Publications by authors named "Daniel J Klionsky"

445 Publications

The expanding role of Atg8.

Autophagy 2021 Sep 5:1-2. Epub 2021 Sep 5.

Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.

It would be quite convenient if every protein had one distinct function, one distinct role in just a single cellular process. In the field of macroautophagy/autophagy, however, we are increasingly finding that this is not the case; several autophagy proteins have two or more roles within the process of autophagy and many even "moonlight" as functional members of entirely different cellular processes. This is perhaps best exemplified by the Atg8-family proteins. These dynamic proteins have already been reported to serve several functions both within autophagy (membrane tethering, membrane fusion, binding to cargo receptors, binding to autophagy machinery) and beyond (LC3-associated phagocytosis, formation of EDEMosomes, immune signaling) but as Maruyama and colleagues suggest in their recent report, this list of functions may not yet be complete.
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http://dx.doi.org/10.1080/15548627.2021.1967566DOI Listing
September 2021

A perspective on the role of autophagy in cancer.

Biochim Biophys Acta Mol Basis Dis 2021 Sep 1;1867(12):166262. Epub 2021 Sep 1.

Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address:

Autophagy refers to a ubiquitous set of catabolic pathways required to achieve proper cellular homeostasis. Aberrant autophagy has been implicated in a multitude of diseases including cancer. In this review, we highlight pioneering and groundbreaking research that centers on delineating the role of autophagy in cancer initiation, proliferation and metastasis. First, we discuss the autophagy-related (ATG) proteins and their respective roles in the de novo formation of autophagosomes and the subsequent delivery of cargo to the lysosome for recycling. Next, we touch upon the history of cancer research that centers upon ATG proteins and regulatory mechanisms that control an appropriate autophagic response and how these are altered in the diseased state. Then, we discuss the various discoveries that led to the idea of autophagy as a double-edged sword when it comes to cancer therapy. This review also briefly narrates how different types of autophagy-selective macroautophagy and chaperone-mediated autophagy, have been linked to different cancers. Overall, these studies build upon a steadfast trajectory that aims to solve the monumentally daunting challenge of finding a cure for many types of cancer by modulating autophagy either through inhibition or induction.
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http://dx.doi.org/10.1016/j.bbadis.2021.166262DOI Listing
September 2021

Nutrition acquisition by human immunity, transient overnutrition and the cytokine storm in severe cases of COVID-19.

Med Hypotheses 2021 Aug 21;155:110668. Epub 2021 Aug 21.

Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States.

The human immunity has a pivotal role in nutrition acquisition from the pathogens and damaged body tissue during the SARS-CoV-2 virus infection, which may lead to transient overnutrition in the patients, lead to lipotoxicity and further damage in non-adipose tissues, and cause hyperinflammation and cytokine storm in severe cases of COVID-19. In view of this, high-quality clinical trials on restrictive eating should be designed to investigate the possible benefits of food intake restriction on patients' recovery from COVID-19 disease.
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http://dx.doi.org/10.1016/j.mehy.2021.110668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8379086PMC
August 2021

Autophagy in major human diseases.

EMBO J 2021 Aug 30:e108863. Epub 2021 Aug 30.

Signalling Programme, Babraham Institute, Cambridge, UK.

Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.
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http://dx.doi.org/10.15252/embj.2021108863DOI Listing
August 2021

Vorinostat in autophagic cell death: A critical insight into autophagy-mediated, -associated and -dependent cell death for cancer prevention.

Drug Discov Today 2021 Aug 13. Epub 2021 Aug 13.

Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela 769008, Odisha, India. Electronic address:

Histone deacetylases (HDACs) inhibit the acetylation of crucial autophagy genes, thereby deregulating autophagy and autophagic cell death (ACD) and facilitating cancer cell survival. Vorinostat, a broad-spectrum pan-HDAC inhibitor, inhibits the deacetylation of key autophagic markers and thus interferes with ACD. Vorinostat-regulated ACD can have an autophagy-mediated, -associated or -dependent mechanism depending on the involvement of apoptosis. Molecular insights revealed that hyperactivation of the PIK3C3/VPS34-BECN1 complex increases lysosomal disparity and enhances mitophagy. These changes are followed by reduced mitochondrial biogenesis and by secondary signals that enable superactivated, nonselective or bulk autophagy, leading to ACD. Although the evidence is limited, this review focuses on molecular insights into vorinostat-regulated ACD and describes critical concepts for clinical translation.
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http://dx.doi.org/10.1016/j.drudis.2021.08.004DOI Listing
August 2021

An AMPK-ULK1-PIKFYVE signaling axis for PtdIns5P-dependent autophagy regulation upon glucose starvation.

Autophagy 2021 Aug 9:1-2. Epub 2021 Aug 9.

Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.

Glucose deprivation induces macroautophagy/autophagy primarily through AMPK activation. However, little is known about the exact mechanism of this signaling. A recent study from Dr. David C. Rubinsztein's lab showed that ULK1 is activated by AMPK upon glucose starvation, resulting in the phosphorylation of the lipid kinase PIKFYVE on S1548. The activated PIKFYVE consequently enhances the formation of phosphatidylinositol-5-phosphate (PtdIns5P)-containing autophagosomes, and therefore drives autophagy upregulation. The novel discovery of how ULK1 regulates the non-canonical autophagy signaling (PtdIns5P-dependent autophagy), not only expands our knowledge of autophagy, but also sheds light on therapeutic strategies for curing human disorders, where glucose-induced starvation can play an important role.
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http://dx.doi.org/10.1080/15548627.2021.1959240DOI Listing
August 2021

Multiple structural rearrangements mediated by high-plasticity regions in Atg3 are key for efficient conjugation of Atg8 to PE during autophagy.

Autophagy 2021 08 31;17(8):1805-1808. Epub 2021 Jul 31.

Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.

The Atg3 protein is highly homologous from yeast to human. Atg3 functions as an E2-like enzyme promoting conjugation of Atg8-family proteins to phosphatidylethanolamine (PE), a lipid molecule embedded in the growing phagophore membrane during stress-induced autophagy. Over the last decade, Atg3 became one of the most explored autophagy proteins, resulting in observations that provided specific insights into the structural mechanisms of its function. In this article, we describe a recent study by Ye et al. that reveals, using the human ATG3, how the membrane binding capability of the enzyme is tightly linked to its conjugation activity. We summarize the current knowledge on important mechanisms that involve protein-protein or protein-membrane interactions of Atg3 and that ultimately lead to efficient Atg8-PE conjugation. AH: amphipathic helix; FR: flexible region; HR: handle region; NMR: nuclear magnetic resonance.
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http://dx.doi.org/10.1080/15548627.2021.1954457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386745PMC
August 2021

Not lowering the bar, just providing a step stool.

Autophagy 2021 07 21;17(7):1569-1570. Epub 2021 Jun 21.

Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.

There have been a couple of times when we have reviewed papers that are essentially publishable as initially submitted; the "criticisms" were more along the lines of constructive suggestions that the authors might want to consider when they submitted a revised version of the paper, but those changes were not required. However, a much more common experience is for the authors to receive a series of comments from multiple reviewers. Most of those comments are critical for the authors to address, to ensure that the data in the paper are of sufficient quality and rigor, with adequate controls, to support the stated conclusions. That said, reviewers sometimes make requests, with the best of intentions, which might be reasonably considered as "beyond the scope of the present study". Thus, there needs to be a balance between addressing each and every comment of a review and completing a story even though there are additional avenues and questions that remain unexplored. Sometimes, even after a repeated round(s) of review, such questions linger and may impede acceptance of a worthy study.
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http://dx.doi.org/10.1080/15548627.2021.1936360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354666PMC
July 2021

Yeast mitophagy: Unanswered questions.

Biochim Biophys Acta Gen Subj 2021 08 19;1865(8):129932. Epub 2021 May 19.

Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA. Electronic address:

Superfluous and damaged mitochondria need to be efficiently repaired or removed. Mitophagy is a selective type of autophagy that can engulf a portion of mitochondria within a double-membrane structure, called a mitophagosome, and deliver it to the vacuole for degradation. Mitophagy has significant physiological functions from yeast to human, and recent advances in yeast mitophagy shed light on the molecular mechanisms of mitophagy, especially the regulation of mitophagy induction. This review summarizes our current knowledge about yeast mitophagy and considers several unsolved questions, with a particular focus on Saccharomyces cerevisiae.
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http://dx.doi.org/10.1016/j.bbagen.2021.129932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8205991PMC
August 2021

ATG4-family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system.

Autophagy 2021 06 19;17(6):1293-1295. Epub 2021 May 19.

Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.

In eukaryotes, ATG4/Atg4 is a critical regulator of macroautophagy/autophagy. The protease activity of Atg4/ATG4, involved in conjugation and deconjugation of Atg8-family proteins, was so far regarded as its sole functional contribution. However, the role of individual ATG4-family proteins during mammalian autophagy had previously not been examined . During their recent investigation, Nguyen et al. discovered a hitherto unexplored role for mammalian ATG4s during mitophagy - the recruitment of ATG9A-containing vesicles. Their article, highlighted here, discusses the finding, which uses a novel artificial intelligence (AI)-directed analysis technique for focused ion beam-scanning electron microscopy (FIB-SEM) imaging to demonstrate the role of ATG4s in promoting phagophore growth and establishing phagophore-ER contacts.
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http://dx.doi.org/10.1080/15548627.2021.1917284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8204968PMC
June 2021

Ferritinophagy and ferroptosis in the management of metabolic diseases.

Trends Endocrinol Metab 2021 07 15;32(7):444-462. Epub 2021 May 15.

Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital Fudan University, Shanghai 200032, China; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA. Electronic address:

Ferroptosis is a form of regulated cell death modality associated with disturbed iron-homeostasis and unrestricted lipid peroxidation. Ample evidence has depicted an essential role for ferroptosis as either the cause or consequence for human diseases, denoting the likely therapeutic promises for targeting ferroptosis in the preservation of human health. Ferritinophagy, a selective form of autophagy, contributes to the initiation of ferroptosis through degradation of ferritin, which triggers labile iron overload (IO), lipid peroxidation, membrane damage, and cell death. In this review, we will delineate the role of ferritinophagy in ferroptosis, and its underlying regulatory mechanisms, to unveil the therapeutic value of ferritinophagy as a target in the combat of ferroptosis to manage metabolic diseases.
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http://dx.doi.org/10.1016/j.tem.2021.04.010DOI Listing
July 2021

The role of autophagy in cardiovascular pathology.

Cardiovasc Res 2021 May 6. Epub 2021 May 6.

Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.

Macroautophagy/autophagy is a conserved catabolic recycling pathway in which cytoplasmic components are sequestered, degraded, and recycled to survive various stress conditions. Autophagy dysregulation has been observed and linked with the development and progression of several pathologies, including cardiovascular diseases, the leading cause of death in the developed world. In this review, we aim to provide a broad understanding of the different molecular factors that govern autophagy regulation and how these mechanisms are involved in the development of specific cardiovascular pathologies, including ischemic and reperfusion injury, myocardial infarction, cardiac hypertrophy, cardiac remodeling, and heart failure.
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http://dx.doi.org/10.1093/cvr/cvab158DOI Listing
May 2021

Moments in autophagy and disease: Past and present.

Mol Aspects Med 2021 Apr 27:100966. Epub 2021 Apr 27.

Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA. Electronic address:

Over the past several decades, research on autophagy, a highly conserved lysosomal degradation pathway, has been advanced by studies in different model organisms, especially in the field of its molecular mechanism and regulation. The malfunction of autophagy is linked to various diseases, among which cancer and neurodegenerative diseases are the major focus. In this review, we cover some other important diseases, including cardiovascular diseases, infectious and inflammatory diseases, and metabolic disorders, as well as rare diseases, with a hope of providing a more complete understanding of the spectrum of autophagy's role in human health.
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http://dx.doi.org/10.1016/j.mam.2021.100966DOI Listing
April 2021

Targeting autophagy in ischemic stroke: From molecular mechanisms to clinical therapeutics.

Pharmacol Ther 2021 Sep 3;225:107848. Epub 2021 Apr 3.

Department of Laboratory Medicine and Pathology, University of Washington Seattle, Seattle, WA 98195, USA; Shanghai Institute of Cardiovascular Diseases, Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China. Electronic address:

Stroke constitutes the second leading cause of death and a major cause of disability worldwide. Stroke is normally classified as either ischemic or hemorrhagic stroke (HS) although 87% of cases belong to ischemic nature. Approximately 700,000 individuals suffer an ischemic stroke (IS) in the US each year. Recent evidence has denoted a rather pivotal role for defective macroautophagy/autophagy in the pathogenesis of IS. Cellular response to stroke includes autophagy as an adaptive mechanism that alleviates cellular stresses by removing long-lived or damaged organelles, protein aggregates, and surplus cellular components via the autophagosome-lysosomal degradation process. In this context, autophagy functions as an essential cellular process to maintain cellular homeostasis and organismal survival. However, unchecked or excessive induction of autophagy has been perceived to be detrimental and its contribution to neuronal cell death remains largely unknown. In this review, we will summarize the role of autophagy in IS, and discuss potential strategies, particularly, employment of natural compounds for IS treatment through manipulation of autophagy.
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http://dx.doi.org/10.1016/j.pharmthera.2021.107848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8263472PMC
September 2021

Adaptive immunity at the crossroads of autophagy and metabolism.

Cell Mol Immunol 2021 May 30;18(5):1096-1105. Epub 2021 Mar 30.

University of Michigan, Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, Ann Arbor, MI, USA.

The function of lymphocytes is dependent on their plasticity, particularly their adaptation to energy availability and environmental stress, and their protein synthesis machinery. Lymphocytes are constantly under metabolic stress, and macroautophagy/autophagy is the primary metabolic pathway that helps cells overcome stressors. The intrinsic role of autophagy in regulating the metabolism of adaptive immune cells has recently gained increasing attention. In this review, we summarize and discuss the versatile roles of autophagy in regulating cellular metabolism and the implications of autophagy for immune cell function and fate, especially for T and B lymphocytes.
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http://dx.doi.org/10.1038/s41423-021-00662-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8093269PMC
May 2021

New functions of a known autophagy regulator: VCP and autophagy initiation.

Autophagy 2021 05 31;17(5):1063-1064. Epub 2021 Mar 31.

Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.

VCP, a conserved ATPase, is involved in several cellular processes, and mutations in this protein are associated with various diseases. VCP also plays a role in autophagosome maturation. However, because a deficiency in autophagosome maturation presents a readily observable phenotype, other roles of VCP in autophagy regulation, in particular in the initial steps of autophagosome formation, may have been overlooked. In a recently published paper, using small-molecule inhibitors, Hill . showed that VCP regulates autophagy initiation through both stabilization of BECN1 and enhancement of phosphati-dylinositol 3-kinase (PtdIns3K) complex assembly.
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http://dx.doi.org/10.1080/15548627.2021.1905974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8143236PMC
May 2021

ER stress in Cardiometabolic Diseases: from Molecular Mechanisms to Therapeutics.

Endocr Rev 2021 Mar 8. Epub 2021 Mar 8.

University of Wyoming College of Health Sciences, Laramie, USA.

The endoplasmic reticulum (ER) hosts linear polypeptides and fosters natural folding of proteins through ER-residing chaperones and enzymes. Failure of the ER to align and compose proper protein architecture leads to accumulation of misfolded/unfolded proteins in the ER lumen, which disturbs ER homeostasis to provoke ER stress. Presence of ER stress initiates the cytoprotective unfolded protein response (UPR) to restore ER homeostasis or instigates a rather maladaptive UPR to promote cell death. Although a wide array of cellular processes such as persistent autophagy, dysregulated mitophagy, and secretion of pro-inflammatory cytokines may contribute to the onset and progression of cardiometabolic diseases, it is well perceived that ER stress also evokes onset and development of cardiometabolic diseases, particularly, cardiovascular diseases, diabetes mellitus, obesity, and chronic kidney disease. Meanwhile, these pathological conditions further aggravate ER stress, creating a rather vicious cycle. Here in this review, we aimed at summarizing and updating the available information on ER stress in cardiovascular diseases, diabetes mellitus, obesity, and chronic kidney disease, hoping to offer novel insights for the management of these cardiometabolic comorbidities through regulation of ER stress.
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http://dx.doi.org/10.1210/endrev/bnab006DOI Listing
March 2021

Ion Channels and Transporters in Autophagy.

Autophagy 2021 Mar 3:1-20. Epub 2021 Mar 3.

Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA.

Ion exchange between intracellular and extracellular spaces is the basic mechanism for controlling cell metabolism and signal transduction. This process is mediated by ion channels and transporters on the plasma membrane, or intracellular membranes that surround various organelles, in response to environmental stimuli. Macroautophagy (hereafter referred to as autophagy) is one of the lysosomal-dependent degradation pathways that maintains homeostasis through the degradation and recycling of cellular components (e.g., dysfunctional proteins and damaged organelles). Although autophagy-related (ATG) proteins play a central role in regulating the formation of autophagy-related member structures (e.g., phagophores, autophagosomes, and autolysosomes), the autophagic process also involves changes in expression and function of ion channels and transporters. Here we discuss current knowledge of the mechanisms that regulate autophagy in mammalian cells, with special attention to the ion channels and transporters. We also highlight prospects for the development of drugs targeting ion channels and transporters in autophagy.
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http://dx.doi.org/10.1080/15548627.2021.1885147DOI Listing
March 2021

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition).

Autophagy 2021 Jan 8;17(1):1-382. Epub 2021 Feb 8.

University of Crete, School of Medicine, Laboratory of Clinical Microbiology and Microbial Pathogenesis, Voutes, Heraklion, Crete, Greece; Foundation for Research and Technology, Institute of Molecular Biology and Biotechnology (IMBB), Heraklion, Crete, Greece.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
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http://dx.doi.org/10.1080/15548627.2020.1797280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7996087PMC
January 2021

Membrane Binding and Homodimerization of Atg16 Via Two Distinct Protein Regions is Essential for Autophagy in Yeast.

J Mol Biol 2021 03 21;433(5):166809. Epub 2021 Jan 21.

Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States.

Macroautophagy is a bulk degradation mechanism in eukaryotic cells. Efficiency of an essential step of this process in yeast, Atg8 lipidation, relies on the presence of Atg16, a subunit of the Atg12-Atg5-Atg16 complex acting as the E3-like enzyme in the ubiquitination-like reaction. A current view on the functional structure of Atg16 in the yeast S. cerevisiae comes from the two crystal structures that reveal the Atg5-interacting α-helix linked via a flexible linker to another α-helix of Atg16, which then assembles into a homodimer. This view does not explain the results of previous in vitro studies revealing Atg16-dependent deformations of membranes and liposome-binding of the Atg12-Atg5 conjugate upon addition of Atg16. Here we show that Atg16 acts as both a homodimerizing and peripheral membrane-binding polypeptide. These two characteristics are imposed by the two distinct regions that are disordered in the nascent protein. Atg16 binds to membranes in vivo via the amphipathic α-helix (amino acid residues 113-131) that has a coiled-coil-like propensity and a strong hydrophobic face for insertion into the membrane. The other protein region (residues 64-99) possesses a coiled-coil propensity, but not amphipathicity, and is dispensable for membrane anchoring of Atg16. This region acts as a Leu-zipper essential for formation of the Atg16 homodimer. Mutagenic disruption in either of these two distinct domains renders Atg16 proteins that, in contrast to wild type, completely fail to rescue the autophagy-defective phenotype of atg16Δ cells. Together, the results of this study yield a model for the molecular mechanism of Atg16 function in macroautophagy.
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http://dx.doi.org/10.1016/j.jmb.2021.166809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7924733PMC
March 2021

Downregulation of autophagy by Met30-mediated Atg9 ubiquitination.

Proc Natl Acad Sci U S A 2021 01;118(1)

Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109;

Macroautophagy/autophagy is a highly conserved eukaryotic molecular process that facilitates the recycling of superfluous cytoplasmic materials, damaged organelles, and invading pathogens, resulting in proper cellular homeostasis and survival during stress conditions. Autophagy is stringently regulated at multiple stages, including control at transcriptional, translational, and posttranslational levels. In this work, we identified a mechanism by which regulation of autophagy is achieved through the posttranslational modification of Atg9. Here, we show that, in order to limit autophagy to a low, basal level during normal conditions, Atg9 is ubiquitinated and subsequently targeted for degradation in a proteasome-dependent manner through the action of the E3 ligase Met30. When cells require increased autophagy flux to respond to nutrient deprivation, the proteolysis of Atg9 is significantly reduced. Overall, this work reveals an additional layer of mechanistic regulation that allows cells to further maintain appropriate levels of autophagy and to rapidly induce this process in response to stress.
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http://dx.doi.org/10.1073/pnas.2005539118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817162PMC
January 2021

Did evolution choose Atg11 as the scaffolding platform beyond selective autophagy?

Autophagy 2021 04 14;17(4):835-836. Epub 2021 Jan 14.

Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.

It has been well established that Atg11 plays a critical role in selective macroautophagy/autophagy, but not in nonselective autophagy in the budding yeast . However, its mammalian ortholog RB1CC1/FIP200 is indispensable for both types of autophagy, and the molecular mechanism behind its function is a mystery. Recently, Pan et al. showed that in the fission yeast , Atg11 could also promote nonselective autophagy via activation of Atg1 kinase. These results prompt an interesting idea that Atg11 might have gained an additional ability to mediate nonselective autophagy through evolution.
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http://dx.doi.org/10.1080/15548627.2021.1872176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8078765PMC
April 2021

Tumor heterogeneity in autophagy-dependent ferroptosis.

Autophagy 2021 Jan 15:1-14. Epub 2021 Jan 15.

Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA.

Macroautophagy (hereafter referred to as "autophagy") is a lysosome-mediated degradation process that plays a complex role in cellular stress, either promoting survival or triggering death. Early studies suggest that ferroptosis, an iron-dependent form of regulated cell death, is not related to autophagy. Conversely, recent evidence indicates that the molecular machinery of autophagy facilitates ferroptosis through the selective degradation of anti-ferroptosis regulators. However, the mechanism of autophagy-dependent ferroptosis remains incompletely understood. Here, we examine the early dynamic change in protein expression of autophagic (e.g., MAP1LC3B and SQSTM1) or ferroptotic (e.g., SLC7A11 and GPX4) regulators in 60 human cancer cell lines in response to two classical ferroptosis activators (erastin and RSL3) in the absence or presence of the lysosomal inhibitor chloroquine. Compared to erastin, RSL3 exhibits wider and stronger activity in the upregulation of MAP1LC3B-II or downregulation of SQSTM1 in 80% (48/60) or 63% (38/60) of cell lines, respectively. Both RSL3 and erastin failed to affect SLC7A11 expression, but they led to GPX4 downregulation in 12% (7/60) and 3% (2/60) of cell lines, respectively. Additionally, the intracellular iron exporter SLC40A1/ferroportin-1 was identified as a new substrate for autophagic elimination, and its degradation by SQSTM1 promoted ferroptosis and in xenograft tumor mouse models. Together, these findings show tumor heterogeneity in autophagy-dependent ferroptosis, which might have different biological behaviors with regard to the dynamic characteristics of cell death.
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http://dx.doi.org/10.1080/15548627.2021.1872241DOI Listing
January 2021

Incomplete mitophagy in the mevalonate kinase-deficient Saccharomyces cerevisiae and its relation to the MKD-related autoinflammatory disease in humans.

Biochim Biophys Acta Mol Basis Dis 2021 04 29;1867(4):166053. Epub 2020 Dec 29.

Department of Genetics, Federal University of Pernambuco, Avenida Moraes Rego, No. 1235, Recife, PE 50760-901, Brazil. Electronic address:

Mevalonate kinase deficiency (MKD) is an autosomal recessive disorder in humans that causes systemic autoinflammatory problems to children. Previously, we used a yeast model to show that MKD results in mitochondrial malfunctioning that may finally induce mitophagy. Here, we proved that MKD indeed induced general autophagy as well as mitophagy in yeast, but these mechanisms did not go to completion. Therefore, the limitation of mevalonate kinase activity produces dysfunctional mitochondria that might not be recycled, causing metabolic dysfunctions in the cells. Understanding this mechanism may provide a piece in solving the nonspecific autoinflammatory response puzzle observed in MKD patients.
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http://dx.doi.org/10.1016/j.bbadis.2020.166053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8011287PMC
April 2021

A multifactorial score including autophagy for prognosis and care of COVID-19 patients.

Autophagy 2020 12 29;16(12):2276-2281. Epub 2020 Nov 29.

Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Centre Antoine Lacassagne , Nice, France.

In less than eleven months, the world was brought to a halt by the COVID-19 outbreak. With hospitals becoming overwhelmed, one of the highest priorities concerned critical care triage to ration the scarce resources of intensive care units. Which patient should be treated first? Based on what clinical and biological criteria? A global joint effort rapidly led to sequencing the genomes of tens of thousands of COVID-19 patients to determine the patients' genetic signature that causes them to be at risk of suddenly developing severe disease. In this commentary, we would like to consider some points concerning the use of a multifactorial risk score for COVID-19 severity. This score includes macroautophagy (hereafter referred to as autophagy), a critical host process that controls all steps harnessed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. ATG5: autophagy related 5; BECN1: beclin 1; COVID-19: coronavirus infectious disease-2019; EGR1: early growth response 1; ER: endoplasmic reticulum; DMVs: double-membrane vesicles; IBV: infectious bronchitis virus; MAP1LC3: microtubule associated protein 1 light chain 3; LC3-I: proteolytically processed, non-lipidated MAP1LC3; LC3-II: lipidated MAP1LC3; MEFs: mouse embryonic fibroblasts; MERS-CoV: Middle East respiratory syndrome-coronavirus; MHV: mouse hepatitis virus; NSP: non-structural protein; PEDV: porcine epidemic diarrhea virus; PLP2-TM: membrane-associated papain-like protease 2; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TGEV: transmissible gastroenteritis virus.
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http://dx.doi.org/10.1080/15548627.2020.1844433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7751655PMC
December 2020

Elevating PI3P drives select downstream membrane trafficking pathways.

Mol Biol Cell 2021 01 25;32(2):143-156. Epub 2020 Nov 25.

Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109.

Phosphoinositide signaling lipids are essential for several cellular processes. The requirement for a phosphoinositide is conventionally studied by depleting the corresponding lipid kinase. However, there are very few reports on the impact of elevating phosphoinositides. That phosphoinositides are dynamically elevated in response to stimuli suggests that, in addition to being required, phosphoinositides drive downstream pathways. To test this hypothesis, we elevated the levels of phosphatidylinositol-3-phosphate (PI3P) by generating hyperactive alleles of the yeast phosphatidylinositol 3-kinase, Vps34. We find that hyperactive Vps34 drives certain pathways, including phosphatidylinositol-3,5-bisphosphate synthesis and retrograde transport from the vacuole. This demonstrates that PI3P is rate limiting in some pathways. Interestingly, hyperactive Vps34 does not affect endosomal sorting complexes required for transport (ESCRT) function. Thus, elevating PI3P does not always increase the rate of PI3P-dependent pathways. Elevating PI3P can also delay a pathway. Elevating PI3P slowed late steps in autophagy, in part by delaying the disassembly of autophagy proteins from mature autophagosomes as well as delaying fusion of autophagosomes with the vacuole. This latter defect is likely due to a more general defect in vacuole fusion, as assessed by changes in vacuole morphology. These studies suggest that stimulus-induced elevation of phosphoinositides provides a way for these stimuli to selectively regulate downstream processes.
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http://dx.doi.org/10.1091/mbc.E20-03-0191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8120694PMC
January 2021

Regulation and function of autophagy in pancreatic cancer.

Autophagy 2020 Nov 20:1-22. Epub 2020 Nov 20.

Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA.

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.: AMPK: AMP-activated protein kinase; CQ: chloroquine; csc: cancer stem cells; DAMP: danger/damage-associated molecular pattern; EMT: epithelial-mesenchymal transition; lncRNA: long noncoding RNA; MIR: microRNA; PanIN: pancreatic intraepithelial neoplasia; PDAC: pancreatic ductal adenocarcinoma; PtdIns3K: phosphatidylinositol 3-kinase; SNARE: soluble NSF attachment protein receptor; UPS: ubiquitin-proteasome system.
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http://dx.doi.org/10.1080/15548627.2020.1847462DOI Listing
November 2020

Highlights in the fight against COVID-19: does autophagy play a role in SARS-CoV-2 infection?

Autophagy 2020 12 5;16(12):2123-2127. Epub 2020 Nov 5.

Life Sciences Institute, University of Michigan , Ann Arbor, MI, USA.

In the preceding months, the novel SARS-CoV-2 pandemic has devastated global communities. The need for safe and effective prophylactic and therapeutic treatments to combat COVID-19 - the human disease resulting from SARS-CoV-2 infection - is clear. Here, we present recent developments in the effort to combat COVID-19 and consider whether SARS-CoV-2 may potentially interact with the host autophagy pathway. : ACE2, angiotensin converting enzyme II; βCoV, betacoronavirus; COVID-19, Coronavirus Disease 2019; CQ, chloroquine; DMV, double-membrane vesicle; GI, gastrointestinal; HCQ, hydroxychloroquine; IL, interleukin; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MEFs, mouse embryonic fibroblasts; MERS-CoV, Middle East respiratory syndrome coronavirus; MHV, murine hepatitis virus; PE, phosphatidylethanolamine; SARS-CoV, severe acute respiratory syndrome coronavirus; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; TNF, tumor necrosis factor; WHO, World Health Organization.
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http://dx.doi.org/10.1080/15548627.2020.1844940DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7651184PMC
December 2020

A novel reticulophagy receptor, Epr1: a bridge between the phagophore protein Atg8 and ER transmembrane VAP proteins.

Autophagy 2021 03 29;17(3):597-598. Epub 2020 Oct 29.

Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.

Reticulophagy, a type of selective autophagy that specifically targets and degrades parts of the endoplasmic reticulum (ER) network (sheets or tubules), plays a crucial role in the responses to ER stress. The selectivity of the ER cargo recognition relies on the unique reticulophagy receptors, which tether and deliver cargos to phagophores, the precursors to autophagosomes. Various integral membrane proteins have been well characterized as reticulophagy receptors, including Atg39, Atg40, RETREG1/FAM134B, SEC62, RTN3L, CCPG1, TEX264, and ATL3, in both yeast and mammals in the past five years. In a recent paper, Zhao et al. discovered in fission yeast a novel reticulophagy receptor, Epr1, which bridges the ER and phagophore by binding to Atg8 and VAPs, a mechanism different from the aforementioned reticulophagy receptors.
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http://dx.doi.org/10.1080/15548627.2020.1837457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8032234PMC
March 2021

Extracellular SQSTM1 as an inflammatory mediator.

Autophagy 2020 12 8;16(12):2313-2315. Epub 2020 Dec 8.

Department of Surgery, The University of Texas Southwestern Medical Center , Dallas, TX USA.

Excessive inflammation may lead to irreparable injury and even death, but the key mediators and underlying mechanisms remain unclear. Our recent findings indicate that SQSTM1/p62 (sequestosome 1), a well-known macroautophagy/autophagy receptor, is a lethal inflammatory mediator of sepsis and septic shock. The release of SQSTM1 occurs during tissue damage or microbial invasion through two main ways: one is passive and the other is active. Passive release occurs in the context of GSDMD-mediated pyroptosis. Active SQSTM1 secretion requires two basic steps: the first step is the expression and phosphorylation of SQSTM1 mediated by STING1/STING/TMEM173, and then the unconventional secretion of SQSTM1 by secretory lysosomes. After release, the extracellular SQSTM1 binds to membrane receptor INSR to activate glycolysis, leading to subsequent production of pro-inflammatory cytokines in a transcription factor NFKB-dependent manner. Functionally, genetic deletion or pharmacological inhibition of the SQSTM1-INSR pathway limits tissue damage, systemic inflammation, organ failure, and death in experimental sepsis models in mice. Moreover, the activation of the SQSTM1-INSR pathway is related to the severity of sepsis in patients. These findings highlight a pathological role of extracellular SQSTM1 in infection, inflammation, and immunity.
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http://dx.doi.org/10.1080/15548627.2020.1843253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7751561PMC
December 2020
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