bims-auttor 2023-06-25 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2023–06–25
thirty-six papers selected by
Viktor Korolchuk, Newcastle University

The yeast transcription factor Stb5 acts as a negative regulator of autophagy by modulating cellular metabolism.
A paradigm shift: AMPK negatively regulates ULK1 activity.
ER-phagy in neurodegeneration.
Deregulation of mTORC1-TFEB axis in human iPSC model of GBA1-associated Parkinson's disease.
Loss of Macrophage mTORC2 Drives Atherosclerosis via FoxO1 and IL-1β Signaling.
Importance of DJ-1 in autophagy regulation and disease.
The role of ncRNA in the co-regulation of autophagy and exosome pathways during cancer progression.
CHI3L1 induces autophagy through the JNK pathway in lung cancer cells.
Measurement of SQSTM1 by flow cytometry.
Chemical mitophagy modulators: drug development strategies and novel regulatory mechanisms.
Tuberous Sclerosis Complex cell-derived EVs have an altered protein cargo capable of regulating their microenvironment and have potential as disease biomarkers.
Autophagy counteracts Mycobacterium tuberculosis infection at early stages.
Unravelling the complexity of lncRNAs in autophagy to improve potential cancer therapy.
PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems.
Loss of functional peroxisomes leads to increased mitochondrial biogenesis and reduced autophagy that preserve mitochondrial function.
NK Cells from Human Cytomegalovirus-Seropositive Individuals Have a Distinct Metabolic Profile That Correlates with Elevated mTOR Signaling.
A bioinformatics analysis, pre-clinical and clinical conception of autophagy in pancreatic cancer: Complexity and simplicity in crosstalk.
C. elegans ATG-5 mutants associated with ataxia.
Renoprotective Effect of Isoorientin in Diabetic Nephropathy via Activating Autophagy and Inhibiting the PI3K-AKT-TSC2-mTOR Pathway.
Two aminopeptidase I homologs convergently contribute to pathobiology of fungal entomopathogen Beauveria bassiana via divergent physiology-dependent autophagy pathways for vacuolar targeting.
The ER calcium channel Csg2 integrates sphingolipid metabolism with autophagy.
SRF deletion results in earlier disease onset in a mouse model of amyotrophic lateral sclerosis.
A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling.
α-amanitin induces autophagy through AMPK-mTOR-ULK1 signaling pathway in hepatocytes.
VANGL2 inhibits antiviral IFN-I signaling by targeting TBK1 for autophagic degradation.
Autophagy during Maize Endosperm Development Dampens Oxidative Stress and Promotes Mitochondrial Clearance.
Perturbation of endoplasmic reticulum proteostasis triggers tissue injury in the thyroid gland.
Unique amphipathic α helix drives membrane insertion and enzymatic activity of ATG3.
Loss of miR-144/451 alleviates β-thalassemia by stimulating ULK1-mediated autophagy of free α-globin.
miR-146a-5p regulates autophagy and NLRP3 inflammasome activation in epithelial barrier damage in the in vitro cell model of ulcerative colitis through the RNF8/Notch1/mTORC1 pathway.
Unlocking the potential of Mesenchymal stem cells in liver Fibrosis: Insights into the impact of autophagy and aging.
The emerging potential role of p62 in cancer treatment by regulating metabolism.
Mitophagy disorder mediates cardiac deterioration induced by severe hypoglycemia in diabetic mice.
Autophagy Suppresses Ferroptosis by Degrading TFR1 to Alleviate Cognitive Dysfunction in Mice with SAE.
Regulation of TORC2 Function and Localization in Yeast.
Cardiolipin externalization mediates prion protein (PrP) peptide 106-126-associated mitophagy and mitochondrial dysfunction.

Autophagy. 2023 Jun 22.

The yeast transcription factor Stb5 acts as a negative regulator of autophagy by modulating cellular metabolism.

Elizabeth Delorme-Axford, Xin Wen, Daniel J Klionsky.

  Macroautophagy/autophagy is a highly conserved pathway of cellular degradation and recycling that maintains cell health during homeostatic conditions and facilitates survival during stress. Aberrant cellular autophagy contributes to the pathogenesis of human diseases such as cancer, neurodegeneration, and cardiovascular, metabolic and lysosomal storage disorders. Despite decades of research, there remain unanswered questions as to how autophagy modulates cellular metabolism, and, conversely, how cellular metabolism affects autophagy activity. Here, we have identified the yeast metabolic transcription factor Stb5 as a negative regulator of autophagy. Chromosomal deletion of STB5 in the yeast Saccharomyces cerevisiae enhances autophagy. Loss of Stb5 results in the upregulation of select autophagy-related (ATG) transcripts under nutrient-replete conditions; however, the Stb5-mediated impact on autophagy occurs primarily through its effect on genes involved in NADPH production and the pentose phosphate pathway. This work provides insight into the intersection of Stb5 as a transcription factor that regulates both cellular metabolic responses and autophagy activity.

Keywords:  Ald6; NADPH; Ymr315w; Zwf1; autophagosome; macroautophagy; pentose phosphate pathway; stress; yeast

DOI:  https://doi.org/10.1080/15548627.2023.2228533
Autophagy. 2023 Jun 20. 1-3

A paradigm shift: AMPK negatively regulates ULK1 activity.

Ji-Man Park, Do-Hyung Kim.

  In glucose-starved cells, macroautophagy (hereafter referred to as autophagy) is considered to serve as an energy-generating process contributing to cell survival. AMPK (adenosine monophosphate-activated protein kinase) is the primary cellular energy sensor that is activated during glucose starvation. According to the current paradigm in the field, AMPK promotes autophagy in response to energy deprivation by binding and phosphorylating ULK1 (UNC-51 like kinase 1), the protein kinase responsible for autophagy initiation. However, conflicting findings have been reported casting doubts about the current established model. In our recent study, we have thoroughly reevaluated the role of AMPK in autophagy. Contrary to the current paradigm, our study revealed that AMPK functions as a negative regulator of ULK1 activity. The study has elucidated the underlying mechanism and demonstrated the significance of the negative role in controlling autophagy and maintaining cellular resilience during energy depletion.Abbreviations: AMPK: adenosine monophosphate-activated protein kinase; ULK1: UNC-51 like kinase 1; MTORC1: mechanistic target of rapamycin complex 1; ATG14: autophagy-related protein 14; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; ATP: adenosine triphosphate; VPS34: vacuolar protein sorting 34; BECN1: Beclin 1; AMPKα: AMPK catalytic subunit α; LKB1: liver kinase B1; PIK3R4: phosphatidylinositol 3-kinase regulatory subunit 4.

Keywords:  AMPK; LKB1; MTORC1; ULK1; energy stress; glucose starvation

DOI:  https://doi.org/10.1080/15548627.2023.2223465
J Neurosci Res. 2023 Jun 19.

ER-phagy in neurodegeneration.

Melissa A Hill, Alex M Sykes, George D Mellick.

  There are many cellular mechanisms implicated in the initiation and progression of neurodegenerative disorders. However, age and the accumulation of unwanted cellular products are a common theme underlying many neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and Niemann-Pick type C. Autophagy has been studied extensively in these diseases and various genetic risk factors have implicated disruption in autophagy homoeostasis as a major pathogenic mechanism. Autophagy is essential in the maintenance of neuronal homeostasis, as their postmitotic nature makes them particularly susceptible to the damage caused by accumulation of defective or misfolded proteins, disease-prone aggregates, and damaged organelles. Recently, autophagy of the endoplasmic reticulum (ER-phagy) has been identified as a novel cellular mechanism for regulating ER morphology and response to cellular stress. As neurodegenerative diseases are generally precipitated by cellular stressors such as protein accumulation and environmental toxin exposure the role of ER-phagy has begun to be investigated. In this review we discuss the current research in ER-phagy and its involvement in neurodegenerative diseases.

Keywords:  ER-phagy; autophagy; endoplasmic reticulum; neurodegeneration

DOI:  https://doi.org/10.1002/jnr.25225
Front Neurosci. 2023 ;17 1152503

Deregulation of mTORC1-TFEB axis in human iPSC model of GBA1-associated Parkinson's disease.

Fahad Mubariz, Afsoon Saadin, Nicholas Lingenfelter, Chinmoy Sarkar, Aditi Banerjee, Marta M Lipinski, Ola Awad.

  Mutations in the GBA1 gene are the single most frequent genetic risk factor for Parkinson's disease (PD). Neurodegenerative changes in GBA1-associated PD have been linked to the defective lysosomal clearance of autophagic substrates and aggregate-prone proteins. To elucidate novel mechanisms contributing to proteinopathy in PD, we investigated the effect of GBA1 mutations on the transcription factor EB (TFEB), the master regulator of the autophagy-lysosomal pathway (ALP). Using PD patients' induced-pluripotent stem cells (iPSCs), we examined TFEB activity and regulation of the ALP in dopaminergic neuronal cultures generated from iPSC lines harboring heterozygous GBA1 mutations and the CRISPR/Cas9-corrected isogenic controls. Our data showed a significant decrease in TFEB transcriptional activity and attenuated expression of many genes in the CLEAR network in GBA1 mutant neurons, but not in the isogenic gene-corrected cells. In PD neurons, we also detected increased activity of the mammalian target of rapamycin complex1 (mTORC1), the main upstream negative regulator of TFEB. Increased mTORC1 activity resulted in excess TFEB phosphorylation and decreased nuclear translocation. Pharmacological mTOR inhibition restored TFEB activity, decreased ER stress and reduced α-synuclein accumulation, indicating improvement of neuronal protiostasis. Moreover, treatment with the lipid substrate reducing compound Genz-123346, decreased mTORC1 activity and increased TFEB expression in the mutant neurons, suggesting that mTORC1-TFEB alterations are linked to the lipid substrate accumulation. Our study unveils a new mechanism contributing to PD susceptibility by GBA1 mutations in which deregulation of the mTORC1-TFEB axis mediates ALP dysfunction and subsequent proteinopathy. It also indicates that pharmacological restoration of TFEB activity could be a promising therapeutic approach in GBA1-associated neurodegeneration.

Keywords:  GBA1 mutations; Parkinson’s disease; autophagy-lysosomal pathway; induced-pluripotent stem cells; mammalian target of rapamycin complex1; transcription factor EB

DOI:  https://doi.org/10.3389/fnins.2023.1152503
Circ Res. 2023 Jun 23.

Loss of Macrophage mTORC2 Drives Atherosclerosis via FoxO1 and IL-1β Signaling.

Xiangyu Zhang, Trent D Evans, Sunny Chen, Ismail Sergin, Jeremiah Stitham, Se-Jin Jeong, Astrid Rodriguez-Velez, Yu-Sheng Yeh, Arick Park, In-Hyuk Jung, Abhinav Diwan, Joel D Schilling, Oren Rom, Arif Yurdagul, Slava Epelman, Jaehyung Cho, Irfan J Lodhi, Bettina Mittendorfer, Babak Razani.

   BACKGROUND: The mTOR (mechanistic target of rapamycin) pathway is a complex signaling cascade that regulates cellular growth, proliferation, metabolism, and survival. Although activation of mTOR signaling has been linked to atherosclerosis, its direct role in lesion progression and in plaque macrophages remains poorly understood. We previously demonstrated that mTORC1 (mTOR complex 1) activation promotes atherogenesis through inhibition of autophagy and increased apoptosis in macrophages.
METHODS: Using macrophage-specific Rictor- and mTOR-deficient mice, we now dissect the distinct functions of mTORC2 pathways in atherogenesis.
RESULTS: In contrast to the atheroprotective effect seen with blockade of macrophage mTORC1, macrophage-specific mTORC2-deficient mice exhibit an atherogenic phenotype, with larger, more complex lesions and increased cell death. In cultured macrophages, we show that mTORC2 signaling inhibits the FoxO1 (forkhead box protein O1) transcription factor, leading to suppression of proinflammatory pathways, especially the inflammasome/IL (interleukin)-1β response, a key mediator of vascular inflammation and atherosclerosis. In addition, administration of FoxO1 inhibitors efficiently rescued the proinflammatory response caused by mTORC2 deficiency both in vitro and in vivo. Interestingly, collective deletion of macrophage mTOR, which ablates mTORC1- and mTORC2-dependent pathways, leads to minimal change in plaque size or complexity, reflecting the balanced yet opposing roles of these signaling arms.
CONCLUSIONS: Our data provide the first mechanistic details of macrophage mTOR signaling in atherosclerosis and suggest that therapeutic measures aimed at modulating mTOR need to account for its dichotomous functions.

Keywords:  atherosclerosis; inflammation; interleukin; macrophage

DOI:  https://doi.org/10.1161/CIRCRESAHA.122.321542
Arch Biochem Biophys. 2023 Jun 17. pii: S0003-9861(23)00171-6. [Epub ahead of print] 109672

Importance of DJ-1 in autophagy regulation and disease.

Shiyi Liu, Sheng Xu, Song Liu, Heping Chen.

  Autophagy is a highly conserved biological process that has evolved across evolution. It can be activated by various external stimuli including oxidative stress, amino acid starvation, infection, and hypoxia. Autophagy is the primary mechanism for preserving cellular homeostasis and is implicated in the regulation of metabolism, cell differentiation, tolerance to starvation conditions, and resistance to aging. As a multifunctional protein, DJ-1 is commonly expressed in vivo and is associated with a variety of biological processes. Its most widely studied role is its function as an oxidative stress sensor that inhibits the production of excessive reactive oxygen species (ROS) in the mitochondria and subsequently the cellular damage caused by oxidative stress. In recent years, many studies have identified DJ-1 as another important factor regulating autophagy; it regulates autophagy in various ways, most commonly by regulating the oxidative stress response. In particular, DJ-1-regulated autophagy is involved in cancer progression and plays a key role in alleviating neurodegenerative diseases(NDS) and defective reperfusion diseases. It could serve as a potential target for the regulation of autophagy and participate in disease treatment as a meaningful modality. Therefore, exploring DJ-1-regulated autophagy could provide new avenues for future disease treatment.

Keywords:  Autophagic lysosomal pathway; Autophagy; DJ-1; MAM; Oxidative stress

DOI:  https://doi.org/10.1016/j.abb.2023.109672
Biochim Biophys Acta Mol Cell Res. 2023 Jun 20. pii: S0167-4889(23)00095-2. [Epub ahead of print] 119523

The role of ncRNA in the co-regulation of autophagy and exosome pathways during cancer progression.

Naveen Soni, Gargi Nandi, Megha Chaudhary, Bhawana Bissa.

  Since its discovery a few decades ago, autophagy has been recognized as a crucial signaling pathway, linked to the recycling of cellular components in nutrient stress. Autophagy is a two-way sword, playing a dual role in tumorigenesis. In this catabolic process, dysfunctional organelles, biomolecules, and misfolded proteins are sequestered in the autophagosome and sent to the lysosome for degradation. Alongside, there are cellular messengers called exosomes, which are released from cells and are known to communicate and regulate metabolism in recipient cells. Multivesicular bodies (MVB) act as the intricate link between autophagy and exosome pathways. The continuous crosstalk between the two pathways is coordinated and regulated by multiple players among which ncRNA is the emerging candidates. The exosomes carry varied cargo of which non-coding RNA exerts an immediate regulatory effect on recipient cells. ncRNA is known to exhibit dual behavior in both promoting and inhibiting tumor growth. There is increasing evidence for the involvement of ncRNAs' in the regulation of different hallmarks of cancer. Different ncRNAs are involved in the co-regulation of autophagy and exosome pathways and therefore represent a superior therapeutic approach to target cancer chemoresistance. Here, we will discuss the ncRNA involved in regulating autophagy, and exosomes pathways and its relevance in cancer therapeutics.

Keywords:  Autophagy; Cancer; Exosome; ceRNA; miRNA; ncRNA; siRNA

DOI:  https://doi.org/10.1016/j.bbamcr.2023.119523
Sci Rep. 2023 Jun 20. 13(1): 9964

CHI3L1 induces autophagy through the JNK pathway in lung cancer cells.

Da Eun Hong, Ji Eun Yu, Seung Sik Yoo, In Jun Yeo, Dong Ju Son, Jaesuk Yun, Sang-Bae Han, Jin Tae Hong.

CHI3L1 is closely related to the molecular mechanisms of cancer cell migration, growth, and death. According to recent research, autophagy regulates tumor growth during various stages of cancer development. This study examined the association between CHI3L1 and autophagy in human lung cancer cells. In CHI3L1-overexpressing lung cancer cells, the expression of LC3, an autophagosome marker, and the accumulation of LC3 puncta increased. In contrast, CHI3L1 depletion in lung cancer cells decreased the formation of autophagosomes. Additionally, CHI3L1 overexpression promoted the formation of autophagosomes in various cancer cell lines: it also increased the co-localization of LC3 and the lysosome marker protein LAMP-1, indicating an increase in the production of autolysosomes. In mechanism study, CHI3L1 promotes autophagy via activation of JNK signaling. JNK may be crucial for CHI3L1-induced autophagy since pretreatment with the JNK inhibitor reduced the autophagic effect. Consistent with the in vitro model, the expression of autophagy-related proteins was downregulated in the tumor tissues of CHI3L1-knockout mice. Furthermore, the expression of autophagy-related proteins and CHI3L1 increased in lung cancer tissues compared with normal lung tissues. These findings show that CHI3L1-induced autophagy is triggered by JNK signals and that CHI3L1-induced autophagy could be a novel therapeutic approach to lung cancer.

DOI: https://doi.org/10.1038/s41598-023-36844-4
Autophagy. 2023 Jun 19. 1-11

Measurement of SQSTM1 by flow cytometry.

Jessica C Hargarten, Guowu Hu, Waleed Elsegeiny, Peter R Williamson.

  Macroautophagy/autophagy is a regulated cellular degradation process essential as a pro-survival mechanism and integral to the regulation of diverse cellular processes in eukaryotes. During cellular stress and nutrient sensing, SQSTM1/p62 (sequestosome 1) functions as a key receptor for selective autophagy by shuttling ubiquitinated cargoes toward autophagic degradation making it a useful marker for monitoring autophagic flux. We present a straightforward and rapid flow cytometric assay for the quantitative measurement of intracellular SQSTM1 with improved sensitivity to conventional immunoblotting and with the benefit of higher throughput and reduced requirements for starting cellular materials for adequate analysis. We demonstrate that flow cytometry is able to detect similar trends in the measurement of intracellular SQSTM1 levels following serum starvation, genetic manipulations, and bafilomycin A1/chloroquine treatments. The assays utilizes readily available reagents and equipment without the need for transfection and utilizes standard flow cytometry equipment. In the present studies, expression of reporter proteins was applied to a range of SQSTM1 expression levels generated by genetic and chemical manipulation in both mouse as well as human cells. In combination with appropriate controls and attention to cautionary issues, this assay offers the ability to assess an important measure of autophagic capacity and flux.Abbreviations: ATG5: autophagy related 5 ATG7: autophagy related 7 BafA: bafilomycin A1 BMDM: bone marrow-derived macrophages CQ: chloroquine EBV: Epstein-Barr Virus EDTA: ethylenediaminetetraacetic acid FBS: fetal bovine serum gMFI: geometric mean fluorescent intensity HD: healthy donor MAP1LC3/LC3/Atg8: microtubule associated protein 1 light chain 3 MedianFI: median fluorescent intensity NTC: non-target control PBMC: peripheral blood mononuclear cells RPMI: Roswell Park Memorial Institution SQSTM1/p62: sequestosome 1 WT: wild type.

Keywords:  Autophagy; Bafilomycin A1; Sqstm1/P62; chloroquine; flow cytometry; serum starvation

DOI:  https://doi.org/10.1080/15548627.2023.2224074
Pharmacol Res. 2023 Jun 20. pii: S1043-6618(23)00191-3. [Epub ahead of print] 106835

Chemical mitophagy modulators: drug development strategies and novel regulatory mechanisms.

Yu Dong, Xu-Xu Zhuang, Yi-Ting Wang, Jieqiong Tan, Du Feng, Min Li, Qing Zhong, Zhiyin Song, Han-Ming Shen, Evandro F Fang, Jia-Hong Lu.

  Maintaining mitochondrial homeostasis is a potential therapeutic strategy for various diseases, including neurodegenerative diseases, cardiovascular diseases, metabolic disorders, and cancer. Selective degradation of mitochondria by autophagy (mitophagy) is a fundamental mitochondrial quality control mechanism conserved from yeast to humans. Indeed, small-molecule modulators of mitophagy are valuable pharmaceutical tools that can be used to dissect complex biological processes and turn them into potential drugs. In the past few years, pharmacological regulation of mitophagy has shown promising therapeutic efficacy in various disease models. However, with the increasing number of chemical mitophagy modulator studies, frequent methodological flaws can be observed, leading some studies to draw unreliable or misleading conclusions. This review attempts (a) to summarize the molecular mechanisms of mitophagy; (b) to propose a Mitophagy Modulator Characterization System (MMCS); (c) to perform a comprehensive analysis of methods used to characterize mitophagy modulators, covering publications over the past 20 years; (d) to provide novel targets for pharmacological intervention of mitophagy. We believe this review will provide a panorama of current research on chemical mitophagy modulators and promote the development of safe and robust mitophagy modulators with therapeutic potential by introducing high methodological standards.

Keywords:  cancer; cardiovascular diseases; drug development; metabolic disorders; mitophagy; neurodegenerative diseases

DOI:  https://doi.org/10.1016/j.phrs.2023.106835
J Extracell Vesicles. 2023 06;12(6): e12336

Tuberous Sclerosis Complex cell-derived EVs have an altered protein cargo capable of regulating their microenvironment and have potential as disease biomarkers.

Muireann Ní Bhaoighill, Juan M Falcón-Pérez, Félix Royo, Andrew R Tee, Jason P Webber, Elaine A Dunlop.

  Hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1) is a feature of many solid tumours and is a key pathogenic driver in the inherited condition Tuberous Sclerosis Complex (TSC). Modulation of the tumour microenvironment by extracellular vesicles (EVs) is known to facilitate the development of various cancers. The role of EVs in modulating the tumour microenvironment and their impact on the development of TSC tumours, however, remains unclear. This study, therefore, focuses on the poorly defined contribution of EVs to tumour growth in TSC. We characterised EVs secreted from TSC2-deficient and TSC2-expressing cells and identified a distinct protein cargo in TSC2-deficient EVs, containing an enrichment of proteins thought to be involved in tumour-supporting signalling pathways. We show EVs from TSC2-deficient cells promote cell viability, proliferation and growth factor secretion from recipient fibroblasts within the tumour microenvironment. Rapalogs (mTORC1 inhibitors) are the current therapy for TSC tumours. Here, we demonstrate a previously unknown intercellular therapeutic effect of rapamycin in altering EV cargo and reducing capacity to promote cell proliferation in the tumour microenvironment. Furthermore, EV cargo proteins have the potential for clinical applications as TSC biomarkers, and we reveal three EV-associated proteins that are elevated in plasma from TSC patients compared to healthy donor plasma.

Keywords:  TSC2; extracellular vesicles (EVs); fibroblasts; mTORC1; tuberous sclerosis complex (TSC); tumour microenvironment

DOI:  https://doi.org/10.1002/jev2.12336
Nat Struct Mol Biol. 2023 06;30(6): 720

Autophagy counteracts Mycobacterium tuberculosis infection at early stages.

Dimitris Typas.

DOI: https://doi.org/10.1038/s41594-023-01024-5
Biochim Biophys Acta Rev Cancer. 2023 Jun 16. pii: S0304-419X(23)00081-1. [Epub ahead of print]1878(5): 188932

Unravelling the complexity of lncRNAs in autophagy to improve potential cancer therapy.

Yi Wang, Yuqi Fu, Yingying Lu, Siwei Chen, Jin Zhang, Bo Liu, Yong Yuan.

  Autophagy is well-known as an internal catabolic process that is evolutionarily conserved and performs the key biological function in maintaining cellular homeostasis. It is tightly controlled by several autophagy-related (ATG) proteins, which are closely associated with many types of human cancers. However, what has remained controversial is the janus roles of autophagy in cancer progression. Interestingly, the biological function of long non-coding RNAs (lncRNAs) in autophagy has been gradually understood in different types of human cancers. More recently, numerous studies have demonstrated that several lncRNAs may regulate some ATG proteins and autophagy-related signaling pathways to either activate or inhibit the autophagic process in cancer. Thus, in this review, we summarize the latest advance in the knowledge of the complicated relationships between lncRNAs and autophagy in cancer. Also, the in-depth dissection of the lncRNAs-autophagy-cancers axis involved in this review would shed new light on discovery of more potential cancer biomarkers and therapeutic targets in the future.

Keywords:  Autophagy; Autophagy-related (ATG) protein; Cancer therapy; Long non-coding RNA (lncRNA); Therapeutic target

DOI:  https://doi.org/10.1016/j.bbcan.2023.188932
EMBO Rep. 2023 Jun 19. e56399

PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems.

Felix Kraus, Ellen A Goodall, Ian R Smith, Yizhi Jiang, Julia C Paoli, Frank Adolf, Jiuchun Zhang, Joao A Paulo, Brenda A Schulman, J Wade Harper.

  The protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed-forward mechanism involving ubiquitin (Ub) phosphorylation (pUb), Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support the recruitment of mitophagy receptors. The ubiquitin ligase substrate receptor FBXO7/PARK15 is mutated in an early-onset parkinsonian-pyramidal syndrome. Previous studies have proposed a role for FBXO7 in promoting Parkin-dependent mitophagy. Here, we systematically examine the involvement of FBXO7 in depolarization and mt UPR-dependent mitophagy in the well-established HeLa and induced-neurons cell systems. We find that FBXO7-/- cells have no demonstrable defect in: (i) kinetics of pUb accumulation, (ii) pUb puncta on mitochondria by super-resolution imaging, (iii) recruitment of Parkin and autophagy machinery to damaged mitochondria, (iv) mitophagic flux, and (v) mitochondrial clearance as quantified by global proteomics. Moreover, global proteomics of neurogenesis in the absence of FBXO7 reveals no obvious alterations in mitochondria or other organelles. These results argue against a general role for FBXO7 in Parkin-dependent mitophagy and point to the need for additional studies to define how FBXO7 mutations promote parkinsonian-pyramidal syndrome.

Keywords:  FBXO7; iNeurons; mitophagy; proteomics; ubiquitin ligase

DOI:  https://doi.org/10.15252/embr.202256399
Cell Mol Life Sci. 2023 Jun 20. 80(7): 183

Loss of functional peroxisomes leads to increased mitochondrial biogenesis and reduced autophagy that preserve mitochondrial function.

Lijun Chi, Dorothy Lee, Sharon Leung, Guanlan Hu, Bijun Wen, Paul Delgado-Olguin, Miluska Vissa, Ren Li, John H Brumell, Peter K Kim, Robert H J Bandsma.

  Peroxisomes are essential for mitochondrial health, as the absence of peroxisomes leads to altered mitochondria. However, it is unclear whether the changes in mitochondria are a function of preserving cellular function or a response to cellular damage caused by the absence of peroxisomes. To address this, we developed conditional hepatocyte-specific Pex16 deficient (Pex16 KO) mice that develop peroxisome loss and subjected them to a low-protein diet to induce metabolic stress. Loss of PEX16 in hepatocytes led to increased biogenesis of small mitochondria and reduced autophagy flux but with preserved capacity for respiration and ATP capacity. Metabolic stress induced by low protein feeding led to mitochondrial dysfunction in Pex16 KO mice and impaired biogenesis. Activation of PPARα partially corrected these mitochondrial disturbances, despite the absence of peroxisomes. The findings of this study demonstrate that the absence of peroxisomes in hepatocytes results in a concerted effort to preserve mitochondrial function, including increased mitochondrial biogenesis, altered morphology, and modified autophagy activity. Our study underscores the relationship between peroxisomes and mitochondria in regulating the hepatic metabolic responses to nutritional stressors.

Keywords:  Fenofibrate; Malnutrition; Metabolism; Mitophagy; Nuclear hormone receptor; mTOR

DOI:  https://doi.org/10.1007/s00018-023-04827-3
J Immunol. 2023 Jun 21. pii: ji2200851. [Epub ahead of print]

NK Cells from Human Cytomegalovirus-Seropositive Individuals Have a Distinct Metabolic Profile That Correlates with Elevated mTOR Signaling.

John R Lozada, Bin Zhang, Jeffrey S Miller, Frank Cichocki.

CMV can elicit adaptive immune features in both mouse and human NK cells. Mouse Ly49H+ NK cells expand 100- to 1000-fold in response to mouse CMV infection and persist for months after exposure. Human NKG2C+ NK cells also expand after human CMV (HCMV) infection and persist for months. The clonal expansion of adaptive NK cells is likely an energy-intensive process, and the metabolic requirements that support adaptive NK cell expansion and persistence remain largely uncharacterized. We previously reported that NK cells from HCMV-seropositive donors had increased maximum capacity for both glycolysis and mitochondrial oxidative phosphorylation relative to NK cells from HCMV-seronegative donors. In this article, we report an extension of this work in which we analyzed the metabolomes of NK cells from HCMV-seropositive donors with NKG2C+ expansions and NK cells from HCMV seronegative donors without such expansions. NK cells from HCMV+ donors exhibited striking elevations in purine and pyrimidine deoxyribonucleotides, along with moderate increases in plasma membrane components. Mechanistic target of rapamycin (mTOR) is a serine/threonine protein kinase that, as a part of mTOR complex 1 (mTORC1), bridges nutrient signaling to metabolic processes necessary for cell growth. Signaling through mTORC1 induces both nucleotide and lipid synthesis. We observed elevated mTORC1 signaling on activation in both NKG2C- and NKG2C+ NK cells from HCMV+ donors relative to those from HCMV- donors, demonstrating a correlation between higher mTORC1 activity and synthesis of key metabolites for cell growth and division.

DOI: https://doi.org/10.4049/jimmunol.2200851
Pharmacol Res. 2023 Jun 17. pii: S1043-6618(23)00178-0. [Epub ahead of print] 106822

A bioinformatics analysis, pre-clinical and clinical conception of autophagy in pancreatic cancer: Complexity and simplicity in crosstalk.

Milad Ashrafizadeh, Wei Zhang, Rongjun Zou, Gautam Sethi, Daniel J Klionsky, Xianbin Zhang.

  Pancreatic cancer (PC) is a serious gastrointestinal tract disease for which the 5-year survival rate is less than 10%, even in developed countries such as the USA. The genomic profile alterations and dysregulated biological mechanisms commonly occur in PC. Macroautophagy/autophagy is a cell death process that is maintained at a basal level in physiological conditions, whereas its level often changes during tumorigenesis. The function of autophagy in human cancers is dual and can be oncogenic and onco-suppressor. Autophagy is a potent controller of tumorigenesis in PC. The supportive autophagy in PC escalates the growth rate of PC cells and its suppression can mediate cell death. Autophagy also determines the metastasis of PC cells, and it can control the EMT in affecting migration. Moreover, starvation and hypoxia can stimulate glycolysis, and glycolysis induction can be mediated by autophagy in enhancing tumorigenesis in PC. Furthermore, protective autophagy stimulates drug resistance and gemcitabine resistance in PC cells, and its inhibition can enhance radiosensitivity. Autophagy can degrade MHC-I to mediate immune evasion and also regulates polarization of macrophages in the tumor microenvironment. Modulation of autophagy activity is provided by silibinin, ursolic acid, chrysin and huaier in the treatment of PC. Non-coding RNAs are also controllers of autophagy in PC and its inhibition can improve therapy response in patients. Moreover, mitophagy shows dysregulation in PC, which can enhance the proliferation of PC cells. Therefore, a bioinformatics analysis demonstrates the dysregulation of autophagy-related proteins and genes in PC as biomarkers.

Keywords:  Autophagy; drug resistance; mitophagy; non-coding RNAs; pancreatic cancer

DOI:  https://doi.org/10.1016/j.phrs.2023.106822
MicroPubl Biol. 2023 ;2023

C. elegans ATG-5 mutants associated with ataxia.

Azusa Yugeta, Hiroki Arai, Daiki Takahashi, Nami Haruta, Asako Sugimoto, Hirokazu Arimoto.

Intercellular cleaning via autophagy is crucial for maintaining cellular homeostasis, and impaired autophagy has been associated with the accumulation of protein aggregates that can contribute to neurological diseases. Specifically, the loss-of-function mutation in the human autophagy-related gene 5 (ATG5) at E122D has been linked to the pathogenesis of spinocerebellar ataxia in humans. In this study, we generated two homozygous C. elegans strains with mutations (E121D and E121A) at positions corresponding to the human ATG5 ataxia mutation to investigate the effects of ATG5 mutations on autophagy and motility. Our results showed that both mutants exhibited a reduction in autophagy activity and impaired motility, suggesting that the conserved mechanism of autophagy-mediated regulation of motility extends from C. elegans to humans.

DOI: https://doi.org/10.17912/micropub.biology.000792
Am J Chin Med. 2023 Jun 17. 1-23

Renoprotective Effect of Isoorientin in Diabetic Nephropathy via Activating Autophagy and Inhibiting the PI3K-AKT-TSC2-mTOR Pathway.

Zili Kong, Min Xiao, Bin Wang, Wenjie Zhang, Kui Che, Wenshan Lv, Yahao Wang, Yajing Huang, Han Zhao, Yanyun Zhao, Mengmeng Qi, Jingwei Chi, Yangang Wang.

  Diabetic nephropathy (DN) is one of the most serious complications of diabetes and the most common cause of death. The autophagy of podocytes plays an important role in the pathogenesis of DN. Here, through screening the constituent compounds of practical and useful Chinese herbal formulas, we identified that isoorientin (ISO) strongly promoted the autophagy of podocytes and could effectively protect podocytes from high glucose (HG)-induced injury. ISO significantly improved autophagic clearance of damaged mitochondria under HG conditions. Through a proteomics-based approach, we identified that ISO could reverse the excessive phosphorylation of TSC2 S939 under HG conditions and stimulate autophagy through inhibition of the PI3K-AKT-TSC2-mTOR pathway. Furthermore, ISO was predicted to bind to the SH2 domain of PI3Kp85[Formula: see text], which is crucial for the recruitment and activation of PI3K. The protective effect of ISO and its effects on autophagy and particularly on mitophagy were further proved using a DN mice model. To summarize, our study identified the protective effects of ISO against DN and demonstrated that ISO was a strong activator of autophagy, which could provide a basis for drug development.

Keywords:  Autophagy; Diabetic Nephropathy; Isoorientin; PI3K; TSC2

DOI:  https://doi.org/10.1142/S0192415X23500581
J Adv Res. 2023 Jun 18. pii: S2090-1232(23)00170-4. [Epub ahead of print]

Two aminopeptidase I homologs convergently contribute to pathobiology of fungal entomopathogen Beauveria bassiana via divergent physiology-dependent autophagy pathways for vacuolar targeting.

Jin-Li Ding, Kang Wei, Ming-Guang Feng, Sheng-Hua Ying.

   INTRODUCTION: In yeast, the cytoplasm-to-vacuole targeting (Cvt) pathway acts as a biosynthetic autophagy-related process, in which vacuolar targeting of hydrolase is mediated by the machineries involved in the selective autophagy. However, the mechanistic insights into vacuolar targeting of hydrolases through the selective autophagy pathway still remain enigmatic in filamentous fungi.
OBJECTIVES: Our study aims to investigate the mechanisms involved in vacuolar targeting of hydrolases in filamentous fungi.
METHODS: The filamentous entomopathogenic fungus Beauveria bassiana was used as a representative of filamentous fungi. We identified the homologs of yeast aminopeptidase I (Ape1) in B. bassiana by bioinformatic analyses and characterized their physiological roles by gene function analyses. Pathways for vacuolar targeting of hydrolases were investigated via molecular trafficking analyses.
RESULTS: B. bassiana has two homologs of yeast aminopeptidase I (Ape1) which are designated as BbApe1A and BbApe1B. The two homologs of yeast Ape1 contribute to starvation tolerance, development, and virulence in B. bassiana. Significantly, BbNbr1 acts as a selective autophagy receptor to mediate the vacuolar targeting of the two Ape1 proteins, in which BbApe1B interacts with BbNbr1 also directly interacting with BbAtg8, and BbApe1A has an additional requirement of the scaffold protein BbAtg11 that interacts with BbNbr1 and BbAtg8. Protein processing occurs at both terminuses of BbApe1A and only at carboxyl terminus of BbApe1B, which is also dependent on the autophagy-related proteins. Together, the functions and translocation processes of the two Ape1 proteins are associated with autophagy in fungal lifecycle.
CONCLUSION: This study reveals the functions and translocation processes for vacuolar hydrolases in the insect-pathogenic fungi and improves our understandings of the Nbr1-mediated vacuolar targeting pathway in the filamentous fungi.

Keywords:  Aminopeptidase I; Development; Insect parasitic fungus; Vacuolar targeting; Virulence

DOI:  https://doi.org/10.1016/j.jare.2023.06.007
Nat Commun. 2023 Jun 22. 14(1): 3725

The ER calcium channel Csg2 integrates sphingolipid metabolism with autophagy.

Shiyan Liu, Mutian Chen, Yichang Wang, Yuqing Lei, Ting Huang, Yabin Zhang, Sin Man Lam, Huihui Li, Shiqian Qi, Jia Geng, Kefeng Lu.

Sphingolipids are ubiquitous components of membranes and function as bioactive lipid signaling molecules. Here, through genetic screening and lipidomics analyses, we find that the endoplasmic reticulum (ER) calcium channel Csg2 integrates sphingolipid metabolism with autophagy by regulating ER calcium homeostasis in the yeast Saccharomyces cerevisiae. Csg2 functions as a calcium release channel and maintains calcium homeostasis in the ER, which enables normal functioning of the essential sphingolipid synthase Aur1. Under starvation conditions, deletion of Csg2 causes increases in calcium levels in the ER and then disturbs Aur1 stability, leading to accumulation of the bioactive sphingolipid phytosphingosine, which specifically and completely blocks autophagy and induces loss of starvation resistance in cells. Our findings indicate that calcium homeostasis in the ER mediated by the channel Csg2 translates sphingolipid metabolism into autophagy regulation, further supporting the role of the ER as a signaling hub for calcium homeostasis, sphingolipid metabolism and autophagy.

DOI: https://doi.org/10.1038/s41467-023-39482-6
JCI Insight. 2023 Jun 20. pii: e167694. [Epub ahead of print]

SRF deletion results in earlier disease onset in a mouse model of amyotrophic lateral sclerosis.

Jialei Song, Natalie Yashoda Dikwella, Daniela Sinske, Francesco Roselli, Bernd Knöll.

  Changes in neuronal activity modulate the vulnerability of motoneurons (MNs) in neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). So far, the molecular basis of neuronal activity's impact in ALS is poorly understood. Herein we investigated the impact of deleting the neuronal activity stimulated transcription factor (TF) serum response factor (SRF) in MNs of SOD1G93A mice. SRF was present in vulnerable MMP9 positive MNs. Ablation of SRF in MNs induced an earlier disease onset starting around 7-8 weeks after birth revealed by enhanced weight loss and decreased motor ability. This earlier disease onset in SRF depleted MNs was accompanied by mild elevation of neuroinflammation and neuromuscular synapse degeneration whereas overall MN numbers and mortality were unaffected. In SRF deficient mice, MNs showed impaired induction of autophagy encoding genes suggesting a new SRF function in transcriptional regulation of autophagy. Complementary, constitutive-active SRF-VP16 enhanced autophagy encoding gene transcription and autophagy progression in cells. Furthermore, SRF-VP16 decreased ALS-associated aggregate induction. Chemogenetic modulation of neuronal activity uncovered SRF as important TF mediating activity-dependent effects which might be beneficial to reduce ALS disease burden. Thus, our data identify with SRF a new gene regulator connecting neuronal activity with the cellular autophagy program initiated in degenerating MNs.

Keywords:  ALS; Autophagy; Mouse models; Neuroscience

DOI:  https://doi.org/10.1172/jci.insight.167694
bioRxiv. 2023 Apr 13. pii: 2023.04.13.536717. [Epub ahead of print]

A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling.

Sun Woo Sophie Kang, Rory P Cunningham, Colin B Miller, Constance M Cultraro, Jonathan Hernandez, Lisa M Jenkins, Alexei Lobanov, Maggie Cam, Natalie Porat-Shliom.

In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal (PP) and pericentral (PC) axis. How these mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combined intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We found that PP and PC mitochondria are morphologically and functionally distinct; beta-oxidation and mitophagy were elevated in PP regions, while lipid synthesis was predominant in the PC mitochondria. In addition, comparative phosphoproteomics revealed that mitophagy and lipid synthesis are regulated by phosphorylation in a zonated manner. Furthermore, we demonstrated that acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifted mitochondrial phenotypes in the PP and PC regions of the intact liver. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. The findings have important implications for liver physiology and disease.

DOI: https://doi.org/10.1101/2023.04.13.536717
Toxicol Lett. 2023 Jun 15. pii: S0378-4274(23)00204-7. [Epub ahead of print]

α-amanitin induces autophagy through AMPK-mTOR-ULK1 signaling pathway in hepatocytes.

Yue Xu, Shangwen Wang, Chi-Kwan Leung, Hao Chen, Chan Wang, Huijie Zhang, Shuwei Zhang, Yi Tan, Haowei Wang, Lin Miao, Yi Li, Yizhen Huang, Xiaoxing Zhang, Genmeng Yang, Ruilin Zhang, Xiaofeng Zeng.

  Amanitin poisoning is one of the most life-threatening mushroom poisonings. α-Amanitin plays a key role in Amanita phalloides intoxication. α-Amanitin shows toxic effects on the liver. However, the mechanism by which α-amanitin induces liver injury has not been elucidated. Autophagy plays a crucial role in maintaining cellular homeostasis and is closely related to the occurrence of a variety of diseases. Studies have shown that autophagy may play an important role in the process of α-amanitin-induced liver injury. However, the mechanism of α-amanitin-induced autophagy remains unclear. Thus, this study aimed to explore the mechanisms of α-amanitin in inducing hepatotoxicity in Sprague Dawley (SD) rats and the normal human liver cell line L02 cells. The SD rats and L02 cells exposed to α-amanitin were observed to determine whether α-amanitin could induce the autophagy of rat liver and L02 cells. The regulatory relationship between autophagy and the AMPK-mTOR- ULK pathway by exposing the autophagy agonist (rapamycin (RAPA)), autophagy inhibitor (3-methylademine (3-MA)), and AMPK inhibitor (compound C) was also explored. Autophagy-related proteins and AMPK-mTOR-ULK pathway-related proteins were detected using Western blot. The results of the study indicated that exposure to different concentrations of α-amanitin led to morphological changes in liver cells and significantly elevated levels of ALT and AST in the serum of SD rats. Additionally, the expression levels of LC3-II, Beclin-1, ATG5, ATG7, AMPK, p-AMPK, mTOR, p-mTOR, and ULK1 were significantly increased in the rat liver. And we found that L02 cells exposed to 0.5μM α-amanitin for 6h significantly induced autophagy and activated the AMPK-mTOR-ULK1 pathway. Pretreated with RAPA, 3-MA, and compound C for 1h, the expression levels of autophagy-related proteins and AMPK-mTOR-ULK pathway-related proteins significantly changed. Our results indicates that autophagy and the AMPK-mTOR-ULK pathway are involved in the process of α-amanitin-induced liver injury. This study may foster the identification of actionable therapeutic targets for A. phalloides intoxication.

Keywords:  AMPK-mTOR-ULK1 signaling pathway; L02 cells; autophagy; liver injury; α-amanitin

DOI:  https://doi.org/10.1016/j.toxlet.2023.06.004
Sci Adv. 2023 Jun 23. 9(25): eadg2339

VANGL2 inhibits antiviral IFN-I signaling by targeting TBK1 for autophagic degradation.

Zhiqiang Hu, Yingchao Xie, Jiansen Lu, Jianwu Yang, Jiahuan Zhang, Huaji Jiang, Hongyu Li, Yufeng Zhang, Dan Wu, Ke Zeng, Xiaochun Bai, Xiao Yu.

Stringent control of type I interferon (IFN-I) signaling is critical to potent innate immune responses against viral infection, yet the underlying molecular mechanisms are still elusive. Here, we found that Van Gogh-like 2 (VANGL2) acts as an IFN-inducible negative feedback regulator to suppress IFN-I signaling during vesicular stomatitis virus (VSV) infection. Mechanistically, VANGL2 interacted with TBK1 and promoted the selective autophagic degradation of TBK1 via K48-linked polyubiquitination at Lys372 by the E3 ligase TRIP, which serves as a recognition signal for the cargo receptor OPTN. Furthermore, myeloid-specific deletion of VANGL2 in mice showed enhanced IFN-I production against VSV infection and improved survival. In general, these findings revealed a negative feedback loop of IFN-I signaling through the VANGL2-TRIP-TBK1-OPTN axis and highlighted the cross-talk between IFN-I and autophagy in preventing viral infection. VANGL2 could be a potential clinical therapeutic target for viral infectious diseases, including COVID-19.

DOI: https://doi.org/10.1126/sciadv.adg2339
Plant Physiol. 2023 Jun 19. pii: kiad340. [Epub ahead of print]

Autophagy during Maize Endosperm Development Dampens Oxidative Stress and Promotes Mitochondrial Clearance.

Jessica A S Barros, Elizabeth C Chatt, Robert C Augustine, Fionn McLoughlin, Faqiang Li, Marisa S Otegui, Richard D Vierstra.

The selective turnover of macromolecules by autophagy provides a critical homeostatic mechanism for recycling cellular constituents and for removing superfluous and damaged organelles, membranes, and proteins. To better understand how autophagy impacts seed maturation and nutrient storage, we studied maize (Zea mays) endosperm in its early and middle developmental stages via an integrated multi-omics approach using mutants impacting the core macroautophagy factor AUTOPHAGY (ATG)-12 required for autophagosome assembly. Surprisingly, the mutant endosperm in these developmental windows accumulated normal amounts of starch and Zein storage proteins. However, the tissue acquired a substantially altered metabolome, especially for compounds related to oxidative stress and sulfur metabolism, including increases in cystine, dehydroascorbate, cys-glutathione disulfide, glucarate and galactarate, and decreases in peroxide and the anti-oxidant glutathione. While changes in the associated transcriptome were mild, the proteome was strongly altered in the atg12 endosperm, especially for increased levels of mitochondrial proteins without a concomitant increase in mRNA abundances. Although fewer mitochondria were seen cytologically, a heightened number appeared dysfunctional based on the accumulation of dilated cristae, consistent with attenuated mitophagy. Collectively, our results confirm that macroautophagy plays a minor role in the accumulation of starch and storage proteins during maize endosperm development, but likely helps protect against oxidative stress and clears unneeded/dysfunctional mitochondria during tissue maturation.

DOI: https://doi.org/10.1093/plphys/kiad340
JCI Insight. 2023 06 22. pii: e169937. [Epub ahead of print]8(12):

Perturbation of endoplasmic reticulum proteostasis triggers tissue injury in the thyroid gland.

Xiaohan Zhang, Crystal Young, Xiao-Hui Liao, Samuel Refetoff, Mauricio Torres, Yaron Tomer, Mihaela Stefan-Lifshitz, Hao Zhang, Dennis Larkin, Deyu Fang, Ling Qi, Peter Arvan.

  Defects in endoplasmic reticulum (ER) proteostasis have been linked to diseases in multiple organ systems. Here we examined the impact of perturbation of ER proteostasis in mice bearing thyrocyte-specific knockout of either HRD1 (to disable ER-associated protein degradation [ERAD]) or ATG7 (to disable autophagy) in the absence or presence of heterozygous expression of misfolded mutant thyroglobulin (the most highly expressed thyroid gene product, synthesized in the ER). Misfolding-inducing thyroglobulin mutations are common in humans but are said to yield only autosomal-recessive disease - perhaps because misfolded thyroglobulin protein might undergo disposal by ERAD or ER macroautophagy. We find that as single defects, neither ERAD, nor autophagy, nor heterozygous thyroglobulin misfolding altered circulating thyroxine levels, and neither defective ERAD nor defective autophagy caused any gross morphological change in an otherwise WT thyroid gland. However, heterozygous expression of misfolded thyroglobulin itself triggered significant ER stress and individual thyrocyte death while maintaining integrity of the surrounding thyroid epithelium. In this context, deficiency of ERAD (but not autophagy) resulted in patchy whole-follicle death with follicular collapse and degeneration, accompanied by infiltration of bone marrow-derived macrophages. Perturbation of thyrocyte ER proteostasis is thus a risk factor for both cell death and follicular demise.

Keywords:  Cell Biology; Protein misfolding

DOI:  https://doi.org/10.1172/jci.insight.169937
Sci Adv. 2023 Jun 23. 9(25): eadh1281

Unique amphipathic α helix drives membrane insertion and enzymatic activity of ATG3.

Taki Nishimura, Gianmarco Lazzeri, Noboru Mizushima, Roberto Covino, Sharon A Tooze.

Autophagosome biogenesis requires a localized perturbation of lipid membrane dynamics and a unique protein-lipid conjugate. Autophagy-related (ATG) proteins catalyze this biogenesis on cellular membranes, but the underlying molecular mechanism remains unclear. Focusing on the final step of the protein-lipid conjugation reaction, the ATG8/LC3 lipidation, we show how the membrane association of the conjugation machinery is organized and fine-tuned at the atomistic level. Amphipathic α helices in ATG3 proteins (AHATG3) have low hydrophobicity and contain less bulky residues. Molecular dynamics simulations reveal that AHATG3 regulates the dynamics and accessibility of the thioester bond of the ATG3~LC3 conjugate to lipids, enabling the covalent lipidation of LC3. Live-cell imaging shows that the transient membrane association of ATG3 with autophagic membranes is governed by the less bulky-hydrophobic feature of AHATG3. The unique properties of AHATG3 facilitate protein-lipid bilayer association, leading to the remodeling of the lipid bilayer required for the formation of autophagosomes.

DOI: https://doi.org/10.1126/sciadv.adh1281
Blood. 2023 Jun 20. pii: blood.2022017265. [Epub ahead of print]

Loss of miR-144/451 alleviates β-thalassemia by stimulating ULK1-mediated autophagy of free α-globin.

Julia Keith, Georgios E Christakopoulos, Alfonso G Fernandez, Yu Yao, Jingjing Zhang, Kalin Mayberry, Rahul Telange, Razan B A Sweileh, Michael W Dudley, Camilla Westbrook, Heather Sheppard, Mitchell J Weiss, Christophe Lechauve.

Most cells can eliminate unstable or misfolded proteins through quality control mechanisms. In the inherited red blood cell disorder β-thalassemia, mutations in the β-globin gene (HBB) lead to a reduction of the corresponding protein and the accumulation of cytotoxic free α-globin, which causes maturation arrest and apoptosis of erythroid precursors and reductions in the lifespan of circulating red blood cells. We showed previously that excess α-globin is eliminated by ULK1-dependent autophagy and that stimulation of this pathway by systemic mTORC1 inhibition alleviates β-thalassemia pathologies. We show here that disruption of the bi-cistronic microRNA locus miR-144/451 alleviates β-thalassemia by reducing mTORC1 activity and stimulating ULK1-mediated autophagy of free α-globin through two mechanisms. Loss of miR-451 upregulated its target mRNA, Cab39, which encodes a cofactor for LKB1, a serine-threonine kinase that phosphorylates and activates the central metabolic sensor, AMPK. The resultant enhancement of LKB1 activity stimulated AMPK and its downstream effects, including repression of mTORC1 and direct activation of ULK1. Additionally, loss of miR-144/451 inhibited the expression of erythroblast transferrin receptor 1 (TfR1), causing intracellular iron restriction, which has been shown to inhibit mTORC1, reduce free α-globin precipitates and improve hematological indices in β-thalassemia. The beneficial effects of miR-144/451 loss in β-thalassemia were inhibited by disruption of the Cab39 or Ulk1 genes. Our findings link the severity of a common hemoglobinopathy to a highly expressed erythroid microRNA locus and to a fundamental, metabolically regulated protein quality control pathway that is amenable to therapeutic manipulation.

DOI: https://doi.org/10.1182/blood.2022017265
Immunobiology. 2023 Apr 14. pii: S0171-2985(23)00054-2. [Epub ahead of print]228(4): 152386

miR-146a-5p regulates autophagy and NLRP3 inflammasome activation in epithelial barrier damage in the in vitro cell model of ulcerative colitis through the RNF8/Notch1/mTORC1 pathway.

Zepeng Chen, Qinglong Gu, Ruichao Chen.

  Ulcerative colitis (UC) is a chronic inflammatory disease affecting the colon that can be influenced by microRNAs (miRNAs). This study aims to investigate the impact of miR-146a-5p on lipopolysaccharide (LPS)-induced Caco-2/HT-29 cell autophagy and NLRP3 inflammasome activation and the underlying mechanism, with the aim of identifying potential therapeutic targets. We used LPS to establish Caco-2/HT-29 cell models and measured cell viability by CCK-8. The levels of miR-146a-5p, RNF8, markers of NLRP3 inflammasome activation and autophagy, proteins involved in the Notch1/mTORC1 pathway, and inflammatory factors were assessed by RT-qPCR, Western blot, and ELISA. Intestinal epithelial barrier function was evaluated by measuring transepithelial electrical resistance. Autophagic flux was measured using tandem fluorescent-labeled LC3. miR-146a-5p was highly-expressed in LPS-induced Caco-2/HT-29 cells, and autophagy flux was blocked at the autolysosomal stage after LPS induction. Inhibition of miR-146a-5p suppressed NLRP3 inflammasome activation, reduced intestinal epithelial barrier damage, and facilitated autophagy inhibition in LPS-induced Caco-2/HT-29 cells. The autophagy inhibitor NH4Cl partially nullified the inhibitory effects of miR-146a-5p inhibition on NLRP3 inflammation activation. miR-146a-5p targeted RNF8, and silencing RNF8 partly abrogated the action of miR-146a-5p inhibition on promoting autophagy and inhibiting NLRP3 inflammasome activation. miR-146a-5p inhibition suppressed the Notch1/mTORC1 pathway activation by upregulating RNF8. Inhibition of the Notch1/mTORC1 pathway partially nullified the function of silencing RNF8 on inhibiting autophagy and bolstering NLRP3 inflammasome activation. In conclusion, miR-146a-5p inhibition may be a potential therapeutic approach for UC, as it facilitates autophagy of LPS-stimulated Caco-2/HT-29 cells, inhibits NLRP3 inflammasome activation, and reduces intestinal epithelial barrier damage by upregulating RNF8 and suppressing the Notch1/mTORC1 pathway.

Keywords:  Autophagy; Caco-2 cells; NLRP3 inflammasome; Notch1; RNF8; Ulcerative colitis; mTORC1; miR-146a-5p

DOI:  https://doi.org/10.1016/j.imbio.2023.152386
Int Immunopharmacol. 2023 Jun 15. pii: S1567-5769(23)00820-2. [Epub ahead of print]121 110497

Unlocking the potential of Mesenchymal stem cells in liver Fibrosis: Insights into the impact of autophagy and aging.

Hongxia Tao, Qianglin Liu, Anqi Zeng, Linjiang Song.

  Liver fibrosis is a chronic liver disease characterized by extracellular matrix protein accumulation, potentially leading to cirrhosis or hepatocellular carcinoma. Liver cell damage, inflammatory responses, and apoptosis due to various reasons induce liver fibrosis. Although several treatments, such as antiviral drugs and immunosuppressive therapies, are available for liver fibrosis, they only provide limited efficacy. Mesenchymal stem cells (MSCs) have become a promising therapeutic option for liver fibrosis, because they can modulate the immune response, promote liver regeneration, and inhibit the activation of hepatic stellate cells that contribute to disease development. Recent studies have suggested that the mechanisms through which MSCs gain their antifibrotic properties involve autophagy and senescence. Autophagy, a vital cellular self-degradation process, is critical for maintaining homeostasis and protecting against nutritional, metabolic, and infection-mediated stress. The therapeutic effects of MSCs depend on appropriate autophagy levels, which can improve the fibrotic process. Nonetheless, aging-related autophagic damage is associated with a decline in MSC number and function, which play a crucial role in liver fibrosis development. This review summarizes the recent advancements in the understanding of autophagy and senescence in MSC-based liver fibrosis treatment, presenting the key findings from relevant studies.

Keywords:  Aging; Autophagy; Liver fibrosis; Mesenchymal stem cells

DOI:  https://doi.org/10.1016/j.intimp.2023.110497
Trends Endocrinol Metab. 2023 Jun 20. pii: S1043-2760(23)00106-6. [Epub ahead of print]

The emerging potential role of p62 in cancer treatment by regulating metabolism.

Xiaochuan Zhang, Mengge Dai, Shaotong Li, Meng Li, Bing Cheng, Ting Ma, Zheng Zhou.

  p62 is an important multifunctional adaptor protein participating in autophagy and many other activities. Many studies have revealed that p62 is highly expressed in multiple cancers and decreasing its level can effectively lower the proliferation ability of cancer cells. Moreover, much research has highlighted the significant role of the regulation of cancer cell metabolism in helping to treat tumors. Recent reports demonstrate that p62 could regulate cancer cell metabolism through various mechanisms. However, the relationship between p62 and cancer cell metabolism as well as the related mechanisms has not been fully elucidated. In this review, we describe glucose, glutamine, and fatty acid metabolism in tumor cells and some signaling pathways that can regulate cancer metabolism and are mediated by p62.

Keywords:  autophagy; cancer cell metabolism; inhibitors; p62

DOI:  https://doi.org/10.1016/j.tem.2023.05.004
Mol Cell Endocrinol. 2023 Jun 15. pii: S0303-7207(23)00145-4. [Epub ahead of print] 111994

Mitophagy disorder mediates cardiac deterioration induced by severe hypoglycemia in diabetic mice.

Cuihua Huang, Lishan Huang, Qintao Huang, Lu Lin, Lijing Wang, Yubin Wu, Kejun Wu, Ruonan Gao, Xiaoying Liu, XiaoHong Liu, Liqin Qi, Libin Liu.

  Severe hypoglycemia is closely related to adverse cardiovascular outcomes in patients with diabetes; however, the specific mechanism remains unclear. We previously found that severe hypoglycemia aggravated myocardial injury and cardiac dysfunction in diabetic mice, and that the mechanism of damage was related to mitochondrial oxidative stress and dysfunction. Based on the key regulatory role of mitophagy in mitochondrial quality control, this study aimed to further explore whether the myocardial damage caused by severe hypoglycemia is related to insufficient mitophagy and to clarify their underlying regulatory relationship. After severe hypoglycemia, mitochondrial reactive oxygen species increased, mitochondrial membrane potential and ATP content decreased, and pathological mitochondrial damage was aggravated in the myocardium of diabetic mice. This was accompanied by decreased mitochondrial biosynthesis, increased fusion, and downregulated PTEN-induced kinase 1 (PINK1)/Parkin-dependent mitophagy. Treating diabetic mice with the mitophagy activator and polyphenol metabolite urolithin A activated PINK1/Parkin-dependent mitophagy, reduced myocardial oxidative stress and mitochondrial damage associated with severe hypoglycemia, improved mitochondrial function, alleviated myocardial damage, and ultimately improved cardiac function. Thus, we provide insight into the prevention and treatment of diabetic myocardial injury caused by hypoglycemia to reduce adverse cardiovascular outcomes in patients with diabetes.

Keywords:  Diabetes mellitus; Mitophagy; Myocardial injury; Severe hypoglycemia

DOI:  https://doi.org/10.1016/j.mce.2023.111994
Cell Mol Neurobiol. 2023 Jun 21.

Autophagy Suppresses Ferroptosis by Degrading TFR1 to Alleviate Cognitive Dysfunction in Mice with SAE.

Lixia Du, You Wu, Qi Jia, Jin Li, Yi Li, Hongwei Ma, Zhongmin Fan, Xiaofeng Guo, Ling Li, Yuliang Peng, Jing Li, Zongping Fang, Xijing Zhang.

  Sepsis-associated encephalopathy (SAE) is a serious complication of sepsis that is characterized by long-term cognitive impairment, which imposes a heavy burden on families and society. However, its pathological mechanism has not been elucidated. Ferroptosis is a novel form of programmed cell death that is involved in multiple neurodegenerative diseases. In the current study, we found that ferroptosis also participated in the pathological process of cognitive dysfunction in SAE, while Liproxstatin-1 (Lip-1) effectively inhibited ferroptosis and alleviated cognitive impairment. Additionally, since an increasing number of studies have suggested the crosstalk between autophagy and ferroptosis, we further proved the essential role of autophagy in this process and demonstrated the key molecular mechanism of the autophagy-ferroptosis interaction. Currently, we showed that autophagy in the hippocampus was downregulated within 3 days of lipopolysaccharide injection into the lateral ventricle. Moreover, enhancing autophagy ameliorated cognitive dysfunction. Importantly, we found that autophagy suppressed ferroptosis by downregulating transferrin receptor 1 (TFR1) in the hippocampus, thereby alleviating cognitive impairment in mice with SAE. In conclusion, our findings indicated that hippocampal neuronal ferroptosis is associated with cognitive impairment. In addition, enhancing autophagy can inhibit ferroptosis via degradation of TFR1 to ameliorate cognitive impairment in SAE, which shed new light on the prevention and therapy for SAE.

Keywords:  Autophagy; Cognitive impairment; Ferroptosis; Sepsis-associated encephalopathy; TFR1

DOI:  https://doi.org/10.1007/s10571-023-01370-4
Annu Rev Cell Dev Biol. 2023 Jun 20.

Regulation of TORC2 Function and Localization in Yeast.

Anita Emmerstorfer-Augustin, Jeremy Thorner.

Every eukaryotic cell contains two, distinct multisubunit protein kinase complexes that each contain a TOR (target of rapamycin) protein as the catalytic subunit. These ensembles, designated TORC1 and TORC2, serve as nutrient and stress sensors, signal integrators, and regulators of cell growth and homeostasis, but they differ in their composition, localization, and function. TORC1, activated on the cytosolic surface of the vacuole (or, in mammalian cells, on the cytosolic surface of the lysosome), promotes biosynthesis and suppresses autophagy. TORC2, located primarily at the plasma membrane (PM), maintains the proper levels and bilayer distribution of all PM components (sphingolipids, glycerophospholipids, sterols, and integral membrane proteins), which are needed for the membrane expansion that accompanies cell growth and division and for combating insults to PM integrity. This review summarizes our current understanding of the assembly, structural features, subcellular distribution, and function and regulation of TORC2, obtained largely through studies conducted with Saccharomyces cerevisiae. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 39 is October 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-cellbio-011723-030346
Front Mol Neurosci. 2023 ;16 1163981

Cardiolipin externalization mediates prion protein (PrP) peptide 106-126-associated mitophagy and mitochondrial dysfunction.

Dongming Yang, Jie Li, Zhiping Li, Mengyang Zhao, Dongdong Wang, Zhixin Sun, Pei Wen, Fengting Gou, Yuexin Dai, Yilan Ji, Wen Li, Deming Zhao, Lifeng Yang.

  Proper mitochondrial performance is imperative for the maintenance of normal neuronal function to prevent the development of neurodegenerative diseases. Persistent accumulation of damaged mitochondria plays a role in prion disease pathogenesis, which involves a chain of events that culminate in the generation of reactive oxygen species and neuronal death. Our previous studies have demonstrated that PINK1/Parkin-mediated mitophagy induced by PrP106-126 is defective and leads to an accumulation of damaged mitochondria after PrP106-126 treatment. Externalized cardiolipin (CL), a mitochondria-specific phospholipid, has been reported to play a role in mitophagy by directly interacting with LC3II at the outer mitochondrial membrane. The involvement of CL externalization in PrP106-126-induced mitophagy and its significance in other physiological processes of N2a cells treated with PrP106-126 remain unknown. We demonstrate that the PrP106-126 peptide caused a temporal course of mitophagy in N2a cells, which gradually increased and subsequently decreased. A similar trend in CL externalization to the mitochondrial surface was seen, resulting in a gradual decrease in CL content at the cellular level. Inhibition of CL externalization by knockdown of CL synthase, responsible for de novo synthesis of CL, or phospholipid scramblase-3 and NDPK-D, responsible for CL translocation to the mitochondrial surface, significantly decreased PrP106-126-induced mitophagy in N2a cells. Meanwhile, the inhibition of CL redistribution significantly decreased PINK1 and DRP1 recruitment in PrP106-126 treatment but had no significant decrease in Parkin recruitment. Furthermore, the inhibition of CL externalization resulted in impaired oxidative phosphorylation and severe oxidative stress, which led to mitochondrial dysfunction. Our results indicate that CL externalization induced by PrP106-126 on N2a cells plays a positive role in the initiation of mitophagy, leading to the stabilization of mitochondrial function.

Keywords:  autophagy; cardiolipin; mitophagy; neurodegenerative disease; prion disease

DOI:  https://doi.org/10.3389/fnmol.2023.1163981