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Wang W, Zheng P, Yan L, Chen X, Wang Z, Liu Q. Mechanism of non-thermal atmospheric plasma in anti-tumor: influencing intracellular RONS and regulating signaling pathways. Free Radic Res 2024:1-21. [PMID: 38767976 DOI: 10.1080/10715762.2024.2358026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024]
Abstract
Non-thermal atmospheric plasma (NTAP) has been proven to be an effective anti-tumor tool, with various biological effects such as inhibiting tumor proliferation, metastasis, and promoting tumor cell apoptosis. At present, the main conclusion is that ROS and RNS are the main effector components of NTAP, but the mechanisms of which still lack systematic summary. Therefore, in this review, we first summarized the mechanism by which NTAP directly or indirectly causes an increase in intracellular RONS concentration, and the multiple pathways dysregulation (i.e. NRF2, PI3K, MAPK, NF-κB) induced by intracellular RONS. Then, we generalized the relationship between NTAP induced pathways dysregulation and the various biological effects it brought. The summary of the anti-tumor mechanism of NTAP is helpful for its further research and clinical transformation.
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Affiliation(s)
- Wenjie Wang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- School of Stomatology, Southern Medical University, Guangzhou, China
| | - Peijia Zheng
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- School of Stomatology, Southern Medical University, Guangzhou, China
| | - Liang Yan
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- School of Stomatology, Southern Medical University, Guangzhou, China
| | - Xiaoman Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- School of Stomatology, Southern Medical University, Guangzhou, China
| | - Zhicheng Wang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- School of Stomatology, Southern Medical University, Guangzhou, China
| | - Qi Liu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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2
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Lieu DJ, Crowder MK, Kryza JR, Tamilselvam B, Kaminski PJ, Kim IJ, Li Y, Jeong E, Enkhbaatar M, Chen H, Son SB, Mok H, Bradley KA, Phillips H, Blanke SR. Autophagy suppression in DNA damaged cells occurs through a newly identified p53-proteasome-LC3 axis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595139. [PMID: 38826216 PMCID: PMC11142043 DOI: 10.1101/2024.05.21.595139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Macroautophagy is thought to have a critical role in shaping and refining cellular proteostasis in eukaryotic cells recovering from DNA damage. Here, we report a mechanism by which autophagy is suppressed in cells exposed to bacterial toxin-, chemical-, or radiation-mediated sources of genotoxicity. Autophagy suppression is directly linked to cellular responses to DNA damage, and specifically the stabilization of the tumor suppressor p53, which is both required and sufficient for regulating the ubiquitination and proteasome-dependent reduction in cellular pools of microtubule-associated protein 1 light chain 3 (LC3A/B), a key precursor of autophagosome biogenesis and maturation, in both epithelial cells and an ex vivo organoid model. Our data indicate that suppression of autophagy, through a newly identified p53-proteasome-LC3 axis, is a conserved cellular response to multiple sources of genotoxicity. Such a mechanism could potentially be important for realigning proteostasis in cells undergoing DNA damage repair.
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3
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Tsvilovskyy V, Ottenheijm R, Kriebs U, Schütz A, Diakopoulos KN, Jha A, Bildl W, Wirth A, Böck J, Jaślan D, Ferro I, Taberner FJ, Kalinina O, Hildebrand S, Wissenbach U, Weissgerber P, Vogt D, Eberhagen C, Mannebach S, Berlin M, Kuryshev V, Schumacher D, Philippaert K, Camacho-Londoño JE, Mathar I, Dieterich C, Klugbauer N, Biel M, Wahl-Schott C, Lipp P, Flockerzi V, Zischka H, Algül H, Lechner SG, Lesina M, Grimm C, Fakler B, Schulte U, Muallem S, Freichel M. OCaR1 endows exocytic vesicles with autoregulatory competence by preventing uncontrolled Ca2+ release, exocytosis, and pancreatic tissue damage. J Clin Invest 2024; 134:e169428. [PMID: 38557489 PMCID: PMC10977991 DOI: 10.1172/jci169428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/13/2024] [Indexed: 04/04/2024] Open
Abstract
Regulated exocytosis is initiated by increased Ca2+ concentrations in close spatial proximity to secretory granules, which is effectively prevented when the cell is at rest. Here we showed that exocytosis of zymogen granules in acinar cells was driven by Ca2+ directly released from acidic Ca2+ stores including secretory granules through NAADP-activated two-pore channels (TPCs). We identified OCaR1 (encoded by Tmem63a) as an organellar Ca2+ regulator protein integral to the membrane of secretory granules that controlled Ca2+ release via inhibition of TPC1 and TPC2 currents. Deletion of OCaR1 led to extensive Ca2+ release from NAADP-responsive granules under basal conditions as well as upon stimulation of GPCR receptors. Moreover, OCaR1 deletion exacerbated the disease phenotype in murine models of severe and chronic pancreatitis. Our findings showed OCaR1 as a gatekeeper of Ca2+ release that endows NAADP-sensitive secretory granules with an autoregulatory mechanism preventing uncontrolled exocytosis and pancreatic tissue damage.
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Affiliation(s)
- Volodymyr Tsvilovskyy
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Ottenheijm
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Ulrich Kriebs
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Aline Schütz
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Kalliope Nina Diakopoulos
- Comprehensive Cancer Center München, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Archana Jha
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, USA
| | - Wolfgang Bildl
- Institute for Physiology, University of Freiburg, Freiburg, Germany
| | - Angela Wirth
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Julia Böck
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dawid Jaślan
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Irene Ferro
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Francisco J. Taberner
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández–Consejo Superior de Investigaciones Científicas, Sant Joan d’Alacant, Spain
| | - Olga Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
| | - Staffan Hildebrand
- Institut für Pharmakologie und Toxikologie, Universität Bonn, Bonn, Germany
| | - Ulrich Wissenbach
- Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Petra Weissgerber
- Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Dominik Vogt
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Carola Eberhagen
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefanie Mannebach
- Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Michael Berlin
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Vladimir Kuryshev
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Dagmar Schumacher
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Koenraad Philippaert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | | | - Ilka Mathar
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Christoph Dieterich
- University Hospital Heidelberg, Department of Medicine III: Cardiology, Angiology and Pneumology, Heidelberg, Germany
| | - Norbert Klugbauer
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Fakultät für Medizin, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich (CIPS-M) and Center for Drug Research, Department of Pharmacy, Ludwig-Maximilians-Universität München, and DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Christian Wahl-Schott
- Walter Brendel Centre of Experimental Medicine, Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Medical Faculty, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Peter Lipp
- Institute for Molecular Cell Biology, Center for Molecular Signaling (PZMS), Universität des Saarlandes, Homburg, Germany
| | - Veit Flockerzi
- Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Toxicology and Environmental Hygiene, Technical University Munich, School of Medicine, Munich, Germany
| | - Hana Algül
- Comprehensive Cancer Center München, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Stefan G. Lechner
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Marina Lesina
- Comprehensive Cancer Center München, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Christian Grimm
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Ludwig-Maximilians-Universität München, Munich, Germany
- Immunology, Infection and Pandemic Research (IIP), Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Munich, Germany
| | - Bernd Fakler
- Institute for Physiology, University of Freiburg, Freiburg, Germany
| | - Uwe Schulte
- Institute for Physiology, University of Freiburg, Freiburg, Germany
| | - Shmuel Muallem
- Epithelial Signaling and Transport Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, USA
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
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4
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Lee D, Lee PCW, Hong JH. UBA6 Inhibition Accelerates Lysosomal TRPML1 Depletion and Exosomal Secretion in Lung Cancer Cells. Int J Mol Sci 2024; 25:2843. [PMID: 38474091 PMCID: PMC10932338 DOI: 10.3390/ijms25052843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Ubiquitin-like modifier-activating enzyme 6 (UBA6) is a member of the E1 enzyme family, which initiates the ubiquitin-proteasome system (UPS). The UPS plays critical roles not only in protein degradation but also in various cellular functions, including neuronal signaling, myocardial remodeling, immune cell differentiation, and cancer development. However, the specific role of UBA6 in cellular functions is not fully elucidated in comparison with the roles of the UPS. It has been known that the E1 enzyme is associated with the motility of cancer cells. In this study, we verified the physiological roles of UBA6 in lung cancer cells through gene-silencing siRNA targeting UBA6 (siUBA6). The siUBA6 treatment attenuated the migration of H1975 cells, along with a decrease in lysosomal Ca2+ release. While autophagosomal proteins remained unchanged, lysosomal proteins, including TRPML1 and TPC2, were decreased in siUBA6-transfected cells. Moreover, siUBA6 induced the production of multivesicular bodies (MVBs), accompanied by an increase in MVB markers in siUBA6-transfected H1975 cells. Additionally, the expression of the exosomal marker CD63 and extracellular vesicles was increased by siUBA6 treatment. Our findings suggest that knock-down of UBA6 induces lysosomal TRPML1 depletion and inhibits endosomal trafficking to lysosome, and subsequently, leads to the accumulation of MVBs and enhanced exosomal secretion in lung cancer cells.
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Affiliation(s)
- Dongun Lee
- Department of Health Sciences and Technology, Lee Gil Ya Cancer and Diabetes Institute, GAIHST, Gachon University, 155 Getbeolro, Yeonsu-gu, Incheon 21999, Republic of Korea;
| | - Peter Chang-Whan Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Republic of Korea;
| | - Jeong Hee Hong
- Department of Health Sciences and Technology, Lee Gil Ya Cancer and Diabetes Institute, GAIHST, Gachon University, 155 Getbeolro, Yeonsu-gu, Incheon 21999, Republic of Korea;
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5
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Liu SS, Jiang TX, Bu F, Zhao JL, Wang GF, Yang GH, Kong JY, Qie YF, Wen P, Fan LB, Li NN, Gao N, Qiu XB. Molecular mechanisms underlying the BIRC6-mediated regulation of apoptosis and autophagy. Nat Commun 2024; 15:891. [PMID: 38291026 PMCID: PMC10827748 DOI: 10.1038/s41467-024-45222-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/16/2024] [Indexed: 02/01/2024] Open
Abstract
Procaspase 9 is the initiator caspase for apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor-of-Apoptosis Protein BIRC6/BRUCE/Apollon inhibits both apoptosis and autophagy by promoting ubiquitylation of proapoptotic factors and the key autophagic protein LC3, respectively. Here we show that BIRC6 forms an anti-parallel U-shaped dimer with multiple previously unannotated domains, including a ubiquitin-like domain, and the proapoptotic factor Smac/DIABLO binds BIRC6 in the central cavity. Notably, Smac outcompetes the effector caspase 3 and the pro-apoptotic protease HtrA2, but not procaspase 9, for binding BIRC6 in cells. BIRC6 also binds LC3 through its LC3-interacting region, probably following dimer disruption of this BIRC6 region. Mutation at LC3 ubiquitylation site promotes autophagy and autophagic degradation of BIRC6. Moreover, induction of autophagy promotes autophagic degradation of BIRC6 and caspase 9, but not of other effector caspases. These results are important to understand how the balance between apoptosis and autophagy is regulated under pathophysiological conditions.
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Affiliation(s)
- Shuo-Shuo Liu
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Tian-Xia Jiang
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Fan Bu
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Ji-Lan Zhao
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Guang-Fei Wang
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Guo-Heng Yang
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Jie-Yan Kong
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Yun-Fan Qie
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China
| | - Pei Wen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
- College of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Li-Bin Fan
- College of Life Sciences, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Ning-Ning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Xiao-Bo Qiu
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China.
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China.
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6
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Wei H, Zhao H, Cheng D, Zhu Z, Xia Z, Lu D, Yu J, Dong R, Yue J. miR-148a and miR-551b-5p regulate inflammatory responses via regulating autophagy in acute pancreatitis. Int Immunopharmacol 2024; 127:111438. [PMID: 38159552 DOI: 10.1016/j.intimp.2023.111438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Acute pancreatitis (AP) is a common inflammatory response that occurs in the pancreas with mortality rates as high as 30 %. However, there is still no consistent and effective treatment for AP now. MicroRNA-148 was reported to be involved in AP through IL-6 signaling pathway. Therefore, we aimed to further explore the detailed mechanisms of AP, to develop more therapeutic approach for AP. Exosomes were isolated from peripheral blood mononuclear cells of 20 AP patients and 20 healthy volunteers to evaluate the abnormally expressed miRNA. Then pancreatic acinar cells (PACs) were transfected with retrovirus to overexpress miR-148a/miR-551b-5p to evaluate their function. Both miR-148a and miR-551b-5p were highly expressed in AP patients than these in healthy cases. Then overexpressing miR-551b-5p in PACs could regulate autophagy through directly binding to Baculoviral IAP Repeat Containing 6, leading to the increased secretions of interleukin-1β (IL-1β) and interleukin-18 (IL-18) through interleukin-1 (IL-1) signaling pathway. Moreover, overexpressing miR-148a in PACs could decrease the secretions of IL-1β and IL-18 to modulate autophagy. The exosomal miRNA-148a and miRNA-551b-5p derived from peripheral blood mononuclear cells of AP patients may two-way mediate autophagy damage through IL-6/STAT3 signaling pathway, which participated in the AP pathogenesis. Our findings may provide new targets for the diagnosis and treatment of AP.
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Affiliation(s)
- Huiping Wei
- Department of Emergency, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Hui Zhao
- Department of Emergency, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China.
| | - Dongliang Cheng
- Pediatric Intensive Care Unit, Henan Provincial People's Hospital, No. 7 Weiwu Road, Jinshui District, Zhengzhou 450000, Henan Province, China
| | - Zhenni Zhu
- Pediatric Gastroenterology Department, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Zhi Xia
- Pediatric Intensive Care Unit, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Dan Lu
- Department of Clinical Examination, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Jing Yu
- Department of General Surgery, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Ran Dong
- Department of Emergency, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
| | - Jing Yue
- Department of Emergency, Hubei Maternal and Child Health Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 745 Wuluo Road, Hongshan District, Wuhan 430070, Hubei, China
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7
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Li HY, Wei TT, Zhuang M, Tan CY, Xie TH, Cai J, Yao Y, Zhu L. Iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway. Cell Death Discov 2023; 9:419. [PMID: 37980349 PMCID: PMC10657394 DOI: 10.1038/s41420-023-01712-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Cellular senescence is a hallmark of aging and has been linked to age-related diseases. Age-related macular degeneration (AMD), the most common aging-related retinal disease, is prospectively associated with retinal pigment epithelial (RPE) senescence. However, the mechanism of RPE cell senescence remains unknown. In this study, tert-butyl hydroperoxide (TBH)-induced ARPE-19 cells and D-galactose-treated C57 mice were used to examine the cause of elevated iron in RPE cell senescence. Ferric ammonium citrate (FAC)-treated ARPE-19 cells and C57 mice were used to elucidated the mechanism of iron overload-induced RPE cell senescence. Molecular biology techniques for the assessment of iron metabolism, cellular senescence, autophagy, and mitochondrial function in vivo and in vitro. We found that iron level was increased during the senescence process. Ferritin, a major iron storage protein, is negatively correlated with intracellular iron levels and cell senescence. NCOA4, a cargo receptor for ferritinophagy, mediates degradation of ferritin and contributes to iron accumulation. Besides, we found that iron overload leads to mitochondrial dysfunction. As a result, mitochondrial DNA (mtDNA) is released from damaged mitochondria to cytoplasm. Cytoplasm mtDNA activates the cGAS-STING pathway and promotes inflammatory senescence-associated secretory phenotype (SASP) and cell senescence. Meanwhile, iron chelator Deferoxamine (DFO) significantly rescues RPE senescence and retinopathy induced by FAC or D-gal in mice. Taken together, these findings imply that iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway. Inhibiting iron accumulation may represent a promising therapeutic approach for age-related diseases such as AMD.
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Affiliation(s)
- Hong-Ying Li
- Department of Ophthalmology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Ting-Ting Wei
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Miao Zhuang
- Department of Ophthalmology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Cheng-Ye Tan
- Department of Ophthalmology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Tian-Hua Xie
- Department of Ophthalmology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Jiping Cai
- Department of Ophthalmology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China
| | - Yong Yao
- Department of Ophthalmology, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China.
| | - Lingpeng Zhu
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, China.
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8
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Shi X, Wu W, Feng Z, Fan P, Shi R, Zhang X. MARCH7-mediated ubiquitination decreases the solubility of ATG14 to inhibit autophagy. Cell Rep 2023; 42:113045. [PMID: 37632749 DOI: 10.1016/j.celrep.2023.113045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023] Open
Abstract
Autophagy is a fundamental biological process critical to all eukaryotic cellular life. Although autophagy has been increasingly studied, how its process is precisely coordinated remains an open question. ATG14 (ATG14L/Barkor) is known to play a crucial role in both autophagosome formation and autophagosome-lysosome fusion. However, how ATG14 is regulated, especially at the post-translation level, is still not clear. Here, we report that MARCH7 (membrane-associated ring-CH-type finger 7), an E3 ubiquitin ligase, inhibits autophagy by ubiquitinating ATG14. MARCH7 significantly promotes K6-, K11-, and K63-linked mixed polyubiquitination on ATG14, triggering the aggregation of ATG14 and reducing its solubility in cells. Functionally, we find that MARCH7 depletion decreases the number of aggresome-like induced structures (ALISs). Mechanistically, we show that ubiquitinated ATG14 has fewer interactions with STX17, leading to the inhibition of autophagy flux. Collectively, our study reveals a mechanism in regulating autophagy and suggests a potential strategy for the treatment of autophagy-related diseases.
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Affiliation(s)
- Xue Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfeng Wu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China
| | - Zhenhuan Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyang Fan
- SanQuan College, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China.
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9
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Cen X, Li Z, Chen X. Ubiquitination in the regulation of autophagy. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1348-1357. [PMID: 37587758 PMCID: PMC10520486 DOI: 10.3724/abbs.2023149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/01/2023] [Indexed: 08/18/2023] Open
Abstract
Autophagy, an efficient and effective approach to clear rapidly damaged organelles, macromolecules, and other harmful cellular components, enables the recycling of nutrient materials and supply of nutrients to maintain cellular homeostasis. Ubiquitination plays an important regulatory role in autophagy. This paper summarizes the most recent progress in ubiquitin modification in various stages of autophagy, including initiation, elongation, and termination. Moreover, this paper shows that ubiquitination is an important way through which selective autophagy achieves substrate specificity. Furthermore, we note the distinction between monoubiquitination and polyubiquitination in the regulation of autophagy. Compared with monoubiquitination, polyubiquitination is a more common strategy to regulate the activity of the autophagy molecular machinery. In addition, the role of ubiquitination in the closure and fusion of autophagosomes warrants further study. This article not only clarifies the regulatory mechanism of autophagy but also contributes to a deeper understanding of the importance of ubiquitination modification.
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Affiliation(s)
- Xueyan Cen
- Hubei Key laboratory of Edible Wild Plants Conservation & UtilizationHubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologySchool of Life ScienceHubei Normal UniversityHuangshi435002China
| | - Ziling Li
- Hubei Key laboratory of Edible Wild Plants Conservation & UtilizationHubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologySchool of Life ScienceHubei Normal UniversityHuangshi435002China
| | - Xinpeng Chen
- Hubei Key laboratory of Edible Wild Plants Conservation & UtilizationHubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization TechnologySchool of Life ScienceHubei Normal UniversityHuangshi435002China
- National Laboratory of BiomacromoleculesCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
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10
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Nieto-Torres JL, Zaretski S, Liu T, Adams PD, Hansen M. Post-translational modifications of ATG8 proteins - an emerging mechanism of autophagy control. J Cell Sci 2023; 136:jcs259725. [PMID: 37589340 PMCID: PMC10445744 DOI: 10.1242/jcs.259725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Autophagy is a recycling mechanism involved in cellular homeostasis with key implications for health and disease. The conjugation of the ATG8 family proteins, which includes LC3B (also known as MAP1LC3B), to autophagosome membranes, constitutes a hallmark of the canonical autophagy process. After ATG8 proteins are conjugated to the autophagosome membranes via lipidation, they orchestrate a plethora of protein-protein interactions that support key steps of the autophagy process. These include binding to cargo receptors to allow cargo recruitment, association with proteins implicated in autophagosome transport and autophagosome-lysosome fusion. How these diverse and critical protein-protein interactions are regulated is still not well understood. Recent reports have highlighted crucial roles for post-translational modifications of ATG8 proteins in the regulation of ATG8 functions and the autophagy process. This Review summarizes the main post-translational regulatory events discovered to date to influence the autophagy process, mostly described in mammalian cells, including ubiquitylation, acetylation, lipidation and phosphorylation, as well as their known contributions to the autophagy process, physiology and disease.
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Affiliation(s)
- Jose L. Nieto-Torres
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- Department of Biomedical Sciences, School of Health Sciences and Veterinary, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Moncada, Spain
| | - Sviatlana Zaretski
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Tianhui Liu
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Peter D. Adams
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- The Buck Institute for Aging Research, Novato, CA 94945, USA
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11
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Elcocks H, Brazel AJ, McCarron KR, Kaulich M, Husnjak K, Mortiboys H, Clague MJ, Urbé S. FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels. EMBO J 2023; 42:e112799. [PMID: 37102372 PMCID: PMC10308357 DOI: 10.15252/embj.2022112799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/17/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023] Open
Abstract
Selective autophagy of mitochondria, mitophagy, is linked to mitochondrial quality control and as such is critical to a healthy organism. We have used a CRISPR/Cas9 approach to screen human E3 ubiquitin ligases for influence on mitophagy under both basal cell culture conditions and upon acute mitochondrial depolarization. We identify two cullin-RING ligase substrate receptors, VHL and FBXL4, as the most profound negative regulators of basal mitophagy. We show that these converge, albeit via different mechanisms, on control of the mitophagy adaptors BNIP3 and BNIP3L/NIX. FBXL4 restricts NIX and BNIP3 levels via direct interaction and protein destabilization, while VHL acts through suppression of HIF1α-mediated transcription of BNIP3 and NIX. Depletion of NIX but not BNIP3 is sufficient to restore mitophagy levels. Our study contributes to an understanding of the aetiology of early-onset mitochondrial encephalomyopathy that is supported by analysis of a disease-associated mutation. We further show that the compound MLN4924, which globally interferes with cullin-RING ligase activity, is a strong inducer of mitophagy, thus providing a research tool in this context and a candidate therapeutic agent for conditions linked to mitochondrial dysfunction.
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Affiliation(s)
- Hannah Elcocks
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Ailbhe J Brazel
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
- Present address:
Department of BiologyMaynooth UniversityMaynoothIreland
| | - Katy R McCarron
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Manuel Kaulich
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
| | - Koraljka Husnjak
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Michael J Clague
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Sylvie Urbé
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
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12
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Badawi S, Mohamed FE, Varghese DS, Ali BR. Genetic disruption of mammalian endoplasmic reticulum-associated protein degradation: Human phenotypes and animal and cellular disease models. Traffic 2023. [PMID: 37188482 DOI: 10.1111/tra.12902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Endoplasmic reticulum-associated protein degradation (ERAD) is a stringent quality control mechanism through which misfolded, unassembled and some native proteins are targeted for degradation to maintain appropriate cellular and organelle homeostasis. Several in vitro and in vivo ERAD-related studies have provided mechanistic insights into ERAD pathway activation and its consequent events; however, a majority of these have investigated the effect of ERAD substrates and their consequent diseases affecting the degradation process. In this review, we present all reported human single-gene disorders caused by genetic variation in genes that encode ERAD components rather than their substrates. Additionally, after extensive literature survey, we present various genetically manipulated higher cellular and mammalian animal models that lack specific components involved in various stages of the ERAD pathway.
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Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
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13
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Dietz L, Ellison CJ, Riechmann C, Cassidy CK, Felfoldi FD, Pinto-Fernández A, Kessler BM, Elliott PR. Structural basis for SMAC-mediated antagonism of caspase inhibition by the giant ubiquitin ligase BIRC6. Science 2023; 379:1112-1117. [PMID: 36758106 DOI: 10.1126/science.ade8840] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Certain inhibitor of apoptosis (IAP) family members are sentinel proteins that prevent untimely cell death by inhibiting caspases. Antagonists, including second mitochondria-derived activator of caspases (SMAC), regulate IAPs and drive cell death. Baculoviral IAP repeat-containing protein 6 (BIRC6), a giant IAP with dual E2 and E3 ubiquitin ligase activity, regulates programmed cell death through unknown mechanisms. We show that BIRC6 directly restricts executioner caspase-3 and -7 and ubiquitinates caspase-3, -7, and -9, working exclusively with noncanonical E1, UBA6. Notably, we show that SMAC suppresses both mechanisms. Cryo-electron microscopy structures of BIRC6 alone and in complex with SMAC reveal that BIRC6 is an antiparallel dimer juxtaposing the substrate-binding module against the catalytic domain. Furthermore, we discover that SMAC multisite binding to BIRC6 results in a subnanomolar affinity interaction, enabling SMAC to competitively displace caspases, thus antagonizing BIRC6 anticaspase function.
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Affiliation(s)
- Larissa Dietz
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Cara J Ellison
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Carlos Riechmann
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - F Daniel Felfoldi
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Paul R Elliott
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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14
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Ehrmann JF, Grabarczyk DB, Heinke M, Deszcz L, Kurzbauer R, Hudecz O, Shulkina A, Gogova R, Meinhart A, Versteeg GA, Clausen T. Structural basis for regulation of apoptosis and autophagy by the BIRC6/SMAC complex. Science 2023; 379:1117-1123. [PMID: 36758105 DOI: 10.1126/science.ade8873] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023]
Abstract
Inhibitor of apoptosis proteins (IAPs) bind to pro-apoptotic proteases, keeping them inactive and preventing cell death. The atypical ubiquitin ligase BIRC6 is the only essential IAP, additionally functioning as a suppressor of autophagy. We performed a structure-function analysis of BIRC6 in complex with caspase-9, HTRA2, SMAC, and LC3B, which are critical apoptosis and autophagy proteins. Cryo-electron microscopy structures showed that BIRC6 forms a megadalton crescent shape that arcs around a spacious cavity containing receptor sites for client proteins. Multivalent binding of SMAC obstructs client binding, impeding ubiquitination of both autophagy and apoptotic substrates. On the basis of these data, we discuss how the BIRC6/SMAC complex can act as a stress-induced hub to regulate apoptosis and autophagy drivers.
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Affiliation(s)
- Julian F Ehrmann
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Daniel B Grabarczyk
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Maria Heinke
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Luiza Deszcz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Robert Kurzbauer
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Otto Hudecz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Alexandra Shulkina
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Rebeca Gogova
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Gijs A Versteeg
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Tim Clausen
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
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15
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Hunkeler M, Jin CY, Fischer ES. Structures of BIRC6-client complexes provide a mechanism of SMAC-mediated release of caspases. Science 2023; 379:1105-1111. [PMID: 36758104 DOI: 10.1126/science.ade5750] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Tight regulation of apoptosis is essential for metazoan development and prevents diseases such as cancer and neurodegeneration. Caspase activation is central to apoptosis, and inhibitor of apoptosis proteins (IAPs) are the principal actors that restrain caspase activity and are therefore attractive therapeutic targets. IAPs, in turn, are regulated by mitochondria-derived proapoptotic factors such as SMAC and HTRA2. Through a series of cryo-electron microscopy structures of full-length human baculoviral IAP repeat-containing protein 6 (BIRC6) bound to SMAC, caspases, and HTRA2, we provide a molecular understanding for BIRC6-mediated caspase inhibition and its release by SMAC. The architecture of BIRC6, together with near-irreversible binding of SMAC, elucidates how the IAP inhibitor SMAC can effectively control a processive ubiquitin ligase to respond to apoptotic stimuli.
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Affiliation(s)
- Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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16
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Mace PD, Day CL. A massive machine regulates cell death. Science 2023; 379:1093-1094. [PMID: 36927032 DOI: 10.1126/science.adg9605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Structural analysis reveals how the decision to induce apoptotic cell death is regulated.
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Affiliation(s)
- Peter D Mace
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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17
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Advanced Bioinformatics Analysis and Genetic Technologies for Targeting Autophagy in Glioblastoma Multiforme. Cells 2023; 12:cells12060897. [PMID: 36980238 PMCID: PMC10047676 DOI: 10.3390/cells12060897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
As the most malignant primary brain tumor in adults, a diagnosis of glioblastoma multiforme (GBM) continues to carry a poor prognosis. GBM is characterized by cytoprotective homeostatic processes such as the activation of autophagy, capability to confer therapeutic resistance, evasion of apoptosis, and survival strategy even in the hypoxic and nutrient-deprived tumor microenvironment. The current gold standard of therapy, which involves radiotherapy and concomitant and adjuvant chemotherapy with temozolomide (TMZ), has been a game-changer for patients with GBM, relatively improving both overall survival (OS) and progression-free survival (PFS); however, TMZ is now well-known to upregulate undesirable cytoprotective autophagy, limiting its therapeutic efficacy for induction of apoptosis in GBM cells. The identification of targets utilizing bioinformatics-driven approaches, advancement of modern molecular biology technologies such as clustered regularly interspaced short palindromic repeats (CRISPR)—CRISPR-associated protein (Cas9) or CRISPR-Cas9 genome editing, and usage of microRNA (miRNA)-mediated regulation of gene expression led to the selection of many novel targets for new therapeutic development and the creation of promising combination therapies. This review explores the current state of advanced bioinformatics analysis and genetic technologies and their utilization for synergistic combination with TMZ in the context of inhibition of autophagy for controlling the growth of GBM.
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18
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Cervia LD, Shibue T, Borah AA, Gaeta B, He L, Leung L, Li N, Moyer SM, Shim BH, Dumont N, Gonzalez A, Bick NR, Kazachkova M, Dempster JM, Krill-Burger JM, Piccioni F, Udeshi ND, Olive ME, Carr SA, Root DE, McFarland JM, Vazquez F, Hahn WC. A Ubiquitination Cascade Regulating the Integrated Stress Response and Survival in Carcinomas. Cancer Discov 2023; 13:766-795. [PMID: 36576405 PMCID: PMC9975667 DOI: 10.1158/2159-8290.cd-22-1230] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/12/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Systematic identification of signaling pathways required for the fitness of cancer cells will facilitate the development of new cancer therapies. We used gene essentiality measurements in 1,086 cancer cell lines to identify selective coessentiality modules and found that a ubiquitin ligase complex composed of UBA6, BIRC6, KCMF1, and UBR4 is required for the survival of a subset of epithelial tumors that exhibit a high degree of aneuploidy. Suppressing BIRC6 in cell lines that are dependent on this complex led to a substantial reduction in cell fitness in vitro and potent tumor regression in vivo. Mechanistically, BIRC6 suppression resulted in selective activation of the integrated stress response (ISR) by stabilization of the heme-regulated inhibitor, a direct ubiquitination target of the UBA6/BIRC6/KCMF1/UBR4 complex. These observations uncover a novel ubiquitination cascade that regulates ISR and highlight the potential of ISR activation as a new therapeutic strategy. SIGNIFICANCE We describe the identification of a heretofore unrecognized ubiquitin ligase complex that prevents the aberrant activation of the ISR in a subset of cancer cells. This provides a novel insight on the regulation of ISR and exposes a therapeutic opportunity to selectively eliminate these cancer cells. See related commentary Leli and Koumenis, p. 535. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Lisa D. Cervia
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Tsukasa Shibue
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ashir A. Borah
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Benjamin Gaeta
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Linh He
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Lisa Leung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Naomi Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Sydney M. Moyer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Brian H. Shim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Nancy Dumont
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Nolan R. Bick
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | | | - Meagan E. Olive
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | - William C. Hahn
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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19
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Autophagy/Mitophagy Regulated by Ubiquitination: A Promising Pathway in Cancer Therapeutics. Cancers (Basel) 2023; 15:cancers15041112. [PMID: 36831455 PMCID: PMC9954143 DOI: 10.3390/cancers15041112] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Autophagy is essential for organismal development, maintenance of energy homeostasis, and quality control of organelles and proteins. As a selective form of autophagy, mitophagy is necessary for effectively eliminating dysfunctional mitochondria. Both autophagy and mitophagy are linked with tumor progression and inhibition. The regulation of mitophagy and autophagy depend upon tumor type and stage. In tumors, mitophagy has dual roles: it removes damaged mitochondria to maintain healthy mitochondria and energy production, which are necessary for tumor growth. In contrast, mitophagy has been shown to inhibit tumor growth by mitigating excessive ROS production, thus preventing mutation and chromosomal instability. Ubiquitination and deubiquitination are important modifications that regulate autophagy. Multiple E3 ubiquitin ligases and DUBs modulate the activity of the autophagy and mitophagy machinery, thereby influencing cancer progression. In this review, we summarize the mechanistic association between cancer development and autophagy/mitophagy activities regulated by the ubiquitin modification of autophagic proteins. In addition, we discuss the function of multiple proteins involved in autophagy/mitophagy in tumors that may represent potential therapeutic targets.
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20
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Gil-Kulik P, Leśniewski M, Bieńko K, Wójcik M, Więckowska M, Przywara D, Petniak A, Kondracka A, Świstowska M, Szymanowski R, Wilińska A, Wiliński M, Płachno BJ, Kostuch M, Rahnama-Hezavach M, Szuta M, Kwaśniewska A, Bogucka-Kocka A, Kocki J. Influence of Perinatal Factors on Gene Expression of IAPs Family and Main Factors of Pluripotency: OCT4 and SOX2 in Human Breast Milk Stem Cells-A Preliminary Report. Int J Mol Sci 2023; 24:ijms24032476. [PMID: 36768802 PMCID: PMC9917041 DOI: 10.3390/ijms24032476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
Due to their therapeutic potential, mesenchymal stem cells are the subject of intensive research on the use of their potential in the treatment of, among others, neurodegenerative diseases or immunological diseases. They are among the newest in the field of medicine. The presented study aimed to evaluate the expression of eight genes from the IAP family and the gene regulating IAP-XAF1-in stem cells derived from human milk, using the qPCR method. The relationships between the expression of genes under study and clinical data, such as maternal age, maternal BMI, week of pregnancy in which the delivery took place, bodyweight of the newborn, the number of pregnancies and deliveries, and the time elapsed since delivery, were also analyzed. The research was carried out on samples of human milk collected from 42 patients hospitalized in The Clinic of Obstetrics and Perinatology of the Independent Public Clinical Hospital No. 4, in Lublin. The conducted research confirmed the expression of the following genes in the tested material: NAIP, BIRC2, BIRC3, BIRC5, BIRC6, BIRC8, XIAP, XAF1, OCT4 and SOX2. Moreover, several dependencies of the expression of individual genes on the maternal BMI (BIRC5, XAF1 and NAIP), the time since childbirth (BIRC5, BIRC6, XAF1 and NAIP), the number of pregnancies and deliveries (BIRC2, BIRC5, BIRC6 and XAF1), the manner of delivery (XAF1 and OCT4), preterm labor (BIRC6 and NAIP) were demonstrated. Additionally, we found positive relationships between gene expression of BIRC7, BIRC8 and XAF1 and the main factors of pluripotency: SOX2 and OCT4. This work is the first to investigate the expression of genes from the IAPs family in mother's milk stem cells.
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Affiliation(s)
- Paulina Gil-Kulik
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Michał Leśniewski
- Student Scientific Society of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Karolina Bieńko
- Student Scientific Society of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Monika Wójcik
- Student Scientific Society of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Marta Więckowska
- Student Scientific Society of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Dominika Przywara
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Alicja Petniak
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Adrianna Kondracka
- Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, 11 Staszica Str., 20-081 Lublin, Poland
| | - Małgorzata Świstowska
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Rafał Szymanowski
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Agnieszka Wilińska
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Mateusz Wiliński
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Cracow, Poland
| | - Marzena Kostuch
- Department of Neonatology, Independent Public Clinical Hospital No. 4, 8 Jaczewskiego St., 20-954 Lublin, Poland
| | - Mansur Rahnama-Hezavach
- Chair and Department of Dental Surgery, Medical University of Lublin, 6 Chodzki St., 20-093 Lublin, Poland
| | - Mariusz Szuta
- Chair of Oral Surgery, Jagiellonian University Medical College, 4 Montelupich St., 31-155 Kraków, Poland
| | - Anna Kwaśniewska
- Department of Obstetrics and Pathology of Pregnancy, Medical University of Lublin, 11 Staszica Str., 20-081 Lublin, Poland
| | - Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20–093 Lublin, Poland
| | - Janusz Kocki
- Department of Clinical Genetics, Medical University of Lublin, 11 Radziwillowska Str., 20-080 Lublin, Poland
- Correspondence:
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21
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Shariq M, Quadir N, Alam A, Zarin S, Sheikh JA, Sharma N, Samal J, Ahmad U, Kumari I, Hasnain SE, Ehtesham NZ. The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection. Autophagy 2023; 19:3-23. [PMID: 35000542 PMCID: PMC9809970 DOI: 10.1080/15548627.2021.2021495] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca2+-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Neha Quadir
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Sheeba Zarin
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Javaid A. Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Neha Sharma
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,Department of Molecular Medicine, Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Jasmine Samal
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Uzair Ahmad
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), New Delhi, India,Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, India,Seyed E. Hasnain ; ; Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110 016, India
| | - Nasreen Z. Ehtesham
- Inflammation Biology and Cell Signaling Laboratory, National Institute of Pathology-ICMR, Ansari Nagar West, New Delhi, India,CONTACT Nasreen Z. Ehtesham ; ICMR-National Institute of Pathology, Ansari Nagar West, New Delhi110029, India
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22
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Yin Y, Zhou Y, Yang X, Xu Z, Yang B, Luo P, Yan H, He Q. The participation of non-canonical autophagic proteins in the autophagy process and their potential as therapeutic targets. Expert Opin Ther Targets 2023; 27:71-86. [PMID: 36735300 DOI: 10.1080/14728222.2023.2177151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Autophagy is a conserved catabolic process that helps recycle intracellular components to maintain homeostasis. The completion of autophagy requires the synergistic effect of multiple canonical autophagic proteins. Defects in autophagy machinery have been reported to promote diseases, rendering autophagy a bone fide health-modifying agent. However, the clinical implication of canonical pan-autophagic activators or inhibitors has often led to undesirable side effects, making it urgent to find a safer autophagy-related therapeutic target. The discovery of non-canonical autophagic proteins has been found to specifically affect the development of diseases without causing a universal impact on autophagy and has shed light on finding a safer way to utilize autophagy in the therapeutic context. AREAS COVERED This review summarizes recently discovered non-canonical autophagic proteins, how these proteins influence autophagy, and their potential therapeutic role in the disease due to their interaction with autophagy. EXPERT OPINION Several therapies have been studied thus far and continued research is needed to identify the potential that non-canonical autophagic proteins have for treating certain diseases. In the meantime, continue to uncover new non-canonical autophagic proteins and examine which are likely to have therapeutic implications.
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Affiliation(s)
- Yiming Yin
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yourong Zhou
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaochun Yang
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhifei Xu
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Peihua Luo
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Pharmacology and Toxicology, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hao Yan
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiaojun He
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, Hangzhou, Zhejiang, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang, China
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23
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Liang JR, Corn JE. A CRISPR view on autophagy. Trends Cell Biol 2022; 32:1008-1022. [PMID: 35581059 DOI: 10.1016/j.tcb.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/21/2023]
Abstract
Autophagy is a fundamental pathway for the degradation of cytoplasmic content in response to pleiotropic extracellular and intracellular stimuli. Recent advances in the autophagy field have demonstrated that different organelles can also be specifically targeted for autophagy with broad implications on cellular and organismal health. This opens new dimensions in the autophagy field and more unanswered questions on the rationale and underlying mechanisms to degrade different organelles. Functional genomics via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-based screening has gained popularity in the autophagy field to understand the common and unique factors that are implicated in the signaling, recognition, and execution of different cargo-specific autophagies. We focus on recent applications of CRISPR-based screens in the autophagy field, their discoveries, and the future directions of autophagy screens.
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Affiliation(s)
- Jin Rui Liang
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland; Medical Research Council, Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland.
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24
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Identification Markers of Carotid Vulnerable Plaques: An Update. Biomolecules 2022; 12:biom12091192. [PMID: 36139031 PMCID: PMC9496377 DOI: 10.3390/biom12091192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Vulnerable plaques have been a hot topic in the field of stroke and carotid atherosclerosis. Currently, risk stratification and intervention of carotid plaques are guided by the degree of luminal stenosis. Recently, it has been recognized that the vulnerability of plaques may contribute to the risk of stroke. Some classical interventions, such as carotid endarterectomy, significantly reduce the risk of stroke in symptomatic patients with severe carotid stenosis, while for asymptomatic patients, clinically silent plaques with rupture tendency may expose them to the risk of cerebrovascular events. Early identification of vulnerable plaques contributes to lowering the risk of cerebrovascular events. Previously, the identification of vulnerable plaques was commonly based on imaging technologies at the macroscopic level. Recently, some microscopic molecules pertaining to vulnerable plaques have emerged, and could be potential biomarkers or therapeutic targets. This review aimed to update the previous summarization of vulnerable plaques and identify vulnerable plaques at the microscopic and macroscopic levels.
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25
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Yuan L, Gao F, Lv Z, Nayak D, Nayak A, Santos Bury PD, Cano KE, Jia L, Oleinik N, Atilgan FC, Ogretmen B, Williams KM, Davies C, El Oualid F, Wasmuth EV, Olsen SK. Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6. Nat Commun 2022; 13:4880. [PMID: 35986001 PMCID: PMC9391358 DOI: 10.1038/s41467-022-32613-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/08/2022] [Indexed: 11/11/2022] Open
Abstract
The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.
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Affiliation(s)
- Lingmin Yuan
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Fei Gao
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Research & Development, Beijing IPE Center for Clinical Laboratory CO, Beijing, 100176, China
| | - Zongyang Lv
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Priscila Dos Santos Bury
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kristin E Cano
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Natalia Oleinik
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Firdevs Cansu Atilgan
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Katelyn M Williams
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Christopher Davies
- Department of Biochemistry & Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Farid El Oualid
- UbiQ Bio B.V., Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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26
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Tong F, Xu L, Xu S, Zhang M. Identification of an autophagy-related 12-lncRNA signature and evaluation of NFYC-AS1 as a pro-cancer factor in lung adenocarcinoma. Front Genet 2022; 13:834935. [PMID: 36105077 PMCID: PMC9466988 DOI: 10.3389/fgene.2022.834935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: To develop an autophagy-related lncRNA-based risk signature and corresponding nomogram to predict overall survival (OS) for LUAD patients and investigate the possible meaning of screened factors.Methods: Differentially expressed lncRNAs and autophagy genes were screened between normal and LUAD tumor samples from the TCGA LUAD dataset. Univariate and multivariate Cox regression analyses were performed to construct the lncRNA-based risk signature and nomogram incorporating clinical information. Then, the accuracy and sensitivity were confirmed by the AUC of ROC curves in both training and validation cohorts. qPCR, immunoblot, shRNA, and ectopic expression were used to verify the positive regulation of NFYC-AS1 on BIRC6. CCK-8, immunofluorescence, and flow cytometry were used to confirm the influence of NFYC-AS1 on cell proliferation, autophagy, and apoptosis via BIRC6.Results: A 12-lncRNA risk signature and a nomogram combining related clinical information were constructed. Furthermore, the abnormal increase of NFYC-AS1 may promote LUAD progression through the autophagy-related gene BIRC6.Conclusion: 12-lncRNA signature may function as a predictive marker for LUAD patients, and NFYC-AS1 along with BIRC6 may function as carcinogenic factors in a combinatorial manner.
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Affiliation(s)
- Fang Tong
- Department of Medical Immunology, School of Medicine, Anhui University of Science and Technology, Anhui, China
- Anhui Province Engineering Laboratory of Occupational Health and Safety, Anhui University of Science and Technology, Anhui, China
| | - Lifa Xu
- Department of Medical Immunology, School of Medicine, Anhui University of Science and Technology, Anhui, China
| | - Sheng Xu
- The First Affiliated Hospital, Anhui University of Science and Technology, Anhui, China
| | - Mingming Zhang
- Department of Medical Immunology, School of Medicine, Anhui University of Science and Technology, Anhui, China
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
- *Correspondence: Mingming Zhang,
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27
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Degradation Mechanism of Autophagy-Related Proteins and Research Progress. Int J Mol Sci 2022; 23:ijms23137301. [PMID: 35806307 PMCID: PMC9266641 DOI: 10.3390/ijms23137301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/21/2022] Open
Abstract
In all eukaryotes, autophagy is the main pathway for nutrient recycling, which encapsulates parts of the cytoplasm and organelles in double-membrane vesicles, and then fuses with lysosomes/vacuoles to degrade them. Autophagy is a highly dynamic and relatively complex process influenced by multiple factors. Under normal growth conditions, it is maintained at basal levels. However, when plants are subjected to biotic and abiotic stresses, such as pathogens, drought, waterlogging, nutrient deficiencies, etc., autophagy is activated to help cells to survive under stress conditions. At present, the regulation of autophagy is mainly reflected in hormones, second messengers, post-transcriptional regulation, and protein post-translational modification. In recent years, the degradation mechanism of autophagy-related proteins has attracted much attention. In this review, we have summarized how autophagy-related proteins are degraded in yeast, animals, and plants, which will help us to have a more comprehensive and systematic understanding of the regulation mechanisms of autophagy. Moreover, research progress on the degradation of autophagy-related proteins in plants has been discussed.
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28
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Schwalm MP, Berger LM, Meuter MN, Vasta JD, Corona CR, Röhm S, Berger BT, Farges F, Beinert SM, Preuss F, Morasch V, Rogov VV, Mathea S, Saxena K, Robers MB, Müller S, Knapp S. A Toolbox for the Generation of Chemical Probes for Baculovirus IAP Repeat Containing Proteins. Front Cell Dev Biol 2022; 10:886537. [PMID: 35721509 PMCID: PMC9204419 DOI: 10.3389/fcell.2022.886537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/29/2022] [Indexed: 12/12/2022] Open
Abstract
E3 ligases constitute a large and diverse family of proteins that play a central role in regulating protein homeostasis by recruiting substrate proteins via recruitment domains to the proteasomal degradation machinery. Small molecules can either inhibit, modulate or hijack E3 function. The latter class of small molecules led to the development of selective protein degraders, such as PROTACs (PROteolysis TArgeting Chimeras), that recruit protein targets to the ubiquitin system leading to a new class of pharmacologically active drugs and to new therapeutic options. Recent efforts have focused on the E3 family of Baculovirus IAP Repeat (BIR) domains that comprise a structurally conserved but diverse 70 amino acid long protein interaction domain. In the human proteome, 16 BIR domains have been identified, among them promising drug targets such as the Inhibitors of Apoptosis (IAP) family, that typically contain three BIR domains (BIR1, BIR2, and BIR3). To date, this target area lacks assay tools that would allow comprehensive evaluation of inhibitor selectivity. As a consequence, the selectivity of current BIR domain targeting inhibitors is unknown. To this end, we developed assays that allow determination of inhibitor selectivity in vitro as well as in cellulo. Using this toolbox, we have characterized available BIR domain inhibitors. The characterized chemical starting points and selectivity data will be the basis for the generation of new chemical probes for IAP proteins with well-characterized mode of action and provide the basis for future drug discovery efforts and the development of PROTACs and molecular glues.
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Affiliation(s)
- Martin P Schwalm
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Lena M Berger
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Maximilian N Meuter
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | | | | | - Sandra Röhm
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Benedict-Tilman Berger
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Frederic Farges
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - Sebastian M Beinert
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
| | - Franziska Preuss
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Viktoria Morasch
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Vladimir V Rogov
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Sebastian Mathea
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Krishna Saxena
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | | | - Susanne Müller
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Stefan Knapp
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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29
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Doeppner TR, Coman C, Burdusel D, Ancuta DL, Brockmeier U, Pirici DN, Yaoyun K, Hermann DM, Popa-Wagner A. Long-term treatment with chloroquine increases lifespan in middle-aged male mice possibly via autophagy modulation, proteasome inhibition and glycogen metabolism. Aging (Albany NY) 2022; 14:4195-4210. [PMID: 35609021 PMCID: PMC9186778 DOI: 10.18632/aging.204069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/28/2022] [Indexed: 11/25/2022]
Abstract
Previous studies have shown that the polyamine spermidine increased the maximum life span in C. elegans and the median life span in mice. Since spermidine increases autophagy, we asked if treatment with chloroquine, an inhibitor of autophagy, would shorten the lifespan of mice. Recently, chloroquine has intensively been discussed as a treatment option for COVID-19 patients. To rule out unfavorable long-term effects on longevity, we examined the effect of chronic treatment with chloroquine given in the drinking water on the lifespan and organ pathology of male middle-aged NMRI mice. We report that, surprisingly, daily treatment with chloroquine extended the median life span by 11.4% and the maximum life span of the middle-aged male NMRI mice by 11.8%. Subsequent experiments show that the chloroquine-induced lifespan elevation is associated with dose-dependent increase in LC3B-II, a marker of autophagosomes, in the liver and heart that was confirmed by transmission electron microscopy. Quite intriguingly, chloroquine treatment was also associated with a decrease in glycogenolysis in the liver suggesting a compensatory mechanism to provide energy to the cell. Accumulation of autophagosomes was paralleled by an inhibition of proteasome-dependent proteolysis in the liver and the heart as well as with decreased serum levels of insulin growth factor binding protein-3 (IGFBP3), a protein associated with longevity. We propose that inhibition of proteasome activity in conjunction with an increased number of autophagosomes and decreased levels of IGFBP3 might play a central role in lifespan extension by chloroquine in male NMRI mice.
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Affiliation(s)
- Thorsten R Doeppner
- Department of Neurology, University Medical Center Göttingen, Göttingen 37075, Germany.,Research Institute for Health Sciences and Technologies (SABITA), Medipol University, Istanbul, Turkey.,Department of Anatomy and Cell Biology, Medical University of Varna, Varna, Bulgaria
| | - Cristin Coman
- Cantacuzino National Medico-Military Institute for Research and Development, Bucharest 050096, Romania
| | - Daiana Burdusel
- Department of Biochemistry, University of Medicine and Pharmacy Craiova, Craiova 200349, Romania
| | - Diana-Larisa Ancuta
- Cantacuzino National Medico-Military Institute for Research and Development, Bucharest 050096, Romania.,Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Ulf Brockmeier
- Vascular Neurology and Dementia, Department of Neurology, University of Medicine Essen, Essen 45147, Germany
| | - Daniel Nicolae Pirici
- Department of Biochemistry, University of Medicine and Pharmacy Craiova, Craiova 200349, Romania
| | - Kuang Yaoyun
- Department of Neurology, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Dirk M Hermann
- Vascular Neurology and Dementia, Department of Neurology, University of Medicine Essen, Essen 45147, Germany
| | - Aurel Popa-Wagner
- Vascular Neurology and Dementia, Department of Neurology, University of Medicine Essen, Essen 45147, Germany.,Experimental Research Center for Normal and Pathological Aging, ARES, University of Medicine and Pharmacy Craiova, Craiova 200349, Romania
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30
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CRISPR/Cas9-mediated genome editing assists protein dynamics studies in live cells. Eur J Cell Biol 2022; 101:151203. [DOI: 10.1016/j.ejcb.2022.151203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/18/2022] Open
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31
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Vargas G, Cortés O, Arias-Muñoz E, Hernández S, Cerda-Troncoso C, Hernández L, González AE, Tatham MH, Bustamante HA, Retamal C, Cancino J, Varas-Godoy M, Hay RT, Rojas-Fernández A, Cavieres VA, Burgos PV. Negative Modulation of Macroautophagy by Stabilized HERPUD1 is Counteracted by an Increased ER-Lysosomal Network With Impact in Drug-Induced Stress Cell Survival. Front Cell Dev Biol 2022; 10:743287. [PMID: 35309917 PMCID: PMC8924303 DOI: 10.3389/fcell.2022.743287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/27/2022] [Indexed: 11/25/2022] Open
Abstract
Macroautophagy and the ubiquitin proteasome system work as an interconnected network in the maintenance of cellular homeostasis. Indeed, efficient activation of macroautophagy upon nutritional deprivation is sustained by degradation of preexisting proteins by the proteasome. However, the specific substrates that are degraded by the proteasome in order to activate macroautophagy are currently unknown. By quantitative proteomic analysis we identified several proteins downregulated in response to starvation independently of ATG5 expression. Among them, the most significant was HERPUD1, an ER membrane protein with low expression and known to be degraded by the proteasome under normal conditions. Contrary, under ER stress, levels of HERPUD1 increased rapidly due to a blockage in its proteasomal degradation. Thus, we explored whether HERPUD1 stability could work as a negative regulator of autophagy. In this work, we expressed a version of HERPUD1 with its ubiquitin-like domain (UBL) deleted, which is known to be crucial for its proteasome degradation. In comparison to HERPUD1-WT, we found the UBL-deleted version caused a negative role on basal and induced macroautophagy. Unexpectedly, we found stabilized HERPUD1 promotes ER remodeling independent of unfolded protein response activation observing an increase in stacked-tubular structures resembling previously described tubular ER rearrangements. Importantly, a phosphomimetic S59D mutation within the UBL mimics the phenotype observed with the UBL-deleted version including an increase in HERPUD1 stability and ER remodeling together with a negative role on autophagy. Moreover, we found UBL-deleted version and HERPUD1-S59D trigger an increase in cellular size, whereas HERPUD1-S59D also causes an increased in nuclear size. Interestingly, ER remodeling by the deletion of the UBL and the phosphomimetic S59D version led to an increase in the number and function of lysosomes. In addition, the UBL-deleted version and phosphomimetic S59D version established a tight ER-lysosomal network with the presence of extended patches of ER-lysosomal membrane-contact sites condition that reveals an increase of cell survival under stress conditions. Altogether, we propose stabilized HERPUD1 downregulates macroautophagy favoring instead a closed interplay between the ER and lysosomes with consequences in drug-cell stress survival.
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Affiliation(s)
- Gabriela Vargas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Omar Cortés
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Eloisa Arias-Muñoz
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Sergio Hernández
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Cristobal Cerda-Troncoso
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Laura Hernández
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Alexis E González
- Facultad de Medicina, Instituto de Fisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Michael H Tatham
- Center for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hianara A Bustamante
- Facultad de Medicina, Instituto de Microbiología Clínica, Universidad Austral de Chile, Valdivia, Chile
| | - Claudio Retamal
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Jorge Cancino
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Manuel Varas-Godoy
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ronald T Hay
- Center for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alejandro Rojas-Fernández
- Center for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom.,Instituto de Medicina & Centro Interdisciplinario de Estudios del Sistema Nervioso (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile.,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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32
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Lu X, Zhang J, Li YQ, Liu QX, Zhou D, Deng XF, Qiu Y, Chen Q, Li MY, Liu XQ, Dai JG, Zheng H. Plasmodium Circumsporozoite Protein Enhances the Efficacy of Gefitinib in Lung Adenocarcinoma Cells by Inhibiting Autophagy via Proteasomal Degradation of LC3B. Front Cell Dev Biol 2022; 10:830046. [PMID: 35186935 PMCID: PMC8851824 DOI: 10.3389/fcell.2022.830046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Almost all lung adenocarcinoma (LUAD) patients with EGFR mutant will develop resistance to EGFR-TKIs, which limit the long-term clinical application of these agents. Accumulating evidence shows one of the main reasons for resistance to EGFR-TKIs is induction of autophagy in tumor cells. Our previous study found that circumsporozoite protein (CSP) in Plasmodium can suppress autophagy in host hepatocytes. However, it is unknown whether CSP-mediated inhibition of autophagy could improve the anti-tumor effect of EGFR-TKIs. Methods: We constructed A549 and H1975 cell lines with stable overexpression of CSP (OE-CSP cells). CCK-8, Lactate Dehydrogenase (LDH), flow cytometry, and colony analysis were performed to observe the effect of CSP overexpression on cell viability, apoptosis rate, and colony formation ratio. The sensitizing effect of CSP on gefitinib was evaluated in vivo using a subcutaneous tumor model in nude mice and immunohistochemical assay. The role of CSP in regulation of autophagy was investigated by laser confocal microscopy assay and western blotting. A transcriptome sequencing assay and real-time polymerase chain reaction were used to determine the levels of mRNA for autophagy-related proteins. Cycloheximide (CHX), MG132, TAK-243, and immunoprecipitation assays were used to detect and confirm proteasomal degradation of LC3B. Results: OE-CSP A549 and H1975 cells were more sensitive to gefitinib, demonstrating significant amounts of apoptosis and decreased viability. In the OE-CSP group, autophagy was significantly inhibited, and there was a decrease in LC3B protein after exposure to gefitinib. Cell viability and colony formed ability were recovered when OE-CSP cells were exposed to rapamycin. In nude mice with xenografts of LUAD cells, inhibition of autophagy by CSP resulted in suppression of cell growth, and more marked apoptosis during exposure to gefitinib. CSP promoted ubiquitin-proteasome degradation of LC3B, leading to inhibition of autophagy in LUAD cells after treatment with gefitinib. When LUAD cells were treated with ubiquitin activating enzyme inhibitor TAK-243, cell viability, apoptosis, and growth were comparable between the OE-CSP group and a control group both in vivo and in vitro. Conclusion: CSP can inhibit gefitinib-induced autophagy via proteasomal degradation of LC3B, which suggests that CSP could be used as an autophagy inhibitor to sensitize EGFR-TKIs.
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Affiliation(s)
- Xiao Lu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Jiao Zhang
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yan-Qi Li
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Quan-Xing Liu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Dong Zhou
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xu-Feng Deng
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yuan Qiu
- Department of General Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Qian Chen
- Cancer Center of Daping Hospital, Army Medical University, Chongqing, China
| | - Man-Yuan Li
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xiao-Qing Liu
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Ji-Gang Dai
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
- *Correspondence: Hong Zheng, ; Ji-Gang Dai,
| | - Hong Zheng
- Department of Thoracic Surgery, Xinqiao Hospital, Army Medical University, Chongqing, China
- *Correspondence: Hong Zheng, ; Ji-Gang Dai,
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33
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Stempels FC, Janssens MH, Ter Beest M, Mesman RJ, Revelo NH, Ioannidis M, van den Bogaart G. Novel and conventional inhibitors of canonical autophagy differently affect LC3-associated phagocytosis. FEBS Lett 2022; 596:491-509. [PMID: 35007347 DOI: 10.1002/1873-3468.14280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2022]
Abstract
In autophagy, LC3-positive autophagophores fuse and encapsulate the autophagic cargo in a double-membrane structure. In contrast, lipidated LC3 (LC3-II) is directly formed at the phagosomal membrane in LC3-associated phagocytosis (LAP). In this study, we dissected the effects of autophagy inhibitors on LAP. SAR405, an inhibitor of VPS34, reduced levels of LC3-II and inhibited LAP. In contrast, the inhibitors of endosomal acidification bafilomycin A1 and chloroquine increased levels of LC3-II, due to reduced degradation in acidic lysosomes. However, while bafilomycin A1 inhibited LAP, chloroquine did not. Finally, EACC, which inhibits the fusion of autophagosomes with lysosomes, promoted LC3 degradation possibly by the proteasome. Targeting LAP with small molecule inhibitors is important given its emerging role in infectious and autoimmune diseases.
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Affiliation(s)
- Femmy C Stempels
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Maaike H Janssens
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Martin Ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob J Mesman
- Department of Microbiology, RIBES, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Natalia H Revelo
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Melina Ioannidis
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Geert van den Bogaart
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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34
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Gilchrist JJ, Kariuki SN, Watson JA, Band G, Uyoga S, Ndila CM, Mturi N, Mwarumba S, Mohammed S, Mosobo M, Alasoo K, Rockett KA, Mentzer AJ, Kwiatkowski DP, Hill AVS, Maitland K, Scott JAG, Williams TN. BIRC6 modifies risk of invasive bacterial infection in Kenyan children. eLife 2022; 11:77461. [PMID: 35866869 PMCID: PMC9391038 DOI: 10.7554/elife.77461] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Invasive bacterial disease is a major cause of morbidity and mortality in African children. Despite being caused by diverse pathogens, children with sepsis are clinically indistinguishable from one another. In spite of this, most genetic susceptibility loci for invasive infection that have been discovered to date are pathogen specific and are not therefore suggestive of a shared genetic architecture of bacterial sepsis. Here, we utilise probabilistic diagnostic models to identify children with a high probability of invasive bacterial disease among critically unwell Kenyan children with Plasmodium falciparum parasitaemia. We construct a joint dataset including 1445 bacteraemia cases and 1143 severe malaria cases, and population controls, among critically unwell Kenyan children that have previously been genotyped for human genetic variation. Using these data, we perform a cross-trait genome-wide association study of invasive bacterial infection, weighting cases according to their probability of bacterial disease. In doing so, we identify and validate a novel risk locus for invasive infection secondary to multiple bacterial pathogens, that has no apparent effect on malaria risk. The locus identified modifies splicing of BIRC6 in stimulated monocytes, implicating regulation of apoptosis and autophagy in the pathogenesis of sepsis in Kenyan children.
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Affiliation(s)
- James J Gilchrist
- Department of Paediatrics, University of OxfordOxfordUnited Kingdom,MRC–Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom,Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Silvia N Kariuki
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - James A Watson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Salim Mwarumba
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Shebe Mohammed
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Moses Mosobo
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Kaur Alasoo
- Institute of Computer Science, University of TartuTartuEstonia
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom,Wellcome Sanger InstituteCambridgeUnited Kingdom
| | - Adrian VS Hill
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom,The Jenner Institute, University of OxfordOxfordUnited Kingdom
| | - Kathryn Maitland
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Division of Medicine, Imperial CollegeLondonUnited Kingdom
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial CollegeLondonUnited Kingdom
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35
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Nowosad A, Besson A. A high-throughput protocol for monitoring starvation-induced autophagy in real time in mouse embryonic fibroblasts. STAR Protoc 2021; 2:100966. [PMID: 34825223 PMCID: PMC8605097 DOI: 10.1016/j.xpro.2021.100966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Autophagy measurement has been challenging due to the transient nature of autophagy vesicles, in which degradation of cargo occurs. Here, we present a protocol to monitor starvation-induced autophagy using a live high-throughput microscopy system in a fast and automated manner without the need for sample preparation. We provide a detailed protocol describing the generation of turboGFP-LC3B expressing mouse embryonic fibroblasts (MEFs), the measurement of autophagy over time and the analysis of data. For complete details on the use and execution of this protocol, please refer to Nowosad et al. (2020, 2021).
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Affiliation(s)
- Ada Nowosad
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France.,Laboratory of Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
| | - Arnaud Besson
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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36
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Bata N, Cosford NDP. Cell Survival and Cell Death at the Intersection of Autophagy and Apoptosis: Implications for Current and Future Cancer Therapeutics. ACS Pharmacol Transl Sci 2021; 4:1728-1746. [PMID: 34927007 DOI: 10.1021/acsptsci.1c00130] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Indexed: 12/25/2022]
Abstract
Autophagy and apoptosis are functionally distinct mechanisms for cytoplasmic and cellular turnover. While these two pathways are distinct, they can also regulate each other, and central components of the apoptosis or autophagy pathway regulate both processes directly. Furthermore, several upstream stress-inducing signaling pathways can influence both autophagy and apoptosis. The crosstalk between autophagy and apoptosis has an integral role in pathological processes, including those related to cancer, homeostasis, and aging. Apoptosis is a form of programmed cell death, tightly regulated by various cellular and biochemical mechanisms, some of which have been the focus of drug discovery efforts targeting cancer therapeutics. Autophagy is a cellular degradation pathway whereby cells recycle macromolecules and organelles to generate energy when subjected to stress. Autophagy can act as either a prodeath or a prosurvival process and is both tissue and microenvironment specific. In this review we describe five groups of proteins that are integral to the apoptosis pathway and discuss their role in regulating autophagy. We highlight several apoptosis-inducing small molecules and biologics that have been developed and advanced into the clinic and discuss their effects on autophagy. For the most part, these apoptosis-inducing compounds appear to elevate autophagy activity. Under certain circumstances autophagy demonstrates cytoprotective functions and is overactivated in response to chemo- or radiotherapy which can lead to drug resistance, representing a clinical obstacle for successful cancer treatment. Thus, targeting the autophagy pathway in combination with apoptosis-inducing compounds may be a promising strategy for cancer therapy.
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Affiliation(s)
- Nicole Bata
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nicholas D P Cosford
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States
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37
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Foster B, Attwood M, Gibbs-Seymour I. Tools for Decoding Ubiquitin Signaling in DNA Repair. Front Cell Dev Biol 2021; 9:760226. [PMID: 34950659 PMCID: PMC8690248 DOI: 10.3389/fcell.2021.760226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022] Open
Abstract
The maintenance of genome stability requires dedicated DNA repair processes and pathways that are essential for the faithful duplication and propagation of chromosomes. These DNA repair mechanisms counteract the potentially deleterious impact of the frequent genotoxic challenges faced by cells from both exogenous and endogenous agents. Intrinsic to these mechanisms, cells have an arsenal of protein factors that can be utilised to promote repair processes in response to DNA lesions. Orchestration of the protein factors within the various cellular DNA repair pathways is performed, in part, by post-translational modifications, such as phosphorylation, ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs). In this review, we firstly explore recent advances in the tools for identifying factors involved in both DNA repair and ubiquitin signaling pathways. We then expand on this by evaluating the growing repertoire of proteomic, biochemical and structural techniques available to further understand the mechanistic basis by which these complex modifications regulate DNA repair. Together, we provide a snapshot of the range of methods now available to investigate and decode how ubiquitin signaling can promote DNA repair and maintain genome stability in mammalian cells.
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Affiliation(s)
| | | | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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38
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Translation Inhibitors Activate Autophagy Master Regulators TFEB and TFE3. Int J Mol Sci 2021; 22:ijms222112083. [PMID: 34769510 PMCID: PMC8584619 DOI: 10.3390/ijms222112083] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023] Open
Abstract
The autophagy-lysosome pathway is a major protein degradation pathway stimulated by multiple cellular stresses, including nutrient or growth factor deprivation, hypoxia, misfolded proteins, damaged organelles, and intracellular pathogens. Recent studies have revealed that transcription factor EB (TFEB) and transcription factor E3 (TFE3) play a pivotal role in the biogenesis and functions of autophagosome and lysosome. Here we report that three translation inhibitors (cycloheximide, lactimidomycin, and rocaglamide A) can facilitate the nuclear translocation of TFEB/TFE3 via dephosphorylation and 14-3-3 dissociation. In addition, the inhibitor-mediated TFEB/TFE3 nuclear translocation significantly increases the transcriptional expression of their downstream genes involved in the biogenesis and function of autophagosome and lysosome. Furthermore, we demonstrated that translation inhibition increased autophagosome biogenesis but impaired the degradative autolysosome formation because of lysosomal dysfunction. These results highlight the previously unrecognized function of the translation inhibitors as activators of TFEB/TFE3, suggesting a novel biological role of translation inhibition in autophagy regulation.
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39
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Fas BA, Maiani E, Sora V, Kumar M, Mashkoor M, Lambrughi M, Tiberti M, Papaleo E. The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer. Autophagy 2021; 17:2818-2841. [PMID: 33302793 PMCID: PMC8525936 DOI: 10.1080/15548627.2020.1847443] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
Macroautophagy/autophagy is a cellular process to recycle damaged cellular components, and its modulation can be exploited for disease treatments. A key autophagy player is the ubiquitin-like protein MAP1LC3B/LC3B. Mutations and changes in MAP1LC3B expression occur in cancer samples. However, the investigation of the effects of these mutations on MAP1LC3B protein structure is still missing. Despite many LC3B structures that have been solved, a comprehensive study, including dynamics, has not yet been undertaken. To address this knowledge gap, we assessed nine physical models for biomolecular simulations for their capabilities to describe the structural ensemble of MAP1LC3B. With the resulting MAP1LC3B structural ensembles, we characterized the impact of 26 missense mutations from pan-cancer studies with different approaches, and we experimentally validated our prediction for six variants using cellular assays. Our findings shed light on damaging or neutral mutations in MAP1LC3B, providing an atlas of its modifications in cancer. In particular, P32Q mutation was found detrimental for protein stability with a propensity to aggregation. In a broader context, our framework can be applied to assess the pathogenicity of protein mutations or to prioritize variants for experimental studies, allowing to comprehensively account for different aspects that mutational events alter in terms of protein structure and function.Abbreviations: ATG: autophagy-related; Cα: alpha carbon; CG: coarse-grained; CHARMM: Chemistry at Harvard macromolecular mechanics; CONAN: contact analysis; FUNDC1: FUN14 domain containing 1; FYCO1: FYVE and coiled-coil domain containing 1; GABARAP: GABA type A receptor-associated protein; GROMACS: Groningen machine for chemical simulations; HP: hydrophobic pocket; LIR: LC3 interacting region; MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 B; MD: molecular dynamics; OPTN: optineurin; OSF: open software foundation; PE: phosphatidylethanolamine, PLEKHM1: pleckstrin homology domain-containing family M 1; PSN: protein structure network; PTM: post-translational modification; SA: structural alphabet; SLiM: short linear motif; SQSTM1/p62: sequestosome 1; WT: wild-type.
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Affiliation(s)
- Burcu Aykac Fas
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Emiliano Maiani
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Valentina Sora
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mukesh Kumar
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Maliha Mashkoor
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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40
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Bastien J, Menon S, Messa M, Nyfeler B. Molecular targets and approaches to restore autophagy and lysosomal capacity in neurodegenerative disorders. Mol Aspects Med 2021; 82:101018. [PMID: 34489092 DOI: 10.1016/j.mam.2021.101018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023]
Abstract
Autophagy is a catabolic process that promotes cellular fitness by clearing aggregated protein species, pathogens and damaged organelles through lysosomal degradation. The autophagic process is particularly important in the nervous system where post-mitotic neurons rely heavily on protein and organelle quality control in order to maintain cellular health throughout the lifetime of the organism. Alterations of autophagy and lysosomal function are hallmarks of various neurodegenerative disorders. In this review, we conceptualize some of the mechanistic and genetic evidence pointing towards autophagy and lysosomal dysfunction as a causal driver of neurodegeneration. Furthermore, we discuss rate-limiting pathway nodes and potential approaches to restore pathway activity, from autophagy initiation, cargo sequestration to lysosomal capacity.
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Affiliation(s)
- Julie Bastien
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Suchithra Menon
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mirko Messa
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Beat Nyfeler
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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41
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Russo M, Sobh A, Zhang P, Loguinov A, Tagmount A, Vulpe CD, Liu B. Functional Pathway Identification With CRISPR/Cas9 Genome-wide Gene Disruption in Human Dopaminergic Neuronal Cells Following Chronic Treatment With Dieldrin. Toxicol Sci 2021; 176:366-381. [PMID: 32421776 DOI: 10.1093/toxsci/kfaa071] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Organochlorine pesticides, once widely used, are extremely persistent and bio-accumulative in the environment. Epidemiological studies have implicated that environmental exposure to organochlorine pesticides including dieldrin is a risk factor for the development of Parkinson's disease. However, the pertinent mechanisms of action remain poorly understood. In this study, we carried out a genome-wide (Brunello library, 19 114 genes, 76 411 sgRNAs) CRISPR/Cas9 screen in human dopaminergic SH-SY5Y neuronal cells exposed to a chronic treatment (30 days) with dieldrin to identify cellular pathways that are functionally related to the chronic cellular toxicity. Our results indicate that dieldrin toxicity was enhanced by gene disruption of specific components of the ubiquitin proteasome system as well as, surprisingly, the protein degradation pathways previously implicated in inherited forms of Parkinson's disease, centered on Parkin. In addition, disruption of regulatory components of the mTOR pathway which integrates cellular responses to both intra- and extracellular signals and is a central regulator for cell metabolism, growth, proliferation, and survival, led to increased sensitivity to dieldrin-induced cellular toxicity. This study is one of the first to apply a genome-wide CRISPR/Cas9-based functional gene disruption screening approach in an adherent neuronal cell line to globally decipher cellular mechanisms that contribute to environmental toxicant-induced neurotoxicity and provides novel insight into the dopaminergic neurotoxicity associated with chronic exposure to dieldrin.
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Affiliation(s)
- Max Russo
- Department of Pharmacodynamics, College of Pharmacy
| | - Amin Sobh
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32610
| | - Ping Zhang
- Department of Pharmacodynamics, College of Pharmacy
| | - Alex Loguinov
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32610
| | - Abderrahmane Tagmount
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32610
| | - Chris D Vulpe
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32610
| | - Bin Liu
- Department of Pharmacodynamics, College of Pharmacy
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42
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Diehl V, Wegner M, Grumati P, Husnjak K, Schaubeck S, Gubas A, Shah V, Polat I, Langschied F, Prieto-Garcia C, Müller K, Kalousi A, Ebersberger I, Brandts C, Dikic I, Kaulich M. Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. Nucleic Acids Res 2021; 49:5684-5704. [PMID: 33956155 PMCID: PMC8191801 DOI: 10.1093/nar/gkab309] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/01/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale.
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Affiliation(s)
- Valentina Diehl
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Paolo Grumati
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Simone Schaubeck
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Andrea Gubas
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Varun Jayeshkumar Shah
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ibrahim H Polat
- Department of Medicine, Hematology/Oncology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
| | - Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Cristian Prieto-Garcia
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Konstantin Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alkmini Kalousi
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Christian H Brandts
- Department of Medicine, Hematology/Oncology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- University Cancer Center Frankfurt (UCT), University Hospital, Goethe University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
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Mimura K, Sakamaki JI, Morishita H, Kawazu M, Mano H, Mizushima N. Genome-wide CRISPR screening reveals nucleotide synthesis negatively regulates autophagy. J Biol Chem 2021; 296:100780. [PMID: 34000301 PMCID: PMC8191307 DOI: 10.1016/j.jbc.2021.100780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/12/2021] [Accepted: 05/12/2021] [Indexed: 02/06/2023] Open
Abstract
Macroautophagy (hereafter, autophagy) is a process that directs the degradation of cytoplasmic material in lysosomes. In addition to its homeostatic roles, autophagy undergoes dynamic positive and negative regulation in response to multiple forms of cellular stress, thus enabling the survival of cells. However, the precise mechanisms of autophagy regulation are not fully understood. To identify potential negative regulators of autophagy, we performed a genome-wide CRISPR screen using the quantitative autophagic flux reporter GFP-LC3-RFP. We identified phosphoribosylformylglycinamidine synthase, a component of the de novo purine synthesis pathway, as one such negative regulator of autophagy. Autophagy was activated in cells lacking phosphoribosylformylglycinamidine synthase or phosphoribosyl pyrophosphate amidotransferase, another de novo purine synthesis enzyme, or treated with methotrexate when exogenous levels of purines were insufficient. Purine starvation-induced autophagy activation was concomitant with mammalian target of rapamycin complex 1 (mTORC1) suppression and was profoundly suppressed in cells deficient for tuberous sclerosis complex 2, which negatively regulates mTORC1 through inhibition of Ras homolog enriched in brain, suggesting that purines regulate autophagy through the tuberous sclerosis complex-Ras homolog enriched in brain-mTORC1 signaling axis. Moreover, depletion of the pyrimidine synthesis enzymes carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase and dihydroorotate dehydrogenase activated autophagy as well, although mTORC1 activity was not altered by pyrimidine shortage. These results suggest a different mechanism of autophagy induction between purine and pyrimidine starvation. These findings provide novel insights into the regulation of autophagy by nucleotides and possibly the role of autophagy in nucleotide metabolism, leading to further developing anticancer strategies involving nucleotide synthesis and autophagy.
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Affiliation(s)
- Kaito Mimura
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideaki Morishita
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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44
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Jia R, Bonifacino JS. The ubiquitin isopeptidase USP10 deubiquitinates LC3B to increase LC3B levels and autophagic activity. J Biol Chem 2021; 296:100405. [PMID: 33577797 PMCID: PMC7960534 DOI: 10.1016/j.jbc.2021.100405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/30/2022] Open
Abstract
Components of the autophagy machinery are subject to regulation by various posttranslational modifications. Previous studies showed that monoubiquitination of LC3B catalyzed by the ubiquitin-activating enzyme UBA6 and ubiquitin-conjugating enzyme/ubiquitin ligase BIRC6 targets LC3B for proteasomal degradation, thus reducing LC3B levels and autophagic activity under conditions of stress. However, mechanisms capable of counteracting this process are not known. Herein, we report that LC3B ubiquitination is reversed by the action of the deubiquitinating enzyme USP10. We identified USP10 in a CRISPR-Cas9 knockout screen for ubiquitination-related genes that regulate LC3B levels. Biochemical analyses showed that silencing of USP10 reduces the levels of both the LC3B-I and LC3B-II forms of LC3B through increased ubiquitination and proteasomal degradation. In turn, the reduced LC3B levels result in slower degradation of the autophagy receptors SQSTM1 and NBR1 and an increased accumulation of puromycin-induced aggresome-like structures. Taken together, these findings indicate that the levels of LC3B and autophagic activity are controlled through cycles of LC3B ubiquitination and deubiquitination.
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Affiliation(s)
- Rui Jia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA.
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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45
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Alloza I, Salegi A, Mena J, Navarro RT, Martin C, Aspichueta P, Salazar LM, Carpio JU, Cagigal PDLH, Vega R, Triviño JC, Freijo MDM, Vandenbroeck K. BIRC6 Is Associated with Vulnerability of Carotid Atherosclerotic Plaque. Int J Mol Sci 2020; 21:ijms21249387. [PMID: 33317170 PMCID: PMC7763522 DOI: 10.3390/ijms21249387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 11/16/2022] Open
Abstract
Carotid atherosclerotic plaque rupture can lead to cerebrovascular accident (CVA). By comparing RNA-Seq data from vascular smooth muscle cells (VSMC) extracted from carotid atheroma surgically excised from a group of asymptomatic and symptomatic subjects, we identified more than 700 genomic variants associated with symptomatology (p < 0.05). From these, twelve single nucleotide polymorphisms (SNPs) were selected for further validation. Comparing genotypes of a hospital-based cohort of asymptomatic with symptomatic patients, an exonic SNP in the BIRC6 (BRUCE/Apollon) gene, rs35286811, emerged as significantly associated with CVA symptomatology (p = 0.002; OR = 2.24). Moreover, BIRC6 mRNA levels were significantly higher in symptomatic than asymptomatic subjects upon measurement by qPCR in excised carotid atherosclerotic tissue (p < 0.0001), and significantly higher in carriers of the rs35286811 risk allele (p < 0.0001). rs35286811 is a proxy of a GWAS SNP reported to be associated with red cell distribution width (RDW); RDW was increased in symptomatic patients (p < 0.03), but was not influenced by the rs35286811 genotype in our cohort. BIRC6 is a negative regulator of both apoptosis and autophagy. This work introduces BIRC6 as a novel genetic risk factor for stroke, and identifies autophagy as a genetically regulated mechanism of carotid plaque vulnerability.
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Affiliation(s)
- Iraide Alloza
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.A.); (A.S.); (J.M.); (R.T.N.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Andrea Salegi
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.A.); (A.S.); (J.M.); (R.T.N.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Jorge Mena
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.A.); (A.S.); (J.M.); (R.T.N.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Raquel Tulloch Navarro
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.A.); (A.S.); (J.M.); (R.T.N.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - César Martin
- Biofisika Institute (UPV/EHU, CSIC), 48940 Leioa, Spain;
| | - Patricia Aspichueta
- Department of Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain
| | - Lucía Martínez Salazar
- Department of Laboratory Medicine, Osakidetza, Bilbao-Basurto IHO, Basurto University Hospital, 48013 Bilbao, Spain; (L.M.S.); (J.U.C.); (P.D.-l.-H.C.)
| | - Jon Uriarte Carpio
- Department of Laboratory Medicine, Osakidetza, Bilbao-Basurto IHO, Basurto University Hospital, 48013 Bilbao, Spain; (L.M.S.); (J.U.C.); (P.D.-l.-H.C.)
| | - Patricia De-la-Hera Cagigal
- Department of Laboratory Medicine, Osakidetza, Bilbao-Basurto IHO, Basurto University Hospital, 48013 Bilbao, Spain; (L.M.S.); (J.U.C.); (P.D.-l.-H.C.)
| | - Reyes Vega
- Neurovascular Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (R.V.); (M.d.M.F.)
| | | | - Maria del Mar Freijo
- Neurovascular Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (R.V.); (M.d.M.F.)
| | - Koen Vandenbroeck
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.A.); (A.S.); (J.M.); (R.T.N.)
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Correspondence:
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46
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Mizushima N, Murphy LO. Autophagy Assays for Biological Discovery and Therapeutic Development. Trends Biochem Sci 2020; 45:1080-1093. [DOI: 10.1016/j.tibs.2020.07.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022]
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47
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The Roles of Ubiquitin in Mediating Autophagy. Cells 2020; 9:cells9092025. [PMID: 32887506 PMCID: PMC7564124 DOI: 10.3390/cells9092025] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Ubiquitination, the post-translational modification essential for various intracellular processes, is implicated in multiple aspects of autophagy, the major lysosome/vacuole-dependent degradation pathway. The autophagy machinery adopted the structural architecture of ubiquitin and employs two ubiquitin-like protein conjugation systems for autophagosome biogenesis. Ubiquitin chains that are attached as labels to protein aggregates or subcellular organelles confer selectivity, allowing autophagy receptors to simultaneously bind ubiquitinated cargos and autophagy-specific ubiquitin-like modifiers (Atg8-family proteins). Moreover, there is tremendous crosstalk between autophagy and the ubiquitin-proteasome system. Ubiquitination of autophagy-related proteins or regulatory components plays significant roles in the precise control of the autophagy pathway. In this review, we summarize and discuss the molecular mechanisms and functions of ubiquitin and ubiquitination, in the process and regulation of autophagy.
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48
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Wesch N, Kirkin V, Rogov VV. Atg8-Family Proteins-Structural Features and Molecular Interactions in Autophagy and Beyond. Cells 2020; 9:E2008. [PMID: 32882854 PMCID: PMC7564214 DOI: 10.3390/cells9092008] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a common name for a number of catabolic processes, which keep the cellular homeostasis by removing damaged and dysfunctional intracellular components. Impairment or misbalance of autophagy can lead to various diseases, such as neurodegeneration, infection diseases, and cancer. A central axis of autophagy is formed along the interactions of autophagy modifiers (Atg8-family proteins) with a variety of their cellular counter partners. Besides autophagy, Atg8-proteins participate in many other pathways, among which membrane trafficking and neuronal signaling are the most known. Despite the fact that autophagy modifiers are well-studied, as the small globular proteins show similarity to ubiquitin on a structural level, the mechanism of their interactions are still not completely understood. A thorough analysis and classification of all known mechanisms of Atg8-protein interactions could shed light on their functioning and connect the pathways involving Atg8-proteins. In this review, we present our views of the key features of the Atg8-proteins and describe the basic principles of their recognition and binding by interaction partners. We discuss affinity and selectivity of their interactions as well as provide perspectives for discovery of new Atg8-interacting proteins and therapeutic approaches to tackle major human diseases.
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Affiliation(s)
- Nicole Wesch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
| | - Vladimir Kirkin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research London, Sutton SM2 5NG, UK;
| | - Vladimir V. Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany;
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany
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49
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Koepke L, Winter B, Grenzner A, Regensburger K, Engelhart S, van der Merwe JA, Krebs S, Blum H, Kirchhoff F, Sparrer KMJ. An improved method for high-throughput quantification of autophagy in mammalian cells. Sci Rep 2020; 10:12241. [PMID: 32699244 PMCID: PMC7376206 DOI: 10.1038/s41598-020-68607-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/25/2020] [Indexed: 12/20/2022] Open
Abstract
Autophagy is a cellular homeostatic pathway with functions ranging from cytoplasmic protein turnover to immune defense. Therapeutic modulation of autophagy has been demonstrated to positively impact the outcome of autophagy-dysregulated diseases such as cancer or microbial infections. However, currently available agents lack specificity, and new candidates for drug development or potential cellular targets need to be identified. Here, we present an improved method to robustly detect changes in autophagy in a high-throughput manner on a single cell level, allowing effective screening. This method quantifies eGFP-LC3B positive vesicles to accurately monitor autophagy. We have significantly streamlined the protocol and optimized it for rapid quantification of large numbers of cells in little time, while retaining accuracy and sensitivity. Z scores up to 0.91 without a loss of sensitivity demonstrate the robustness and aptness of this approach. Three exemplary applications outline the value of our protocols and cell lines: (I) Examining autophagy modulating compounds on four different cell types. (II) Monitoring of autophagy upon infection with e.g. measles or influenza A virus. (III) CRISPR/Cas9 screening for autophagy modulating factors in T cells. In summary, we offer ready-to-use protocols to generate sensitive autophagy reporter cells and quantify autophagy in high-throughput assays.
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Affiliation(s)
- Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Benjamin Winter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Alexander Grenzner
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Kerstin Regensburger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Susanne Engelhart
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | | | - Stefan Krebs
- Gene Center and Laboratory for Functional Genome Analysis, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Helmut Blum
- Gene Center and Laboratory for Functional Genome Analysis, Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
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The Role of Deubiquitinating Enzymes in the Various Forms of Autophagy. Int J Mol Sci 2020; 21:ijms21124196. [PMID: 32545524 PMCID: PMC7352190 DOI: 10.3390/ijms21124196] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
Deubiquitinating enzymes (DUBs) have an essential role in several cell biological processes via removing the various ubiquitin patterns as posttranslational modification forms from the target proteins. These enzymes also contribute to the normal cytoplasmic ubiquitin pool during the recycling of this molecule. Autophagy, a summary name of the lysosome dependent self-degradative processes, is necessary for maintaining normal cellular homeostatic equilibrium. Numerous forms of autophagy are known depending on how the cellular self-material is delivered into the lysosomal lumen. In this review we focus on the colorful role of DUBs in autophagic processes and discuss the mechanistic contribution of these molecules to normal cellular homeostasis via the possible regulation forms of autophagic mechanisms.
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