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Gubas A, Dikic I. ER remodeling via ER-phagy. Mol Cell 2022; 82:1492-1500. [PMID: 35452617 PMCID: PMC9098120 DOI: 10.1016/j.molcel.2022.02.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/01/2023]
Abstract
The endoplasmic reticulum (ER) is a hotspot for many essential cellular functions. The ER membrane is highly dynamic, which affects many cellular processes that take place within the ER. One such process is ER-phagy, a selective degradation of ER fragments (including membranes and luminal content), which serves to preserve the size of ER while adapting its morphology under basal and stress conditions. In order to be degraded, the ER undergoes selective fragmentation facilitated by specialized ER-shaping proteins that also act as ER-phagy receptors. Their ability to sense and induce membrane curvature, as well as to bridge the ER with autophagy machinery, allows for a successful ER fragmentation and delivery of these fragments to the lysosome for degradation and recycling. In this review, we provide insights into ER-phagy from the perspective of membrane remodeling. We highlight the importance of ER membrane dynamics during ER-phagy and emphasize how its dysregulation reflects on human physiology and pathology.
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Affiliation(s)
- Andrea Gubas
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany; Max Planck Institute of Biophysics, Frankfurt, Germany.
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202
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Ma X, Lu C, Chen Y, Li S, Ma N, Tao X, Li Y, Wang J, Zhou M, Yan YB, Li P, Heydari K, Deng H, Zhang M, Yi C, Ge L. CCT2 is an aggrephagy receptor for clearance of solid protein aggregates. Cell 2022; 185:1325-1345.e22. [PMID: 35366418 DOI: 10.1016/j.cell.2022.03.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/13/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a hallmark of multiple human pathologies. Autophagy selectively degrades protein aggregates via aggrephagy. How selectivity is achieved has been elusive. Here, we identify the chaperonin subunit CCT2 as an autophagy receptor regulating the clearance of aggregation-prone proteins in the cell and the mouse brain. CCT2 associates with aggregation-prone proteins independent of cargo ubiquitination and interacts with autophagosome marker ATG8s through a non-classical VLIR motif. In addition, CCT2 regulates aggrephagy independently of the ubiquitin-binding receptors (P62, NBR1, and TAX1BP1) or chaperone-mediated autophagy. Unlike P62, NBR1, and TAX1BP1, which facilitate the clearance of protein condensates with liquidity, CCT2 specifically promotes the autophagic degradation of protein aggregates with little liquidity (solid aggregates). Furthermore, aggregation-prone protein accumulation induces the functional switch of CCT2 from a chaperone subunit to an autophagy receptor by promoting CCT2 monomer formation, which exposes the VLIR to ATG8s interaction and, therefore, enables the autophagic function.
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Affiliation(s)
- Xinyu Ma
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Caijing Lu
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuting Chen
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ningjia Ma
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuan Tao
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ying Li
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing Wang
- State Key Laboratory of Membrane Biology, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Min Zhou
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Yong-Bin Yan
- State Key Laboratory of Membrane Biology, Beijing, China; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pilong Li
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China
| | - Kartoosh Heydari
- Cancer Research Laboratory FACS Core Facility, University of California, Berkeley, CA 94720, USA
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing 100084, China; MOE Key Laboratory of Bioinformatics, Beijing, China
| | - Min Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
| | - Cong Yi
- Department of Biochemistry, and Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Beijing, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; School of Life Sciences, Tsinghua University, Beijing 100084, China.
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203
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Ke PY, Chang CW, Hsiao YC. Baicalein Activates Parkin-Dependent Mitophagy through NDP52 and OPTN. Cells 2022; 11:cells11071132. [PMID: 35406696 PMCID: PMC8997844 DOI: 10.3390/cells11071132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
The elimination of intracellular components by autophagy maintains metabolic homeostasis and is a quality-control pathway that enables organelle regeneration. Mitophagy is a type of selective autophagy that regulates mitochondrial turnover, and the dysregulation of mitophagy has been implicated in the pathogenesis of liver diseases. However, the detailed molecular mechanism underlying mitophagy regulation in liver cells remains unclear, and the small molecules that may potentially modulate hepatic mitophagy are still unavailable. Here, we report that baicalein, a flavonoid extracted from Scutellaria baicalensis, induces the entire autophagy that proceeds through the autolysosome maturation stage in human hepatoma cells. In addition, baicalein-induced autophagy is demonstrated to target mitochondria for degradation. Further studies show that baicalein triggers the translocation of Parkin and TBK1 to mitochondria to induce mitophagy. Moreover, the phosphorylation of TBK1 at Ser172 and ubiquitin at Ser65 is shown to trigger mitophagy in baicalein-treated cells. Furthermore, two specific autophagy cargo receptors, NDP52 and OPTN, that function in baicalein-activated mitophagy are identified. Taken together, these findings not only delineate the molecular process of Parkin-dependent mitophagy in liver cells, but also reveal baicalein as a novel inducer of hepatic mitophagy.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-W.C.); (Y.-C.H.)
- Liver Research Center, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
- Correspondence: ; Tel.: +886-3-2118800 (ext. 5115); Fax: +886-3-211-8700
| | - Chih-Wei Chang
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-W.C.); (Y.-C.H.)
| | - Yuan-Chao Hsiao
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; (C.-W.C.); (Y.-C.H.)
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204
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Herb M, Gluschko A, Farid A, Krönke M. When the Phagosome Gets Leaky: Pore-Forming Toxin-Induced Non-Canonical Autophagy (PINCA). Front Cell Infect Microbiol 2022; 12:834321. [PMID: 35372127 PMCID: PMC8968195 DOI: 10.3389/fcimb.2022.834321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Macrophages remove bacteria from the extracellular milieu via phagocytosis. While most of the engulfed bacteria are degraded in the antimicrobial environment of the phagolysosome, several bacterial pathogens have evolved virulence factors, which evade degradation or allow escape into the cytosol. To counter this situation, macrophages activate LC3-associated phagocytosis (LAP), a highly bactericidal non-canonical autophagy pathway, which destroys the bacterial pathogens in so called LAPosomes. Moreover, macrophages can also target intracellular bacteria by pore-forming toxin-induced non-canonical autophagy (PINCA), a recently described non-canonical autophagy pathway, which is activated by phagosomal damage induced by bacteria-derived pore-forming toxins. Similar to LAP, PINCA involves LC3 recruitment to the bacteria-containing phagosome independently of the ULK complex, but in contrast to LAP, this process does not require ROS production by Nox2. As last resort of autophagic targeting, macrophages activate xenophagy, a selective form of macroautophagy, to recapture bacteria, which evaded successful targeting by LAP or PINCA through rupture of the phagosome. However, xenophagy can also be hijacked by bacterial pathogens for their benefit or can be completely inhibited resulting in intracellular growth of the bacterial pathogen. In this perspective, we discuss the molecular differences and similarities between LAP, PINCA and xenophagy in macrophages during bacterial infections.
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Affiliation(s)
- Marc Herb
- Faculty of Medicine and University Hospital of Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Cologne, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Marc Herb,
| | - Alexander Gluschko
- Faculty of Medicine and University Hospital of Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Cologne, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Alina Farid
- Faculty of Medicine and University Hospital of Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Cologne, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Martin Krönke
- Faculty of Medicine and University Hospital of Cologne, Institute for Medical Microbiology, Immunology and Hygiene, Cologne, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- German Center for Infection Research, Bonn-Cologne, Germany
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205
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Marshall RS, Vierstra RD. A trio of ubiquitin ligases sequentially drives ubiquitylation and autophagic degradation of dysfunctional yeast proteasomes. Cell Rep 2022; 38:110535. [PMID: 35294869 DOI: 10.1016/j.celrep.2022.110535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/08/2021] [Accepted: 02/25/2022] [Indexed: 12/22/2022] Open
Abstract
As central effectors of ubiquitin (Ub)-mediated proteolysis, proteasomes are regulated at multiple levels, including degradation of unwanted or dysfunctional particles via autophagy (termed proteaphagy). In yeast, inactive proteasomes are exported from the nucleus, sequestered into cytoplasmic aggresomes via the Hsp42 chaperone, extensively ubiquitylated, and then tethered to the expanding phagophore by the autophagy receptor Cue5. Here, we demonstrate the need for ubiquitylation driven by the trio of Ub ligases (E3s), San1, Rsp5, and Hul5, which together with their corresponding E2s work sequentially to promote nuclear export and Cue5 recognition. Whereas San1 functions prior to nuclear export, Rsp5 and Hul5 likely decorate aggresome-localized proteasomes in concert. Ultimately, topologically complex Ub chain(s) containing both K48 and K63 Ub-Ub linkages are assembled, mainly on the regulatory particle, to generate autophagy-competent substrates. Because San1, Rsp5, Hul5, Hsp42, and Cue5 also participate in general proteostasis, proteaphagy likely engages a fundamental mechanism for eliminating inactive/misfolded proteins.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, Missouri 63130, USA.
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, Missouri 63130, USA.
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206
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Qin C, Lu Y, Bai L, Wang K. The molecular regulation of autophagy in antimicrobial immunity. J Mol Cell Biol 2022; 14:6547771. [PMID: 35278083 PMCID: PMC9335221 DOI: 10.1093/jmcb/mjac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 11/25/2022] Open
Abstract
Autophagy is a catabolic process that can degrade worn-out organelles and invading pathogens. The activation of autophagy regulates innate and adaptive immunity, playing a key role in the response to microbial invasion. Microbial infection may cause different consequences such as the elimination of invaders through autophagy or xenophagy, host cell death, and symbiotic relationships. Pathogens adapt to the autophagy mechanism and further relieve intracellular stress, which is conducive to host cell survival and microbial growth. The regulation of autophagy forms a complex network through which host immunity is modulated, resulting in a variety of pathophysiological manifestations. Modification of the autophagic pathway is an essential target for the development of antimicrobial drugs.
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Affiliation(s)
- Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Beijing 100021, China
| | - Yalan Lu
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Beijing 100021, China
| | - Lin Bai
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Beijing 100021, China
| | - Kewei Wang
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Beijing 100021, China
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207
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Toxoplasma TgAtg8-TgAtg3 Interaction Primarily Contributes to Apicoplast Inheritance and Parasite Growth in Tachyzoite. Microbiol Spectr 2022; 10:e0149521. [PMID: 35196797 PMCID: PMC8865545 DOI: 10.1128/spectrum.01495-21] [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] [Indexed: 11/20/2022] Open
Abstract
The apicoplast, which harbors key pathways involved in biosynthesis of vital metabolites, is a unique and essential nonphotosynthetic plastid organelle in apicomplexan parasites. Intriguingly, autophagy-related protein 8 (Atg8), a highly conserved eukaryotic protein, can localize to the outermost membrane of the apicoplast and modulate its inheritance in both Toxoplasma and Plasmodium parasites. The Atg8-Atg3 interaction plays a key role in Atg8 lipidation and localization, and our previously work in Toxoplasma has suggested that the core Atg8-family interacting motif (AIM) in TgAtg3, 239FADI242, and the R27 residue of TgAtg8 contribute to TgAtg8-TgAtg3 interaction in vitro. However, little is known about the function of this interaction or its importance in tachyzoite growth in Toxoplasma gondii. Here, we generated two complemented cell lines, TgAtg3F239A/I242A and TgAtg8R27E, based on the TgAtg3 and TgAtg8 conditional knockdown cell lines, respectively. We found that both mutant complemented cell lines were severely affected in terms of tachyzoite growth and displayed delayed death upon conditional knockdown of endogenous TgAtg3 or TgAtg8. Intriguingly, both complemented lines appeared to be defective in TgAtg8 lipidation and apicoplast inheritance. Moreover, we showed that the interaction of TgAtg8 and TgAtg3 is critical for TgAtg8 apicoplast localization. In addition, we found that the TgAtg3F239A/I242A complemented line exhibits an integral mitochondrial network upon ablation of endogenous TgAtg3, which is distinct from TgAtg3-depleted parasites with a fragmented mitochondrial network. Taken together, this work solidifies the contribution of the TgAtg8-TgAtg3 interaction to apicoplast inheritance and the growth of T. gondii tachyzoites. IMPORTANCEToxoplasma gondiiis a widespread intracellular parasite infecting a variety of warm-blooded animals, including humans. Current frontline treatment of toxoplasmosis suffers many drawbacks, including toxicity, drug resistance, and failure to eradicate tissue cysts, underscoring the need to identify novel drug targets for suppression or treatment of toxoplasmosis. TgAtg8 is thought to serve multiple functions in lipidation and is considered essential to the growth and development of both tachyzoites and bradyzoites. Here, we show that Toxoplasma gondii has adapted a conserved Atg8-Atg3 interaction, required for canonical autophagy in other eukaryotes, to function specifically in apicoplast inheritance. Our finding not only highlights the importance of TgAtg8-TgAtg3 interaction in tachyzoite growth but also suggests that this interaction is a promising drug target for the therapy of toxoplasmosis.
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208
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Reggiori F, Molinari M. ER-phagy: mechanisms, regulation and diseases connected to the lysosomal clearance of the endoplasmic reticulum. Physiol Rev 2022; 102:1393-1448. [PMID: 35188422 PMCID: PMC9126229 DOI: 10.1152/physrev.00038.2021] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
ER-phagy (reticulo-phagy) defines the degradation of portions of the endoplasmic reticulum (ER) within lysosomes or vacuoles. It is part of the self-digestion (i.e., auto-phagic) programs recycling cytoplasmic material and organelles, which rapidly mobilize metabolites in cells confronted with nutrient shortage. Moreover, selective clearance of ER subdomains participates to the control of ER size and activity during ER stress, the re-establishment of ER homeostasis after ER stress resolution and the removal of ER parts, in which aberrant and potentially cytotoxic material has been segregated. ER-phagy relies on the individual and/or concerted activation of the ER-phagy receptors, ER peripheral or integral membrane proteins that share the presence of LC3/Atg8-binding motifs in their cytosolic domains. ER-phagy involves the physical separation of portions of the ER from the bulk ER network, and their delivery to the endolysosomal/vacuolar catabolic district. This last step is accomplished by a variety of mechanisms including macro-ER-phagy (in which ER fragments are sequestered by double-membrane autophagosomes that eventually fuse with lysosomes/vacuoles), micro-ER-phagy (in which ER fragments are directly engulfed by endosomes/lysosomes/vacuoles), or direct fusion of ER-derived vesicles with lysosomes/vacuoles. ER-phagy is dysfunctional in specific human diseases and its regulators are subverted by pathogens, highlighting its crucial role for cell and organism life.
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Affiliation(s)
- Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, grid.4830.fUniversity of Groningen, Netherlands
| | - Maurizio Molinari
- Protein Folding and Quality Control, grid.7722.0Institute for Research in Biomedicine, Bellinzona, Switzerland
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209
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TRIM14 inhibits OPTN-mediated autophagic degradation of KDM4D to epigenetically regulate inflammation. Proc Natl Acad Sci U S A 2022; 119:2113454119. [PMID: 35145029 PMCID: PMC8851536 DOI: 10.1073/pnas.2113454119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/11/2022] Open
Abstract
Histone methylation regulates gene transcription through a variety of methylases and demethylases. The regulatory role of autophagy, an important process of protein degradation and recycling, in these histone modifiers is still unclear. We report that TRIM14 stabilized the histone demethylase KDM4D to facilitate the transcription of interleukin 12 (Il12) and Il23 by inhibiting histone H3K9 trimethylation in vitro and in vivo. Mechanistically, TRIM14 recruited the deubiquitinases USP14 and BRCC3 to remove the K63-linked ubiquitin chains of KDM4D and prevented it from undergoing optineurin-mediated autophagic degradation. This study is valuable not only for increasing our understanding of the cross-talk between autophagy and epigenetic regulation, but also for demonstrating the potential of TRIM14 as a target for therapeutic interventions for inflammation-related diseases. Autophagy is a fundamental cellular process of protein degradation and recycling that regulates immune signaling pathways via multiple mechanisms. However, it remains unclear how autophagy epigenetically regulates the immune response. Here, we identified TRIM14 as an epigenetic regulator that reduces histone H3K9 trimethylation by inhibiting the autophagic degradation of the histone demethylase KDM4D. TRIM14 recruited the deubiquitinases USP14 and BRCC3 to cleave the K63-linked ubiquitin chains of KDM4D, which prevented KDM4D from undergoing optineurin (OPTN)-mediated selective autophagy. Tripartite motif-containing 14 (TRIM14) deficiency in dendritic cells significantly impaired the expression of the KDM4D-directed proinflammatory cytokines interleukin 12 (Il12) and Il23 and protected mice from autoimmune inflammation. Taken together, these findings highlight the cross-talk between epigenetic regulation and autophagy and suggest TRIM14 is a potential target of therapeutic intervention for inflammation-related diseases.
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210
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Non-canonical roles of ATG8 for TFEB activation. Biochem Soc Trans 2022; 50:47-54. [PMID: 35166325 DOI: 10.1042/bst20210813] [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: 09/08/2021] [Revised: 12/23/2021] [Accepted: 01/18/2022] [Indexed: 11/17/2022]
Abstract
Autophagy is an evolutionally conserved cytoplasmic degradation pathway in which the double membrane structure, autophagosome sequesters cytoplasmic material and delivers them to lysosomes for degradation. Many autophagy related (ATG) proteins participate in the regulation of the several steps of autophagic process. Among ATGs, ubiquitin-like protein, ATG8 plays a pivotal role in autophagy. ATG8 is directly conjugated on lipid in autophagosome membrane upon induction of autophagy thus providing a good marker to monitor and analyze autophagy process. However, recent discoveries suggest that ATG8 has autophagy independent non-canonical functions and ATG8 positive structures are not always autophagosomes. This review briefly overviews canonical and non-canonical roles of ATG8 and introduce novel function of ATG8 to activate Transcriptional Factor EB(TFEB), a master transcription factor of autophagy and lysosome function during lysosomal damage.
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211
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Zada S, Hwang JS, Lai TH, Pham TM, Ahmed M, Elashkar O, Kim W, Kim DR. Autophagy-mediated degradation of NOTCH1 intracellular domain controls the epithelial to mesenchymal transition and cancer metastasis. Cell Biosci 2022; 12:17. [PMID: 35164848 PMCID: PMC8842742 DOI: 10.1186/s13578-022-00752-3] [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: 09/29/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
Backgound Autophagy controls levels of cellular components during normal and stress conditions; thus, it is a pivotal process for the maintenance of cell homeostasis. In cancer, autophagy protects cells from cancerous transformations that can result from genomic instability induced by reactive oxygen species or other damaged components, but it can also promote cancer survival by providing essential nutrients during the metabolic stress condition of cancer progression. However, the molecular mechanism underlying autophagy-dependent regulation of the epithelial to mesenchymal transition (EMT) and metastasis is still elusive. Methods The intracellular level of NOTCH1 intracellular domain (NICD) in several cancer cells was studied under starvation, treatment with chloroquine or ATG7-knockdown. The autophagy activity in these cells was assessed by immunocytochemistry and molecular analyses. Cancer cell migration and invasion under modulation of autophagy were determined by in vitro scratch and Matrigel assays. Results In the study, autophagy activation stimulated degradation of NICD, a key transcriptional regulator of the EMT and cancer metastasis. We also found that NICD binds directly to LC3 and that the NICD/LC3 complex associates with SNAI1 and sequestosome 1 (SQSTM1)/p62 proteins. Furthermore, the ATG7 knockdown significantly inhibited degradation of NICD under starvation independent of SQSTM1-associated proteasomal degradation. In addition, NICD degradation by autophagy associated with the cellular level of SNAI1. Indeed, autophagy inhibited nuclear translocation of NICD protein and consequently decreased the transcriptional activity of its target genes. Autophagy activation substantially suppressed in vitro cancer cell migration and invasion. We also observed that NICD and SNAI1 levels in tissues from human cervical and lung cancer patients correlated inversely with expression of autophagy-related proteins. Conclusions These findings suggest that the cellular level of NICD is regulated by autophagy during cancer progression and that targeting autophagy-dependent NICD/SNAI1 degradation could be a strategy for the development of cancer therapeutics. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00752-3.
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Affiliation(s)
- Sahib Zada
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea.,Cancer Biology and Immunology Laboratory, College of Dental Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Jin Seok Hwang
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Trang Huyen Lai
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Trang Minh Pham
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Mahmoud Ahmed
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Omar Elashkar
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Wanil Kim
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea.
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212
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Visintin R, Ray SK. Specific microRNAs for Modulation of Autophagy in Spinal Cord Injury. Brain Sci 2022; 12:brainsci12020247. [PMID: 35204010 PMCID: PMC8870708 DOI: 10.3390/brainsci12020247] [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: 12/31/2021] [Revised: 02/02/2022] [Accepted: 02/06/2022] [Indexed: 02/05/2023] Open
Abstract
The treatment of spinal cord injury (SCI) is currently a major challenge, with a severe lack of effective therapies for yielding meaningful improvements in function. Therefore, there is a great opportunity for the development of novel treatment strategies for SCI. The modulation of autophagy, a process by which a cell degrades and recycles unnecessary or harmful components (protein aggregates, organelles, etc.) to maintain cellular homeostasis and respond to a changing microenvironment, is thought to have potential for treating many neurodegenerative conditions, including SCI. The discovery of microRNAs (miRNAs), which are short ribonucleotide transcripts for targeting of specific messenger RNAs (mRNAs) for silencing, shows prevention of the translation of mRNAs to the corresponding proteins affecting various cellular processes, including autophagy. The number of known miRNAs and their targets continues to grow rapidly. This review article aims to explore the relationship between autophagy and SCI, specifically with the intent of identifying specific miRNAs that can be useful to modulate autophagy for neuroprotection and the improvement of functional recovery in SCI.
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Affiliation(s)
- Rhett Visintin
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA;
| | - Swapan K. Ray
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA
- Correspondence: ; Tel.: +1-803-216-3420; Fax: +1-803-216-3428
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213
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Lau N, Thomas DR, Lee YW, Knodler LA, Newton HJ. Perturbation of ATG16L1 function impairs the biogenesis of Salmonella and Coxiella replication vacuoles. Mol Microbiol 2022; 117:235-251. [PMID: 34874584 PMCID: PMC8844213 DOI: 10.1111/mmi.14858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 02/03/2023]
Abstract
Anti-bacterial autophagy, known as xenophagy, is a host innate immune response that targets invading pathogens for degradation. Some intracellular bacteria, such as the enteric pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), utilize effector proteins to interfere with autophagy. One such S. Typhimurium effector, SopF, inhibits recruitment of ATG16L1 to damaged Salmonella-containing vacuoles (SCVs), thereby inhibiting the host xenophagic response. SopF is also required to maintain the integrity of the SCV during the early stages of infection. Here we show disruption of the SopF-ATG16L1 interaction leads to an increased proportion of cytosolic S. Typhimurium. Furthermore, SopF was utilized as a molecular tool to examine the requirement for ATG16L1 in the intracellular lifestyle of Coxiella burnetii, a bacterium that requires a functional autophagy pathway to replicate efficiently and form a single, spacious vacuole called the Coxiella-containing vacuole (CCV). ATG16L1 is required for CCV expansion and fusion but does not influence C. burnetii replication. In contrast, SopF did not affect CCV formation or replication, demonstrating that the contribution of ATG16L1 to CCV biogenesis is via its role in autophagy, not xenophagy. This study highlights the diverse capabilities of bacterial effector proteins to dissect the molecular details of host-pathogen interactions.
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Affiliation(s)
- Nicole Lau
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - David R Thomas
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Yi Wei Lee
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Leigh A Knodler
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Hayley J Newton
- The Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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214
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Research Progress and Prospects of Autophagy in the Mechanism of Multidrug Resistance in Tumors. JOURNAL OF ONCOLOGY 2022; 2022:7032614. [PMID: 35136409 PMCID: PMC8818414 DOI: 10.1155/2022/7032614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
Although the treatment of cancer has made great strides in clinical practice, its high morbidity and fatality rates remain a major threat to human health. Multidrug resistance (MDR) often appears in the process of tumor treatment, leading to tumor refractory and aggravating the risk of tumor recurrence. Therefore, antitumor MDR plays a key role in tumor chemotherapy. Autophagy is an important process for the turnover of intracellular materials, which is commonly seen in the treatment of sensitive and multidrug-resistant tumors, and it can play different roles in various types of MDR tumor cells and tissues. Autophagy plays a dual regulatory role in MDR tumors. On the one hand, autophagy can promote the formation of MDR in tumor cells, weaken the killing effect of chemotherapy drugs on tumor cells, and play a protective role in tumor survival. On the other hand, autophagy production in the cellular environment can kill MDR tumor cells, reverse tumor resistance and enhance the efficiency of chemotherapy drugs. Therefore, the regulation of autophagy to overcome MDR has become increasingly significant in tumor chemotherapy. In this article, we discussed and summarized the research progress of autophagy in MDR tumors, mainly involving the different characteristics of autophagy in MDR cancer cells.
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215
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Wu W, Luo X, Ren M. Clearance or Hijack: Universal Interplay Mechanisms Between Viruses and Host Autophagy From Plants to Animals. Front Cell Infect Microbiol 2022; 11:786348. [PMID: 35047417 PMCID: PMC8761674 DOI: 10.3389/fcimb.2021.786348] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/10/2021] [Indexed: 12/24/2022] Open
Abstract
Viruses typically hijack the cellular machinery of their hosts for successful infection and replication, while the hosts protect themselves against viral invasion through a variety of defense responses, including autophagy, an evolutionarily ancient catabolic pathway conserved from plants to animals. Double-membrane vesicles called autophagosomes transport trapped viral cargo to lysosomes or vacuoles for degradation. However, during an ongoing evolutionary arms race, viruses have acquired a strong ability to disrupt or even exploit the autophagy machinery of their hosts for successful invasion. In this review, we analyze the universal role of autophagy in antiviral defenses in animals and plants and summarize how viruses evade host immune responses by disrupting and manipulating host autophagy. The review provides novel insights into the role of autophagy in virus–host interactions and offers potential targets for the prevention and control of viral infection in both plants and animals.
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Affiliation(s)
- Wenxian Wu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu Agricultural Science and Technology Center, Chengdu, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou, China.,Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiumei Luo
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu Agricultural Science and Technology Center, Chengdu, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou, China.,Hainan Yazhou Bay Seed Laboratory, Sanya, China.,Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu Agricultural Science and Technology Center, Chengdu, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Science of Zhengzhou University, Zhengzhou, China.,Hainan Yazhou Bay Seed Laboratory, Sanya, China
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216
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Tsapras P, Petridi S, Chan S, Geborys M, Jacomin AC, Sagona AP, Meier P, Nezis IP. Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 axis. Cell Rep 2022; 38:110286. [PMID: 35081354 DOI: 10.1016/j.celrep.2021.110286] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
Selective autophagy is a catabolic route that turns over specific cellular material for degradation by lysosomes, and whose role in the regulation of innate immunity is largely unexplored. Here, we show that the apical kinase of the Drosophila immune deficiency (IMD) pathway Tak1, as well as its co-activator Tab2, are both selective autophagy substrates that interact with the autophagy protein Atg8a. We also present a role for the Atg8a-interacting protein Sh3px1 in the downregulation of the IMD pathway, by facilitating targeting of the Tak1/Tab2 complex to the autophagy platform through its interaction with Tab2. Our findings show the Tak1/Tab2/Sh3px1 interactions with Atg8a mediate the removal of the Tak1/Tab2 signaling complex by selective autophagy. This in turn prevents constitutive activation of the IMD pathway in Drosophila. This study provides mechanistic insight on the regulation of innate immune responses by selective autophagy.
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Affiliation(s)
| | - Stavroula Petridi
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | - Selina Chan
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | - Marta Geborys
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Antonia P Sagona
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Ioannis P Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK.
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217
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Kliche J, Ivarsson Y. Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. Biochem J 2022; 479:1-22. [PMID: 34989786 PMCID: PMC8786283 DOI: 10.1042/bcj20200714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
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218
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NEAT1 Confers Radioresistance to Hepatocellular Carcinoma Cells by Inducing Autophagy through GABARAP. Int J Mol Sci 2022; 23:ijms23020711. [PMID: 35054896 PMCID: PMC8775719 DOI: 10.3390/ijms23020711] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023] Open
Abstract
A long noncoding RNA (lncRNA), nuclear enriched abundant transcript 1 (NEAT1) variant 1 (NEAT1v1), is involved in the maintenance of cancer stem cells (CSCs) in hepatocellular carcinoma (HCC). CSCs are suggested to play important roles in therapeutic resistance. Therefore, we investigated whether NEAT1v1 is involved in the sensitivity to radiation therapy in HCC. Gene knockdown was performed using short hairpin RNAs, and NEAT1v1-overexpressing HCC cell lines were generated by stable transfection with a NEAT1v1-expressing plasmid DNA. Cells were irradiated using an X-ray generator. We found that NEAT1 knockdown enhanced the radiosensitivity of HCC cell lines and concomitantly inhibited autophagy. NEAT1v1 overexpression enhanced autophagy in the irradiated cells and conferred radioresistance. Gamma-aminobutyric acid receptor-associated protein (GABARAP) expression was downregulated by NEAT1 knockdown, whereas it was upregulated in NEAT1v1-overexpressing cells. Moreover, GABARAP was required for NEAT1v1-induced autophagy and radioresistance as its knockdown significantly inhibited autophagy and sensitized the cells to radiation. Since GABARAP is a crucial protein for the autophagosome-lysosome fusion, our results suggest that NEAT1v1 confers radioresistance to HCC by promoting autophagy through GABARAP.
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219
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Acute Myeloid Leukemia-Related Proteins Modified by Ubiquitin and Ubiquitin-like Proteins. Int J Mol Sci 2022; 23:ijms23010514. [PMID: 35008940 PMCID: PMC8745615 DOI: 10.3390/ijms23010514] [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: 10/27/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/17/2022] Open
Abstract
Acute myeloid leukemia (AML), the most common form of an acute leukemia, is a malignant disorder of stem cell precursors of the myeloid lineage. Ubiquitination is one of the post-translational modifications (PTMs), and the ubiquitin-like proteins (Ubls; SUMO, NEDD8, and ISG15) play a critical role in various cellular processes, including autophagy, cell-cycle control, DNA repair, signal transduction, and transcription. Also, the importance of Ubls in AML is increasing, with the growing research defining the effect of Ubls in AML. Numerous studies have actively reported that AML-related mutated proteins are linked to Ub and Ubls. The current review discusses the roles of proteins associated with protein ubiquitination, modifications by Ubls in AML, and substrates that can be applied for therapeutic targets in AML.
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220
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Sun C, Rosenstock TR, Cohen MA, Sarkar S. Autophagy Dysfunction as a Phenotypic Readout in hiPSC-Derived Neuronal Cell Models of Neurodegenerative Diseases. Methods Mol Biol 2022; 2549:103-136. [PMID: 34490597 DOI: 10.1007/7651_2021_420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Autophagy is an evolutionarily conserved catabolic pathway for the degradation of cytoplasmic constituents in eukaryotic cells. It is the primary disposal route for selective removal of undesirable cellular materials like aggregation-prone proteins and damaged organelles for maintaining cellular homeostasis, and for bulk degradation of intracellular macromolecules and recycling the breakdown products for providing energy homeostasis during starvation. These functions of autophagy are attributed to cellular survival and thus pertinent for human health; however, malfunction of this process is detrimental to the cells, particularly for post-mitotic neurons. Thus, basal autophagy is vital for maintaining neuronal homeostasis, whereas autophagy dysfunction contributes to neurodegeneration. Defective autophagy has been demonstrated in several neurodegenerative diseases wherein pharmacological induction of autophagy is beneficial in many of these disease models. Elucidating the mechanisms underlying defective autophagy is imperative for the development of therapies targeting this process. Disease-affected human neuronal cells can be established from patient-derived human induced pluripotent stem cells (hiPSCs) that provide a clinically relevant platform for studying disease mechanisms and drug discovery. Thus, modeling autophagy dysfunction as a phenotypic readout in patient-derived neurons provides a more direct platform for investigating the mechanisms underlying defective autophagy and evaluating the therapeutic efficacy of autophagy inducers. Toward this, several hiPSC-derived neuronal cell models of neurodegenerative diseases have been employed. In this review, we highlight the key methodologies pertaining to hiPSC maintenance and neuronal differentiation, and studying autophagy at an endogenous level in hiPSC-derived neuronal cells.
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Affiliation(s)
- Congxin Sun
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tatiana R Rosenstock
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Pharmacology, University of São Paulo, São Paulo, Brazil
| | - Malkiel A Cohen
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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221
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Choubey V, Zeb A, Kaasik A. Molecular Mechanisms and Regulation of Mammalian Mitophagy. Cells 2021; 11:38. [PMID: 35011599 PMCID: PMC8750762 DOI: 10.3390/cells11010038] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria in the cell are the center for energy production, essential biomolecule synthesis, and cell fate determination. Moreover, the mitochondrial functional versatility enables cells to adapt to the changes in cellular environment and various stresses. In the process of discharging its cellular duties, mitochondria face multiple types of challenges, such as oxidative stress, protein-related challenges (import, folding, and degradation) and mitochondrial DNA damage. They mitigate all these challenges with robust quality control mechanisms which include antioxidant defenses, proteostasis systems (chaperones and proteases) and mitochondrial biogenesis. Failure of these quality control mechanisms leaves mitochondria as terminally damaged, which then have to be promptly cleared from the cells before they become a threat to cell survival. Such damaged mitochondria are degraded by a selective form of autophagy called mitophagy. Rigorous research in the field has identified multiple types of mitophagy processes based on targeting signals on damaged or superfluous mitochondria. In this review, we provide an in-depth overview of mammalian mitophagy and its importance in human health and diseases. We also attempted to highlight the future area of investigation in the field of mitophagy.
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Affiliation(s)
- Vinay Choubey
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411 Tartu, Estonia; (A.Z.); (A.K.)
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222
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Prats-Ejarque G, Lorente H, Villalba C, Anguita R, Lu L, Vázquez-Monteagudo S, Fernández-Millán P, Boix E. Structure-Based Design of an RNase Chimera for Antimicrobial Therapy. Int J Mol Sci 2021; 23:95. [PMID: 35008522 PMCID: PMC8745102 DOI: 10.3390/ijms23010095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Bacterial resistance to antibiotics urges the development of alternative therapies. Based on the structure-function of antimicrobial members of the RNase A superfamily, we have developed a hybrid enzyme. Within this family, RNase 1 exhibits the highest catalytic activity and the lowest cytotoxicity; in contrast, RNase 3 shows the highest bactericidal action, alas with a reduced catalytic activity. Starting from both parental proteins, we designed a first RNase 3/1-v1 chimera. The construct had a catalytic activity much higher than RNase 3, unfortunately without reaching an equivalent antimicrobial activity. Thus, two new versions were created with improved antimicrobial properties. Both of these versions (RNase 3/1-v2 and -v3) incorporated an antimicrobial loop characteristic of RNase 3, while a flexible RNase 1-specific loop was removed in the latest construct. RNase 3/1-v3 acquired both higher antimicrobial and catalytic activities than previous versions, while retaining the structural determinants for interaction with the RNase inhibitor and displaying non-significant cytotoxicity. Following, we tested the constructs' ability to eradicate macrophage intracellular infection and observed an enhanced ability in both RNase 3/1-v2 and v3. Interestingly, the inhibition of intracellular infection correlates with the variants' capacity to induce autophagy. We propose RNase 3/1-v3 chimera as a promising lead for applied therapeutics.
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Affiliation(s)
- Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Helena Lorente
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Clara Villalba
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Raúl Anguita
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625014, China
| | - Sergi Vázquez-Monteagudo
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Pablo Fernández-Millán
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
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223
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Sharma K, Asp NT, Harrison SP, Siller R, Baumgarten SF, Gupta S, Chollet ME, Andersen E, Sullivan GJ, Simonsen A. Autophagy modulates cell fate decisions during lineage commitment. Autophagy 2021; 18:1915-1931. [PMID: 34923909 PMCID: PMC9450964 DOI: 10.1080/15548627.2021.2008691] [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] [Indexed: 12/17/2022] Open
Abstract
Early events during development leading to exit from a pluripotent state and commitment toward a specific germ layer still need in depth understanding. Autophagy has been shown to play a crucial role in both development and differentiation. This study employs human embryonic and induced pluripotent stem cells to understand the early events of lineage commitment with respect to the role of autophagy in this process. Our data indicate that a dip in autophagy facilitates exit from pluripotency. Upon exit, we demonstrate that the modulation of autophagy affects SOX2 levels and lineage commitment, with induction of autophagy promoting SOX2 degradation and mesendoderm formation, whereas inhibition of autophagy causes SOX2 accumulation and neuroectoderm formation. Thus, our results indicate that autophagy-mediated SOX2 turnover is a determining factor for lineage commitment. These findings will deepen our understanding of development and lead to improved methods to derive different lineages and cell types.Abbreviations: ACTB: Actin, beta; ATG: Autophagy-related; BafA1: Bafilomycin A1; CAS9: CRISPR associated protein 9; CQ: Chloroquine; DE: Definitive endoderm; hESCs: Human Embryonic Stem Cells; hiPSCs: Human Induced Pluripotent Stem Cells; LAMP1: Lysosomal Associated Membrane Protein 1; MAP1LC3: Microtubule-Associated Protein 1 Light Chain 3; MTOR: Mechanistic Target Of Rapamycin Kinase; NANOG: Nanog Homeobox; PAX6: Paired Box 6; PE: Phosphatidylethanolamine; POU5F1: POU class 5 Homeobox 1; PRKAA2: Protein Kinase AMP-Activated Catalytic Subunit Alpha 2; SOX2: SRY-box Transcription Factor 2; SQSTM1: Sequestosome 1; ULK1: unc-51 like Autophagy Activating Kinase 1; WDFY3: WD Repeat and FYVE Domain Containing 3.
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Affiliation(s)
- Kulbhushan Sharma
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Stem Cell and Gene Therapy Research, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, India.,Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Nagham T Asp
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sean P Harrison
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Richard Siller
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Saphira F Baumgarten
- Hybrid Technology Hub, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Swapnil Gupta
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Maria E Chollet
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Elisabeth Andersen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,Department of Haematology, Oslo University Hospital, Oslo, Norway
| | - Gareth J Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Department of Pediatric Research, Oslo University Hospital, Oslo, Norway.,Hybrid Technology Hub, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Norwegian Center for Stem Cell Research, Oslo University Hospital and University of Oslo, Oslo, Norway.,Institute of Immunology, Oslo University Hospital, Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital Montebello, Oslo, Norway
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224
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Investigation of the role of the autophagic protein LC3B in the regulation of human airway epithelium cell differentiation in COPD using a biomimetic model. Mater Today Bio 2021; 13:100182. [PMID: 34917923 PMCID: PMC8668979 DOI: 10.1016/j.mtbio.2021.100182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 12/04/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the most lethal chronic disease worldwide; however, the establishment of reliable in vitro models for exploring the biological mechanisms of COPD remains challenging. Here, we determined the differences in the expression and characteristics of the autophagic protein LC3B in normal and COPD human small airway epithelial cells and found that the nucleus of COPD cells obviously accumulated LC3B. We next established 3D human small airway tissues with distinct disease characteristics by regulating the biological microenvironment, extracellular matrix, and air-liquid interface culture methods. Using this biomimetic model, we found that LC3B affects the differentiation of COPD cells into basal, secretory, mucous, and ciliated cells. Moreover, although chloroquine and ivermectin effectively inhibited the expression of LC3B in the nucleus, chloroquine specifically maintained the performance of LC3B in cytoplasm, thereby contributing to the differentiation of ciliated cells and subsequent improvement in the beating functions of the cilia, whereas ivermectin only facilitated differentiation of goblet cells. We demonstrated that the autophagic mechanism of LC3B in the nucleus is one factor regulating the ciliary differentiation and function of COPD cells. Our innovative model can be used to further analyze the physiological mechanisms in the in vitro airway environment.
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225
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Schreiber A, Collins BC, Davis C, Enchev RI, Sedra A, D'Antuono R, Aebersold R, Peter M. Multilayered regulation of autophagy by the Atg1 kinase orchestrates spatial and temporal control of autophagosome formation. Mol Cell 2021; 81:5066-5081.e10. [PMID: 34798055 PMCID: PMC8693860 DOI: 10.1016/j.molcel.2021.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/23/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022]
Abstract
Autophagy is a conserved intracellular degradation pathway exerting various cytoprotective and homeostatic functions by using de novo double-membrane vesicle (autophagosome) formation to target a wide range of cytoplasmic material for vacuolar/lysosomal degradation. The Atg1 kinase is one of its key regulators, coordinating a complex signaling program to orchestrate autophagosome formation. Combining in vitro reconstitution and cell-based approaches, we demonstrate that Atg1 is activated by lipidated Atg8 (Atg8-PE), stimulating substrate phosphorylation along the growing autophagosomal membrane. Atg1-dependent phosphorylation of Atg13 triggers Atg1 complex dissociation, enabling rapid turnover of Atg1 complex subunits at the pre-autophagosomal structure (PAS). Moreover, Atg1 recruitment by Atg8-PE self-regulates Atg8-PE levels in the growing autophagosomal membrane by phosphorylating and thus inhibiting the Atg8-specific E2 and E3. Our work uncovers the molecular basis for positive and negative feedback imposed by Atg1 and how opposing phosphorylation and dephosphorylation events underlie the spatiotemporal regulation of autophagy.
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Affiliation(s)
- Anne Schreiber
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
| | - Ben C Collins
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; School of Biological Sciences, Queen's University of Belfast, 19 Chlorine Gardens, BT9 5DL Belfast, UK
| | - Colin Davis
- Cellular Degradation Systems Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Radoslav I Enchev
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Angie Sedra
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy (CALM) STP, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
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226
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Ion Channels and Pumps in Autophagy: A Reciprocal Relationship. Cells 2021; 10:cells10123537. [PMID: 34944044 PMCID: PMC8700256 DOI: 10.3390/cells10123537] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
Autophagy, the process of cellular self-degradation, is intrinsically tied to the degradative function of the lysosome. Several diseases have been linked to lysosomal degradative defects, including rare lysosomal storage disorders and neurodegenerative diseases. Ion channels and pumps play a major regulatory role in autophagy. Importantly, calcium signaling produced by TRPML1 (transient receptor potential cation channel, mucolipin subfamily) has been shown to regulate autophagic progression through biogenesis of autophagic-lysosomal organelles, activation of mTORC1 (mechanistic target of rapamycin complex 1) and degradation of autophagic cargo. ER calcium channels such as IP3Rs supply calcium for the lysosome, and lysosomal function is severely disrupted in the absence of lysosomal calcium replenishment by the ER. TRPML1 function is also regulated by LC3 (microtubule-associated protein light chain 3) and mTORC1, two critical components of the autophagic network. Here we provide an overview of the current knowledge about ion channels and pumps-including lysosomal V-ATPase (vacuolar proton-ATPase), which is required for acidification and hence proper enzymatic activity of lysosomal hydrolases-in the regulation of autophagy, and discuss how functional impairment of some of these leads to diseases.
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227
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Collier JJ, Suomi F, Oláhová M, McWilliams TG, Taylor RW. Emerging roles of ATG7 in human health and disease. EMBO Mol Med 2021; 13:e14824. [PMID: 34725936 PMCID: PMC8649875 DOI: 10.15252/emmm.202114824] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/08/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
The cardinal stages of macroautophagy are driven by core autophagy-related (ATG) proteins, whose ablation largely abolishes intracellular turnover. Disrupting ATG genes is paradigmatic of studying autophagy deficiency, yet emerging data suggest that ATG proteins have extensive biological importance beyond autophagic elimination. An important example is ATG7, an essential autophagy effector enzyme that in concert with other ATG proteins, also regulates immunity, cell death and protein secretion, and independently regulates the cell cycle and apoptosis. Recently, a direct association between ATG7 dysfunction and disease was established in patients with biallelic ATG7 variants and childhood-onset neuropathology. Moreover, a prodigious body of evidence supports a role for ATG7 in protecting against complex disease states in model organisms, although how dysfunctional ATG7 contributes to manifestation of these diseases, including cancer, neurodegeneration and infection, in humans remains unclear. Here, we systematically review the biological functions of ATG7, discussing the impact of its impairment on signalling pathways and human pathology. Future studies illuminating the molecular relationship between ATG7 dysfunction and disease will expedite therapies for disorders involving ATG7 deficiency and/or impaired autophagy.
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Affiliation(s)
- Jack J Collier
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK
- Present address:
Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill UniversityMontrealQCCanada
| | - Fumi Suomi
- Translational Stem Cell Biology & Metabolism Program, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Thomas G McWilliams
- Translational Stem Cell Biology & Metabolism Program, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
- Department of AnatomyFaculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders of Adults and ChildrenNewcastle UniversityNewcastle upon TyneUK
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228
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Ke PY. Autophagy and antiviral defense. IUBMB Life 2021; 74:317-338. [PMID: 34859938 DOI: 10.1002/iub.2582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Targeting intracellular components for lysosomal degradation by autophagy not only maintains cellular homeostasis but also counteracts the effects of external stimuli, including invading pathogens. Among various kinds of pathogens, viruses have been extensively shown to induce autophagy to benefit viral growth in infected cells and to modulate host defense responses, such as innate antiviral immunity. Recently, numerous lines of evidence have implied that virus-induced autophagy triggers multilayer mechanisms to regulate the innate antiviral response of host cells, thus promoting a balance in virus-host cell interactions. In this review, the detailed mechanisms underlying autophagy and the innate antiviral immune response are first described. Then, I summarize the current information regarding the diverse functional role(s) of autophagy in the control of antiviral defenses against different types of viral infections. Moreover, the physiological significance of autophagy-regulated antiviral responses on the viral life cycle and the potential autophagy alterations induced by virus-associated antiviral signaling is further discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC
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229
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Zhao J, Li Z, Li J. The crystal structure of the FAM134B-GABARAP complex provides mechanistic insights into the selective binding of FAM134 to the GABARAP subfamily. FEBS Open Bio 2021; 12:320-331. [PMID: 34854256 PMCID: PMC8727931 DOI: 10.1002/2211-5463.13340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/07/2021] [Accepted: 11/30/2021] [Indexed: 01/18/2023] Open
Abstract
The mammalian Atg8 family (Atg8s proteins) consists of two subfamilies: GABARAP and LC3. All members can bind to the LC3‐interacting region (LIR) or Atg8‐interacting motif and participate in multiple steps of autophagy. The endoplasmic reticulum (ER) autophagy receptor FAM134B contains an LIR motif that can bind to Atg8s, but whether it can differentially bind to the two subfamilies and, if so, the structural basis for this preference remains unknown. Here, we found that FAM134B bound to the GABARAP subfamily more strongly than to the LC3 subfamily. We then solved the crystal structure of the FAM134B–GABARAP complex and demonstrated that FAM134B used both its LIR core and the C‐terminal helix to bind to GABARAP. We further showed that these properties might be conserved in FAM134A or FAM134C. The structure also allowed us to identify the structural determinants for the binding selectivity. Our work may be valuable for studying the differential functions of GABARAP and LC3 subfamilies in ER phagy in future.
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Affiliation(s)
- Junfeng Zhao
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Zhiwei Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jianchao Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China.,Department of Otorhinolaryngology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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230
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Abstract
Selective degradation of protein aggregates by macroautophagy/autophagy is an essential homeostatic process of safeguarding cells from the effects of proteotoxicity. Among the ubiquitin-like proteins, NEDD8 conjugation to misfolded proteins is prominent in stress-induced protein aggregates, albeit the function of neddylation in autophagy is unclear. Here, we report that polyneddylation functions as a post-translational modification for autophagic degradation of proteotoxic-stress induced protein aggregates. We also show that HYPK functions as an autophagy receptor in the polyneddylation-dependent aggrephagy. The scaffolding function of HYPK is facilitated by its C-terminal ubiquitin-associated domain and N-terminal tyrosine-type LC3-interacting region which bind to NEDD8 and LC3 respectively. Both NEDD8 and HYPK are positive modulators of basal and proteotoxicity-induced autophagy, leading to protection of cells from protein aggregates, such as aggregates of mutant HTT exon 1. Thus, we propose an indispensable and additive role of neddylation and HYPK in clearance of protein aggregates by autophagy, resulting in cytoprotective effect during proteotoxic stress.Abbreviations: ATG5, autophagy related 5; ATG12, autophagy related 12; ATG14, autophagy related 14; BECN1, beclin 1; CBL, casitas B-lineage lymphoma; CBLB, Cbl proto-oncogene B; GABARAP, GABA type A receptor-associated protein; GABARAPL1, GABA type A receptor associated protein like 1; GABARAPL2, GABA type A receptor associated protein like 2; GFP, green fluorescent protein; HTT, huntingtin; HTT97Q exon 1, huntingtin 97-glutamine exon 1; HUWE1, HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1; HYPK, huntingtin interacting protein K; IgG, immunoglobulin G; IMR-32, Institute for Medical Research-32; KD, knockdown; Kd, dissociation constant; LAMP1, lysosomal associated membrane protein 1; LIR, LC3 interacting region; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MAP1LC3A/LC3A, microtubule associated protein 1 light chain 3 alpha; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; MARK1, microtubule affinity regulating kinase 1; MARK2, microtubule affinity regulating kinase 2; MARK3, microtubule affinity regulating kinase 3; MARK4, microtubule affinity regulating kinase 4; MCF7, Michigan Cancer Foundation-7; MTOR, mechanistic target of rapamycin kinase; NAE1, NEDD8 activating enzyme E1 subunit 1; NBR1, NBR1 autophagy cargo receptor; NEDD8, NEDD8 ubiquitin like modifier; Ni-NTA, nickel-nitrilotriacetic acid; NUB1, negative regulator of ubiquitin like proteins 1; PIK3C3, phosphatidylinositol 3-kinase catalytic subunit type 3; PolyQ, poly-glutamine; PSMD8, proteasome 26S subunit, non-ATPase 8; RAD23A, RAD23 homolog A, nucleotide excision repair protein; RAD23B, RAD23 homolog B, nucleotide excision repair protein; RFP, red fluorescent protein; RPS27A, ribosomal protein S27a; RSC1A1, regulator of solute carriers 1; SNCA, synuclein alpha; SIK1, salt inducible kinase 1; siRNA, small interfering ribonucleic acid; SOD1, superoxide dismutase 1; SPR, surface plasmon resonance; SQSTM1, sequestosome 1; SUMO1, small ubiquitin like modifier 1; TAX1BP1, Tax1 binding protein 1; TDRD3, tudor domain containing 3; TNRC6C, trinucleotide repeat containing adaptor 6C; TOLLIP, toll interacting protein; TUBA, tubulin alpha; TUBB, tubulin beta class I; UBA, ubiquitin-associated; UBA1, ubiquitin like modifier activating enzyme 1; UBA5, ubiquitin like modifier activating enzyme 5; UBAC1, UBA domain containing 1; UBAC2, UBA domain containing 2; UBAP1, ubiquitin associated protein 1; UBAP2, ubiquitin associated protein 2; UBASH3B, ubiquitin associated and SH3 domain containing B; UBD/FAT10, ubiquitin D; UBE2K, ubiquitin conjugating enzyme E2 K; UBLs, ubiquitin-like proteins; UBL7, ubiquitin like 7; UBQLN1, ubiquilin 1; UBQLN2, ubiquilin 2; UBQLN3, ubiquilin 3; UBQLN4, ubiquilin 4; UBXN1, UBX domain protein 1; ULK1, unc-51 like autophagy activating kinase 1; URM1, ubiquitin related modifier 1; USP5, ubiquitin specific peptidase 5; USP13, ubiquitin specific peptidase 13; VPS13D, vacuolar protein sorting 13 homolog D.
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Affiliation(s)
- Debasish Kumar Ghosh
- Computational and Functional Genomics Group Centre for Dna Fingerprinting and Diagnostics Uppal Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Akash Ranjan
- Computational and Functional Genomics Group Centre for Dna Fingerprinting and Diagnostics Uppal Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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231
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Yim WWY, Kurikawa Y, Mizushima N. An exploratory text analysis of the autophagy research field. Autophagy 2021; 18:1648-1661. [PMID: 34812110 PMCID: PMC9298454 DOI: 10.1080/15548627.2021.1995151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
After its discovery in the 1950 s, the autophagy research field has seen its annual number of publications climb from tens to thousands. The ever-growing number of autophagy publications is a wealth of information but presents a challenge to researchers, especially those new to the field, who are looking for a general overview of the field to, for example, determine current topics of the field or formulate new hypotheses. Here, we employed text mining tools to extract research trends in the autophagy field, including those of genes, terms, and topics. The publication trend of the field can be separated into three phases. The exponential rise in publication number began in the last phase and is most likely spurred by a series of highly cited research papers published in previous phases. The exponential increase in papers has resulted in a larger variety of research topics, with the majority involving those that are directly physiologically relevant, such as disease and modulating autophagy. Our findings provide researchers a summary of the history of the autophagy research field and perhaps hints of what is to come.Abbreviations: 5Y-IF: 5-year impact factor; AIS: article influence score; EM: electron microscopy; HGNC: HUGO gene nomenclature committee; LDA: latent Dirichlet allocation; MeSH: medical subject headings; ncRNA: non-coding RNA.
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Affiliation(s)
- Willa Wen-You Yim
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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232
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Mailler E, Guardia CM, Bai X, Jarnik M, Williamson CD, Li Y, Maio N, Golden A, Bonifacino JS. The autophagy protein ATG9A enables lipid mobilization from lipid droplets. Nat Commun 2021; 12:6750. [PMID: 34799570 PMCID: PMC8605025 DOI: 10.1038/s41467-021-26999-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/26/2021] [Indexed: 01/18/2023] Open
Abstract
The multispanning membrane protein ATG9A is a scramblase that flips phospholipids between the two membrane leaflets, thus contributing to the expansion of the phagophore membrane in the early stages of autophagy. Herein, we show that depletion of ATG9A does not only inhibit autophagy but also increases the size and/or number of lipid droplets in human cell lines and C. elegans. Moreover, ATG9A depletion blocks transfer of fatty acids from lipid droplets to mitochondria and, consequently, utilization of fatty acids in mitochondrial respiration. ATG9A localizes to vesicular-tubular clusters (VTCs) that are tightly associated with an ER subdomain enriched in another multispanning membrane scramblase, TMEM41B, and also in close proximity to phagophores, lipid droplets and mitochondria. These findings indicate that ATG9A plays a critical role in lipid mobilization from lipid droplets to autophagosomes and mitochondria, highlighting the importance of ATG9A in both autophagic and non-autophagic processes.
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Affiliation(s)
- Elodie Mailler
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Carlos M Guardia
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Xiaofei Bai
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michal Jarnik
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nunziata Maio
- Metals Biology and Molecular Medicine Group, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 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, MD, USA.
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233
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Non-canonical roles of autophagy proteins in endocytosis and exocytosis. Biochem Soc Trans 2021; 49:2841-2851. [PMID: 34783341 DOI: 10.1042/bst20210811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 01/18/2023]
Abstract
Autophagy, the pathways that degrade cytoplasmic constituents in lysosomes, contribute to most biological processes from aging and neurodegeneration to pathogen restriction and immunity. In recent years, it was realized that the autophagy machinery serves additional functions, primarily in endo- and exocytosis. In this review, I summarize recent advances in our understanding on how these non-canonical functions differ from canonical macroautophagy, and contribute to immune activation and viral replication. Understanding these pathways will allow us to harness them for the treatment of human diseases, as well as appreciate how cells use modules of membrane remodeling and trafficking for multiple biological functions.
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234
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Direct Interaction of ATP7B and LC3B Proteins Suggests a Cooperative Role of Copper Transportation and Autophagy. Cells 2021; 10:cells10113118. [PMID: 34831341 PMCID: PMC8625360 DOI: 10.3390/cells10113118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
Macroautophagy/autophagy plays an important role in cellular copper clearance. The means by which the copper metabolism and autophagy pathways interact mechanistically is vastly unexplored. Dysfunctional ATP7B, a copper-transporting ATPase, is involved in the development of monogenic Wilson disease, a disorder characterized by disturbed copper transport. Using in silico prediction, we found that ATP7B contains a number of potential binding sites for LC3, a central protein in the autophagy pathway, the so-called LC3 interaction regions (LIRs). The conserved LIR3, located at the C-terminal end of ATP7B, was found to directly interact with LC3B in vitro. Replacing the two conserved hydrophobic residues W1452 and L1455 of LIR3 significantly reduced interaction. Furthermore, autophagy was induced in normal human hepatocellular carcinoma cells (HepG2) leading to enhanced colocalization of ATP7B and LC3B on the autophagosome membranes. By contrast, HepG2 cells deficient of ATP7B (HepG2 ATP7B-/-) showed autophagy deficiency at elevated copper condition. This phenotype was complemented by heterologous ATP7B expression. These findings suggest a cooperative role of ATP7B and LC3B in autophagy-mediated copper clearance.
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235
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Primary cilium-dependent autophagy in the response to shear stress. Biochem Soc Trans 2021; 49:2831-2839. [PMID: 34747995 DOI: 10.1042/bst20210810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022]
Abstract
Mechanical forces, such as compression, shear stress and stretching, play major roles during development, tissue homeostasis and immune processes. These forces are translated into a wide panel of biological responses, ranging from changes in cell morphology, membrane transport, metabolism, energy production and gene expression. Recent studies demonstrate the role of autophagy in the integration of these physical constraints. Here we focus on the role of autophagy in the integration of shear stress induced by blood and urine flows in the circulatory system and the kidney, respectively. Many studies highlight the involvement of the primary cilium, a microtubule-based antenna present at the surface of many cell types, in the integration of extracellular stimuli. The cross-talk between the molecular machinery of autophagy and that of the primary cilium in the context of shear stress is revealed to be an important dialog in cell biology.
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236
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Hanley SE, Willis SD, Cooper KF. Snx4-assisted vacuolar targeting of transcription factors defines a new autophagy pathway for controlling ATG expression. Autophagy 2021; 17:3547-3565. [PMID: 33678121 PMCID: PMC8632336 DOI: 10.1080/15548627.2021.1877934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
Autophagy, in part, is controlled by the repression and activation of autophagy-related (ATG) genes. Here, we describe a new selective autophagy pathway that targets functional transcriptional regulators to control their activity. This pathway is activated in response to nitrogen starvation and recycles transcriptional activators (Msn2 and Rim15) and a repressor (Ssn2/Med13) of ATG expression. Further analysis of Ssn2/Med13 vacuolar proteolysis revealed that this pathway utilizes the core autophagic machinery. However, it is independent of known nucleophagy mechanisms, receptor proteins, and the scaffold protein Atg11. Instead, Ssn2/Med13 exits the nucleus through the nuclear pore complex (NPC) and associates with the cytoplasmic nucleoporin Gle1, a member of the RNA remodeling complex. Dbp5 and Nup159, that act in concert with Gle1, are also required for Ssn2/Med13 clearance. Ssn2/Med13 is retrieved from the nuclear periphery and degraded by Atg17-initiated phagophores anchored to the vacuole. Efficient transfer to phagophores depends on the sorting nexin heterodimer Snx4/Atg24-Atg20, which binds to Atg17, and relocates to the perinucleus following nitrogen starvation. To conclude, this pathway defines a previously undescribed autophagy mechanism that targets select transcriptional regulators for rapid vacuolar proteolysis, utilizing the RNA remodeling complex, the sorting nexin heterodimer Snx4-Atg20, Atg17, and the core autophagic machinery. It is physiologically relevant as this Snx4-assisted vacuolar targeting pathway permits cells to fine-tune the autophagic response by controlling the turnover of both positive and negative regulators of ATG transcription.Abbreviations: AIM: Atg8 interacting motif; ATG: autophagy-related; CKM: CDK8 kinase module; IDR: intrinsically disordered region; IP6: phosphoinositide inositol hexaphosphate; NPC: nuclear pore complex; PAS: phagophore assembly site; UPS: ubiquitin-proteasomal system.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
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237
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Li J, Chen X, Kang R, Zeh H, Klionsky DJ, Tang D. Regulation and function of autophagy in pancreatic cancer. Autophagy 2021; 17:3275-3296. [PMID: 33161807 PMCID: PMC8632104 DOI: 10.1080/15548627.2020.1847462] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
Oncogenic KRAS mutation-driven pancreatic ductal adenocarcinoma is currently the fourth-leading cause of cancer-related deaths in the United States. Macroautophagy (hereafter "autophagy") is one of the lysosome-dependent degradation systems that can remove abnormal proteins, damaged organelles, or invading pathogens by activating dynamic membrane structures (e.g., phagophores, autophagosomes, and autolysosomes). Impaired autophagy (including excessive activation and defects) is a pathological feature of human diseases, including pancreatic cancer. However, dysfunctional autophagy has many types and plays a complex role in pancreatic tumor biology, depending on various factors, such as tumor stage, microenvironment, immunometabolic state, and death signals. As a modulator connecting various cellular events, pharmacological targeting of nonselective autophagy may lead to both good and bad therapeutic effects. In contrast, targeting selective autophagy could reduce potential side effects of the drugs used. In this review, we describe the advances and challenges of autophagy in the development and therapy of pancreatic cancer.Abbreviations: AMPK: AMP-activated protein kinase; CQ: chloroquine; csc: cancer stem cells; DAMP: danger/damage-associated molecular pattern; EMT: epithelial-mesenchymal transition; lncRNA: long noncoding RNA; MIR: microRNA; PanIN: pancreatic intraepithelial neoplasia; PDAC: pancreatic ductal adenocarcinoma; PtdIns3K: phosphatidylinositol 3-kinase; SNARE: soluble NSF attachment protein receptor; UPS: ubiquitin-proteasome system.
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Affiliation(s)
- Jingbo Li
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Xin Chen
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Herbert Zeh
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
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238
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Tóth D, Horváth GV, Juhász G. The interplay between pathogens and Atg8 family proteins: thousand-faced interactions. FEBS Open Bio 2021; 11:3237-3252. [PMID: 34670023 PMCID: PMC8634866 DOI: 10.1002/2211-5463.13318] [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: 06/29/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 01/18/2023] Open
Abstract
Autophagy is an intracellular degradation and recycling process that can also remove pathogenic intracellular bacteria and viruses from within cells (referred to as xenophagy) and activate the adaptive immune responses. But autophagy-especially Atg proteins including Atg8 family members-can also have proviral and probacterial effects. In this review, we summarize known interactions of bacterial, parasitic, and viral proteins with Atg8 family proteins and the outcome of these interactions on pathogen replication, autophagy, or mitophagy. We discuss the value of prediction software and the research methodology in the study of pathogen protein-Atg8 family protein interactions, with selected examples of potential LC3-interacting region motif-containing SARS-CoV-2 proteins.
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Affiliation(s)
- Dávid Tóth
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Gábor V Horváth
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Gábor Juhász
- Institute of Genetics, Biological Research Centre, Szeged, Hungary.,Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
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239
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The Cytotoxicity and Clearance of Mutant Huntingtin and Other Misfolded Proteins. Cells 2021; 10:cells10112835. [PMID: 34831058 PMCID: PMC8616338 DOI: 10.3390/cells10112835] [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: 09/29/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023] Open
Abstract
Protein misfolding and aggregation are implicated in many neurodegenerative diseases. One of these diseases is Huntington's, which is caused by increased glutamine-encoding trinucleotide repeats within the Huntingtin gene. Like other misfolded proteins, mutated Huntingtin proteins with polyglutamine expansions are prone to aggregation. Misfolded proteins exist as soluble monomers, small aggregates, or as large insoluble inclusion bodies. Misfolded protein aggregates are believed to be cytotoxic by stressing the protein degradation machinery, disrupting membrane structure, or sequestering other proteins. We recently showed that expression of misfolded proteins lowers cellular free ubiquitin levels, which compromises the protein degradation machinery. Therefore, the efficient degradation of misfolded proteins is critical to preserve cell health. Cells employ two major mechanisms to degrade misfolded proteins. The first is the ubiquitin-proteasome system (UPS), which ubiquitinates and degrades misfolded proteins with the assistance of segregase Cdc48/p97. The UPS pathway is mainly responsible for the clearance of misfolded proteins present as monomers or smaller aggregates. The second pathway is macroautophagy/autophagy, in which protein aggregates or inclusion bodies are recruited into an autophagosome before transport to the vacuole/lysosome for degradation. This review is focused on the current understanding of the cytotoxicity of misfolded proteins as well as their clearance pathways, with a particular emphasis on mutant Huntingtin.
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Demasi M, Augusto O, Bechara EJH, Bicev RN, Cerqueira FM, da Cunha FM, Denicola A, Gomes F, Miyamoto S, Netto LES, Randall LM, Stevani CV, Thomson L. Oxidative Modification of Proteins: From Damage to Catalysis, Signaling, and Beyond. Antioxid Redox Signal 2021; 35:1016-1080. [PMID: 33726509 DOI: 10.1089/ars.2020.8176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: The systematic investigation of oxidative modification of proteins by reactive oxygen species started in 1980. Later, it was shown that reactive nitrogen species could also modify proteins. Some protein oxidative modifications promote loss of protein function, cleavage or aggregation, and some result in proteo-toxicity and cellular homeostasis disruption. Recent Advances: Previously, protein oxidation was associated exclusively to damage. However, not all oxidative modifications are necessarily associated with damage, as with Met and Cys protein residue oxidation. In these cases, redox state changes can alter protein structure, catalytic function, and signaling processes in response to metabolic and/or environmental alterations. This review aims to integrate the present knowledge on redox modifications of proteins with their fate and role in redox signaling and human pathological conditions. Critical Issues: It is hypothesized that protein oxidation participates in the development and progression of many pathological conditions. However, no quantitative data have been correlated with specific oxidized proteins or the progression or severity of pathological conditions. Hence, the comprehension of the mechanisms underlying these modifications, their importance in human pathologies, and the fate of the modified proteins is of clinical relevance. Future Directions: We discuss new tools to cope with protein oxidation and suggest new approaches for integrating knowledge about protein oxidation and redox processes with human pathophysiological conditions. Antioxid. Redox Signal. 35, 1016-1080.
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Affiliation(s)
- Marilene Demasi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brazil
| | - Ohara Augusto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Etelvino J H Bechara
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Renata N Bicev
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda M Cerqueira
- CENTD, Centre of Excellence in New Target Discovery, Instituto Butantan, São Paulo, Brazil
| | - Fernanda M da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Denicola
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Fernando Gomes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Sayuri Miyamoto
- Departamento de Bioquímica and Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Luis E S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Lía M Randall
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
| | - Cassius V Stevani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Leonor Thomson
- Laboratorios Fisicoquímica Biológica-Enzimología, Facultad de Ciencias, Instituto de Química Biológica, Universidad de la República, Montevideo, Uruguay
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241
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Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Schultz SW, Aman Y, Lystad AH, Singh S, Singh S, Wesche J, Fang EF, Simonsen A. GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nat Commun 2021; 12:6101. [PMID: 34671015 DOI: 10.1101/2020.11.05.369496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/29/2021] [Indexed: 05/28/2023] Open
Abstract
The mechanisms involved in programmed or damage-induced removal of mitochondria by mitophagy remains elusive. Here, we have screened for regulators of PRKN-independent mitophagy using an siRNA library targeting 197 proteins containing lipid interacting domains. We identify Cyclin G-associated kinase (GAK) and Protein Kinase C Delta (PRKCD) as regulators of PRKN-independent mitophagy, with both being dispensable for PRKN-dependent mitophagy and starvation-induced autophagy. We demonstrate that the kinase activity of both GAK and PRKCD are required for efficient mitophagy in vitro, that PRKCD is present on mitochondria, and that PRKCD facilitates recruitment of ULK1/ATG13 to early autophagic structures. Importantly, we demonstrate in vivo relevance for both kinases in the regulation of basal mitophagy. Knockdown of GAK homologue (gakh-1) in C. elegans or knockout of PRKCD homologues in zebrafish led to significant inhibition of basal mitophagy, highlighting the evolutionary relevance of these kinases in mitophagy regulation.
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Affiliation(s)
- Michael J Munson
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Benan J Mathai
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Matthew Yoke Wui Ng
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura Trachsel-Moncho
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura R de la Ballina
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sebastian W Schultz
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Yahyah Aman
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Alf H Lystad
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sakshi Singh
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sachin Singh
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Jørgen Wesche
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Anne Simonsen
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway.
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242
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Mitochondria as a Cellular Hub in Infection and Inflammation. Int J Mol Sci 2021; 22:ijms222111338. [PMID: 34768767 PMCID: PMC8583510 DOI: 10.3390/ijms222111338] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are the energy center of the cell. They are found in the cell cytoplasm as dynamic networks where they adapt energy production based on the cell’s needs. They are also at the center of the proinflammatory response and have essential roles in the response against pathogenic infections. Mitochondria are a major site for production of Reactive Oxygen Species (ROS; or free radicals), which are essential to fight infection. However, excessive and uncontrolled production can become deleterious to the cell, leading to mitochondrial and tissue damage. Pathogens exploit the role of mitochondria during infection by affecting the oxidative phosphorylation mechanism (OXPHOS), mitochondrial network and disrupting the communication between the nucleus and the mitochondria. The role of mitochondria in these biological processes makes these organelle good targets for the development of therapeutic strategies. In this review, we presented a summary of the endosymbiotic origin of mitochondria and their involvement in the pathogen response, as well as the potential promising mitochondrial targets for the fight against infectious diseases and chronic inflammatory diseases.
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243
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Munson MJ, Mathai BJ, Ng MYW, Trachsel-Moncho L, de la Ballina LR, Schultz SW, Aman Y, Lystad AH, Singh S, Singh S, Wesche J, Fang EF, Simonsen A. GAK and PRKCD are positive regulators of PRKN-independent mitophagy. Nat Commun 2021; 12:6101. [PMID: 34671015 PMCID: PMC8528926 DOI: 10.1038/s41467-021-26331-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 09/29/2021] [Indexed: 12/26/2022] Open
Abstract
The mechanisms involved in programmed or damage-induced removal of mitochondria by mitophagy remains elusive. Here, we have screened for regulators of PRKN-independent mitophagy using an siRNA library targeting 197 proteins containing lipid interacting domains. We identify Cyclin G-associated kinase (GAK) and Protein Kinase C Delta (PRKCD) as regulators of PRKN-independent mitophagy, with both being dispensable for PRKN-dependent mitophagy and starvation-induced autophagy. We demonstrate that the kinase activity of both GAK and PRKCD are required for efficient mitophagy in vitro, that PRKCD is present on mitochondria, and that PRKCD facilitates recruitment of ULK1/ATG13 to early autophagic structures. Importantly, we demonstrate in vivo relevance for both kinases in the regulation of basal mitophagy. Knockdown of GAK homologue (gakh-1) in C. elegans or knockout of PRKCD homologues in zebrafish led to significant inhibition of basal mitophagy, highlighting the evolutionary relevance of these kinases in mitophagy regulation.
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Affiliation(s)
- Michael J Munson
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Benan J Mathai
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Matthew Yoke Wui Ng
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura Trachsel-Moncho
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Laura R de la Ballina
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sebastian W Schultz
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Yahyah Aman
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Alf H Lystad
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sakshi Singh
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
| | - Sachin Singh
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Jørgen Wesche
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway
- Department of Tumor Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Anne Simonsen
- Division of Biochemistry, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, N-0372, Oslo, Norway.
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0316, Oslo, Norway.
- Department of Molecular Cell Biology, The Norwegian Radium Hospital Montebello, N-0379, Oslo, Norway.
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244
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Villarejo-Zori B, Jiménez-Loygorri JI, Zapata-Muñoz J, Bell K, Boya P. New insights into the role of autophagy in retinal and eye diseases. Mol Aspects Med 2021; 82:101038. [PMID: 34620506 DOI: 10.1016/j.mam.2021.101038] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/12/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
Autophagy is a fundamental homeostatic pathway that mediates the degradation and recycling of intracellular components. It serves as a key quality control mechanism, especially in non-dividing cells such as neurons. Proteins, lipids, and even whole organelles are engulfed in autophagosomes and delivered to the lysosome for elimination. The retina is a light-sensitive tissue located in the back of the eye that detects and processes visual images. Vision is a highly demanding process, making the eye one of the most metabolically active tissues in the body and photoreceptors display glycolytic metabolism, even in the presence of oxygen. The retina and eye are also exposed to other stressors that can impair their function, including genetic mutations and age-associated changes. Autophagy, among other pathways, is therefore a key process for the preservation of retinal homeostasis. Here, we review the roles of both canonical and non-canonical autophagy in normal retinal function. We discuss the most recent studies investigating the participation of autophagy in eye diseases such as age-related macular degeneration, glaucoma, and diabetic retinopathy and its role protecting photoreceptors in several forms of retinal degeneration. Finally, we consider the therapeutic potential of strategies that target autophagy pathways to treat prevalent retinal and eye diseases.
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Affiliation(s)
- Beatriz Villarejo-Zori
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Ramiro de Maetzu, 9, 28040, Madrid, Spain
| | - Juan Ignacio Jiménez-Loygorri
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Ramiro de Maetzu, 9, 28040, Madrid, Spain
| | - Juan Zapata-Muñoz
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Ramiro de Maetzu, 9, 28040, Madrid, Spain
| | - Katharina Bell
- Singapore Eye Research Institute, Singapore National Eye Centre, Republic of Singapore
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Margarita Salas Center for Biological Research, CSIC, Ramiro de Maetzu, 9, 28040, Madrid, Spain.
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245
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Goodwin JM, Walkup WG, Hooper K, Li T, Kishi-Itakura C, Ng A, Lehmberg T, Jha A, Kommineni S, Fletcher K, Garcia-Fortanet J, Fan Y, Tang Q, Wei M, Agrawal A, Budhe SR, Rouduri SR, Baird D, Saunders J, Kiselar J, Chance MR, Ballabio A, Appleton BA, Brumell JH, Florey O, Murphy LO. GABARAP sequesters the FLCN-FNIP tumor suppressor complex to couple autophagy with lysosomal biogenesis. SCIENCE ADVANCES 2021; 7:eabj2485. [PMID: 34597140 PMCID: PMC10938568 DOI: 10.1126/sciadv.abj2485] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/11/2021] [Indexed: 05/28/2023]
Abstract
Adaptive changes in lysosomal capacity are driven by the transcription factors TFEB and TFE3 in response to increased autophagic flux and endolysosomal stress, yet the molecular details of their activation are unclear. LC3 and GABARAP members of the ATG8 protein family are required for selective autophagy and sensing perturbation within the endolysosomal system. Here, we show that during the conjugation of ATG8 to single membranes (CASM), Parkin-dependent mitophagy, and Salmonella-induced xenophagy, the membrane conjugation of GABARAP, but not LC3, is required for activation of TFEB/TFE3 to control lysosomal capacity. GABARAP directly binds to a previously unidentified LC3-interacting motif (LIR) in the FLCN/FNIP tumor suppressor complex and mediates sequestration to GABARAP-conjugated membrane compartments. This disrupts FLCN/FNIP GAP function toward RagC/D, resulting in impaired substrate-specific mTOR-dependent phosphorylation of TFEB. Thus, the GABARAP-FLCN/FNIP-TFEB axis serves as a molecular sensor that coordinates lysosomal homeostasis with perturbations and cargo flux within the autophagy-lysosomal network.
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Affiliation(s)
| | - Ward G. Walkup
- Casma Therapeutics, 400 Technology Sq, Cambridge, MA 02139, USA
| | - Kirsty Hooper
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Taoyingnan Li
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Aylwin Ng
- Casma Therapeutics, 400 Technology Sq, Cambridge, MA 02139, USA
| | | | - Archana Jha
- Casma Therapeutics, 400 Technology Sq, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | - Asmita Agrawal
- Sai Life Sciences Limited, Pune 411057, Maharashtra, India
| | - Sagar R. Budhe
- Sai Life Sciences Limited, Pune 411057, Maharashtra, India
| | | | - Dan Baird
- Casma Therapeutics, 400 Technology Sq, Cambridge, MA 02139, USA
| | - Jeff Saunders
- Casma Therapeutics, 400 Technology Sq, Cambridge, MA 02139, USA
| | | | - Mark R. Chance
- NEO Proteomics Inc., Cleveland, OH 44106, USA
- School of Medicine, Case Western Reserve University, Cleveland, OH 44016, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- SSM School for Advanced Studies, Federico II University, Naples, Italy
| | | | - John H. Brumell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- SickKids IBD Centre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Oliver Florey
- Signalling Programme, Babraham Institute, Cambridge, UK
| | - Leon O. Murphy
- Casma Therapeutics, 400 Technology Sq, Cambridge, MA 02139, USA
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Nieto-Torres JL, Durgan J, Franco-Romero A, Grumati P, Guardia CM, Leidal AM, Mandell MA, Towers CG, Wang F. The Autophagy, Inflammation and Metabolism Center international eSymposium - an early-career investigators' seminar series during the COVID-19 pandemic. J Cell Sci 2021; 134:jcs259268. [PMID: 34622922 PMCID: PMC8520733 DOI: 10.1242/jcs.259268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Autophagy, Inflammation and Metabolism (AIM) Center organized a globally accessible, virtual eSymposium during the COVID-19 pandemic in 2020. The conference included presentations from scientific leaders, as well as a career discussion panel, and provided a much-needed platform for early-career investigators (ECIs) to showcase their research in autophagy. This Perspective summarizes the science presented by the ECIs during the event and discusses the lessons learned from a virtual meeting of this kind during the pandemic. The meeting was a learning experience for all involved, and the ECI participants herein offer their thoughts on the pros and cons of virtual meetings as a modality, either as standalone or hybrid events, with a view towards the post-pandemic world.
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Affiliation(s)
- Jose L Nieto-Torres
- Program of Development, Aging and Regeneration, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Anais Franco-Romero
- Department of Biomedical Science, University of Padova, via U.Bassi 58b, 35121 Padova, Italy
- Venetian Institute of Molecular Medicine, via Orus 2, 35129 Padova, Italy
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | - Carlos M Guardia
- Section on Intracellular Protein Trafficking, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew M Leidal
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0502, USA
| | - Michael A Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Christina G Towers
- The Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037-1002, USA
| | - Fei Wang
- UT Southwestern Medical Center, Department of Cell Biology, Dallas, TX 75390-9039, USA
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247
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Eapen VV, Swarup S, Hoyer MJ, Paulo JA, Harper JW. Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy. eLife 2021; 10:72328. [PMID: 34585663 PMCID: PMC8523161 DOI: 10.7554/elife.72328] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022] Open
Abstract
Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the damaged organelle, prior to fusion with the degradative lysosomal compartment. Lysosomes themselves are also prone to damage and are degraded through the process of lysophagy. While early steps involve recognition of ruptured lysosomal membranes by glycan-binding galectins and ubiquitylation of transmembrane lysosomal proteins, many steps in the process, and their interrelationships, remain poorly understood, including the role and identity of cargo receptors required for completion of lysophagy. Here, we employ quantitative organelle capture and proximity biotinylation proteomics of autophagy adaptors, cargo receptors, and galectins in response to acute lysosomal damage, thereby revealing the landscape of lysosome-associated proteome remodeling during lysophagy. Among the proteins dynamically recruited to damaged lysosomes were ubiquitin-binding autophagic cargo receptors. Using newly developed lysophagic flux reporters including Lyso-Keima, we demonstrate that TAX1BP1, together with its associated kinase TBK1, are both necessary and sufficient to promote lysophagic flux in both HeLa cells and induced neurons (iNeurons). While the related receptor Optineurin (OPTN) can drive damage-dependent lysophagy when overexpressed, cells lacking either OPTN or CALCOCO2 still maintain significant lysophagic flux in HeLa cells. Mechanistically, TAX1BP1-driven lysophagy requires its N-terminal SKICH domain, which binds both TBK1 and the autophagy regulatory factor RB1CC1, and requires upstream ubiquitylation events for efficient recruitment and lysophagic flux. These results identify TAX1BP1 as a central component in the lysophagy pathway and provide a proteomic resource for future studies of the lysophagy process.
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Affiliation(s)
- Vinay V Eapen
- Department of Cell Biology, Harvard Medical School, Boston, Boston, United States.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States
| | - Sharan Swarup
- Department of Cell Biology, Harvard Medical School, Boston, Boston, United States.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States
| | - Melissa J Hoyer
- Department of Cell Biology, Harvard Medical School, Boston, Boston, United States.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Boston, United States
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Boston, United States.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States
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Hu Z, Sankar DS, Vu B, Leytens A, Vionnet C, Wu W, Stumpe M, Martínez-Martínez E, Stork B, Dengjel J. ULK1 phosphorylation of striatin activates protein phosphatase 2A and autophagy. Cell Rep 2021; 36:109762. [PMID: 34592149 DOI: 10.1016/j.celrep.2021.109762] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 01/18/2023] Open
Abstract
The evolutionarily conserved ULK1 kinase complex acts as gatekeeper of canonical autophagy and regulates induction of autophagosome biogenesis. To better understand control of ULK1 and analyze whether ULK1 has broader functions that are also linked to the later steps of autophagy, we perform comprehensive phosphoproteomic analyses. Combining in vivo with in vitro data, we identify numerous direct ULK1 target sites within autophagy-relevant proteins that are critical for autophagosome maturation and turnover. In addition, we highlight an intimate crosstalk between ULK1 and several phosphatase complexes. ULK1 is not only a PP2A target but also directly phosphorylates the regulatory PP2A subunit striatin, activating PP2A and serving as positive feedback to promote autophagy-dependent protein turnover. Thus, ULK1 and phosphatase activities are tightly coordinated to robustly regulate protein degradation by autophagy.
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Affiliation(s)
- Zehan Hu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | | | - Bich Vu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Alexandre Leytens
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christine Vionnet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Wenxian Wu
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | | | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
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249
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Sukhorukov V, Voronkov D, Baranich T, Mudzhiri N, Magnaeva A, Illarioshkin S. Impaired Mitophagy in Neurons and Glial Cells during Aging and Age-Related Disorders. Int J Mol Sci 2021; 22:10251. [PMID: 34638589 PMCID: PMC8508639 DOI: 10.3390/ijms221910251] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Aging is associated with a decline in cognitive function, which can partly be explained by the accumulation of damage to the brain cells over time. Neurons and glia undergo morphological and ultrastructure changes during aging. Over the past several years, it has become evident that at the cellular level, various hallmarks of an aging brain are closely related to mitophagy. The importance of mitochondria quality and quantity control through mitophagy is highlighted by the contribution that defects in mitochondria-autophagy crosstalk make to aging and age-related diseases. In this review, we analyze some of the more recent findings regarding the study of brain aging and neurodegeneration in the context of mitophagy. We discuss the data on the dynamics of selective autophagy in neurons and glial cells during aging and in the course of neurodegeneration, focusing on three mechanisms of mitophagy: non-receptor-mediated mitophagy, receptor-mediated mitophagy, and transcellular mitophagy. We review the role of mitophagy in neuronal/glial homeostasis and in the molecular pathogenesis of neurodegenerative disorders, such as Parkinson's disease, Alzheimer's disease, and other disorders. Common mechanisms of aging and neurodegeneration that are related to different mitophagy pathways provide a number of promising targets for potential therapeutic agents.
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Affiliation(s)
- Vladimir Sukhorukov
- Research Center of Neurology, Department for Brain Research, 125367 Moscow, Russia; (D.V.); (T.B.); (N.M.); (A.M.); (S.I.)
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250
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Tian R, Han K, Geng Y, Yang C, Shi C, Thomas PB, Pearce C, Moffatt K, Ma S, Xu S, Yang G, Zhou X, Gladyshev VN, Liu X, Fisher DO, Chopin LK, Leiner NO, Baker AM, Fan G, Seim I. A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating. Mol Ecol Resour 2021; 22:740-754. [PMID: 34486812 PMCID: PMC9290055 DOI: 10.1111/1755-0998.13501] [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: 05/23/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022]
Abstract
The 15 species of small carnivorous marsupials that comprise the genus Antechinus exhibit semelparity, a rare life-history strategy in mammals where synchronized death occurs after one breeding season. Antechinus males, but not females, age rapidly (demonstrate organismal senescence) during the breeding season and show promise as new animal models of ageing. Some antechinus species are also threatened or endangered. Here, we report a chromosome-level genome of a male yellow-footed antechinus Antechinus flavipes. The genome assembly has a total length of 3.2 Gb with a contig N50 of 51.8 Mb and a scaffold N50 of 636.7 Mb. We anchored and oriented 99.7% of the assembly on seven pseudochromosomes and found that repetitive DNA sequences occupy 51.8% of the genome. Draft genome assemblies of three related species in the subfamily Phascogalinae, two additional antechinus species (Antechinus argentus and A. arktos) and the iteroparous sister species Murexia melanurus, were also generated. Preliminary demographic analysis supports the hypothesis that climate change during the Pleistocene isolated species in Phascogalinae and shaped their population size. A transcriptomic profile across the A. flavipes breeding season allowed us to identify genes associated with aspects of the male die-off. The chromosome-level A. flavipes genome provides a steppingstone to understanding an enigmatic life-history strategy and a resource to assist the conservation of antechinuses.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Kai Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chen Yang
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Patrick B Thomas
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.,Queensland Bladder Cancer Initiative, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Coral Pearce
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kate Moffatt
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Siming Ma
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Diana O Fisher
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Lisa K Chopin
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Natália O Leiner
- Laboratório de Ecologia de Mamíferos, Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia.,Natural Environments Program, Queensland Museum, South Brisbane, QLD, Australia
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
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