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Peng K, Zhao G, Zhao H, Noda NN, Zhang H. The autophagy protein ATG-9 regulates lysosome function and integrity. J Cell Biol 2025; 224:e202411092. [PMID: 40202485 PMCID: PMC11980680 DOI: 10.1083/jcb.202411092] [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] [Received: 11/13/2024] [Revised: 03/05/2025] [Accepted: 03/11/2025] [Indexed: 04/10/2025] Open
Abstract
The transmembrane autophagy protein ATG9 has multiple functions essential for autophagosome formation. Here, we uncovered a novel function of ATG-9 in regulating lysosome biogenesis and integrity in Caenorhabditis elegans. Through a genetic screen, we identified that mutations attenuating the lipid scrambling activity of ATG-9 suppress the autophagy defect in epg-5 mutants, in which non-degradative autolysosomes accumulate. The scramblase-attenuated ATG-9 mutants promote lysosome biogenesis and delivery of lysosome-localized hydrolases and also facilitate the maintenance of lysosome integrity. Through manipulation of phospholipid levels, we found that a reduction in phosphatidylethanolamine (PE) also suppresses the autophagy defects and lysosome damage associated with impaired lysosomal degradation. Our results reveal that modulation of phospholipid composition and distribution, e.g., by attenuating the scramblase activity of ATG-9 or reducing the PE level, regulates lysosome function and integrity.
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Affiliation(s)
- Kangfu Peng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Guoxiu Zhao
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
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2
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Xia F, Li W, Wang W, Liu J, Li X, Cai J, Shan H, Cai Z, Cui J. S-palmitoylation coordinates the trafficking of ATG9A to mediate autophagy initiation. Autophagy 2025:1-21. [PMID: 40394978 DOI: 10.1080/15548627.2025.2509376] [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: 10/09/2024] [Revised: 05/15/2025] [Accepted: 05/17/2025] [Indexed: 05/22/2025] Open
Abstract
ABBREVIATION 17-ODYA: 17-octadecynoic acid; 293T: HEK293T; 2-BP: 2-bromopalmitate; 2CS: Cys155Ser and Cys156Ser; ABE: acyl-biotin exchange; AP: adaptor protein; APEX2: ascorbate peroxidase 2; ATG: autophagy related; baf A1: bafilomycin A1; CRISPR: clustered regularly interspaced short palindromic repeats; CTD: C-terminal domain; Cys: cysteine; DAB: 3,3'-diaminobenzidine; EV: empty vector; H2O2: hydrogen peroxide; IF: immunofluorescence; IP: immunoprecipitation; KO: knockout; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; NTD: N-terminal domain; PAS: phagophore assembly site; PBS: phosphate-buffered saline; PtdIns3K-CI: class III phosphatidylinositol 3-kinase complex I; PM: plasma membrane; PTM: post-translational modifications; Ser: serine; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy; TGN: trans-Golgi network; ULK1: unc-51 like autophagy activating kinase 1; WCL, whole cell lysates; WDR45/WIPI4: WD repeat domain 45; WT: wild-type; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1.
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Affiliation(s)
- Fan Xia
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, Innovation Center of the Sixth Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weining Li
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, Innovation Center of the Sixth Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenru Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, Innovation Center of the Sixth Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiru Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, Innovation Center of the Sixth Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaolin Li
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, Innovation Center of the Sixth Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jing Cai
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, Innovation Center of the Sixth Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hao Shan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Zhe Cai
- The Department of Rheumatology, Guangzhou Women and Children's Medical Centre, Guangzhou, Guangdong, China
| | - Jun Cui
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, Innovation Center of the Sixth Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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3
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Jia H, Wei J, Zheng W, Li Z. The dual role of autophagy in cancer stem cells: implications for tumor progression and therapy resistance. J Transl Med 2025; 23:583. [PMID: 40414839 DOI: 10.1186/s12967-025-06595-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Accepted: 05/08/2025] [Indexed: 05/27/2025] Open
Abstract
Cancer stem cells (CSCs) constitute a small yet crucial subgroup in tumors, known for their capacity to self-renew, differentiate, and promote tumor growth, metastasis, and resistance to therapy. These characteristics position CSCs as significant factors in tumor recurrence and unfavorable clinical results, emphasizing their role as targets for therapy. Autophagy, an evolutionarily preserved cellular mechanism for degradation and recycling, has a complex function in cancer by aiding cell survival during stress and preserving balance by eliminating damaged organelles and proteins. Although autophagy can hinder tumor growth by reducing genomic instability, it also aids tumor advancement, particularly in harsh microenvironments, highlighting its dual characteristics. Recent research has highlighted the complex interactions between autophagy and CSCs, showing that autophagy governs CSC maintenance, boosts survival, and aids in resistance to chemotherapy and radiotherapy. On the other hand, in specific situations, autophagy may restrict CSC growth by increasing differentiation or inducing cell death. These intricate interactions offer both obstacles and possibilities for therapeutic intervention. Pharmacological modulation of autophagy, via inhibitors like chloroquine or by enhancing autophagy when advantageous, has demonstrated potential in making CSCs more responsive to standard treatments. Nonetheless, applying these strategies in clinical settings necessitates a better understanding of context-dependent autophagy dynamics and the discovery of dependable biomarkers indicating autophagic activity in CSCs. Progressing in this area might unveil novel, accurate strategies to tackle therapy resistance, lessen tumor recurrence, and ultimately enhance patient outcomes.
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Affiliation(s)
- Haiqing Jia
- Department of Gynecology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, No.44 xiaoheyan road, Shenyang, 110042, China
| | - Jing Wei
- Department of Gynecology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, No.44 xiaoheyan road, Shenyang, 110042, China
| | - Wei Zheng
- Department of Gynecology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, No.44 xiaoheyan road, Shenyang, 110042, China.
| | - Zhuo Li
- Department of Gynecology, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, No.44 xiaoheyan road, Shenyang, 110042, China.
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4
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Sisto A, van Wermeskerken T, Pancher M, Gatto P, Asselbergh B, Assunção Carreira ÁS, De Winter V, Adami V, Provenzani A, Timmerman V. Autophagy induction by piplartine ameliorates axonal degeneration caused by mutant HSPB1 and HSPB8 in Charcot-Marie-Tooth type 2 neuropathies. Autophagy 2025; 21:1116-1143. [PMID: 39698979 PMCID: PMC12013449 DOI: 10.1080/15548627.2024.2439649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 12/01/2024] [Accepted: 12/04/2024] [Indexed: 12/20/2024] Open
Abstract
HSPB1 [heat shock protein family B (small) member 1] and HSPB8 are essential molecular chaperones for neuronal proteostasis, as they prevent protein aggregation. Mutant HSPB1 and HSPB8 primarily harm peripheral neurons, resulting in axonal Charcot-Marie-Tooth neuropathies (CMT2). Macroautophagy/autophagy is a shared mechanism by which HSPB1 and HSPB8 mutations cause neuronal dysfunction. Autophagosome formation is reduced in mutant HSPB1-induced pluripotent stem-cell-derived motor neurons from CMT type 2F patients. Likewise, the HSPB8K141N knockin mouse model, mimicking CMT type 2 L, exhibits axonal degeneration and muscle atrophy, with SQSTM1/p62-positive deposits. We show here that mouse embryonic fibroblasts isolated from a HSPB8K141N/green fluorescent protein (GFP)-LC3 model have diminished autophagosome production under conditions of MTOR inhibition. To correct the autophagic deficits in the HSPB1 and HSPB8 models, we screened by high-throughput autophagosome quantification the repurposing Spectrum Collection library for molecules that could boost the autophagic activity above the canonical MTOR inhibition. Hit compounds were validated on motor neurons obtained by differentiation of HSPB1P182L and HSPB8K141N patient-derived induced pluripotent stem cells, focusing on autophagy induction as well as neurite network density, axonal degeneration, and mitochondrial morphology. We identified molecules that specifically stimulate autophagosome formation in the HSPB8K141N cells, without affecting autophagy flux. Two top lead compounds induced autophagy and reduced axonal degeneration, thus promoting neuronal network maturation in the CMT2 patient-derived motor neurons. Based on these findings, the phenotypical screen revealed that piplartine rescued autophagy deficiencies in both the HSPB1 and HSPB8 models, demonstrating autophagy induction as an effective therapeutic strategy for CMT neuropathies and other chaperonopathies.
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Affiliation(s)
- Angela Sisto
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Tamira van Wermeskerken
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Pamela Gatto
- HTS Core Facility, University of Trento, Trento, Italy
| | - Bob Asselbergh
- Neuromics Support Facility, VIB - Center for Molecular Neurology, Antwerp, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Vicky De Winter
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | | | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
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5
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Song JZ, Li H, Yang H, Liu R, Zhang W, He T, Xie MX, Chen C, Cui L, Wu S, Rong Y, Pan LF, Zhu J, Gong Q, Wang J, Qin Z, Xie Z. Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries. Nat Struct Mol Biol 2025:10.1038/s41594-025-01546-0. [PMID: 40295771 DOI: 10.1038/s41594-025-01546-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 03/24/2025] [Indexed: 04/30/2025]
Abstract
Autophagy-related (Atg) proteins catalyze autophagosome formation at the phagophore assembly site (PAS). The assembly of Atg proteins at the PAS follows a semihierarchical order, in which Atg8 is thought to be quite downstream but still able to control the size of autophagosomes. Yet, how Atg8 coordinates multiple branches of autophagy machinery to regulate autophagosomal size is not clear. Here, we show that, in yeast, Atg8 positively regulates the autophagy-specific phosphatidylinositol 3-OH kinase complex and the retrograde trafficking of Atg9 vesicles through interaction with Atg1. Mechanistically, Atg8 does not enhance the kinase activity of Atg1; instead, it recruits Atg1 to the surface of the phagophore likely to orient Atg1's activity toward select substrates, leading to efficient phagophore expansion. Artificial tethering of Atg1 kinase domains to Atg8s enhanced autophagy in yeast, human and plant cells and improved muscle performance in worms. We propose that Atg8-mediated relocation of Atg1 from the PAS scaffold to the phagophore is a critical step in positive autophagy regulation.
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Affiliation(s)
- Jing-Zhen Song
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyan Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rui Liu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Tianlong He
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Meng-Xi Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Chen
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Cui
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shian Wu
- School of Life Sciences, Nankai University, Tianjin, China
| | - Yueguang Rong
- School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Feng Pan
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Jing Zhu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Juan Wang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China.
| | - Zhao Qin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China.
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, China.
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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6
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Campisi D, Hawkins N, Bonjour K, Wollert T. The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy. J Mol Biol 2025:169138. [PMID: 40221132 DOI: 10.1016/j.jmb.2025.169138] [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: 12/05/2024] [Revised: 02/24/2025] [Accepted: 04/07/2025] [Indexed: 04/14/2025]
Abstract
Autophagy is a conserved cellular recycling pathway that delivers damaged or superfluous cytoplasmic material to lysosomes for degradation. In response to cytotoxic stress or starvation, autophagy can also sequester bulk cytoplasm and deliver it to lysosomes to regenerate building blocks. In macroautophagy, a membrane cisterna termed phagophore that encloses autophagic cargo is generated. The formation of the phagophore depends on a conserved machinery of autophagy related proteins. The phosphatidylinositol(3)-phosphate binding protein WIPI2 facilitates the transition from phagophore initiation to phagophore expansion by recruiting the ATG12-ATG5-ATG16L1 complex to phagophores. This complex functions as an E3-ligase to conjugate ubiquitin-like ATG8 proteins to phagophore membranes, which promotes tethering of cargo to phagophore membranes, phagophore expansion, maturation and the fusion of autophagosomes with lysosomes. ATG16L1 also has important functions independently of ATG12-ATG5 in autophagy and beyond. In this review, we will summarize the functions of WIPI2 and ATG16L1 in selective and nonselective autophagy.
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Affiliation(s)
- Daniele Campisi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - N'Toia Hawkins
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Kennedy Bonjour
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France.
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7
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Fesenko M, Moore DJ, Ewbank P, Courthold E, Royle SJ. ATG9A vesicles are a subtype of intracellular nanovesicle. J Cell Sci 2025; 138:jcs263852. [PMID: 40067248 PMCID: PMC12045599 DOI: 10.1242/jcs.263852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 02/27/2025] [Indexed: 04/10/2025] Open
Abstract
Cells are filled with thousands of vesicles, which mediate protein transport and ensure homeostasis of the endomembrane system. Distinguishing these vesicles functionally and molecularly represents a major challenge. Intracellular nanovesicles (INVs) are a large class of transport vesicles that likely comprise multiple subtypes. Here, we define the INV proteome and find that it is molecularly heterogeneous and enriched for transmembrane cargo molecules, including integrins, transporters and ATG9A, a lipid scramblase associated with autophagy. ATG9A is known to reside in 'ATG9A vesicles' - small vesicles that contribute to autophagosome formation. Here, using in-cell vesicle capture assays, we found that ATG9A, as well as other ATG9A vesicle cargoes, are in INVs. Quantitative analysis showed that virtually all ATG9A vesicles are INVs, but that only ∼20% of INVs are ATG9A vesicles, suggesting that ATG9A vesicles are in fact a subtype of INV, which we term ATG9A-flavor INVs. Finally, we show that perturbing ATG9A-flavor INVs impairs the autophagy response induced by starvation.
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Affiliation(s)
- Mary Fesenko
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Daniel J. Moore
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Peyton Ewbank
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Elizabeth Courthold
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Stephen J. Royle
- Centre for Mechanochemical Cell Biology and Warwick Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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8
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Scavone F, Lian S, Eskelinen EL, Cohen RE, Yao T. Trafficking of K63-polyubiquitin-modified membrane proteins in a macroautophagy-independent pathway is linked to ATG9A. Mol Biol Cell 2025; 36:ar42. [PMID: 39969968 PMCID: PMC12005115 DOI: 10.1091/mbc.e24-12-0535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 02/03/2025] [Accepted: 02/05/2025] [Indexed: 02/20/2025] Open
Abstract
Cytoplasmic K63-linked polyubiquitin signals have well-established roles in endocytosis and selective autophagy. However, how these signals help to direct different cargos to different intracellular trafficking routes is unclear. Here we report that, when the K63-polyubiquitin signal is blocked by intracellular expression of a high-affinity sensor (named Vx3), many proteins originating from the plasma membrane are found trapped in clusters of small vesicles that colocalize with ATG9A, a transmembrane protein that plays an essential role in autophagy. Importantly, whereas ATG9A is required for cluster formation, other core autophagy machinery as well as selective autophagy cargo receptors are not required. Although the cargos are sequestered in the vesicular clusters in an ATG9-dependent manner, additional signals are needed to induce LC3 conjugation. Upon removal of the Vx3 block, K63-polyubiquitylated cargos are rapidly delivered to lysosomes. These observations suggest that ATG9A plays an unexpected role in the trafficking of K63-polyubiquitin-modified membrane proteins.
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Affiliation(s)
- Francesco Scavone
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sharon Lian
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Eeva-Liisa Eskelinen
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, 00014, Finland
- Institute of Biomedicine, University of Turku, Turku, FI-20520, Finland
| | - Robert E. Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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9
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Wang S, Ren J, Chi J, Guan Y, Zheng R, Wang J, Liu X, Huang H. RHOD mediates ATG9A trafficking to promote autophagosome formation during autophagy in cancer. Autophagy 2025:1-19. [PMID: 40143438 DOI: 10.1080/15548627.2025.2484604] [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: 08/15/2024] [Revised: 03/19/2025] [Accepted: 03/22/2025] [Indexed: 03/28/2025] Open
Abstract
ATG9A is a transmembrane protein essential for macroautophagy/autophagy that drives autophagosome formation by delivering essential proteins and lipids to the phagophore through vesicle trafficking. Here, we demonstrate that the atypical Rho GTPase RHOD is required for ATG9A trafficking and stimulates autophagosome formation. Upon starvation, RHOD interacted with ATG9A and accompanied ATG9A trafficking from the Golgi toward phagophores. In addition, starvation-induced high levels of RHOD resulted in Golgi fragmentation to further promote ATG9A vesicle export from the trans-Golgi network to the peripheral region. Loss of RHOD suppressed ATG9A trafficking and reduced the distribution of ATG9A on the phagophore. Moreover, WHAMM (WASP homolog associated with actin, golgi membranes and microtubules) forms a complex with RHOD and participates in this process in a RHOD-dependent manner. Importantly, RHOD mutants, which lack the exon II-containing effector region motif that is required for ATG9A binding or lack the CAAX box that is responsible for membrane targeting, fail to stimulate ATG9A trafficking and autophagosome formation. Furthermore, RHOD plays a distinct suppressor role in tumor development, partly associated with its regulatory effect on autophagy. These findings reveal the important roles of RHOD in autophagy and tumor development.Abbreviation: ATG9A: autophagy related 9A; BafA1: bafilomycin A1; BiFC: bimolecular fluorescence complementation; co-IP: co-immunoprecipitation; EBSS: Earle's balanced salt solution; FM: full culture medium; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PUP-IT: pupylation-based interaction tagging; RHOD: ras homolog family member D; SQSTM1: sequestosome 1; TGN: trans-Golgi network; VC: Venus C-terminal; VN: Venus N-terminal; WHAMM: WASP homolog associated with actin, golgi membranes and microtubules; WIPI2: WD repeat domain, phosphoinositide interacting 2; WT: wild-type; 3-MA: phosphatidylinositol 3-kinase (PtdIns3K) inhibitor 3-methyladenine.
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Affiliation(s)
- Sijia Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jinghan Chi
- Senior Department of Pediatrics, The Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Yifei Guan
- Beijing Key Laboratory of Environmental and Viral Oncology, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Ran Zheng
- Beijing Key Laboratory of Environmental and Viral Oncology, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Juan Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xinhui Liu
- Beijing Key Laboratory of Environmental and Viral Oncology, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Hua Huang
- Beijing Key Laboratory of Environmental and Viral Oncology, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
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10
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Moreno TM, Nieto-Torres JL, Kumsta C. Monitoring Autophagy in Human Aging: Key Cell Models and Insights. FRONT BIOSCI-LANDMRK 2025; 30:27091. [PMID: 40152379 PMCID: PMC12042822 DOI: 10.31083/fbl27091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/08/2024] [Accepted: 11/22/2024] [Indexed: 03/29/2025]
Abstract
Autophagy, a key cellular degradation and recycling pathway, is critical for maintaining cellular homeostasis and responding to metabolic and environmental stress. Evidence for age-related autophagic dysfunction and its implications in chronic age-related diseases including neurodegeneration is accumulating. However, as a complex, multi-step process, autophagy can be challenging to measure, particularly in humans and human aging- and disease-relevant models. This review describes the links between macroautophagy, aging, and chronic age-related diseases. We present three novel human cell models, peripheral blood mononuclear cells (PBMCs), primary dermal fibroblasts (PDFs), and induced neurons (iNs), which serve as essential tools for studying autophagy flux and assessing its potential as a biomarker for aging. Unlike traditional models, these cell models retain age- and disease-associated molecular signatures, enhancing their relevance for human studies. The development of robust tools and methodologies for measuring autophagy flux in human cell models holds promise for advancing our understanding of autophagy's role in aging and age-related diseases, ultimately facilitating the discovery of therapies to enhance health outcomes.
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Affiliation(s)
- Tatiana M. Moreno
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jose L. Nieto-Torres
- Department of Biomedical Sciences, School of Health Sciences, Universidad Cardenal Herrera-CEU, CEU Universities, 46115 Valencia, Spain
| | - Caroline Kumsta
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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11
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Javed R, Mari M, Trosdal E, Duque T, Paddar MA, Allers L, Mudd MH, Claude-Taupin A, Akepati PR, Hendrix E, He Y, Salemi M, Phinney B, Uchiyama Y, Reggiori F, Deretic V. ATG9A facilitates the closure of mammalian autophagosomes. J Cell Biol 2025; 224:e202404047. [PMID: 39745851 PMCID: PMC11694768 DOI: 10.1083/jcb.202404047] [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] [Received: 04/17/2024] [Revised: 08/29/2024] [Accepted: 11/11/2024] [Indexed: 01/04/2025] Open
Abstract
Canonical autophagy captures within specialized double-membrane organelles, termed autophagosomes, an array of cytoplasmic components destined for lysosomal degradation. An autophagosome is completed when the growing phagophore undergoes ESCRT-dependent membrane closure, a prerequisite for its subsequent fusion with endolysosomal organelles and degradation of the sequestered cargo. ATG9A, a key integral membrane protein of the autophagy pathway, is best known for its role in the formation and expansion of phagophores. Here, we report a hitherto unappreciated function of mammalian ATG9A in directing autophagosome closure. ATG9A partners with IQGAP1 and key ESCRT-III component CHMP2A to facilitate this final stage in autophagosome formation. Thus, ATG9A is a central hub governing all major aspects of autophagosome membrane biogenesis, from phagophore formation to its closure, and is a unique ATG factor with progressive functionalities affecting the physiological outputs of autophagy.
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Affiliation(s)
- Ruheena Javed
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Muriel Mari
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Einar Trosdal
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Thabata Duque
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Masroor Ahmad Paddar
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Lee Allers
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Michal H. Mudd
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Aurore Claude-Taupin
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Prithvi Reddy Akepati
- Gastroenterology Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Emily Hendrix
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Yi He
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Brett Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
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12
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Broadbent DG, McEwan CM, Jayatunge D, Kaminsky EG, Tsang TM, Poole DM, Naylor BC, Price JC, Schmidt JC, Andersen JL. Ubiquitin-mediated recruitment of the ATG9A-ATG2 lipid transfer complex drives clearance of phosphorylated p62 aggregates. Mol Biol Cell 2025; 36:ar20. [PMID: 39718773 PMCID: PMC11809316 DOI: 10.1091/mbc.e24-03-0101] [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] [Received: 03/05/2024] [Revised: 11/04/2024] [Accepted: 12/19/2024] [Indexed: 12/25/2024] Open
Abstract
Autophagy is an essential cellular recycling process that maintains protein and organelle homeostasis. ATG9A vesicle recruitment is a critical early step in autophagy to initiate autophagosome biogenesis. The mechanisms of ATG9A vesicle recruitment are best understood in the context of starvation-induced nonselective autophagy, whereas less is known about the signals driving ATG9A vesicle recruitment to autophagy initiation sites in the absence of nutrient stress. Here we demonstrate that loss of ATG9A, or the lipid transfer protein ATG2, leads to the accumulation of phosphorylated p62 aggregates in nutrient replete conditions. Furthermore, we show that p62 degradation requires the lipid scramblase activity of ATG9A. Last, we present evidence that polyubiquitin is an essential signal that recruits ATG9A and mediates autophagy foci assembly in nutrient replete cells. Together, our data support a ubiquitin-driven model of ATG9A recruitment and autophagosome formation during basal autophagy.
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Affiliation(s)
- David G Broadbent
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI 48824
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824
- Department of Physiology, College of Natural Sciences, Michigan State University, East Lansing, MI 48824
| | - Colten M McEwan
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Dasun Jayatunge
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Emily G Kaminsky
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI 48824
| | - Tsz-Min Tsang
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Daniel M Poole
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Jens C Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI 48824
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI 48824
| | - Josh L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
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13
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Acheson J, Joanisse S, Sale C, Hodson N. Recycle, repair, recover: the role of autophagy in modulating skeletal muscle repair and post-exercise recovery. Biosci Rep 2025; 45:1-30. [PMID: 39670455 PMCID: PMC12096956 DOI: 10.1042/bsr20240137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 12/03/2024] [Accepted: 12/11/2024] [Indexed: 12/14/2024] Open
Abstract
Skeletal muscle is a highly plastic tissue that can adapt relatively rapidly to a range of stimuli. In response to novel mechanical loading, e.g. unaccustomed resistance exercise, myofibers are disrupted and undergo a period of ultrastructural remodeling to regain full physiological function, normally within 7 days. The mechanisms that underpin this remodeling are believed to be a combination of cellular processes including ubiquitin-proteasome/calpain-mediated degradation, immune cell infiltration, and satellite cell proliferation/differentiation. A relatively understudied system that has the potential to be a significant contributing mechanism to repair and recovery is the autophagolysosomal system, an intracellular process that degrades damaged and redundant cellular components to provide constituent metabolites for the resynthesis of new organelles and cellular structures. This review summarizes our current understanding of the autophagolysosomal system in the context of skeletal muscle repair and recovery. In addition, we also provide hypothetical models of how this system may interact with other processes involved in skeletal muscle remodeling and provide avenues for future research to improve our understanding of autophagy in human skeletal muscle.
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Affiliation(s)
- Jordan Acheson
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Institute of Sport, Manchester, U.K.
| | - Sophie Joanisse
- School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, U.K.
| | - Craig Sale
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Institute of Sport, Manchester, U.K.
| | - Nathan Hodson
- Department of Sport and Exercise Sciences, Manchester Metropolitan University, Institute of Sport, Manchester, U.K.
- Faculty of Kinesiology and Physical Education, University of Toronto, Toronto, Ontario, Canada
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14
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Wang L, Yi S, Zhang S, Tsai YT, Cheng YH, Lin YT, Lin CC, Lee YH, Wang H, Ho MS. New Atg9 Phosphorylation Sites Regulate Autophagic Trafficking in Glia. ASN Neuro 2025; 17:2443442. [PMID: 39807990 PMCID: PMC11877618 DOI: 10.1080/17590914.2024.2443442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 12/07/2024] [Accepted: 12/11/2024] [Indexed: 01/30/2025] Open
Abstract
We previously identified a role for dAuxilin (dAux), the fly homolog of Cyclin G-associated kinase, in glial autophagy contributing to Parkinson's disease (PD). To further dissect the mechanism, we present evidence here that lack of glial dAux enhanced the phosphorylation of the autophagy-related protein Atg9 at two newly identified threonine residues, T62 and T69. The enhanced Atg9 phosphorylation in the absence of dAux promotes autophagosome formation and Atg9 trafficking to the autophagosomes in glia. Whereas the expression of the non-phosphorylatable Atg9 variants suppresses the lack of dAux-induced increase in both autophagosome formation and Atg9 trafficking to autophagosome, the expression of the phosphomimetic Atg9 variants restores the lack of Atg1-induced decrease in both events. In relation to pathophysiology, Atg9 phosphorylation at T62 and T69 contributes to dopaminergic neurodegeneration and locomotor dysfunction in a Drosophila PD model. Notably, increased expression of the master autophagy regulator Atg1 promotes dAux-Atg9 interaction. Thus, we have identified a dAux-Atg1-Atg9 axis relaying signals through the Atg9 phosphorylation at T62 and T69; these findings further elaborate the mechanism of dAux regulating glial autophagy and highlight the significance of protein degradation pathway in glia contributing to PD.
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Affiliation(s)
- Linfang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- The Institute of Seed Industry, Xianghu Laboratory, Qiantang River International Innovation Belt of the Xiaoshan Economic and Technological Development Zone, Hangzhou, China
| | - Shuanglong Yi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiping Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu-Ting Tsai
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Hsuan Cheng
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Tung Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-Ching Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Hua Lee
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Honglei Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Margaret S. Ho
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
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15
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Bhardwaj K, Jha A, Roy A, Kumar H. The crucial role of VPS35 and SHH in Parkinson's disease: Understanding the mechanisms behind the neurodegenerative disorder. Brain Res 2024; 1845:149204. [PMID: 39197569 DOI: 10.1016/j.brainres.2024.149204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/10/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
Parkinson's disease (PD) is indeed a complex neurodegenerative disorder recognized by the progressive depletion of dopaminergic neurons in the brain, particularly in the substantia nigra region, leading to motor impairments and other symptoms. But at the molecular level, the study about PD still lacks. As the number of cases worldwide continues to increase, it is critical to focus on the cellular and molecular mechanisms of the disease's presentation and neurodegeneration to develop novel therapeutic approaches. At the molecular level, the complexity is more due to the involvement of vacuolar protein sorting 35 (VPS35) and sonic hedgehog (SHH) signaling in PD (directly or indirectly), leading to one of the most prominent hallmarks of the disease, which is an accumulation of α-synuclein. This elevated pathogenesis may result from impaired autophagy due to mutation in the case of VPS35 and impairment in SHH signaling at the molecular level. The traditional understanding of PD is marked by the disruption of dopaminergic neurons and dopaminergic signaling, which exacerbates symptoms of motor function deficits. However, the changes at the molecular level that are being disregarded also impact the overall health of the dopaminergic system. Gaining insight into these two unique mechanisms is essential to determine whether they give neuroprotection or have no effect on the health of neurons. Hence, here we tried to simplify the understanding of the role of VPS35 and SHH signaling to comprehend it in one direction.
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Affiliation(s)
- Kritika Bhardwaj
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Akanksha Jha
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Abhishek Roy
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Hemant Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar, Gujarat 382355, India.
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16
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Pimentel JM, Zhou JY, Wu GS. Autophagy and cancer therapy. Cancer Lett 2024; 605:217285. [PMID: 39395780 DOI: 10.1016/j.canlet.2024.217285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 09/25/2024] [Accepted: 10/03/2024] [Indexed: 10/14/2024]
Abstract
Autophagy is an intracellular degradation process that sequesters cytoplasmic components in double-membrane vesicles known as autophagosomes, which are degraded upon fusion with lysosomes. This pathway maintains the integrity of proteins and organelles while providing energy and nutrients to cells, particularly under nutrient deprivation. Deregulation of autophagy can cause genomic instability, low protein quality, and DNA damage, all of which can contribute to cancer. Autophagy can also be overactivated in cancer cells to aid in cancer cell survival and drug resistance. Emerging evidence indicates that autophagy has functions beyond cargo degradation, including roles in tumor immunity and cancer stem cell survival. Additionally, autophagy can also influence the tumor microenvironment. This feature warrants further investigation of the role of autophagy in cancer, in which autophagy manipulation can improve cancer therapies, including cancer immunotherapy. This review discusses recent findings on the regulation of autophagy and its role in cancer therapy and drug resistance.
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Affiliation(s)
- Julio M Pimentel
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA; Institutional Research Academic Career Development Award Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jun Ying Zhou
- Molecular Therapeutics Program, Karmanos Cancer Institute, Detroit, MI, 48201, USA; Department of Oncology, Wayne State University, Detroit, MI, 48201, USA
| | - Gen Sheng Wu
- Molecular Therapeutics Program, Karmanos Cancer Institute, Detroit, MI, 48201, USA; Department of Oncology, Wayne State University, Detroit, MI, 48201, USA; Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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17
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Mohseni M, Behzad G, Farhadi A, Behroozi J, Mohseni H, Valipour B. MicroRNAs regulating autophagy: opportunities in treating neurodegenerative diseases. Front Neurosci 2024; 18:1397106. [PMID: 39582602 PMCID: PMC11582054 DOI: 10.3389/fnins.2024.1397106] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 10/15/2024] [Indexed: 11/26/2024] Open
Abstract
Neurodegenerative diseases (NDs) are increasingly prevalent in our aging population, imposing significant social and economic burdens. Currently, most ND patients receive only symptomatic treatment due to limited understanding of their underlying causes. Consequently, there is a pressing need for comprehensive research into the pathological mechanisms of NDs by both researchers and clinicians. Autophagy, a cellular mechanism responsible for maintaining cellular equilibrium by removing dysfunctional organelles and misfolded proteins, plays a vital role in cell health and is implicated in various diseases. MicroRNAs (miRNAs) exert influence on autophagy and hold promise for treating these diseases. These small oligonucleotides bind to the 3'-untranslated region (UTR) of target mRNAs, leading to mRNA silencing, degradation, or translation blockade. This review explores recent findings on the regulation of autophagy and autophagy-related genes by different miRNAs in various pathological conditions, including neurodegeneration and inflammation-related diseases. The recognition of miRNAs as key regulators of autophagy in human diseases has spurred investigations into pharmacological compounds and traditional medicines targeting these miRNAs in disease models. This has catalyzed a new wave of therapeutic interventions aimed at modulating autophagy.
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Affiliation(s)
- Mahdi Mohseni
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghazal Behzad
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arezoo Farhadi
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Javad Behroozi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hamraz Mohseni
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behnaz Valipour
- Department of Basic Sciences and Health, Sarab Faculty of Medical Sciences, Sarab, Iran
- Department of Anatomical Sciences, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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18
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Choi J, Jang H, Xuan Z, Park D. Emerging roles of ATG9/ATG9A in autophagy: implications for cell and neurobiology. Autophagy 2024; 20:2373-2387. [PMID: 39099167 PMCID: PMC11572220 DOI: 10.1080/15548627.2024.2384349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 07/01/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024] Open
Abstract
Atg9, the only transmembrane protein among many autophagy-related proteins, was first identified in the year 2000 in yeast. Two homologs of Atg9, ATG9A and ATG9B, have been found in mammals. While ATG9B shows a tissue-specific expression pattern, such as in the placenta and pituitary gland, ATG9A is ubiquitously expressed. Additionally, ATG9A deficiency leads to severe defects not only at the molecular and cellular levels but also at the organismal level, suggesting key and fundamental roles for ATG9A. The subcellular localization of ATG9A on small vesicles and its functional relevance to autophagy have suggested a potential role for ATG9A in the lipid supply during autophagosome biogenesis. Nevertheless, the precise role of ATG9A in the autophagic process has remained a long-standing mystery, especially in neurons. Recent findings, however, including structural, proteomic, and biochemical analyses, have provided new insights into its function in the expansion of the phagophore membrane. In this review, we aim to understand various aspects of ATG9 (in invertebrates and plants)/ATG9A (in mammals), including its localization, trafficking, and other functions, in nonneuronal cells and neurons by comparing recent discoveries related to ATG9/ATG9A and proposing directions for future research.Abbreviation: AP-4: adaptor protein complex 4; ATG: autophagy related; cKO: conditional knockout; CLA-1: CLArinet (functional homolog of cytomatrix at the active zone proteins piccolo and fife); cryo-EM: cryogenic electron microscopy; ER: endoplasmic reticulum; KO: knockout; PAS: phagophore assembly site; PtdIns3K: class III phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SV: synaptic vesicle; TGN: trans-Golgi network; ULK: unc-51 like autophagy activating kinase; WIPI2: WD repeat domain, phosphoinositide interacting 2.
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Affiliation(s)
- Jiyoung Choi
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, South Korea
- Department of Biotechnology, The Catholic University of Korea, Bucheon, South Korea
| | - Haeun Jang
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, South Korea
| | - Zhao Xuan
- School of Biology and Ecology, University of Maine, Orono, ME, USA
| | - Daehun Park
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, South Korea
- Department of Biotechnology, The Catholic University of Korea, Bucheon, South Korea
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19
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Nie J, Ma S, Wu L, Li Y, Cao J, Li M, Mei P, Cooper PR, Li A, Pei D. SEC31a-ATG9a Interaction Mediates the Recruitment of COPII Vesicles for Autophagosome Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2405127. [PMID: 39361436 PMCID: PMC11600210 DOI: 10.1002/advs.202405127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/28/2024] [Indexed: 10/05/2024]
Abstract
Autophagy plays an important role in determining stem-cell differentiation. During the osteogenic differentiation of mesenchymal stem cells (MSCs), autophagosome formation is upregulated but the reason is unknown. A long-standing quest in the autophagy field is to find the membrane origin of autophagosomes. In this study, cytoplasmic coat protein complex II (COPII) vesicles, endoplasmic reticulum-derived vesicles responsible for the transport of storage proteins to the Golgi, are demonstrated to be a critical source of osteoblastic autophagosomal membrane. A significant correlation between the number of COPII vesicle and the autophagy level is identified in the rat bone tissues. Disruption of COPII vesicles restrained osteogenesis and decreased the number and size of autophagosomes. SEC31a (an outer coat protein of COPII vesicle) is found to be vital to regulate COPII vesicle-dependent autophagosome formation via interacting with ATG9a of autophagosomal seed vesicles. The interference of Sec31a inhibited autophagosome formation and osteogenesis in vitro and in vivo. These results identified a novel mechanism of autophagosome formation in osteogenic differentiation of stem cells and identified SEC31a as a critical protein that mediates the interplay between COPII and ATG9a vesicles. These findings broaden the understanding of the regulatory mechanism in the osteogenic differentiation of MSCs.
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Affiliation(s)
- Jiaming Nie
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
| | - Shaoyang Ma
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
| | - Linyue Wu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
| | - Ye Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
| | - Jiao Cao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
| | - Meng Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
| | - Peter Mei
- Department of Oral SciencesFaculty of DentistryUniversity of OtagoDunedin9016New Zealand
| | - Paul R. Cooper
- Department of Oral SciencesFaculty of DentistryUniversity of OtagoDunedin9016New Zealand
| | - Ang Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
| | - Dandan Pei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of StomatologyXi'an Jiaotong UniversityXi'anShaanxi710004China
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20
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Lin L, Lin Y, Han Z, Wang K, Zhou S, Wang Z, Wang S, Chen H. Understanding the molecular regulatory mechanisms of autophagy in lung disease pathogenesis. Front Immunol 2024; 15:1460023. [PMID: 39544928 PMCID: PMC11560454 DOI: 10.3389/fimmu.2024.1460023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 10/07/2024] [Indexed: 11/17/2024] Open
Abstract
Lung disease development involves multiple cellular processes, including inflammation, cell death, and proliferation. Research increasingly indicates that autophagy and its regulatory proteins can influence inflammation, programmed cell death, cell proliferation, and innate immune responses. Autophagy plays a vital role in the maintenance of homeostasis and the adaptation of eukaryotic cells to stress by enabling the chelation, transport, and degradation of subcellular components, including proteins and organelles. This process is essential for sustaining cellular balance and ensuring the health of the mitochondrial population. Recent studies have begun to explore the connection between autophagy and the development of different lung diseases. This article reviews the latest findings on the molecular regulatory mechanisms of autophagy in lung diseases, with an emphasis on potential targeted therapies for autophagy.
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Affiliation(s)
- Lin Lin
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yumeng Lin
- Nanjing Tongren Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Zhongyu Han
- School of Medicine, Southeast University, Nanjing, China
- Science Education Department, Chengdu Xinhua Hospital Affiliated to North Sichuan Medical College, Chengdu, China
| | - Ke Wang
- Department of Science and Education, Deyang Hospital Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Deyang, China
| | - Shuwei Zhou
- Department of Radiology, Zhongda Hospital, Nurturing Center of Jiangsu Province for State Laboratory of AI Imaging & Interventional Radiology, School of Medicine, Southeast University, Nanjing, China
| | - Zhanzhan Wang
- Department of Respiratory and Critical Care Medicine, The First People’s Hospital of Lianyungang, Lianyungang, China
| | - Siyu Wang
- Department of Preventive Medicine, Kunshan Hospital of Chinese Medicine, Kunshan, China
| | - Haoran Chen
- Science Education Department, Chengdu Xinhua Hospital Affiliated to North Sichuan Medical College, Chengdu, China
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21
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Norell PN, Campisi D, Mohan J, Wollert T. Biogenesis of omegasomes and autophagosomes in mammalian autophagy. Biochem Soc Trans 2024; 52:2145-2155. [PMID: 39392358 PMCID: PMC11555699 DOI: 10.1042/bst20240015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Autophagy is a highly conserved catabolic pathway that maintains cellular homeostasis by promoting the degradation of damaged or superfluous cytoplasmic material. A hallmark of autophagy is the generation of membrane cisternae that sequester autophagic cargo. Expansion of these structures allows cargo to be engulfed in a highly selective and exclusive manner. Cytotoxic stress or starvation induces the formation of autophagosomes that sequester bulk cytoplasm instead of selected cargo. This rather nonselective pathway is essential for maintaining vital cellular functions during adverse conditions and is thus a major stress response pathway. Both selective and nonselective autophagy rely on the same molecular machinery. However, due to the different nature of cargo to be sequestered, the involved molecular mechanisms are fundamentally different. Although intense research over the past decades has advanced our understanding of autophagy, fundamental questions remain to be addressed. This review will focus on molecular principles and open questions regarding the formation of omegasomes and phagophores in nonselective mammalian autophagy.
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Affiliation(s)
- Puck N. Norell
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Daniele Campisi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Jagan Mohan
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
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22
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Braun MM, Sheehan BK, Shapiro SL, Ding Y, Rubinstein CD, Lehman BP, Puglielli L. Ca +2 and Nε-lysine acetylation regulate the CALR-ATG9A interaction in the lumen of the endoplasmic reticulum. Sci Rep 2024; 14:25532. [PMID: 39462136 PMCID: PMC11513142 DOI: 10.1038/s41598-024-76854-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 10/17/2024] [Indexed: 10/28/2024] Open
Abstract
The acetylation of autophagy protein 9 A (ATG9A) in the lumen of the endoplasmic reticulum (ER) by ATase1 and ATase2 regulates the induction of reticulophagy. Analysis of the ER-specific ATG9A interactome identified calreticulin (CALR), an ER luminal Ca+2-binding chaperone, as key for ATG9A activity. Specifically, if acetylated, ATG9A is sequestered by CALR and prevented from engaging FAM134B and SEC62. Under this condition, ATG9A is unable to activate the autophagy core machinery. In contrast, when non-acetylated, ATG9A is released by CALR and able to engage FAM134B and SEC62. In this study, we report that Ca+2 dynamics across the ER membrane regulate the ATG9A-CALR interaction as well as the ability of ATG9A to trigger reticulophagy. We show that the Ca+2-binding sites situated on the C-domain of CALR are essential for the ATG9A-CALR interaction. Finally, we show that K359 and K363 on ATG9A can influence the ATG9A-CALR interaction. Collectively, our results disclose a previously unidentified aspect of the complex mechanisms that regulate ATG9A activity. They also offer a possible area of intersection between Ca+2 metabolism, acetyl-CoA metabolism, and ER proteostasis.
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Affiliation(s)
- Megan M Braun
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Brendan K Sheehan
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA
- Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Samantha L Shapiro
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA
| | - Yun Ding
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Lilly Oncology, San Diego, CA, 92121, USA
| | - C Dustin Rubinstein
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brent P Lehman
- Biotechnology Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Luigi Puglielli
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Waisman Center, University of Wisconsin-Madison, 1500 Highland Ave, Madison, WI, 53705, USA.
- Geriatric Research Education Clinical Center, Veterans Affairs Medical Center, Madison, WI, 53705, USA.
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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23
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Zhang T, Liu Q, Chen Q, Wu H. Iron regulatory protein two facilitates ferritinophagy and DNA damage/repair through guiding ATG9A trafficking. J Biol Chem 2024; 300:107767. [PMID: 39276939 PMCID: PMC11490887 DOI: 10.1016/j.jbc.2024.107767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/17/2024] [Accepted: 08/25/2024] [Indexed: 09/17/2024] Open
Abstract
Trace elemental iron is an essential nutrient that participates in diverse metabolic processes. Dysregulation of cellular iron homeostasis, both iron deficiency and iron overload, is detrimental and tightly associated with disease pathogenesis. IRPs-IREs system is located at the center for iron homeostasis regulation. Additionally, ferritinophagy, the autophagy-dependent ferritin catabolism for iron recycling, is emerging as a novel mechanism for iron homeostasis regulation. It is still unclear whether IRPs-IREs system and ferritinophagy are synergistic or redundant in determining iron homeostasis. Here we report that IRP2, but not IRP1, is indispensable for ferritinophagy in response to iron depletion. Mechanistically, IRP2 ablation results in compromised AMPK activation and defective ATG9A endosomal trafficking, leading to the decreased engulfment of NCOA4-ferritin complex by endosomes and the subsequent dysregulated endosomal microferritinophagy. Moreover, this defective endosomal microferritinophagy exacerbates DNA damage and reduces colony formation in IRP2-depleted cells. Collectively, this study expands the physiological function of IRP2 in endosomal microferritinophagy and highlights potential crosstalk between IRPs-IREs and ferritinophagy in manipulating iron homeostasis.
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Affiliation(s)
- Ting Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Qian Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Quan Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Hao Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China.
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24
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Sankar DS, Kaeser-Pebernard S, Vionnet C, Favre S, de Oliveira Marchioro L, Pillet B, Zhou J, Stumpe M, Kovacs WJ, Kressler D, Antonioli M, Fimia GM, Dengjel J. The ULK1 effector BAG2 regulates autophagy initiation by modulating AMBRA1 localization. Cell Rep 2024; 43:114689. [PMID: 39207901 DOI: 10.1016/j.celrep.2024.114689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/15/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
Autophagy initiation is regulated by the ULK1 kinase complex. To gain insights into functions of the holo-complex, we generated a deep interactome by combining affinity purification- and proximity labeling-mass spectrometry of all four complex members: ULK1, ATG13, ATG101, and RB1CC1/FIP200. Under starvation conditions, the ULK1 complex interacts with several protein and lipid kinases and phosphatases, implying the formation of a signalosome. Interestingly, several selective autophagy receptors also interact with ULK1, indicating the activation of selective autophagy pathways by nutrient starvation. One effector of the ULK1 complex is the HSC/HSP70 co-chaperone BAG2, which regulates the subcellular localization of the VPS34 lipid kinase complex member AMBRA1. Depending on the nutritional status, BAG2 has opposing roles. In growth conditions, the unphosphorylated form of BAG2 sequesters AMBRA1, attenuating autophagy induction. In starvation conditions, ULK1 phosphorylates BAG2 on Ser31, which supports the recruitment of AMBRA1 to the ER membrane, positively affecting autophagy.
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Affiliation(s)
| | | | - Christine Vionnet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sebastian Favre
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Lais de Oliveira Marchioro
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", 00149 Rome, Italy; Department of Pharmacology, Federal University of São Paulo (UNIFESP), São Paulo CEP 05508-000, Brazil
| | - Benjamin Pillet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jianwen Zhou
- Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Werner Josef Kovacs
- Institute of Molecular Health Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Dieter Kressler
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Manuela Antonioli
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", 00149 Rome, Italy; Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Gian Maria Fimia
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS "L. Spallanzani", 00149 Rome, Italy; Department of Molecular Medicine, University of Rome "Sapienza", 00185 Rome, Italy
| | - Jӧrn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
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25
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Otegui MS, Steelheart C, Ma W, Ma J, Kang BH, De Medina Hernandez VS, Dagdas Y, Gao C, Goto-Yamada S, Oikawa K, Nishimura M. Vacuolar degradation of plant organelles. THE PLANT CELL 2024; 36:3036-3056. [PMID: 38657116 PMCID: PMC11371181 DOI: 10.1093/plcell/koae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Plants continuously remodel and degrade their organelles due to damage from their metabolic activities and environmental stressors, as well as an integral part of their cell differentiation programs. Whereas certain organelles use local hydrolytic enzymes for limited remodeling, most of the pathways that control the partial or complete dismantling of organelles rely on vacuolar degradation. Specifically, selective autophagic pathways play a crucial role in recognizing and sorting plant organelle cargo for vacuolar clearance, especially under cellular stress conditions induced by factors like heat, drought, and damaging light. In these short reviews, we discuss the mechanisms that control the vacuolar degradation of chloroplasts, mitochondria, endoplasmic reticulum, Golgi, and peroxisomes, with an emphasis on autophagy, recently discovered selective autophagy receptors for plant organelles, and crosstalk with other catabolic pathways.
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Affiliation(s)
- Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Charlotte Steelheart
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wenlong Ma
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Juncai Ma
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Byung-Ho Kang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | | | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shino Goto-Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow 30-348, Poland
| | - Kazusato Oikawa
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Mikio Nishimura
- Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
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26
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Choi J, Wu Y, Park D. Absence of ATG9A and synaptophysin demixing on Rab5 mutation-induced giant endosomes. Mol Brain 2024; 17:63. [PMID: 39223639 PMCID: PMC11367939 DOI: 10.1186/s13041-024-01132-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
ATG9A is the only integral membrane protein among core autophagy-related (ATG) proteins. We previously found that ATG9A does not co-assemble into synaptophysin-positive vesicles, but rather, localizes to a distinct pool of vesicles within synapsin condensates in both fibroblasts and nerve terminals. The endocytic origin of these vesicles further suggests the existence of different intracellular sorting or segregation mechanisms for ATG9A and synaptophysin in cells. However, the precise underlying mechanism remains largely unknown. In this follow-up study, we investigated the endosomal localization of these two proteins by exploiting the advantages of a Rab5 mutant that induces the formation of enlarged endosomes. Notably, ATG9A and synaptophysin intermix perfectly and do not segregate on giant endosomes, indicating that the separation of these two proteins is not solely caused by the inherent properties of the proteins, but possibly by other unknown factors.
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Affiliation(s)
- Jiyoung Choi
- Department of Medical and Biological Sciences, The Catholic University of Korea, Gyeonggi-Do, Bucheon, 14662, South Korea
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi-Do, Bucheon, 14662, South Korea
| | - Yumei Wu
- Departments of Neuroscience and of Cell Biology, HHMI, Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Daehun Park
- Department of Medical and Biological Sciences, The Catholic University of Korea, Gyeonggi-Do, Bucheon, 14662, South Korea.
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi-Do, Bucheon, 14662, South Korea.
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27
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Meena D, Jha S. Autophagy in glioblastoma: A mechanistic perspective. Int J Cancer 2024; 155:605-617. [PMID: 38716809 DOI: 10.1002/ijc.34991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 06/20/2024]
Abstract
Glioblastoma (GBM) is one of the most lethal malignancies in humans. Even after surgical resection and aggressive radio- or chemotherapies, patients with GBM can survive for less than 14 months. Extreme inter-tumor and intra-tumor heterogeneity of GBM poses a challenge for resolving recalcitrant GBM pathophysiology. GBM tumor microenvironment (TME) exhibits diverse heterogeneity in cellular composition and processes contributing to tumor progression and therapeutic resistance. Autophagy is such a cellular process; that demonstrates a cell-specific and TME context-dependent role in GBM progression, leading to either the promotion or suppression of GBM progression. Autophagy can regulate GBM cell function directly via regulation of survival, migration, and invasion, or indirectly by affecting GBM TME composition such as immune cell population, tumor metabolism, and glioma stem cells. This review comprehensively investigates the role of autophagy in GBM pathophysiology.
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Affiliation(s)
- Durgesh Meena
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Sushmita Jha
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
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28
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Zheng Y, Zha X, Zhang B, Elsabagh M, Wang H, Wang M, Zhang H. The interaction of ER stress and autophagy in trophoblasts: navigating pregnancy outcome†. Biol Reprod 2024; 111:292-311. [PMID: 38678504 DOI: 10.1093/biolre/ioae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/12/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024] Open
Abstract
The endoplasmic reticulum is a complex and dynamic organelle that initiates unfolded protein response and endoplasmic reticulum stress in response to the accumulation of unfolded or misfolded proteins within its lumen. Autophagy is a paramount intracellular degradation system that facilitates the transportation of proteins, cytoplasmic components, and organelles to lysosomes for degradation and recycling. Preeclampsia and intrauterine growth retardation are two common complications of pregnancy associated with abnormal trophoblast differentiation and placental dysfunctions and have a major impact on fetal development and maternal health. The intricate interplay between endoplasmic reticulum stress, and autophagy and their impact on pregnancy outcomes, through mediating trophoblast differentiation and placental development, has been highlighted in various reports. Autophagy controls trophoblast regulation through a variety of gene expressions and signaling pathways while excessive endoplasmic reticulum stress triggers downstream apoptotic signaling, culminating in trophoblast apoptosis. This comprehensive review delves into the intricacies of placental development and explores the underlying mechanisms of preeclampsia and intrauterine growth retardation. In addition, this review will elucidate the molecular mechanisms of endoplasmic reticulum stress and autophagy, both individually and in their interplay, in mediating placental development and trophoblast differentiation, particularly highlighting their roles in preeclampsia and intrauterine growth retardation development. This research seeks to the interplay between endoplasmic reticulum stress and impaired autophagy in the placental trophoderm, offering novel insights into their contribution to pregnancy complications.
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Affiliation(s)
- Yi Zheng
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Repubic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China
| | - Xia Zha
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Repubic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China
| | - Bei Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Repubic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China
| | - Mabrouk Elsabagh
- Department of Animal Production and Technology, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Nigde, Turkey
- Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Kafrelsheikh University, KafrelSheikh, Egypt
| | - Hongrong Wang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Repubic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China
| | - Mengzhi Wang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Repubic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Science, Shihezi, P. R. China
| | - Hao Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou, People's Repubic of China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, People's Republic of China
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29
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Holzer E, Martens S, Tulli S. The Role of ATG9 Vesicles in Autophagosome Biogenesis. J Mol Biol 2024; 436:168489. [PMID: 38342428 DOI: 10.1016/j.jmb.2024.168489] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Autophagy mediates the degradation and recycling of cellular material in the lysosomal system. Dysfunctional autophagy is associated with a plethora of diseases including uncontrolled infections, cancer and neurodegeneration. In macroautophagy (hereafter autophagy) this material is encapsulated in double membrane vesicles, the autophagosomes, which form upon induction of autophagy. The precursors to autophagosomes, referred to as phagophores, first appear as small flattened membrane cisternae, which gradually enclose the cargo material as they grow. The assembly of phagophores during autophagy initiation has been a major subject of investigation over the past decades. A special focus has been ATG9, the only conserved transmembrane protein among the core machinery. The majority of ATG9 localizes to small Golgi-derived vesicles. Here we review the recent advances and breakthroughs regarding our understanding of how ATG9 and the vesicles it resides in serve to assemble the autophagy machinery and to establish membrane contact sites for autophagosome biogenesis. We also highlight open questions in the field that need to be addressed in the years to come.
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Affiliation(s)
- Elisabeth Holzer
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Campus-Vienna-Biocenter 1, Vienna, Austria.
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
| | - Susanna Tulli
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria; University of Vienna, Max Perutz Labs, Department of Biochemistry and Cell Biology, Vienna, Austria.
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30
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Isola D, Elazar Z. Phospholipid Supply for Autophagosome Biogenesis. J Mol Biol 2024; 436:168691. [PMID: 38944336 DOI: 10.1016/j.jmb.2024.168691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/10/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Autophagy is a cellular degradation pathway where double-membrane autophagosomes form de novo to engulf cytoplasmic material destined for lysosomal degradation. This process requires regulated membrane remodeling, beginning with the initial autophagosomal precursor and progressing to its elongation and maturation into a fully enclosed, fusion-capable vesicle. While the core protein machinery involved in autophagosome formation has been extensively studied over the past two decades, the role of phospholipids in this process has only recently been studied. This review focuses on the phospholipid composition of the phagophore membrane and the mechanisms that supply lipids to expand this unique organelle.
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Affiliation(s)
- Damilola Isola
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zvulun Elazar
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
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31
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Selarka K, Shravage BV. Illuminating intercellular autophagy: A comprehensive review of cell non-autonomous autophagy. Biochem Biophys Res Commun 2024; 716:150024. [PMID: 38701555 DOI: 10.1016/j.bbrc.2024.150024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 04/26/2024] [Indexed: 05/05/2024]
Abstract
Macro-autophagy (autophagy hereafter) is an evolutionarily conserved cellular process that has long been recognized as an intracellular mechanism for maintaining cellular homeostasis. It involves the formation of a membraned structure called the autophagosome, which carries cargo that includes toxic protein aggregates and dysfunctional organelles to the lysosome for degradation and recycling. Autophagy is primarily considered and studied as a cell-autonomous mechanism. However, recent studies have illuminated an underappreciated facet of autophagy, i.e., non-autonomously regulated autophagy. Non-autonomously regulated autophagy involves the degradation of autophagic components, including organelles, cargo, and signaling molecules, and is induced in neighboring cells by signals from primary adjacent or distant cells/tissues/organs. This review provides insight into the complex molecular mechanisms governing non-autonomously regulated autophagy, highlighting the dynamic interplay between cells within tissue/organ or distinct cell types in different tissues/organs. Emphasis is placed on modes of intercellular communication that include secreted molecules, including microRNAs, and their regulatory roles in orchestrating this phenomenon. Furthermore, we explore the multidimensional roles of non-autonomously regulated autophagy in various physiological contexts, spanning tissue development and aging, as well as its importance in diverse pathological conditions, including cancer and neurodegeneration. By studying the complexities of non-autonomously regulated autophagy, we hope to gain insights into the sophisticated intercellular dynamics within multicellular organisms, including mammals. These studies will uncover novel avenues for therapeutic intervention to modulate intercellular autophagic pathways in altered human physiology.
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Affiliation(s)
- Karan Selarka
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India; Department of Biotechnology, Savitribai Phule Pune University, Pune, India
| | - Bhupendra V Shravage
- Developmental Biology Group, MACS-Agharkar Research Institute, Pune, India; Department of Biotechnology, Savitribai Phule Pune University, Pune, India; Department of Zoology, Savitribai Phule Pune University, Pune, India.
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Macke AJ, Divita TE, Pachikov AN, Mahalingam S, Bellamkonda R, Rasineni K, Casey CA, Petrosyan A. Alcohol-induced Golgiphagy is triggered by the downregulation of Golgi GTPase RAB3D. Autophagy 2024; 20:1537-1558. [PMID: 38591519 PMCID: PMC11210917 DOI: 10.1080/15548627.2024.2329476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
The development of alcohol-associated liver disease (ALD) is associated with disorganized Golgi apparatus and accelerated phagophore formation. While Golgi membranes may contribute to phagophores, association between Golgi alterations and macroautophagy/autophagy remains unclear. GOLGA4/p230 (golgin A4), a dimeric Golgi matrix protein, participates in phagophore formation, but the underlying mechanism is elusive. Our prior research identified ethanol (EtOH)-induced Golgi scattering, disrupting intra-Golgi trafficking and depleting RAB3D GTPase from the trans-Golgi. Employing various techniques, we analyzed diverse cellular and animal models representing chronic and chronic/binge alcohol consumption. In trans-Golgi of non-treated hepatocytes, we found a triple complex formed between RAB3D, GOLGA4, and MYH10/NMIIB (myosin, heavy polypeptide 10, non-muscle). However, EtOH-induced RAB3D downregulation led to MYH10 segregation from the Golgi, accompanied by Golgi fragmentation and tethering of the MYH10 isoform, MYH9/NMIIA, to dispersed Golgi membranes. EtOH-activated autophagic flux is evident through increased WIPI2 recruitment to the Golgi, phagophore formation, enhanced LC3B lipidation, and reduced SQSTM1/p62. Although GOLGA4 dimerization and intra-Golgi localization are unaffected, loss of RAB3D leads to an extension of the cytoplasmic N terminal domain of GOLGA4, forming GOLGA4-positive phagophores. Autophagy inhibition by hydroxychloroquine (HCQ) prevents alcohol-mediated Golgi disorganization, restores distribution of ASGR (asialoglycoprotein receptor), and mitigates COL (collagen) deposition and steatosis. In contrast to short-term exposure to HCQ, extended co-treatment with both EtOH and HCQ results in the depletion of LC3B protein via proteasomal degradation. Thus, (a) RAB3D deficiency and GOLGA4 conformational changes are pivotal in MYH9-driven, EtOH-mediated Golgiphagy, and (b) HCQ treatment holds promise as a therapeutic approach for alcohol-induced liver injury.Abbreviation: ACTB: actin, beta; ALD: alcohol-associated liver disease; ASGR: asialoglycoprotein receptor; AV: autophagic vacuoles; EM: electron microscopy; ER: endoplasmic reticulum; EtOH: ethanol; HCQ: hydroxychloroquine; IP: immunoprecipitation; KD: knockdown; KO: knockout; MYH10/NMIIB: myosin, heavy polypeptide 10, non-muscle; MYH9/NMIIA: myosin, heavy polypeptide 9, non-muscle; PLA: proximity ligation assay; ORO: Oil Red O staining; PM: plasma membrane; TGN: trans-Golgi network; SIM: structured illumination super-resolution microscopy.
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Affiliation(s)
- Amanda J. Macke
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Taylor E. Divita
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Artem N. Pachikov
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sundararajan Mahalingam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Omaha Western Iowa Health Care System, VA Service, Department of Research Service, Omaha, NE, USA
| | - Ramesh Bellamkonda
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Omaha Western Iowa Health Care System, VA Service, Department of Research Service, Omaha, NE, USA
| | - Karuna Rasineni
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Omaha Western Iowa Health Care System, VA Service, Department of Research Service, Omaha, NE, USA
| | - Carol A. Casey
- Omaha Western Iowa Health Care System, VA Service, Department of Research Service, Omaha, NE, USA
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Armen Petrosyan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
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Huang L, Guo H. Acetylation modification in the regulation of macroautophagy. ADVANCED BIOTECHNOLOGY 2024; 2:19. [PMID: 39883319 PMCID: PMC11740868 DOI: 10.1007/s44307-024-00027-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 01/31/2025]
Abstract
Macroautophagy, commonly referred to as autophagy, is an evolutionarily conserved cellular process that plays a crucial role in maintaining cellular homeostasis. It orchestrates the delivery of dysfunctional or surplus cellular materials to the vacuole or lysosome for degradation and recycling, particularly during adverse conditions. Over the past few decades, research has unveiled intricate regulatory mechanisms governing autophagy through various post-translational modifications (PTMs). Among these PTMs, acetylation modification has emerged as a focal point in yeast and animal studies. It plays a pivotal role in autophagy by directly targeting core components within the central machinery of autophagy, including autophagy initiation, nucleation, phagophore expansion, and autophagosome maturation. Additionally, acetylation modulates autophagy at the transcriptional level by modifying histones and transcription factors. Despite its well-established significance in yeast and mammals, the role of acetylation in plant autophagy remains largely unexplored, and the precise regulatory mechanisms remain enigmatic. In this comprehensive review, we summarize the current understanding of the function and underlying mechanisms of acetylation in regulating autophagy across yeast, mammals, and plants. We particularly highlight recent advances in deciphering the impact of acetylation on plant autophagy. These insights not only provide valuable guidance but also inspire further scientific inquiries into the intricate role of acetylation in plant autophagy.
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Affiliation(s)
- Li Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hongwei Guo
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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Yu Q, Ding J, Li S, Li Y. Autophagy in cancer immunotherapy: Perspective on immune evasion and cell death interactions. Cancer Lett 2024; 590:216856. [PMID: 38583651 DOI: 10.1016/j.canlet.2024.216856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Both the innate and adaptive immune systems work together to produce immunity. Cancer immunotherapy is a novel approach to tumor suppression that has arisen in response to the ineffectiveness of traditional treatments like radiation and chemotherapy. On the other hand, immune evasion can diminish immunotherapy's efficacy. There has been a lot of focus in recent years on autophagy and other underlying mechanisms that impact the possibility of cancer immunotherapy. The primary feature of autophagy is the synthesis of autophagosomes, which engulf cytoplasmic components and destroy them by lysosomal degradation. The planned cell death mechanism known as autophagy can have opposite effects on carcinogenesis, either increasing or decreasing it. It is autophagy's job to maintain the balance and proper functioning of immune cells like B cells, T cells, and others. In addition, autophagy controls whether macrophages adopt the immunomodulatory M1 or M2 phenotype. The ability of autophagy to control the innate and adaptive immune systems is noteworthy. Interleukins and chemokines are immunological checkpoint chemicals that autophagy regulates. Reducing antigen presentation to induce immunological tolerance is another mechanism by which autophagy promotes cancer survival. Therefore, targeting autophagy is of importance for enhancing potential of cancer immunotherapy.
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Affiliation(s)
- Qiang Yu
- Department of Digestive Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Jiajun Ding
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Shisen Li
- Department of Digestive Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Yunlong Li
- Department of Digestive Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China.
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Yi S, Wang L, Ho MS, Zhang S. The autophagy protein Atg9 functions in glia and contributes to parkinsonian symptoms in a Drosophila model of Parkinson's disease. Neural Regen Res 2024; 19:1150-1155. [PMID: 37862221 PMCID: PMC10749615 DOI: 10.4103/1673-5374.382259] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 10/22/2023] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disease characterized by motor deficits, dopaminergic neuron loss, and brain accumulation of α-synuclein aggregates called Lewy bodies. Dysfunction in protein degradation pathways, such as autophagy, has been demonstrated in neurons as a critical mechanism for eliminating protein aggregates in Parkinson's disease. However, it is less well understood how protein aggregates are eliminated in glia, the other cell type in the brain. In the present study, we show that autophagy-related gene 9 (Atg9), the only transmembrane protein in the autophagy machinery, is highly expressed in Drosophila glia from adult brain. Results from immunostaining and live cell imaging analysis reveal that a portion of Atg9 localizes to the trans-Golgi network, autophagosomes, and lysosomes in glia. Atg9 is persistently in contact with these organelles. Lacking glial atg9 reduces the number of omegasomes and autophagosomes, and impairs autophagic substrate degradation. This suggests that glial Atg9 participates in the early steps of autophagy, and hence the control of autophagic degradation. Importantly, loss of glial atg9 induces parkinsonian symptoms in Drosophila including progressive loss of dopaminergic neurons, locomotion deficits, and glial activation. Our findings identify a functional role of Atg9 in glial autophagy and establish a potential link between glial autophagy and Parkinson's disease. These results may provide new insights on the underlying mechanism of Parkinson's disease.
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Affiliation(s)
- Shuanglong Yi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Linfang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Margaret S. Ho
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shiping Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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Rowlands J, Moore DJ. VPS35 and retromer dysfunction in Parkinson's disease. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220384. [PMID: 38368930 PMCID: PMC10874700 DOI: 10.1098/rstb.2022.0384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024] Open
Abstract
The vacuolar protein sorting 35 ortholog (VPS35) gene encodes a core component of the retromer complex essential for the endosomal sorting and recycling of transmembrane cargo. Endo-lysosomal pathway deficits are suggested to play a role in the pathogenesis of neurodegenerative diseases, including Parkinson's disease (PD). Mutations in VPS35 cause a late-onset, autosomal dominant form of PD, with a single missense mutation (D620N) shown to segregate with disease in PD families. Understanding how the PD-linked D620N mutation causes retromer dysfunction will provide valuable insight into the pathophysiology of PD and may advance the identification of therapeutics. D620N VPS35 can induce LRRK2 hyperactivation and impair endosomal recruitment of the WASH complex but is also linked to mitochondrial and autophagy-lysosomal pathway dysfunction and altered neurotransmitter receptor transport. The clinical similarities between VPS35-linked PD and sporadic PD suggest that defects observed in cellular and animal models with the D620N VPS35 mutation may provide valuable insights into sporadic disease. In this review, we highlight the current knowledge surrounding VPS35 and its role in retromer dysfunction in PD. We provide a critical discussion of the mechanisms implicated in VPS35-mediated neurodegeneration in PD, as well as the interplay between VPS35 and other PD-linked gene products. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'.
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Affiliation(s)
- Jordan Rowlands
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Darren J. Moore
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A trafficking and delivery. Mol Biol Cell 2024; 35:ar56. [PMID: 38381558 PMCID: PMC11064669 DOI: 10.1091/mbc.e23-09-0359-t] [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] [Received: 09/20/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans-Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative LC3-Interacting Region (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B preferentially over other members of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Reintroduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, reintroducing tepsin with a mutated LIR motif or missing N-terminus drives diffuse ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; ensuring delivery of ATG9A-positive vesicles; and in overall maintenance of autophagosome structure.
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Affiliation(s)
- Natalie S. Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - John E. Gadbery
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
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Mayer J, Boeck D, Werner M, Frankenhauser D, Geley S, Farhan H, Shimozawa M, Nilsson P. Inhibition of Autophagy Alters Intracellular Transport of APP Resulting in Increased APP Processing. Traffic 2024; 25:e12934. [PMID: 38613404 DOI: 10.1111/tra.12934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
Abstract
Alzheimer's disease (AD) pathology is characterized by amyloid beta (Aβ) plaques and dysfunctional autophagy. Aβ is generated by sequential proteolytic cleavage of amyloid precursor protein (APP), and the site of intracellular APP processing is highly debated, which may include autophagosomes. Here, we investigated the involvement of autophagy, including the role of ATG9 in APP intracellular trafficking and processing by applying the RUSH system, which allows studying the transport of fluorescently labeled mCherry-APP-EGFP in a systematic way, starting from the endoplasmic reticulum. HeLa cells, expressing the RUSH mCherry-APP-EGFP system, were investigated by live cell imaging, immunofluorescence, and Western blot. We found that mCherry-APP-EGFP passed through the Golgi faster in ATG9 knockout cells. Furthermore, ATG9 deletion shifted mCherry-APP-EGFP from early endosomes and lysosomes toward the plasma membrane concomitant with reduced endocytosis. Importantly, this alteration in mCherry-APP-EGFP transport resulted in increased secreted mCherry-soluble APP and C-terminal fragment-EGFP. These effects were also phenocopied by pharmacological inhibition of ULK1, indicating that autophagy is regulating the intracellular trafficking and processing of APP. These findings contribute to the understanding of the role of autophagy in APP metabolism and could potentially have implications for new therapeutic approaches for AD.
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Affiliation(s)
- Johanna Mayer
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Dominik Boeck
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
- Institute of Molecular Neurogenetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michelle Werner
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | | | - Stephan Geley
- Institute of Pathophysiology, Innsbruck Medical University, Innsbruck, Austria
| | - Hesso Farhan
- Institute of Pathophysiology, Innsbruck Medical University, Innsbruck, Austria
| | - Makoto Shimozawa
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
| | - Per Nilsson
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Solna, Sweden
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Muramoto M, Mineoka N, Fukuda K, Kuriyama S, Masatani T, Fujita A. Coordinated regulation of phosphatidylinositol 4-phosphate and phosphatidylserine levels by Osh4p and Osh5p is an essential regulatory mechanism in autophagy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184308. [PMID: 38437942 DOI: 10.1016/j.bbamem.2024.184308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/26/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
Macroautophagy (hereafter autophagy) is an intracellular degradative pathway in budding yeast cells. Certain lipid types play essential roles in autophagy; yet the precise mechanisms regulating lipid composition during autophagy remain unknown. Here, we explored the role of the Osh family proteins in the modulating lipid composition during autophagy in budding yeast. Our results showed that osh1-osh7∆ deletions lead to autophagic dysfunction, with impaired GFP-Atg8 processing and the absence of autophagosomes and autophagic bodies in the cytosol and vacuole, respectively. Freeze-fracture electron microscopy (EM) revealed elevated phosphatidylinositol 4-phosphate (PtdIns(4)P) levels in cytoplasmic and luminal leaflets of autophagic bodies and vacuolar membranes in all deletion mutants. Phosphatidylserine (PtdSer) levels were significantly decreased in the autophagic bodies and vacuolar membranes in osh4∆ and osh5∆ mutants, whereas no significant changes were observed in other osh deletion mutants. Furthermore, we identified defects in autophagic processes in the osh4∆ and osh5∆ mutants, including rare autophagosome formation in the osh5∆ mutant and accumulation of autophagic bodies in the vacuole in the osh4∆ mutant, even in the absence of the proteinase inhibitor PMSF. These findings suggest that Osh4p and Osh5p play crucial roles in the transport of PtdSer to autophagic bodies and autophagosome membranes, respectively. The precise control of lipid composition in the membranes of autophagosomes and autophagic bodies by Osh4p and Osh5p represents an important regulatory mechanism in autophagy.
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Affiliation(s)
- Moe Muramoto
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Nanaru Mineoka
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Kayoko Fukuda
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Sayuri Kuriyama
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Tatsunori Masatani
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Akikazu Fujita
- Department of Molecular and Cell Biology and Biochemistry, Basic Veterinary Science, Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan.
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40
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Sun D, Zhang Z, Yu X, Li H, Wang X, Chen L. The mechanism of UNC-51-like kinase 1 and the applications of small molecule modulators in cancer treatment. Eur J Med Chem 2024; 268:116273. [PMID: 38432059 DOI: 10.1016/j.ejmech.2024.116273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
Autophagy is a process of self-renewal in cells, which not only provides the necessary nutrients for cells, but also clears necrotic organelles. Autophagy disorders are closely related to diseases such as cancer. UNC-51-like kinase 1 (ULK1) is a serine/threonine protein kinase that plays a crucial role in receiving input from energy and nutrient sensors, activating autophagy to maintain cellular homeostasis under stressful conditions. In recent years, targeting ULK1 has become a highly promising strategy for cancer treatment. This review introduces the regulatory mechanism of ULK1 in autophagy through the AMPK/mTOR/ULK1 pathway and reviews the research progress of ULK1 activators and inhibitors and their applications in cancer treatment. In addition, we analyze the binding modes between ULK1 and modulators through virtual molecular docking, which will provide a reliable basis and theoretical guidance for the design and development of new therapeutic drugs targeting ULK1.
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Affiliation(s)
- Dejuan Sun
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Chinese People's Liberation Army Logistics Support Force, No. 967 Hospital, Dalian, 116021, China
| | - Zhiqi Zhang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xinbo Yu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hua Li
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China; Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.
| | - Xiaobo Wang
- Chinese People's Liberation Army Logistics Support Force, No. 967 Hospital, Dalian, 116021, China.
| | - Lixia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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Chiduza GN, Garza-Garcia A, Almacellas E, De Tito S, Pye VE, van Vliet AR, Cherepanov P, Tooze SA. ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A. Autophagy 2024; 20:557-576. [PMID: 37938170 PMCID: PMC10936676 DOI: 10.1080/15548627.2023.2275905] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/05/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Macroautophagy/autophagy is a fundamental aspect of eukaryotic biology, and the autophagy-related protein ATG9A is part of the core machinery facilitating this process. In addition to ATG9A vertebrates encode ATG9B, a poorly characterized paralog expressed in a subset of tissues. Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein. Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. By establishing the molecular structure and function of ATG9B, our results inform the exploration of niche roles for autophagy machinery in more complex eukaryotes and reveal insights relevant across species.Abbreviation: ATG: autophagy related; CHS: cholesteryl hemisuccinate; cryo-EM: single-particle cryogenic electron microscopy; CTF: contrast transfer function: CTH: C- terminal α helix; FSC: fourier shell correlation; HDIR: HORMA domain interacting region; LMNG: lauryl maltose neopentyl glycol; MD: molecular dynamics simulations; MSA: multiple sequence alignment; NBD-PE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl ammonium salt); POPC: palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; RBG: repeating beta groove domain; RMSD: root mean square deviation; SEC: size-exclusion chromatography; TMH: transmembrane helix.
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Affiliation(s)
- George N. Chiduza
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Acely Garza-Garcia
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
| | - Eugenia Almacellas
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | | | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
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Tang X, Lin S, Luo H, Wang L, Zhong J, Xiong J, Lv H, Zhou F, Wan Z, Cao K. ATG9A as a potential diagnostic marker of intervertebral disc degeneration: Inferences from experiments and bioinformatics analysis incorporating sc-RNA-seq data. Gene 2024; 897:148084. [PMID: 38104954 DOI: 10.1016/j.gene.2023.148084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/02/2023] [Accepted: 12/13/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Disfunctional autophagy plays a pivotal role in Intervertebral Disc Degeneration (IDD) progression. however, the connection between Autophagy-related gene 9A (ATG9A) and IDD has not been reported. METHODS Firstly, transcriptome datasets from the GEO and Autophagy-related genes (ARGs) from GeneCards were carried out using R. Following this, IDD-specific signature genes were identified through methods such as least absolute shrinkage and selection operator (LASSO), random forest (RF), and support vector machine (SVM) analyses. Validation of these findings proceeded through in vitro experiments, evaluation of independent datasets, and analysis of receiver operating characteristic (ROC) curves. Subsequent steps incorporated co-expression analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, Gene Set Enrichment Analysis (GSEA), and construction of competing endogenous RNA (ceRNA) network. The final section established the correlation between immune cell infiltration, ATG9A, and IDD utilizing the CIBERSORT algorithm and single-cell RNA (scRNA) sequencing data. RESULTS Research identified 87 differentially expressed genes, with only ATG9A noted as an IDD signature gene. Analysis of in vitro experiments and independent datasets uncovered a decrease in ATG9A expression within the degeneration group. The area under the curve (AUC) of ATG9A exceeded 0.8 following ROC analysis. Furthermore, immune cell infiltration and scRNA sequencing data analysis elucidated the substantial role of immune cells in IDD progression. A ceRNA network was constructed, centered around ATG9A, included 4 miRNAs and 22 lncRNAs. CONCLUSION ATG9A was identified as a diagnostic gene for IDD, indicating its viability as a effective target for therapy disease.
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Affiliation(s)
- Xiaokai Tang
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Sijian Lin
- The Department of Rehabilitation Medicine, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Hao Luo
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Lixia Wang
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Junlong Zhong
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Jiachao Xiong
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Hao Lv
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Faxin Zhou
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Zongmiao Wan
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China
| | - Kai Cao
- Orthopedic Hospital, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, China.
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Kotani T, Yasuda Y, Nakatogawa H. Molecular Mechanism of Autophagy, Cytoplasmic Zoning by Lipid Membranes. J Biochem 2024; 175:155-165. [PMID: 37983716 DOI: 10.1093/jb/mvad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/02/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
Autophagy is a highly conserved intracellular degradation mechanism. The most distinctive feature of autophagy is the formation of double-membrane structures called autophagosomes, which compartmentalize portions of the cytoplasm. The outer membrane of the autophagosome fuses with the vacuolar/lysosomal membrane, leading to the degradation of the contents of the autophagosome. Approximately 30 years have passed since the identification of autophagy-related (ATG) genes and Atg proteins essential for autophagosome formation, and the primary functions of these Atg proteins have been elucidated. These achievements have significantly advanced our understanding of the mechanism of autophagosome formation. This article summarizes our current knowledge on how the autophagosome precursor is generated, and how the membrane expands and seals to complete the autophagosome.
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Affiliation(s)
- Tetsuya Kotani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-14 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yuri Yasuda
- School of Life Science and Technology, Tokyo Institute of Technology, S2-14 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hitoshi Nakatogawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-14 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, S2-14 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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Bhattacharya A, Torggler R, Reiter W, Romanov N, Licheva M, Ciftci A, Mari M, Kolb L, Kaiser D, Reggiori F, Ammerer G, Hollenstein DM, Kraft C. Decoding the function of Atg13 phosphorylation reveals a role of Atg11 in bulk autophagy initiation. EMBO Rep 2024; 25:813-831. [PMID: 38233718 PMCID: PMC10897315 DOI: 10.1038/s44319-023-00055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024] Open
Abstract
Autophagy is initiated by the assembly of multiple autophagy-related proteins that form the phagophore assembly site where autophagosomes are formed. Atg13 is essential early in this process, and a hub of extensive phosphorylation. How these multiple phosphorylations contribute to autophagy initiation, however, is not well understood. Here we comprehensively analyze the role of phosphorylation events on Atg13 during nutrient-rich conditions and nitrogen starvation. We identify and functionally characterize 48 in vivo phosphorylation sites on Atg13. By generating reciprocal mutants, which mimic the dephosphorylated active and phosphorylated inactive state of Atg13, we observe that disrupting the dynamic regulation of Atg13 leads to insufficient or excessive autophagy, which are both detrimental to cell survival. We furthermore demonstrate an involvement of Atg11 in bulk autophagy even during nitrogen starvation, where it contributes together with Atg1 to the multivalency that drives phase separation of the phagophore assembly site. These findings reveal the importance of post-translational regulation on Atg13 early during autophagy initiation, which provides additional layers of regulation to control bulk autophagy activity and integrate cellular signals.
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Affiliation(s)
- Anuradha Bhattacharya
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Raffaela Torggler
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Wolfgang Reiter
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna, Austria
| | - Natalie Romanov
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Akif Ciftci
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Muriel Mari
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000, Aarhus C, Denmark
| | - Lena Kolb
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Dominik Kaiser
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000, Aarhus C, Denmark
| | - Gustav Ammerer
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - David M Hollenstein
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.
- Department for Biochemistry and Cell Biology, University of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
- Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna, Austria.
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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45
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Zobaroğlu-Özer P, Bora-Akoğlu G. Split but merge: Golgi fragmentation in physiological and pathological conditions. Mol Biol Rep 2024; 51:214. [PMID: 38280063 DOI: 10.1007/s11033-023-09153-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 12/12/2023] [Indexed: 01/29/2024]
Abstract
The Golgi complex is a highly dynamic and tightly regulated cellular organelle with essential roles in the processing as well as the sorting of proteins and lipids. Its structure undergoes rapid disassembly and reassembly during normal physiological processes, including cell division, migration, polarization, differentiation, and cell death. Golgi dispersal or fragmentation also occurs in pathological conditions, such as neurodegenerative diseases, infectious diseases, congenital disorders of glycosylation diseases, and cancer. In this review, current knowledge about both structural organization and morphological alterations in the Golgi in physiological and pathological conditions is summarized together with the methodologies that help to reveal its structure.
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Affiliation(s)
- Pelin Zobaroğlu-Özer
- Faculty of Medicine, Department of Medical Biology, Hacettepe University, Ankara, Turkey
- Faculty of Medicine, Department of Medical Biology, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Gamze Bora-Akoğlu
- Faculty of Medicine, Department of Medical Biology, Hacettepe University, Ankara, Turkey.
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Papadakos S, Issa H, Alamri A, Alamri A, Semlali A. Rapamycin as a Potential Alternative Drug for Squamous Cell Gingiva Carcinoma (Ca9-22): A Focus on Cell Cycle, Apoptosis and Autophagy Genetic Profile. Pharmaceuticals (Basel) 2024; 17:131. [PMID: 38276004 PMCID: PMC10818555 DOI: 10.3390/ph17010131] [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: 12/07/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Oral cancer is considered as one of the most common malignancies worldwide. Its conventional treatment primarily involves surgery with or without postoperative adjuvant therapy. The targeting of signaling pathways implicated in tumorigenesis is becoming increasingly prevalent in the development of new anticancer drug candidates. Based on our recently published data, Rapamycin, an inhibitor of the mTOR pathway, exhibits selective antitumor activity in oral cancer by inhibiting cell proliferation and inducing cancer cell apoptosis, autophagy, and cellular stress. In the present study, our focus is on elucidating the genetic determinants of Rapamycin's action and the interaction networks accountable for tumorigenesis suppression. To achieve this, gingival carcinoma cell lines (Ca9-22) were exposed to Rapamycin at IC50 (10 µM) for 24 h. Subsequently, we investigated the genetic profiles related to the cell cycle, apoptosis, and autophagy, as well as gene-gene interactions, using QPCR arrays and the Gene MANIA website. Overall, our results showed that Rapamycin at 10 µM significantly inhibits the growth of Ca9-22 cells after 24 h of treatment by around 50% by suppression of key modulators in the G2/M transition, namely, Survivin and CDK5RAP1. The combination of Rapamycin with Cisplatin potentializes the inhibition of Ca9-22 cell proliferation. A P1/Annexin-V assay was performed to evaluate the effect of Rapamycin on cell apoptosis. The results obtained confirm our previous findings in which Rapamycin at 10 μM induces a strong apoptosis of Ca9-22 cells. The live cells decreased, and the late apoptotic cells increased when the cells were treated by Rapamycin. To identify the genes responsible for cell apoptosis induced by Rapamycin, we performed the RT2 Profiler PCR Arrays for 84 apoptotic genes. The blocked cells were believed to be directed towards cell death, confirmed by the downregulation of apoptosis inhibitors involved in both the extrinsic and intrinsic pathways, including BIRC5, BNIP3, CD40LG, DAPK1, LTA, TNFRSF21 and TP73. The observed effects of Rapamycin on tumor suppression are likely to involve the autophagy process, evidenced by the inhibition of autophagy modulators (TGFβ1, RGS19 and AKT1), autophagosome biogenesis components (AMBRA1, ATG9B and TMEM74) and autophagy byproducts (APP). Identifying gene-gene interaction (GGI) networks provided a comprehensive view of the drug's mechanism and connected the studied tumorigenesis processes to potential functional interactions of various kinds (physical interaction, co-expression, genetic interactions etc.). In conclusion, Rapamycin shows promise as a clinical agent for managing Ca9-22 gingiva carcinoma cells.
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Affiliation(s)
- Sofia Papadakos
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada; (S.P.); (H.I.)
| | - Hawraa Issa
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada; (S.P.); (H.I.)
| | - Abdulaziz Alamri
- Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.); (A.A.)
| | - Abdullah Alamri
- Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.); (A.A.)
| | - Abdelhabib Semlali
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC G1V 0A6, Canada; (S.P.); (H.I.)
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Saffari A, Brechmann B, Böger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu JE, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore ED, Barrett L, Borner GHH, Davies AK, Ebrahimi-Fakhari D, Sahin M. High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia. Nat Commun 2024; 15:584. [PMID: 38233389 PMCID: PMC10794252 DOI: 10.1038/s41467-023-44264-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adapter protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, BCH-HSP-C01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate potential mechanisms of action of BCH-HSP-C01. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future studies.
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Affiliation(s)
- Afshin Saffari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Child Neurology and Inherited Metabolic Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Brechmann
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cedric Böger
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wardiya Afshar Saber
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hellen Jumo
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Dosh Whye
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Delaney Wood
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lara Wahlster
- Department of Hematology & Oncology, Boston Children's Hospital & Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Julian E Alecu
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marvin Ziegler
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marlene Scheffold
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kellen Winden
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jed Hubbs
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth D Buttermore
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lee Barrett
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Darius Ebrahimi-Fakhari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Mustafa Sahin
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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Liénard C, Pintart A, Bomont P. Neuronal Autophagy: Regulations and Implications in Health and Disease. Cells 2024; 13:103. [PMID: 38201307 PMCID: PMC10778363 DOI: 10.3390/cells13010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Autophagy is a major degradative pathway that plays a key role in sustaining cell homeostasis, integrity, and physiological functions. Macroautophagy, which ensures the clearance of cytoplasmic components engulfed in a double-membrane autophagosome that fuses with lysosomes, is orchestrated by a complex cascade of events. Autophagy has a particularly strong impact on the nervous system, and mutations in core components cause numerous neurological diseases. We first review the regulation of autophagy, from autophagosome biogenesis to lysosomal degradation and associated neurodevelopmental/neurodegenerative disorders. We then describe how this process is specifically regulated in the axon and in the somatodendritic compartment and how it is altered in diseases. In particular, we present the neuronal specificities of autophagy, with the spatial control of autophagosome biogenesis, the close relationship of maturation with axonal transport, and the regulation by synaptic activity. Finally, we discuss the physiological functions of autophagy in the nervous system, during development and in adulthood.
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Affiliation(s)
- Caroline Liénard
- NeuroMyoGene Institute—PGNM, CNRS UMR 5261—INSERM U1315, University of Claude Bernard Lyon 1, 69008 Lyon, France; (C.L.); (A.P.)
- CHU Montpellier, University of Montpellier, 34295 Montpellier, France
| | - Alexandre Pintart
- NeuroMyoGene Institute—PGNM, CNRS UMR 5261—INSERM U1315, University of Claude Bernard Lyon 1, 69008 Lyon, France; (C.L.); (A.P.)
| | - Pascale Bomont
- NeuroMyoGene Institute—PGNM, CNRS UMR 5261—INSERM U1315, University of Claude Bernard Lyon 1, 69008 Lyon, France; (C.L.); (A.P.)
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Khalko RK, Pandeya A, Saxena S, Gosipatala SB. HCMV miR-UL70-3p downregulates the rapamycin-induced autophagy by targeting the autophagy-related protein 9A (ATG9A). Int Rev Immunol 2024; 43:197-210. [PMID: 38164951 DOI: 10.1080/08830185.2023.2296488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/01/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Human cytomegalovirus (HCMV) is a representative β-herpesvirus that establishes persistent infections in humans, and exhibits high seropositivity rates in adults. It has co-evolved with its human host and employs various strategies to evade antiviral mechanisms by utilizing a significant portion of its genome. HCMV-encoded proteins and miRNAs have been implicated in regulating these mechanisms, enabling viral survival within the human body. During viral infections, autophagy, a conserved catabolic process essential for cellular homeostasis, acts as an antiviral defense mechanism. Multiple studies have reported that HCMV can modulate autophagy through its proteins and miRNAs, thereby influencing its survival within the host. In this study, we showed the potential involvement of HCMV miRNAs in cellular autophagy. We employed various bioinformatic tools to predict putative HCMV miRNAs that target autophagy-related genes and their corresponding cellular autophagy genes. Our results show that the 3'UTR of autophagy-related genes, including ATG9A, ATG9B, ATG16L2, SQSTM1, and EIF2AK2, harbors potential binding sites for hcmv-miR-UL70-3p. Experimental manipulation involving ectopic expression of hcmv-miR-UL70-3p demonstrated a significant reduction in rapamycin-induced autophagy, with ATG9A as its functional target. These findings establish that hcmv-miR-UL70-3p acts as an autophagy inhibitor by suppressing the expression of ATG9A.
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Affiliation(s)
- Raj Kumar Khalko
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Abhishek Pandeya
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Sangeeta Saxena
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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50
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Yamashita SI, Kanki T. Mitophagy Responds to the Environmental Temperature and Regulates Mitochondrial Mass in Adipose Tissues. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1461:229-243. [PMID: 39289285 DOI: 10.1007/978-981-97-4584-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
There are at least two types of adipose tissues in the body, defined as brown adipose tissues (BATs) and white adipose tissues (WATs). These tissues comprise brown and white adipocytes, respectively. The adipocytes are commonly endowed with mitochondria, but they have diverse characteristics and roles. Brown adipocytes have abundant mitochondria that contribute to the β-oxidation of fatty acids to produce chemical energy and the production of heat via uncoupling of the mitochondrial membrane potential from ATP synthesis. Alternatively, white adipocytes have fewer mitochondria that contribute to the generation of free fatty acids via lipogenesis by providing key intermediates. Besides the described types of adipocytes, brown-like adipocytes, termed beige adipocytes, are developed in WAT depots during cold exposure. Beige adipocytes also contribute to thermogenesis. Notably, beige adipocytes may transform into white-like adipocytes after the withdrawal of cold exposure. This process is marked by the elimination of mitochondria through the activation of mitochondria autophagy (mitophagy). This review aims to describe the mitophagy that occurs during the beige-to-white transition and discuss recent insights into the molecular mechanisms of this transformation. Additionally, we describe the mitophagy monitoring strategy in adipose tissues using three independent reporter systems and discuss the availabilities and limitations of the method.
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Affiliation(s)
- Shun-Ichi Yamashita
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Tomotake Kanki
- Department of Cellular Physiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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