized by cholesterol accumulation in lysosomes, promotes a cholesterol-lowering effect in a TFEB-dependent manner. Thus, c-Abl is a TFEB regulator that mediates its tyrosine phosphorylation, and the inhibition of c-Abl activates TFEB promoting cholesterol clearance in NPC models.
    Keywords:  Biological Sciences; Cell Biology; Molecular Biology
    DOI:  https://doi.org/10.1016/j.isci.2020.101691
  2. Autophagy. 2020 Nov 13. 1-17
    Siva Sankar D, Dengjel J.
      Autophagy summarizes evolutionarily conserved, intracellular degradation processes targeting cytoplasmic material for lysosomal degradation. These encompass constitutive processes as well as stress responses, which are often found dysregulated in diseases. Autophagy pathways help in the clearance of damaged organelles, protein aggregates and macromolecules, mediating their recycling and maintaining cellular homeostasis. Protein-protein interaction networks contribute to autophagosome biogenesis, substrate loading, vesicular trafficking and fusion, protein translocations across membranes and degradation in lysosomes. Hypothesis-free proteomic approaches tremendously helped in the functional characterization of protein-protein interactions to uncover molecular mechanisms regulating autophagy. In this review, we elaborate on the importance of understanding protein-protein-interactions of varying affinities and on the strengths of mass spectrometry-based proteomic approaches to study these, generating new mechanistic insights into autophagy regulation. We discuss in detail affinity purification approaches and recent developments in proximity labeling coupled to mass spectrometry, which uncovered molecular principles of autophagy mechanisms. Abbreviations: AMPK: AMP-activated protein kinase; AP-MS: affinity purification-mass spectrometry; APEX2: ascorbate peroxidase-2; ATG: autophagy related; BioID: proximity-dependent biotin identification; ER: endoplasmic reticulum; GFP: green fluorescent protein; iTRAQ: isobaric tag for relative and absolute quantification; MS: mass spectrometry; PCA: protein-fragment complementation assay; PL-MS: proximity labeling-mass spectrometry; PtdIns3P: phosphatidylinositol-3-phosphate; PTM: posttranslational modification; PUP-IT: pupylation-based interaction tagging; RFP: red fluorescent protein; SILAC: stable isotope labeling by amino acids in cell culture; TAP: tandem affinity purification; TMT: tandem mass tag.
    Keywords:  Autophagy; affinity purification; mass spectrometry; protein-protein interactions; proximity labeling; quantitative proteomics
    DOI:  https://doi.org/10.1080/15548627.2020.1847461
  3. Cell Rep. 2020 Nov 10. pii: S2211-1247(20)31360-7. [Epub ahead of print]33(6): 108371
    Carey KL, Paulus GLC, Wang L, Balce DR, Luo JW, Bergman P, Ferder IC, Kong L, Renaud N, Singh S, Kost-Alimova M, Nyfeler B, Lassen KG, Virgin HW, Xavier RJ.
      Transcription factor EB (TFEB) activates lysosomal biogenesis genes in response to environmental cues. Given implications of impaired TFEB signaling and lysosomal dysfunction in metabolic, neurological, and infectious diseases, we aim to systematically identify TFEB-directed circuits by examining transcriptional responses to TFEB subcellular localization and stimulation. We reveal that steady-state nuclear TFEB is sufficient to activate transcription of lysosomal, autophagy, and innate immunity genes, whereas other targets require higher thresholds of stimulation. Furthermore, we identify shared and distinct transcriptional signatures between mTOR inhibition and bacterial autophagy. Using a genome-wide CRISPR library, we find TFEB targets that protect cells from or sensitize cells to lysosomal cell death. BHLHE40 and BHLHE41, genes responsive to high, sustained levels of nuclear TFEB, act in opposition to TFEB upon lysosomal cell death induction. Further investigation identifies genes counter-regulated by TFEB and BHLHE40/41, adding this negative feedback to the current understanding of TFEB regulatory mechanisms.
    Keywords:  BHLHE40; BHLHE41; TFEB; autophagy; gene regulation; lysosome; xenophagy
    DOI:  https://doi.org/10.1016/j.celrep.2020.108371
  4. Autophagy. 2020 Nov 08.
    Stephani M, Picchianti L, Dagdas Y.
      Reticulophagy, the autophagic degradation of the endoplasmic reticulum, is crucial to maintain ER homeostasis during stress. Although several reticulophagy receptors have been discovered recently, most of them have been studied using nutrient starvation. How macroautophagy/autophagy cross-talks with other ER-quality control mechanisms is largely unknown. Using ATG8-based affinity proteomics in the model plant Arabidopsis thaliana, we identified AT5G06830/C53, a soluble protein that directly interacts with ATG8. Biochemical and biophysical characterization of C53-ATG8 interaction using both human (CDK5RAP3) and Arabidopsis proteins revealed that C53 binds ATG8 via shuffled Atg8-family interacting motifs (sAIMs) located at its intrinsically disordered region (IDR). C53 is recruited to phagophores, precursors to autophagosomes, during ER stress in an autophagy-dependent manner. Consistently, c53 mutants are highly sensitive to ER stress treatments. C53 senses ER stress by forming a tripartite receptor complex that involves UFL1, the E3 ligase that mediates ufmylation, and its ER-resident adaptor protein DDRGK1. C53 activity is regulated by another ubiquitin-like protein, UFM1, which is transferred from C53 to the ribosomes upon ribosome collision/stalling at the ER, thereby activating the C53 pathway to recycle stalled nascent chains. Altogether our findings suggest C53 forms an ancient quality control pathway that links ribosome-associated quality control with selective autophagy at the ER.
    Keywords:   Arabidopsis thaliana CDK5RAP3; ER-phagy; ER-quality control; UFMylation; ribosome stalling; selective autophagy; selective autophagy receptor
    DOI:  https://doi.org/10.1080/15548627.2020.1846304
  5. Mol Biol Rep. 2020 Nov 13.
    Jeger JL.
      Endosomes and lysosomes are membrane-bound organelles crucial for the normal functioning of the eukaryotic cell. The primary function of endosomes relates to the transportation of extracellular material into the intracellular domain. Lysosomes, on the other hand, are primarily involved in the degradation of macromolecules. Endosomes and lysosomes interact through two distinct pathways: kiss-and-run and direct fusion. In addition to the internalization of particles, endosomes also play an important role in cell signaling and autophagy. Disruptions in either of these processes may contribute to cancer development. Lysosomal proteins, such as cathepsins, can play a role in both tumorigenesis and cancer cell apoptosis. Since endosomal and lysosomal biogenesis and signaling are important components of normal cellular growth and proliferation, proteins involved in these processes are attractive targets for cancer research and, potentially, therapeutics. This literature review provides an overview of the endocytic pathway, endolysosome formation, and the interplay between endosomal/lysosomal biogenesis and carcinogenesis.
    Keywords:  Carcinogenesis; Cathepsins; Endocytosis; Endosomes; Lysosomes
    DOI:  https://doi.org/10.1007/s11033-020-05993-4
  6. Cell Cycle. 2020 Nov 10. 1-13
    Xu Y, Wu Y, Wang L, Qian C, Wang Q, Wan W.
      Ribosomal DNA (rDNA) transcription drives cell growth and cell proliferation via the product ribosomal RNA (rRNA), the essential component of ribosome. Given the fundamental role of rRNA in ribosome biogenesis, rDNA transcription has emerged as one of the effective targets for a number of human diseases including various types of cancers. In this study, we identify curcumin, an ancient drug, as a novel natural inhibitor of rDNA transcription. Curcumin treatment impairs the assembly of the RNA polymerase I preinitiation complex at rDNA promoters and represses rDNA promoter activity, which leads to the decrease of rRNA synthesis. In addition, curcumin treatment stimulates autophagosome formation and promotes autophagic degradation in cells. Mechanistically, curcumin inactivates the mechanistic target of rapamycin complex 1 (mTORC1), the upstream regulator of rDNA transcription and autophagy induction, by inhibiting mTOR lysosomal localization. Functionally, curcumin treatment inhibits protein synthesis, cell growth and cell proliferation. Taken together, these findings identify curcumin as an effective inhibitor of rDNA transcription and provide novel mechanisms for the anticancer properties of curcumin. Abbreviations: Atg: autophagy-related; GFP: green fluorescent protein; LAMP2: lysosomal associated membrane protein 2; LC3: microtubule-associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; mTORC1: mechanistic target of rapamycin complex 1; rDNA: ribosomal DNA; rRNA: ribosomal RNA; TP53INP2: tumor protein p53 inducible nuclear protein 2.
    Keywords:  Acetylation; TP53INP2; autophagy; curcumin; mTOR; rDNA transcription
    DOI:  https://doi.org/10.1080/15384101.2020.1843817
  7. Autophagy. 2020 Nov 10.
    Antonioli M, Pagni B, Vescovo T, Ellis R, Cosway B, Rollo F, Bordoni V, Agrati C, Labus M, Covello R, Benevolo M, Ippolito G, Robinson M, Piacentini M, Lovat P, Fimia GM.
      Oropharyngeal squamous cell carcinoma (OPSCC) is an increasing world health problem with a more favourable prognosis for patients with human papillomavirus (HPV)-positive tumors compared to those with HPV-negative OPSCC. How HPV confers a less aggressive phenotype, however, remains undefined. We demonstrated that HPV-positive OPSCC cells display reduced macroautophagy/autophagy activity, mediated by the ability of HPV-E7 to interact with AMBRA1, to compete with its binding to BECN1 and to trigger its calpain-dependent degradation. Moreover, we have shown that AMBRA1 downregulation and pharmacological inhibition of autophagy sensitized HPV-negative OPSCC cells to the cytotoxic effects of cisplatin. Importantly, semi-quantitative immunohistochemical analysis in primary OPSCCs confirmed that AMBRA1 expression is reduced in HPV-positive compared to HPV-negative tumors. Collectively, these data identify AMBRA1 as a key target of HPV to impair autophagy and propose the targeting of autophagy as a viable therapeutic strategy to improve treatment response of HPV-negative OPSCC.
    Keywords:  AMBRA1; AUTOPHAGY; CALPAINS; HPV-E7; Oropharyngeal squamous cell carcinoma
    DOI:  https://doi.org/10.1080/15548627.2020.1847444
  8. Curr Neurovasc Res. 2020 Nov 11.
    Maiese K.
      Metabolic disorders that include diabetes mellitus present significant challenges for maintaining the welfare of the global population. Metabolic diseases impact all systems of the body and despite current therapies that offer some protection through tight serum glucose control, ultimately such treatments cannot block the progression of disability and death realized with metabolic disorders. As a result, novel therapeutic avenues are critical for further development to address these concerns. An innovative strategy involves the vitamin nicotinamide and the pathways associated with the silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1), the mechanistic target of rapamycin (mTOR), mTOR Complex 1 (mTORC1), mTOR Complex 2 (mTORC2), AMP activated protein kinase (AMPK), and clock genes. Nicotinamide maintains an intimate relationship with these pathways to oversee metabolic disease and improve glucose utilization, limit mitochondrial dysfunction, block oxidative stress, potentially function as antiviral therapy, and foster cellular survival through mechanisms involving autophagy. However, the pathways of nicotinamide, SIRT1, mTOR, AMPK, and clock genes are complex and involve feedback pathways as well as trophic factors such as erythropoietin that require a careful balance to ensure metabolic homeostasis. Future work is warranted to gain additional insight into these vital pathways that can oversee both normal metabolic physiology and metabolic disease.
    Keywords:  AMP activated protein kinase (AMPK); Alzheimer';s disease; SARS-CoV-2; apoptosis; autophagy; circadian rhythm; clock genes; coronavirus disease 2019 (COVID-19); dementia; diabetes mellitus; erythropoietin; mechanistic target of rapamycin (mTOR); metformin; oxidative stress; poly-ADP-ribose polymerase (PARP); silent mating type information regulation 2 homolog 1 (Saccharomyces cerevisiae) (SIRT1); sirtuin; stem cells
    DOI:  https://doi.org/10.2174/1567202617999201111195232
  9. Bioessays. 2020 Nov 09. e2000187
    Ramaian Santhaseela A, Jayavelu T.
      Extensive studies have attributed the lysosomal localization of the mechanistic target of rapamycin complex 1 (mTORC1) during its activation. However, the exact biological significance of this lysosomal localization of mTORC1 remains ill-defined. Interestingly, findings have shown that localization of the lysosome itself is altered under conditions influencing mTORC1 activity. In this perspective, we hypothesize that the localization of mTORC1 and lysosome could be interconnected in a way that manifests regulation of autophagy that is already under progression at the time of mTORC1 activation. This provides a new possibility for autophagy regulation whose complete mechanistic insights remain to be determined.
    Keywords:  autophagy; lysosome; mechanistic target of rapamycin complex 1; signal transduction
    DOI:  https://doi.org/10.1002/bies.202000187
  10. Mol Cell. 2020 Oct 29. pii: S1097-2765(20)30725-5. [Epub ahead of print]
    Chen S, Liu S, Wang J, Wu Q, Wang A, Guan H, Zhang Q, Zhang D, Wang X, Song H, Qin J, Zou J, Jiang Z, Ouyang S, Feng XH, Liang T, Xu P.
      Mitochondrial morphology shifts rapidly to manage cellular metabolism, organelle integrity, and cell fate. It remains unknown whether innate nucleic acid sensing, the central and general mechanisms of monitoring both microbial invasion and cellular damage, can reprogram and govern mitochondrial dynamics and function. Here, we unexpectedly observed that upon activation of RIG-I-like receptor (RLR)-MAVS signaling, TBK1 directly phosphorylated DRP1/DNM1L, which disabled DRP1, preventing its high-order oligomerization and mitochondrial fragmentation function. The TBK1-DRP1 axis was essential for assembly of large MAVS aggregates and healthy antiviral immunity and underlay nutrient-triggered mitochondrial dynamics and cell fate determination. Knockin (KI) strategies mimicking TBK1-DRP1 signaling produced dominant-negative phenotypes reminiscent of human DRP1 inborn mutations, while interrupting the TBK1-DRP1 connection compromised antiviral responses. Thus, our findings establish an unrecognized function of innate immunity governing both morphology and physiology of a major organelle, identify a lacking loop during innate RNA sensing, and report an elegant mechanism of shaping mitochondrial dynamics.
    Keywords:  DRP1; RLR-MAVS; TBK1; antiviral immunity; cell fate determination; innate immunity; mitochondrial dynamics; mitochondrion; nucleic acid sensing; phosphorylation
    DOI:  https://doi.org/10.1016/j.molcel.2020.10.018
  11. Autophagy. 2020 Nov 08.
    Pan ZQ, Du LL.
      The protein kinase Atg1 is a key player in macroautophagy/autophagy, but how its activity is regulated in various organisms is inadequately understood. Our recent study showed that in the fission yeast Schizosaccharomyces pombe, Atg1 kinase activity depends on Atg11, but not Atg13, Atg17, or Atg101. Notably, a 62 amino acid region of S. pombe Atg11 is sufficient for activating Atg1. This region is composed of two parts: an Atg1-binding domain and a homodimerization domain. Atg11 uses this region to dimerize Atg1. Dimerized Atg1 is activated through cis-autophosphorylation.
    Keywords:   Schizosaccharomyces pombe ; Atg1; Atg11; autophagy; cis-autophosphorylation; dimerization; kinase activity
    DOI:  https://doi.org/10.1080/15548627.2020.1846303
  12. Acta Neuropathol Commun. 2020 Nov 09. 8(1): 189
    Quinn PMJ, Moreira PI, Ambrósio AF, Alves CH.
      Mutations in the PTEN-induced kinase 1 (PINK1) and Parkin RBR E3 ubiquitin-protein ligase (PARKIN) genes are associated with familial forms of Parkinson's disease (PD). PINK1, a protein kinase, and PARKIN, an E3 ubiquitin ligase, control the specific elimination of dysfunctional or superfluous mitochondria, thus fine-tuning mitochondrial network and preserving energy metabolism. PINK1 regulates PARKIN translocation in impaired mitochondria and drives their removal via selective autophagy, a process known as mitophagy. As knowledge obtained using different PINK1 and PARKIN transgenic animal models is being gathered, growing evidence supports the contribution of mitophagy impairment to several human pathologies, including PD and Alzheimer's diseases (AD). Therefore, therapeutic interventions aiming to modulate PINK1/PARKIN signalling might have the potential to treat these diseases. In this review, we will start by discussing how the interplay of PINK1 and PARKIN signalling helps mediate mitochondrial physiology. We will continue by debating the role of mitochondrial dysfunction in disorders such as amyotrophic lateral sclerosis, Alzheimer's, Huntington's and Parkinson's diseases, as well as eye diseases such as age-related macular degeneration and glaucoma, and the causative factors leading to PINK1/PARKIN-mediated neurodegeneration and neuroinflammation. Finally, we will discuss PINK1/PARKIN gene augmentation possibilities with a particular focus on AD, PD and glaucoma.
    Keywords:  Alzheimer’s disease; Mitophagy; Neurodegeneration; PARKIN; PINK1; Parkinson’s disease
    DOI:  https://doi.org/10.1186/s40478-020-01062-w
  13. Genes (Basel). 2020 Nov 11. pii: E1331. [Epub ahead of print]11(11):
    Hayashi K, Suzuki Y, Fujimoto C, Kanzaki S.
      The etiology of hearing impairment following cochlear damage can be caused by many factors, including congenital or acquired onset, ototoxic drugs, noise exposure, and aging. Regardless of the many different etiologies, a common pathologic change is auditory cell death. It may be difficult to explain hearing impairment only from the aspect of cell death including apoptosis, necrosis, or necroptosis because the level of hearing loss varies widely. Therefore, we focused on autophagy as an intracellular phenomenon functionally competing with cell death. Autophagy is a dynamic lysosomal degradation and recycling system in the eukaryotic cell, mandatory for controlling the balance between cell survival and cell death induced by cellular stress, and maintaining homeostasis of postmitotic cells, including hair cells (HCs) and spiral ganglion neurons (SGNs) in the inner ear. Autophagy is considered a candidate for the auditory cell fate decision factor, whereas autophagy deficiency could be one of major causes of hearing impairment. In this paper, we review the molecular mechanisms and biologic functions of autophagy in the auditory system and discuss the latest research concerning autophagy-related genes and sensorineural hearing loss to gain insight into the role of autophagic mechanisms in inner-ear disorders.
    Keywords:  autophagy- and lysosomal function-related genes; classical degradative autophagy; congenital disorder; genetics of hearing impairment
    DOI:  https://doi.org/10.3390/genes11111331
  14. Dev Cell. 2020 Nov 09. pii: S1534-5807(20)30797-8. [Epub ahead of print]55(3): 253-254
    Puschmann R, Loewith R.
      In this issue of Developmental Cell, Yang et al. (2020) report that both nutrient- and growth factor-dependent signaling impinge upon the RAG GTPases which in turn control TSC residency time on the lysosome membrane and ultimately mTORC1 activity.
    DOI:  https://doi.org/10.1016/j.devcel.2020.10.007
  15. Autophagy. 2020 Nov 08.
    Li J, Chen X, Kang R, Zeh H, Klionsky DJ, Tang D.
      Oncogenic KRAS mutation-driven pancreatic ductal adenocarcinoma is currently the fourth-leading cause of cancer-related deaths in the United States. Macroautophagy (hereafter "autophagy") is one of the lysosome-dependent degradation systems that can remove abnormal proteins, damaged organelles, or invading pathogens by activating dynamic membrane structures (e.g., phagophores, autophagosomes, and autolysosomes). Impaired autophagy (including excessive activation and defects) is a pathological feature of human diseases, including pancreatic cancer. However, dysfunctional autophagy has many types and plays a complex role in pancreatic tumor biology, depending on various factors, such as tumor stage, microenvironment, immunometabolic state, and death signals. As a modulator connecting various cellular events, pharmacological targeting of nonselective autophagy may lead to both good and bad therapeutic effects. In contrast, targeting selective autophagy could reduce potential side effects of the drugs used. In this review, we describe the advances and challenges of autophagy in the development and therapy of pancreatic cancer.
    Keywords:  PDAC; disease; lysosome; macroautophagy; pancreatic ductal adenocarcinoma; tumor
    DOI:  https://doi.org/10.1080/15548627.2020.1847462
  16. EMBO Mol Med. 2020 Nov 12. e12025
    Chastagner P, Loria F, Vargas JY, Tois J, I Diamond M, Okafo G, Brou C, Zurzolo C.
      Tau accumulation in the form of neurofibrillary tangles in the brain is a hallmark of tauopathies such as Alzheimer's disease (AD). Tau aggregates accumulate in brain regions in a defined spatiotemporal pattern and may induce the aggregation of native Tau in a prion-like manner. However, the underlying mechanisms of cell-to-cell spreading of Tau pathology are unknown and could involve encapsulation within exosomes, trans-synaptic passage, and tunneling nanotubes (TNTs). We have established a neuronal cell model to monitor both internalization of externally added fibrils, synthetic (K18) or Tau from AD brain extracts, and real-time conversion of microtubule-binding domain of Tau fused to a fluorescent marker into aggregates. We found that these endogenously formed deposits colabel with ubiquitin and p62 but are not recruited to macroautophagosomes, eventually escaping clearance. Furthermore, endogenous K18-seeded Tau aggregates spread to neighboring cells where they seed new deposits. Transfer of Tau aggregates depends on direct cell contact, and they are found inside TNTs connecting neuronal cells. We further demonstrate that contact-dependent transfer occurs in primary neurons and between neurons and astrocytes in organotypic cultures.
    Keywords:  Intercellular spreading; Tau aggregates; autophagy; prion-like seeding; tunneling nanotubes
    DOI:  https://doi.org/10.15252/emmm.202012025
  17. Aging Cell. 2020 Nov 09. e13268
    Okur MN, Fang EF, Fivenson EM, Tiwari V, Croteau DL, Bohr VA.
      Cockayne syndrome (CS) is a rare premature aging disease, most commonly caused by mutations of the genes encoding the CSA or CSB proteins. CS patients display cachectic dwarfism and severe neurological manifestations and have an average life expectancy of 12 years. The CS proteins are involved in transcription and DNA repair, with the latter including transcription-coupled nucleotide excision repair (TC-NER). However, there is also evidence for mitochondrial dysfunction in CS, which likely contributes to the severe premature aging phenotype of this disease. While damaged mitochondria and impaired mitophagy were characterized in mice with CSB deficiency, such changes in the CS nematode model and CS patients are not fully known. Our cross-species transcriptomic analysis in CS postmortem brain tissue, CS mouse, and nematode models shows that mitochondrial dysfunction is indeed a common feature in CS. Restoration of mitochondrial dysfunction through NAD+ supplementation significantly improved lifespan and healthspan in the CS nematodes, highlighting mitochondrial dysfunction as a major driver of the aging features of CS. In cerebellar samples from CS patients, we found molecular signatures of dysfunctional mitochondrial dynamics and impaired mitophagy/autophagy. In primary cells depleted for CSA or CSB, this dysfunction can be corrected with supplementation of NAD+ precursors. Our study provides support for the interconnection between major causative aging theories, DNA damage accumulation, mitochondrial dysfunction, and compromised mitophagy/autophagy. Together, these three agents contribute to an accelerated aging program that can be averted by cellular NAD+ restoration.
    Keywords:  AMPK; Cockayne syndrome; NAD+; accelerated ageing; aging; mitochondrial maintenance; mitophagy
    DOI:  https://doi.org/10.1111/acel.13268
  18. Nat Commun. 2020 Nov 13. 11(1): 5755
    Balukoff NC, Ho JJD, Theodoridis PR, Wang M, Bokros M, Llanio LM, Krieger JR, Schatz JH, Lee S.
      Translatome reprogramming is a primary determinant of protein levels during stimuli adaptation. This raises the question: what are the translatome remodelers that reprogram protein output to activate biochemical adaptations. Here, we identify a translational pathway that represses metabolism to safeguard genome integrity. A system-wide MATRIX survey identified the ancient eIF5A as a pH-regulated translation factor that responds to fermentation-induced acidosis. TMT-pulse-SILAC analysis identified several pH-dependent proteins, including the mTORC1 suppressor Tsc2 and the longevity regulator Sirt1. Sirt1 operates as a pH-sensor that deacetylates nuclear eIF5A during anaerobiosis, enabling the cytoplasmic export of eIF5A/Tsc2 mRNA complexes for translational engagement. Tsc2 induction inhibits mTORC1 to suppress cellular metabolism and prevent acidosis-induced DNA damage. Depletion of eIF5A or Tsc2 leads to metabolic re-initiation and proliferation, but at the expense of incurring substantial DNA damage. We suggest that eIF5A operates as a translatome remodeler that suppresses metabolism to shield the genome.
    DOI:  https://doi.org/10.1038/s41467-020-19602-2
  19. Autophagy. 2020 Nov 10. 1-3
    Lloberas J, Muñoz JP, Hernández-Álvarez MI, Cardona PJ, Zorzano A, Celada A.
      MFN2 (mitofusin 2) is required for mitochondrial fusion and for mitochondria-endoplasmic reticulum interaction. Using myeloid-conditional KO mice models, we found that MFN2 but not MFN1 is a prerequisite for the adaptation of mitochondrial respiration to stress conditions as well as for the production of reactive oxygen species (ROS). The deficient ROS production in the absence of MFN2 impairs the induction of cytokines and nitric oxide, and is associated with dysfunctional autophagy, apoptosis, phagocytosis, and antigen processing. The lack of MFN2 in macrophages causes an impaired response in a model of non-septic inflammation in mice, as well as a failure in protection from Listeria, Mycobacterium tuberculosis or LPS endotoxemia. These results reveal an unexpected role of MFN2 to ROS production in macrophages affecting natural and acquired immunity and the immune response.
    Keywords:  Autophagy; ROS; bactericidal activity; cytokine; inflammation; macrophages; phagocytosis
    DOI:  https://doi.org/10.1080/15548627.2020.1839191
  20. Front Med. 2020 Nov 09.
    Sun SY.
      The mammalian target of rapamycin (mTOR) critically regulates several essential biological functions, such as cell growth, metabolism, survival, and immune response by forming two important complexes, namely, mTOR complex 1 (mTORC1) and complex 2 (mTORC2). mTOR signaling is often dysregulated in cancers and has been considered an attractive cancer therapeutic target. Great efforts have been made to develop efficacious mTOR inhibitors, particularly mTOR kinase inhibitors, which suppress mTORC1 and mTORC2; however, major success has not been achieved. With the strong scientific rationale, the intriguing question is why cancers are insensitive or not responsive to mTOR-targeted cancer therapy in clinics. Beyond early findings on induced activation of PI3K/Akt, MEK/ERK, and Mnk/eIF4E survival signaling pathways that compromise the efficacy of rapalog-based cancer therapy, recent findings on the essential role of GSK3 in mediating cancer cell response to mTOR inhibitors and mTORC1 inhibition-induced upregulation of PD-L1 in cancer cells may provide some explanations. These new findings may also offer us the opportunity to rationally utilize mTOR inhibitors in cancer therapy. Further elucidation of the biology of complicated mTOR networks may bring us the hope to develop effective therapeutic strategies with mTOR inhibitors against cancer.
    Keywords:  E3 ubiquitin ligase; GSK3; PD-L1; cancer therapy; mTOR; protein degradation; resistance
    DOI:  https://doi.org/10.1007/s11684-020-0812-7
  21. Expert Rev Neurother. 2020 Nov 09.
    Demaré S, Kothari A, Calcutt NA, Fernyhough P.
      INTRODUCTION: Metformin is currently first line therapy for type 2 diabetes (T2D). The mechanism of action of metformin involves activation of AMP-activated protein kinase (AMPK) to enhance mitochondrial function (for example, biogenesis, refurbishment and dynamics) and autophagy. Many neurodegenerative diseases of the central and peripheral nervous systems arise from metabolic failure and toxic protein aggregation where activated AMPK could prove protective. Areas covered: The authors review literature on metformin treatment in Parkinson's disease, Huntington's disease and other neurological diseases of the CNS along with neuroprotective effects of AMPK activation and suppression of the mammalian target of rapamycin (mTOR) pathway on peripheral neuropathy and neuropathic pain. The authors compare the efficacy of metformin with the actions of resveratrol. Expert opinion: Metformin, through activation of AMPK and autophagy, can enhance neuronal bioenergetics, promote nerve repair and reduce toxic protein aggregates in neurological diseases. A long history of safe use in humans should encourage development of metformin and other AMPK activators in preclinical and clinical research. Future studies in animal models of neurological disease should strive to further dissect in a mechanistic manner the pathways downstream from metformin-dependent AMPK activation, and to further investigate mTOR dependent and independent signaling pathways driving neuroprotection.
    Keywords:  AMP-activated protein kinase (AMPK); PGC-1a; autophagy; axon regeneration; diabetes; mTOR; mitochondria; neurodegenerative disease; neuropathic pain; neuropathy
    DOI:  https://doi.org/10.1080/14737175.2021.1847645
  22. Nat Commun. 2020 11 12. 11(1): 5731
    Cen X, Chen Y, Xu X, Wu R, He F, Zhao Q, Sun Q, Yi C, Wu J, Najafov A, Xia H.
      There is increasing evidence that inducing neuronal mitophagy can be used as a therapeutic intervention for Alzheimer's disease. Here, we screen a library of 2024 FDA-approved drugs or drug candidates, revealing UMI-77 as an unexpected mitophagy activator. UMI-77 is an established BH3-mimetic for MCL-1 and was developed to induce apoptosis in cancer cells. We found that at sub-lethal doses, UMI-77 potently induces mitophagy, independent of apoptosis. Our mechanistic studies discovered that MCL-1 is a mitophagy receptor and directly binds to LC3A. Finally, we found that UMI-77 can induce mitophagy in vivo and that it effectively reverses molecular and behavioral phenotypes in the APP/PS1 mouse model of Alzheimer's disease. Our findings shed light on the mechanisms of mitophagy, reveal that MCL-1 is a mitophagy receptor that can be targeted to induce mitophagy, and identify MCL-1 as a drug target for therapeutic intervention in Alzheimer's disease.
    DOI:  https://doi.org/10.1038/s41467-020-19547-6
  23. Front Immunol. 2020 ;11 591803
    Biasizzo M, Kopitar-Jerala N.
      The NLRP3 inflammasome is cytosolic multi-protein complex that induces inflammation and pyroptotic cell death in response to both pathogen (PAMPs) and endogenous activators (DAMPs). Recognition of PAMPs or DAMPs leads to formation of the inflammasome complex, which results in activation of caspase-1, followed by cleavage and release of pro-inflammatory cytokines. Excessive activation of NLRP3 inflammasome can contribute to development of inflammatory diseases and cancer. Autophagy is vital intracellular process for recycling and removal of damaged proteins and organelles, as well as destruction of intracellular pathogens. Cytosolic components are sequestered in a double-membrane vesicle-autophagosome, which then fuses with lysosome resulting in degradation of the cargo. The autophagy dysfunction can lead to diseases with hyperinflammation and excessive activation of NLRP3 inflammasome and thus acts as a major regulator of inflammasomes. Autophagic removal of NLRP3 inflammasome activators, such as intracellular DAMPs, NLRP3 inflammasome components, and cytokines can reduce inflammasome activation and inflammatory response. Likewise, inflammasome signaling pathways can regulate autophagic process necessary for balance between required host defense inflammatory response and prevention of excessive and detrimental inflammation. Autophagy has a protective role in some inflammatory diseases associated with NLRP3 inflammasome, including gouty arthritis, familial Mediterranean fever (FMF), and sepsis. Understanding the interregulation between these two essential biological processes is necessary to comprehend the biological mechanisms and designing possible treatments for multiple inflammatory diseases.
    Keywords:  NLRP3 inflammasome; autophagy; inflammation; inflammatory diseases; mitophagy
    DOI:  https://doi.org/10.3389/fimmu.2020.591803
  24. Autophagy. 2020 Nov 10.
    Cedric B, Armen S.
      Cell migration is a highly dynamic and energy-intensive process that ensures the correct targeting of cells during embryonic and postnatal development. In recent work, we highlighted the importance of macroautophagy/autophagy in regulating the dynamics of cell migration under baseline conditions and in response to a diverse set of molecular factors. Genetic suppression of autophagy-related genes induced longer stationary phases in migrating cells and cell stalling at the beginning of the migratory stream. We also showed that autophagy is required for recycling of the focal adhesion molecule PXN (paxillin), and is induced by energy levels of cells via AMPK activation. This recent study revealed the importance of autophagy in the maintenance of cell migration, and showed that the dynamic interplay between autophagy and energy levels is required to sustain neuronal migration and to cope with diverse micro-environmental factors.
    Keywords:  AMPK; ATP/ADP; Atg12; Atg5; autophagy; cell migration; paxillin; time-lapse imaging
    DOI:  https://doi.org/10.1080/15548627.2020.1848120
  25. Transl Med Aging. 2020 ;4 117-120
    Mor DE, Murphy CT.
      Mitochondrial dysfunction is thought to contribute to neurodegeneration in Parkinson's disease (PD), yet the cellular events that lead to mitochondrial disruption remain unclear. Post-mortem studies of PD patient brains and the use of complex I inhibitors to model the disease previously suggested a reduction in mitochondrial activity as a causative factor in PD, but this may represent an endpoint in the disease process. In our recent studies, we identified a novel link between branched-chain amino acid metabolism and PD, and uncovered mitochondrial hyperactivity as a potential alternative mechanism of PD pathogenesis. Increased mitochondrial activity may occur in a subset of PD patients, or may be a more common early event that precedes the ultimate loss of mitochondrial function. Therefore, it may be that any imbalance in mitochondrial activity, either increased or decreased, could cause a loss of mitochondrial homeostasis that leads to disease. An effective therapeutic strategy may be to target specific imbalances in activity at selective stages of PD or in specific patients, with any efforts to reduce mitochondrial activity constituting a surprising new avenue for PD treatment.
    Keywords:  Branched-chain amino acid metabolism; Hyperactive mitochondria; Mitochondrial homeostasis; Parkinson’s disease
    DOI:  https://doi.org/10.1016/j.tma.2020.07.007
  26. Exp Biol Med (Maywood). 2020 Nov 09. 1535370220966545
    Jogalekar MP, Veerabathini A, Gangadaran P.
      Autophagy plays a crucial role in cellular development and differentiation as well as in the maintenance of homeostasis in healthy cells. Autophagy is well documented in neurodegenerative disorders, aging, and infectious diseases. However, recognizing its significance in cancer has always been challenging due to its tumor-promoting and suppressive attributes. Various modulators targeting key components of autophagy machinery directly or indirectly have been developed over the years, and have shown promising results in preclinical models. Some of these compounds are even being tested in clinical trials for safety and efficacy. A detailed review of strategies used to target autophagy in cancer is presented including our opinion on developing better therapies and outstanding issues.
    Keywords:  Autophagy; Beclin-1; cancer; chloroquine; mTOR
    DOI:  https://doi.org/10.1177/1535370220966545
  27. Front Mol Neurosci. 2020 ;13 586731
    Jiang S, Bhaskar K.
      Tauopathies are a class of neurodegenerative diseases, including Alzheimer's disease (AD), Frontotemporal Dementia (FTD), Progressive Supranuclear Palsy (PSP), Corticobasal Degeneration (CBD), and many others where microtubule-associated protein tau (MAPT or tau) is hyperphosphorylated and aggregated to form insoluble paired helical filaments (PHFs) and ultimately neurofibrillary tangles (NFTs). Autophagic-endolysosomal networks (AELN) play important roles in tau clearance. Excessive soluble neurotoxic forms of tau and tau hyperphosphorylated at specific sites are cleared through the ubiquitin-proteasome system (UPS), Chaperon-mediated Autophagy (CMA), and endosomal microautophagy (e-MI). On the other hand, intra-neuronal insoluble tau aggregates are often degraded within lysosomes by macroautophagy. AELN defects have been observed in AD, FTD, CBD, and PSP, and lysosomal dysfunction was shown to promote the cleavage and neurotoxicity of tau. Moreover, several AD risk genes (e.g., PICALM, GRN, and BIN1) have been associated with dysregulation of AELN in the late-onset sporadic AD. Conversely, tau dissociation from microtubules interferes with retrograde transport of autophagosomes to lysosomes, and that tau fragments can also lead to lysosomal dysfunction. Recent studies suggest that tau is not merely an intra-neuronal protein, but it can be released to brain parenchyma via extracellular vesicles, like exosomes and ectosomes, and thus spread between neurons. Extracellular tau can also be taken up by microglial cells and astrocytes, either being degraded through AELN or propagated via exosomes. This article reviews the complex roles of AELN in the degradation and transmission of tau, potential diagnostic/therapeutic targets and strategies based on AELN-mediated tau clearance and propagation, and the current state of drug development targeting AELN and tau against tauopathies.
    Keywords:  autophagy; degradation; endo-lysosomal systems; glial cells; neuron; tau; tauopathy; transmission
    DOI:  https://doi.org/10.3389/fnmol.2020.586731
  28. Neurosci Lett. 2020 Nov 09. pii: S0304-3940(20)30763-1. [Epub ahead of print] 135493
    Qi H, Shen D, Jiang C, Wang H, Chang M.
      Neuroprotection targeting mitochondrial dysfunction has been proposed as a potential therapeutic strategy for Parkinson's disease (PD). Ursodeoxycholic acid (UDCA) has been shown to prevent neuronal damage; however, the role of UDCA in PD is poorly understood. This study aimed to investigate the neuroprotective effects of UDCA on PD and its underlying mechanisms. We used MPTP/MPP+-induced PD models, including MPTP-induced mice, primary cultures of mice mesencephalic neurons and MPP+-treated neuro-2a cells to examine the effects of UDCA on PD pathogenesis. The results showed that UDCA improved behavioral performance and protected dopaminergic neurons in MPTP mice. UDCA improved cell viability and decreased cell death in MPP+-treated cells. UDCA inhibited reactive oxygen species accumulation, mitochondrial membrane potential collapse, and ATP depletion in nero-2a cells. UDCA improved movement dysfunction, ameliorated autophagic flux and alleviated apoptosis. Furthermore, UDCA could activate the AMPK/mTOR and PINK1/Parkin pathways. In conclusion, UDCA may improve PD by regulating mitochondrial function, autophagy, and apoptosis, involving AMPK/mTOR and PINK1/Parkin pathways. These results open new perspectives for pharmacological use of UDCA in PD.
    Keywords:  MPTP/MPP(+); Parkinson’s disease; UDCA; apoptosis; autophagy; mitochondrial dysfunction
    DOI:  https://doi.org/10.1016/j.neulet.2020.135493
  29. Autophagy. 2020 Nov 08.
    Bensalem J, Hattersley KJ, Hein LK, Tong Teong X, Carosi JM, Hassiotis S, Grose RH, Fourrier C, Heilbronn LK, Sargeant TJ.
      Autophagic flux is a critical cellular process that is vastly under-appreciated in terms of its importance to human health. Preclinical studies have demonstrated that reductions in autophagic flux cause cancer and exacerbate chronic diseases, including heart disease and the pathological hallmarks of dementia. Autophagic flux can be increased by targeting nutrition-related biochemical signaling. To date, translation of this knowledge has been hampered because there has been no way to directly measure autophagic flux in humans. In this study we detail a method whereby human macroautophagic/autophagic flux can be directly measured from human blood samples. We show that whole blood samples can be treated with the lysosomal inhibitor chloroquine, and peripheral blood mononuclear cells isolated from these samples could be used to measure autophagic machinery protein LC3B-II. Blocking of autophagic flux in cells while still in whole blood represents an important advance because it preserves genetic, nutritional, and signaling parameters inherent to the individual. We show this method was reproducible and defined LC3B-II as the best protein to measure autophagic flux in these cells. Finally, we show that this method is relevant to assess intra-individual variation induced by an intervention by manipulating nutrition signaling with an ex vivo treatment of whole blood that comprised leucine and insulin. Significantly, this method will enable the identification of factors that alter autophagic flux in humans, and better aid their translation in the clinic. With further research, it could also be used as a novel biomarker for risk of age-related chronic disease.
    Keywords:  Autophagy; LC3B; PBMC; biomarker; blood; chloroquine; human; lysosome
    DOI:  https://doi.org/10.1080/15548627.2020.1846302
  30. Ageing Res Rev. 2020 Nov 05. pii: S1568-1637(20)30337-8. [Epub ahead of print] 101202
    Wu AG, Zhou XG, Qiao G, Yu L, Tang Y, Yan L, Qiu WQ, Pan R, Yu CL, Law BY, Qin DL, Wu JM.
      Neuroinflammation is considered as a detrimental factor in neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), etc. Nucleotide-binding oligomerization domain-, leucine-rich repeat- and pyrin domain-containing 3 (NLRP3), the most well-studied inflammasome, is abundantly expressed in microglia and has gained considerable attention. Misfolded proteins are characterized as the common hallmarks of neurodegenerative diseases due to not only their induced neuronal toxicity, but also their effects in over-activating microglia and the NLRP3 inflammasome. The activated NLRP3 inflammasome aggravates the pathology and accelerates the progression of neurodegenerative diseases. Emerging evidence indicates that microglial autophagy plays an important role in the maintenance of brain homeostasis and the negative regulation of NLRP3 inflammasome-mediated neuroinflammation. The excessive activation of NLRP3 inflammasome impairs microglial autophagy and further aggravates the pathogenesis of neurodegenerative diseases. In this review article, we summarize and discuss the NLRP3 inflammasome and its specific inhibitors in microglia. The crucial role of microglial autophagy and its inducers in the removal of misfolded proteins, the clearance of damaged mitochondria and reactive oxygen species (ROS), and the degradation of the NLRP3 inflammasome or its components in neurodegenerative diseases are summarized. Understanding the underlying mechanisms behind the sex differences in NLRP3 inflammasome-mediated neurodegenerative diseases will help researchers to develop more targeted therapies and increase our diagnostic and prognostic abilities. In addition, the superiority of the combined use of microglial autophagy inducers with the specific inhibitors of the NLRP3 inflammasome in the inhibition of NLRP3 inflammasome-mediated neuroinflammation requires further preclinical and clinical validations in the future.
    Keywords:  Microglial autophagy; Misfolded proteins; NLRP3 inflammasome; Neurodegenerative diseases; Neuroinflammation
    DOI:  https://doi.org/10.1016/j.arr.2020.101202
  31. Pharmacol Res. 2020 Nov 05. pii: S1043-6618(20)31587-5. [Epub ahead of print] 105279
    Wu J, Bai Y, Wang Y, Ma J.
      Mitochondria are essential subcellular units that generate basic energy for the cell, as well as influence Ca2+ flux, apoptosis, and cell signaling. Mitophagy can selectively remove impaired mitochondria to preserve mitochondrial function, which is crucial for normal cellular maintenance. Mitochondrial dysfunction and mitophagy are widely reported to be linked to various pathogeneses. In addition, there is increasing evidence regarding the beneficial role of melatonin in the regulation and intervention of mitophagy progression. In this review, we focus on specific pathological conditions, including ischemia/reperfusion injury (IRI), cancer and neurodegenerative diseases, and elucidate the essential role of melatonin in the modulation of mitophagy in each of these distinct disorders.
    Keywords:  Cancer; Ischemia/reperfusion injury; Melatonin; Mitophagy; Neurodegenerative diseases
    DOI:  https://doi.org/10.1016/j.phrs.2020.105279