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Srinivasan S, Álvarez D, John Peter AT, Vanni S. Unbiased MD simulations identify lipid binding sites in lipid transfer proteins. J Cell Biol 2024; 223:e202312055. [PMID: 39105757 PMCID: PMC11303870 DOI: 10.1083/jcb.202312055] [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: 12/13/2023] [Revised: 05/29/2024] [Accepted: 07/16/2024] [Indexed: 08/07/2024] Open
Abstract
The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid binding to bridge LTPs of the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.
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Affiliation(s)
| | - Daniel Álvarez
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, España
| | - Arun T John Peter
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research Bio-inspired Materials, University of Fribourg , Fribourg, Switzerland
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2
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Li Y, Zhuang Y, Chen Y, Wang G, Tang Z, Zhong Y, Zhang Y, Wu L, Ji X, Zhang Q, Pan B, Luo Y. Euphorbia factor L2 alleviated gouty inflammation by specifically suppressing both the priming and activation of NLRP3 inflammasome. Int Immunopharmacol 2024; 138:112598. [PMID: 38981223 DOI: 10.1016/j.intimp.2024.112598] [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: 03/20/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024]
Abstract
Euphorbia L. is a traditionally used herb and contains many newly identified compounds with novel chemical structures. Euphorbia factor L2 (EFL2), a diterpenoid derived from Euphorbia seeds, is reported to alleviate acute lung injury and arthritis by exerting anti-inflammatory effects. In this study, we aimed to test the therapeutic benefit and mechanisms of EFL2 in NLRP3 inflammasome-mediated gouty models and identified the potential molecular mechanism. A cell-based system was used to test the specific inhibitory effect of EFL2 on NLRP3-related inflammation. The gouty arthritis model and an air pouch inflammation model induced by monosodium urate monohydrate (MSU) crystals were used for in vivo experiments. Nlrp3-/- mice and in vitro studies were used for mechanistic exploration. Virtual molecular docking and biophysical assays were performed to identify the direct binding and regulatory target of EFL2. The inhibitory effect of EFL2 on inflammatory cell infiltration was determined by flow cytometry in vivo. The mechanism by which EFL2 activates the NLRP3 inflammasome signaling pathway was evaluated by immunological experiment and transmission electron microscopy. In vitro, EFL2 specifically reduced NLRP3 inflammasome-mediated IL-1β production and alleviated MSU crystal-induced arthritis, as well as inflammatory cell infiltration. EFL2 downregulated NF-κB phosphorylation and NLRP3 inflammasome expression by binding to glucocorticoid receptors. Moreover, EFL2 could specifically suppress the lysosome damage-mediated NLRP3 inflammasome activation process. It is expected that this work may be useful to accelerate the development of anti-inflammatory drugs originated from traditional herbs and improve therapeutics in gout and its complications.
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Affiliation(s)
- Yanhong Li
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuqing Zhuang
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuehong Chen
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guan Wang
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu 6a004a, Sichuan, China
| | - Zhigang Tang
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yutong Zhong
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuanyuan Zhang
- Sichuan Institute of Food Inspection, Chengdu, Sichuan, China
| | - Liang Wu
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xing Ji
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiuping Zhang
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin Pan
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang 262700, Shandong, China
| | - Yubin Luo
- Department of Rheumatology & Immunology, Laboratory of Rheumatology & Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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3
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Ferrari V, Tedesco B, Cozzi M, Chierichetti M, Casarotto E, Pramaggiore P, Cornaggia L, Mohamed A, Patelli G, Piccolella M, Cristofani R, Crippa V, Galbiati M, Poletti A, Rusmini P. Lysosome quality control in health and neurodegenerative diseases. Cell Mol Biol Lett 2024; 29:116. [PMID: 39237893 PMCID: PMC11378602 DOI: 10.1186/s11658-024-00633-2] [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: 04/12/2024] [Accepted: 08/13/2024] [Indexed: 09/07/2024] Open
Abstract
Lysosomes are acidic organelles involved in crucial intracellular functions, including the degradation of organelles and protein, membrane repair, phagocytosis, endocytosis, and nutrient sensing. Given these key roles of lysosomes, maintaining their homeostasis is essential for cell viability. Thus, to preserve lysosome integrity and functionality, cells have developed a complex intracellular system, called lysosome quality control (LQC). Several stressors may affect the integrity of lysosomes, causing Lysosomal membrane permeabilization (LMP), in which membrane rupture results in the leakage of luminal hydrolase enzymes into the cytosol. After sensing the damage, LQC either activates lysosome repair, or induces the degradation of the ruptured lysosomes through autophagy. In addition, LQC stimulates the de novo biogenesis of functional lysosomes and lysosome exocytosis. Alterations in LQC give rise to deleterious consequences for cellular homeostasis. Specifically, the persistence of impaired lysosomes or the malfunctioning of lysosomal processes leads to cellular toxicity and death, thereby contributing to the pathogenesis of different disorders, including neurodegenerative diseases (NDs). Recently, several pieces of evidence have underlined the importance of the role of lysosomes in NDs. In this review, we describe the elements of the LQC system, how they cooperate to maintain lysosome homeostasis, and their implication in the pathogenesis of different NDs.
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Affiliation(s)
- Veronica Ferrari
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Barbara Tedesco
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Marta Cozzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Marta Chierichetti
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Elena Casarotto
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Paola Pramaggiore
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Laura Cornaggia
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Ali Mohamed
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Guglielmo Patelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Margherita Piccolella
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Riccardo Cristofani
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Valeria Crippa
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Mariarita Galbiati
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy.
| | - Paola Rusmini
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Dipartimento Di Eccellenza, 2018-2027, Milan, Italy
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4
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Qi Z, Yang W, Xue B, Chen T, Lu X, Zhang R, Li Z, Zhao X, Zhang Y, Han F, Kong X, Liu R, Yao X, Jia R, Feng S. ROS-mediated lysosomal membrane permeabilization and autophagy inhibition regulate bleomycin-induced cellular senescence. Autophagy 2024; 20:2000-2016. [PMID: 38762757 PMCID: PMC11346523 DOI: 10.1080/15548627.2024.2353548] [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: 06/06/2023] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024] Open
Abstract
Bleomycin exhibits effective chemotherapeutic activity against multiple types of tumors, and also induces various side effects, such as pulmonary fibrosis and neuronal defects, which limit the clinical application of this drug. Macroautophagy/autophagy has been recently reported to be involved in the functions of bleomycin, and yet the mechanisms of their crosstalk remain insufficiently understood. Here, we demonstrated that reactive oxygen species (ROS) produced during bleomycin activation hampered autophagy flux by inducing lysosomal membrane permeabilization (LMP) and obstructing lysosomal degradation. Exhaustion of ROS with N-acetylcysteine relieved LMP and autophagy defects. Notably, we observed that LMP and autophagy blockage preceded the emergence of cellular senescence during bleomycin treatment. In addition, promoting or inhibiting autophagy-lysosome degradation alleviated or exacerbated the phenotypes of senescence, respectively. This suggests the alternation of autophagy activity is more a regulatory mechanism than a consequence of bleomycin-induced cellular senescence. Taken together, we reveal a specific role of bleomycin-induced ROS in mediating defects of autophagic degradation and further regulating cellular senescence in vitro and in vivo. Our findings, conversely, indicate the autophagy-lysosome degradation pathway as a target for modulating the functions of bleomycin. These provide a new perspective for optimizing bleomycin as a clinically applicable chemotherapeutics devoid of severe side-effects.Abbreviations: AT2 cells: type II alveolar epithelial cells; ATG7: autophagy related 7; bEnd.3: mouse brain microvascular endothelial cells; BNIP3L: BCL2/adenovirus E1B interacting protein 3-like; CCL2: C-C motif chemokine ligand 2; CDKN1A: cyclin dependent kinase inhibitor 1A; CDKN2A: cyclin dependent kinase inhibitor 2A; FTH1: ferritin heavy polypeptide 1; γ-H2AX: phosphorylated H2A.X variant histone; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HUVEC: human umbilical vein endothelial cells; HT22: hippocampal neuronal cell lines; Il: interleukin; LAMP: lysosomal-associated membrane protein; LMP: lysosome membrane permeabilization; MTORC1: mechanistic target of rapamycin kinase complex 1; NAC: N-acetylcysteine; NCOA4: nuclear receptor coactivator 4; PI3K: phosphoinositide 3-kinase; ROS: reactive oxygen species; RPS6KB/S6K: ribosomal protein S6 kinase; SA-GLB1/β-gal: senescence-associated galactosidase, beta 1; SAHF: senescence-associated heterochromatic foci; SASP: senescence-associated secretory phenotype; SEC62: SEC62 homolog, preprotein translocation; SEP: superecliptic pHluorin; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB.
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Affiliation(s)
- Zhangyang Qi
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Weiqi Yang
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Baibing Xue
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Tingjun Chen
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, Shandong, China
| | - Xianjie Lu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Rong Zhang
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Zhichao Li
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaoqing Zhao
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yang Zhang
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Fabin Han
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xiaohong Kong
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ruikang Liu
- Shandong Research Institute of Industrial Technology, Jinan, Shandong, China
| | - Xue Yao
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Orthopaedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin Medical University General Hospital, Tianjin, China
| | - Rui Jia
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shiqing Feng
- Department of Orthopaedics, Qilu Hospital, Shandong University Centre for Orthopaedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Orthopaedics, International Science and Technology Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin Medical University General Hospital, Tianjin, China
- Department of Orthopaedics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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5
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Yanagawa K, Kuma A, Hamasaki M, Kita S, Yamamuro T, Nishino K, Nakamura S, Omori H, Kaminishi T, Oikawa S, Kato Y, Edahiro R, Kawagoe R, Taniguchi T, Tanaka Y, Shima T, Tabata K, Iwatani M, Bekku N, Hanayama R, Okada Y, Akimoto T, Kosako H, Takahashi A, Shimomura I, Sakata Y, Yoshimori T. The Rubicon-WIPI axis regulates exosome biogenesis during ageing. Nat Cell Biol 2024; 26:1558-1570. [PMID: 39174742 DOI: 10.1038/s41556-024-01481-0] [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: 08/28/2023] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
Cells release intraluminal vesicles in multivesicular bodies as exosomes to communicate with other cells. Although recent studies suggest an intimate link between exosome biogenesis and autophagy, the detailed mechanism is not fully understood. Here we employed comprehensive RNA interference screening for autophagy-related factors and discovered that Rubicon, a negative regulator of autophagy, is essential for exosome release. Rubicon recruits WIPI2d to endosomes to promote exosome biogenesis. Interactome analysis of WIPI2d identified the ESCRT components that are required for intraluminal vesicle formation. Notably, we found that Rubicon is required for an age-dependent increase of exosome release in mice. In addition, small RNA sequencing of serum exosomes revealed that Rubicon determines the fate of exosomal microRNAs associated with cellular senescence and longevity pathways. Taken together, our current results suggest that the Rubicon-WIPI axis functions as a key regulator of exosome biogenesis and is responsible for age-dependent changes in exosome quantity and quality.
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Affiliation(s)
- Kyosuke Yanagawa
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Akiko Kuma
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Health Promotion System Science, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Maho Hamasaki
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Shunbun Kita
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
- Tokyo New Drug Research Laboratories, Pharmaceutical Business Unit, Kowa Company, Higashimurayama, Japan
| | - Tadashi Yamamuro
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Institute for Advanced Co-Creation Studies, Osaka University, Suita, Japan
- Department of Biochemistry, Nara Medical University, Kashihara, Japan
| | - Hiroko Omori
- Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Tatsuya Kaminishi
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Satoshi Oikawa
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
- Waseda Institute for Sport Sciences, Waseda University, Tokorozawa, Japan
| | - Yoshio Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kawagoe
- i2i-Labo, Yokohama Research Center, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Yokohama, Japan
| | - Takako Taniguchi
- i2i-Labo, Yokohama Research Center, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Yokohama, Japan
| | - Yoko Tanaka
- Division of Cellular Senescence, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takayuki Shima
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Biochemistry, Nara Medical University, Kashihara, Japan
| | - Keisuke Tabata
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Miki Iwatani
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Nao Bekku
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Rikinari Hanayama
- Department of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
- WPI Premium Research Institute for Human Metaverse Medicine, Osaka University, Suita, Japan
| | - Takayuki Akimoto
- Laboratory of Muscle Biology, Faculty of Sport Sciences, Waseda University, Tokorozawa, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Akiko Takahashi
- Division of Cellular Senescence, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Health Promotion System Science, Graduate School of Medicine, Osaka University, Suita, Japan.
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
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6
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Suzuki Y, Hayashi K, Goto F, Nomura Y, Fujimoto C, Makishima M. Premature senescence is regulated by crosstalk among TFEB, the autophagy lysosomal pathway and ROS derived from damaged mitochondria in NaAsO 2-exposed auditory cells. Cell Death Discov 2024; 10:382. [PMID: 39191766 DOI: 10.1038/s41420-024-02139-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 07/13/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024] Open
Abstract
Age-related hearing loss (ARHL) is one of the most prevalent types of sensory decline in a superaging society. Although various studies have focused on the effect of oxidative stress on the inner ear as an inducer of ARHL, there are no effective preventive approaches for ARHL. Recent studies have suggested that oxidative stress-induced DNA damage responses (oxidative DDRs) drive cochlear cell senescence and contribute to accelerated ARHL, and autophagy could function as a defense mechanism against cellular senescence in auditory cells. However, the underlying mechanism remains unclear. Sodium arsenite (NaAsO2) is a unique oxidative stress inducer associated with reactive oxygen species (ROS) that causes high-tone hearing loss similar to ARHL. Transcription factor EB (TFEB) functions as a master regulator of the autophagy‒lysosome pathway (ALP), which is a potential target during aging and the pathogenesis of various age-related diseases. Here, we focused on the function of TFEB and the impact of intracellular ROS as a potential target for ARHL treatment in a NaAsO2-induced auditory premature senescence model. Our results suggested that short exposure to NaAsO2 leads to DNA damage, lysosomal damage and mitochondrial damage in auditory cells, triggering temporary signals for TFEB transport into the nucleus and, as a result, causing insufficient autophagic flux and declines in lysosomal function and biogenesis and mitochondrial quality. Then, intracellular ROS derived from damaged mitochondria play a role as a second messenger to induce premature senescence in auditory cells. These findings suggest that TFEB activation via transport into the nucleus contributes to anti-senescence activity in auditory cells and represents a new therapeutic target for ARHL. We have revealed the potential function of TFEB as a master regulator of the induction of oxidative stress-induced premature senescence and the senescence-associated secretion phenotype (SASP) in auditory cells, which regulates ALP and controls mitochondrial quality through ROS production.
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Affiliation(s)
- Yuna Suzuki
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo, Japan
| | - Ken Hayashi
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo, Japan.
- Department of Otolaryngology, Sakura Koedo Clinic, Saitama, Japan.
- Department of Otolaryngology-Head and Neck Surgery, Keio University, Tokyo, Japan.
| | - Fumiyuki Goto
- Department of Otolaryngology-Head and Neck Surgery, Tokai University, Kanagawa, Japan
| | - Yasuyuki Nomura
- Department of Otolaryngology-Head and Neck Surgery, Nihon University, Tokyo, Japan
| | - Chisato Fujimoto
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo, Japan
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7
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Bonet-Ponce L, Kluss JH, Cookson MR. Mechanisms of lysosomal tubulation and sorting driven by LRRK2. Biochem Soc Trans 2024; 52:1909-1919. [PMID: 39083004 DOI: 10.1042/bst20240087] [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: 05/14/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/29/2024]
Abstract
Lysosomes are dynamic cellular structures that adaptively remodel their membrane in response to stimuli, including membrane damage. Lysosomal dysfunction plays a central role in the pathobiology of Parkinson's disease (PD). Gain-of-function mutations in Leucine-rich repeat kinase 2 (LRRK2) cause familial PD and genetic variations in its locus increase the risk of developing the sporadic form of the disease. We previously uncovered a process we term LYTL (LYsosomal Tubulation/sorting driven by LRRK2), wherein membrane-damaged lysosomes generate tubules sorted into mobile vesicles. Subsequently, these vesicles interact with healthy lysosomes. LYTL is orchestrated by LRRK2 kinase activity, via the recruitment and phosphorylation of a subset of RAB GTPases. Here, we summarize the current understanding of LYTL and its regulation, as well as the unknown aspects of this process.
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Affiliation(s)
- Luis Bonet-Ponce
- Department of Neurology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, U.S.A
| | | | - Mark R Cookson
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, U.S.A
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8
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Li K, Li L, Xie X, Zhu J, Xia D, Xiang L, Cai K, Zhang J. Spatially confined photoacoustic effects of responsive nanoassembly boosts lysosomal membrane permeabilization and immunotherapy of triple-negative breast cancer. Acta Biomater 2024:S1742-7061(24)00465-3. [PMID: 39209130 DOI: 10.1016/j.actbio.2024.08.021] [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: 06/13/2024] [Revised: 08/10/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Although immunogenic cell death (ICD) induced by lysosomal membrane permeabilization (LMP) evidently enhance the effectiveness of antitumor immunity for triple-negative breast cancer (TNBC) with poor immunogenicity, their potential is increasingly restricted by the development of other death pathways and the repair of lysosomes by endoplasmic reticulum (ER) during LMP induction. Herein, a polydopamine nanocomposite with i-motif DNA modified and BNN6 loaded is prepared toward boosting LMP and immunotherapy of TNBC by synergy of spatially confined photoacoustic (PA) effects and nitric oxide. Combining the high-frequency pulsed laser (4000 kHz) with the intra-lysosomal assembly of nanocomposites produced spatially confined and significantly boosted PA effects (4.8-fold higher than the individually dispersed particles extracellular), suppressing damage to other cellular components and selectively reducing lysosomal integrity to 19.2 %. Simultaneously, the releasing of nitric oxide inhibited the repair of lysosomes by ER stress, causing exacerbated LMP. Consequently, efficient immune activation was achieved, including the abundant releasing of CRT/HMGB1 (5.93-6.8-fold), the increasing maturation of dendritic cells (3.41-fold), and the fostered recruitment of CD4+/CD8+T cells (3.99-3.78-fold) in vivo. The study paves a new avenue for the rational design and synergy of confined energy conversion and responsive nanostructures to achieve the treatment of low immunogenicity tumors. STATEMENT OF SIGNIFICANCE: A strategy of boosting lysosomal membrane permeabilization (LMP) and concomitantly preventing the repair was developed to address the immunotherapy challenge of triple-negative breast cancer. Spatially confined and significantly enhanced photoacoustic (PA) effects were achieved through DNA-guided pH-responsive assembly of polydopamine nanocomposites in lysosomes and application of a high-frequency pulsed laser. Efficient immunogenic cell death was guaranteed by selective and powerful damage of lysosomal membranes through the significant contrast of PA intensities for dispersed/assembled particles and nitric oxide release induced endoplasmic reticulum stress. The study paves a new avenue for the rational design and synergy of confined energy conversion and responsive nanostructures to achieve the treatment of low immunogenicity tumors.
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Affiliation(s)
- Kunlin Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China
| | - Lin Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China
| | - Xiyue Xie
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China
| | - Jing Zhu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China
| | - Daqing Xia
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China
| | - Lunli Xiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China
| | - Jixi Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No 174 Shazheng Road, Chongqing 400044, China.
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9
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Wang H, Jiang Y, Zhu M, Li H, Chen H, Wang H, Zhang S, Guo Q, Hui H. LW-213, a derivative of wogonin, triggers reticulophagy-mediated cell death in NSCLC via lysosomal damage combined with NPC1 inhibition. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 134:155958. [PMID: 39241385 DOI: 10.1016/j.phymed.2024.155958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Maintaining intracellular equilibrium is essential for the viability of tumor cells, which tend to be particularly vulnerable to environmental stressors. Consequently, targeting the disruption of this homeostasis offers a promising approach for oncological treatments. LW-213, a novel derivative of wogonin, effectively induces apoptosis in cancer cells by initiating endoplasmic reticulum (ER) stress, although the precise molecular pathways involved remain intricate and multifaceted. PURPOSE This research aimed to explore how LW-213 prompts apoptosis in non-small cell lung cancer (NSCLC) cells and to clarify the detailed mechanisms that govern this process. METHODS Various NSCLC cell lines were utilized to delineate the apoptotic effects induced by LW-213. Advanced methodologies, including RNA sequencing (RNA-seq), Western blotting (WB), immunofluorescence (IF), immunoprecipitation (IP), flow cytometry (Fc), real-time quantitative polymerase chain reaction (RT-qPCR), and electron microscopy, were employed to investigate the underlying molecular interactions. The efficacy and mechanistic action of LW-213 were also assessed in a xenograft model using nude mice. RESULTS We demonstrated that LW-213, a small molecule cationic amphiphilic drug (CAD), inhibited Niemann-Pick C1 (NPC1) function and induced lysosomal membrane damage, thereby activating the phosphoinositide-initiated membrane tethering and lipid transport (PITT) pathway. This activation promoted cholesterol transport from the ER to the lysosome, perpetuating a cholesterol-deficient state in the ER, including massive exocytosis of Ca2+ and activation of FAM134B-mediated reticulophagy. Ultimately, excessive reticulophagy induced lethal ER stress. CONCLUSIONS In summary, our study elucidates an organelle domino reaction initiated by lysosome damage and a series of self-rescue mechanisms that eventually lead to irreversible lethal effects, revealing a potential drug intervention strategy.
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Affiliation(s)
- Hongzheng Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Yuexin Jiang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Mengyuan Zhu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Hui Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Hongyu Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Haidi Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Shuai Zhang
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 21009, PR China
| | - Qinglong Guo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Hui Hui
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
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10
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Donahue E, Hepowit NL, Keuchel B, Mulligan AG, Johnson DJ, Ellisman M, Arrojo E Drigo R, MacGurn J, Burkewitz K. ER-phagy drives age-onset remodeling of endoplasmic reticulum structure-function and lifespan. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607085. [PMID: 39149405 PMCID: PMC11326278 DOI: 10.1101/2024.08.07.607085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The endoplasmic reticulum (ER) comprises an array of structurally distinct subdomains, each with characteristic functions. While altered ER-associated processes are linked to age-onset pathogenesis, whether shifts in ER morphology underlie these functional changes is unclear. We report that ER remodeling is a conserved feature of the aging process in models ranging from yeast to C. elegans and mammals. Focusing on C. elegans as an exemplar of metazoan aging, we find that as animals age, ER mass declines in virtually all tissues and ER morphology shifts from rough sheets to tubular ER. The accompanying large-scale shifts in proteomic composition correspond to the ER turning from protein synthesis to lipid metabolism. To drive this substantial remodeling, ER-phagy is activated early in adulthood, promoting turnover of rough ER in response to rises in luminal protein-folding burden and reduced global protein synthesis. Surprisingly, ER remodeling is a pro-active and protective response during aging, as ER-phagy impairment limits lifespan in yeast and diverse lifespan-extending paradigms promote profound remodeling of ER morphology even in young animals. Altogether our results reveal ER-phagy and ER morphological dynamics as pronounced, underappreciated mechanisms of both normal aging and enhanced longevity.
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Affiliation(s)
- Ekf Donahue
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - N L Hepowit
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - B Keuchel
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - A G Mulligan
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - D J Johnson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - M Ellisman
- National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - R Arrojo E Drigo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37240, USA
| | - J MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - K Burkewitz
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
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11
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Cabukusta B, Borst Pauwels S, Akkermans JJLL, Blomberg N, Mulder AA, Koning RI, Giera M, Neefjes J. The ORP9-ORP11 dimer promotes sphingomyelin synthesis. eLife 2024; 12:RP91345. [PMID: 39106189 PMCID: PMC11302984 DOI: 10.7554/elife.91345] [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] [Indexed: 08/09/2024] Open
Abstract
Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by the loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans-Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.
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Affiliation(s)
- Birol Cabukusta
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Shalom Borst Pauwels
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Jimmy JLL Akkermans
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Niek Blomberg
- Centre for Proteomics and Metabolomics, Leiden University Medical CenterLeidenNetherlands
| | - Aat A Mulder
- Electron Microscopy Facility, Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Roman I Koning
- Electron Microscopy Facility, Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Martin Giera
- Centre for Proteomics and Metabolomics, Leiden University Medical CenterLeidenNetherlands
| | - Jacques Neefjes
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
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12
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Deretic V, Duque T, Trosdal E, Paddar M, Javed R, Akepati P. Membrane atg8ylation in Canonical and Noncanonical Autophagy. J Mol Biol 2024; 436:168532. [PMID: 38479594 PMCID: PMC11260254 DOI: 10.1016/j.jmb.2024.168532] [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: 01/23/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024]
Abstract
Membrane atg8ylation is a homeostatic process responding to membrane remodeling and stress signals. Membranes are atg8ylated by mammalian ATG8 ubiquitin-like proteins through a ubiquitylation-like cascade. A model has recently been put forward which posits that atg8ylation of membranes is conceptually equivalent to ubiquitylation of proteins. Like ubiquitylation, membrane atg8ylation involves E1, E2 and E3 enzymes. The E3 ligases catalyze the final step of atg8ylation of aminophospholipids in membranes. Until recently, the only known E3 ligase for membrane atg8ylation was ATG16L1 in a noncovalent complex with the ATG12-ATG5 conjugate. ATG16L1 was first identified as a factor in canonical autophagy. During canonical autophagy, the ATG16L1-based E3 ligase complex includes WIPI2, which in turn recognizes phosphatidylinositiol 3-phosphate and directs atg8ylation of autophagic phagophores. As an alternative to WIPIs, binding of ATG16L1 to the proton pump V-ATPase guides atg8ylation of endolysosomal and phagosomal membranes in response to lumenal pH changes. Recently, a new E3 complex containing TECPR1 instead of ATG16L1, has been identified that responds to sphingomyelin's presence on the cytofacial side of perturbed endolysosomal membranes. In present review, we cover the principles of membrane atg8ylation, catalog its various presentations, and provide a perspective on the growing repertoire of E3 ligase complexes directing membrane atg8ylation at diverse locations.
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Affiliation(s)
- Vojo Deretic
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA.
| | - Thabata Duque
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Einar Trosdal
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Masroor Paddar
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Ruheena Javed
- Autophagy Inflammation and Metabolism Center of Biochemical Research Excellence, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA; Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Prithvi Akepati
- Gastroenterology Division, Department of Internal Medicine, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
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13
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Alessi DR, Pfeffer SR. Leucine-Rich Repeat Kinases. Annu Rev Biochem 2024; 93:261-287. [PMID: 38621236 DOI: 10.1146/annurev-biochem-030122-051144] [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: 04/17/2024]
Abstract
Activating mutations in leucine-rich repeat kinase 2 (LRRK2) represent the most common cause of monogenic Parkinson's disease. LRRK2 is a large multidomain protein kinase that phosphorylates a specific subset of the ∼65 human Rab GTPases, which are master regulators of the secretory and endocytic pathways. After phosphorylation by LRRK2, Rabs lose the capacity to bind cognate effector proteins and guanine nucleotide exchange factors. Moreover, the phosphorylated Rabs cannot interact with their cognate prenyl-binding retrieval proteins (also known as guanine nucleotide dissociation inhibitors) and, thus, they become trapped on membrane surfaces. Instead, they gain the capacity to bind phospho-Rab-specific effector proteins, such as RILPL1, with resulting pathological consequences. Rab proteins also act upstream of LRRK2 by controlling its activation and recruitment onto membranes. LRRK2 signaling is counteracted by the phosphoprotein phosphatase PPM1H, which selectively dephosphorylates phospho-Rab proteins. We present here our current understanding of the structure, biochemical properties, and cell biology of LRRK2 and its related paralog LRRK1 and discuss how this information guides the generation of LRRK2 inhibitors for the potential benefit of patients.
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Affiliation(s)
- Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, United Kingdom;
| | - Suzanne R Pfeffer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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14
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Han X, Li B, Wang W, Feng B, Tang Q, Qi Y, Zhao R, Qiu W, Zhao S, Pan Z, Guo X, Du H, Qiu J, Liu H, Li G, Xue H. Cerium Vanadate Nanozyme with pH-Dependent Dual Enzymatic Activity for Glioblastoma Targeted Therapy and Postradiotherapy Damage Protection. ACS NANO 2024; 18. [PMID: 39016679 PMCID: PMC11295195 DOI: 10.1021/acsnano.4c06616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Nanocatalytic therapy is an emerging technology that uses synthetic nanoscale enzyme mimics for biomedical treatment. However, in the field of neuroscience, achieving neurological protection while simultaneously killing tumor cells is a technical challenge. Herein, we synthesized a biomimic and translational cerium vanadate (CeVO4) nanozyme for glioblastoma (GBM) therapy and the repair of brain damage after GBM ionizing radiation (IR). This system exhibited pH dependence: it showed potent Superoxide dismutase (SOD) enzyme activity in a neutral environment and Peroxidase (POD) enzyme activity in an acidic environment. In GBM cells, this system acted in lysosomes, causing cellular damage and reactive oxygen species (ROS) accumulation; in neuronal cells, this nanozyme could undergo lysosomal escape and nanozyme aggregation with mitochondria, reversing the mitochondrial damage caused by IR and restoring the expression level of the antiapoptotic BCL-2 protein. Mechanistically, we believe that this distribution difference is related to the specific uptake internalization mechanism and lysosomal repair pathway in neurons, and ultimately led to the dual effect of tumor killing and nerve repair in the in vivo model. In summary, this study provides insight into the repair of brain damage after GBM radiation therapy.
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Affiliation(s)
- Xiao Han
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
- Department
of Neurosurgery, Children’s Hospital
Affiliated to Shandong University, Jinan Children’s Hospital, Jinan, Shandong 250001, P.R. China
| | - Boyan Li
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Wenhan Wang
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Bowen Feng
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Qilin Tang
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Yanhua Qi
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Rongrong Zhao
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Wei Qiu
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Shulin Zhao
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Ziwen Pan
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Xiaofan Guo
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Hao Du
- Department
of Cell Biology, University of Connecticut
School of Medicine, Farmington, Connecticut 06032, United States
| | - Jichuan Qiu
- State
Key Laboratory of Crystal Materials, Shandong
University, Jinan, Shandong 250100, P. R. China
| | - Hong Liu
- State
Key Laboratory of Crystal Materials, Shandong
University, Jinan, Shandong 250100, P. R. China
- Institute
for Advanced Interdisciplinary Research (IAIR), University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Gang Li
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
| | - Hao Xue
- Department
of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute
of Brain and Brain-Inspired Science, Shandong
University, Jinan, Shandong 250012, P. R. China
- Shandong
Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, P. R. China
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15
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Paddar MA, Wang F, Trosdal ES, Hendrix E, He Y, Salemi M, Mudd M, Jia J, Duque TLA, Javed R, Phinney B, Deretic V. Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602886. [PMID: 39026874 PMCID: PMC11257513 DOI: 10.1101/2024.07.10.602886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
ATG5 is one of the core autophagy proteins with additional functions such as noncanonical membrane atg8ylation, which among a growing number of biological outputs includes control of tuberculosis in animal models. Here we show that ATG5 associates with retromer's core components VPS26, VPS29 and VPS35 and modulates retromer function. Knockout of ATG5 blocked trafficking of a key glucose transporter sorted by the retromer, GLUT1, to the plasma membrane. Knockouts of other genes essential for membrane atg8ylation, of which ATG5 is a component, affected GLUT1 sorting, indicating that membrane atg8ylation as a process affects retromer function and endosomal sorting. The contribution of membrane atg8ylation to retromer function in GLUT1 sorting was independent of canonical autophagy. These findings expand the scope of membrane atg8ylation to specific sorting processes in the cell dependent on the retromer and its known interactors.
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Affiliation(s)
- Masroor Ahmad Paddar
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Fulong Wang
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Einar S Trosdal
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Emily Hendrix
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Yi He
- Department of Chemistry & Chemical Biology, The University of New Mexico, Albuquerque, NM, USA
| | - Michelle Salemi
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Michal Mudd
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Jingyue Jia
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Thabata L A Duque
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Ruheena Javed
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
| | - Brett Phinney
- Proteomics Core Facility, UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 915 Camino de Salud, NE, Albuquerque, NM 87131, USA
- Lead Contact
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16
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Li H, Smeriglio N, Ni J, Wang Y, Sekine S, Hao L. Benchmarking and Automating the Biotinylation Proteomics Workflow. RESEARCH SQUARE 2024:rs.3.rs-4590410. [PMID: 39011118 PMCID: PMC11247940 DOI: 10.21203/rs.3.rs-4590410/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Protein biotinylation has been widely used in biotechnology with various labeling and enrichment strategies. However, different enrichment strategies have not been systematically evaluated due to the lack of a benchmarking model for fair comparison. Most biotinylation proteomics workflows suffer from lengthy experimental steps, non-specific bindings, limited throughput, and experimental variability. To address these challenges, we designed a two-proteome model, where biotinylated yeast proteins were spiked in unlabeled human proteins, allowing us to distinguish true enrichment from non-specific bindings. Using this benchmarking model, we compared common biotinylation proteomics methods and provided practical selection guidelines. We significantly optimized and shortened sample preparation from 3 days to 9 hours, enabling fully-automated 96-well plate sample processing. Next, we applied this optimized and automated workflow for proximity labeling to investigate the intricate interplay between mitochondria and lysosomes in living cells under both healthy state and mitochondrial damage. Our results suggested a time-dependent proteome remodeling and dynamic translocation within mitochondria and between mitochondria and lysosomes upon mitochondrial damage. This newly established benchmarking model and the fully-automated 9-hour workflow can be readily applied to the broad fields of protein biotinylation to study protein interaction and organelle dynamics.
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Affiliation(s)
- Haorong Li
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Noah Smeriglio
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Jiawei Ni
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Yan Wang
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Shiori Sekine
- Aging Institute, Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Ling Hao
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
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17
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Guallar-Garrido S, Soldati T. Exploring host-pathogen interactions in the Dictyostelium discoideum-Mycobacterium marinum infection model of tuberculosis. Dis Model Mech 2024; 17:dmm050698. [PMID: 39037280 DOI: 10.1242/dmm.050698] [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] [Indexed: 07/23/2024] Open
Abstract
Mycobacterium tuberculosis is a pathogenic mycobacterium that causes tuberculosis. Tuberculosis is a significant global health concern that poses numerous clinical challenges, particularly in terms of finding effective treatments for patients. Throughout evolution, host immune cells have developed cell-autonomous defence strategies to restrain and eliminate mycobacteria. Concurrently, mycobacteria have evolved an array of virulence factors to counteract these host defences, resulting in a dynamic interaction between host and pathogen. Here, we review recent findings, including those arising from the use of the amoeba Dictyostelium discoideum as a model to investigate key mycobacterial infection pathways. D. discoideum serves as a scalable and genetically tractable model for human phagocytes, providing valuable insights into the intricate mechanisms of host-pathogen interactions. We also highlight certain similarities between M. tuberculosis and Mycobacterium marinum, and the use of M. marinum to more safely investigate mycobacteria in D. discoideum.
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Affiliation(s)
- Sandra Guallar-Garrido
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Science II, 1211 Geneva-4, Switzerland
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Science II, 1211 Geneva-4, Switzerland
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18
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Hu M, Feng X, Liu Q, Liu S, Huang F, Xu H. The ion channels of endomembranes. Physiol Rev 2024; 104:1335-1385. [PMID: 38451235 PMCID: PMC11381013 DOI: 10.1152/physrev.00025.2023] [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: 06/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/08/2024] Open
Abstract
The endomembrane system consists of organellar membranes in the biosynthetic pathway [endoplasmic reticulum (ER), Golgi apparatus, and secretory vesicles] as well as those in the degradative pathway (early endosomes, macropinosomes, phagosomes, autophagosomes, late endosomes, and lysosomes). These endomembrane organelles/vesicles work together to synthesize, modify, package, transport, and degrade proteins, carbohydrates, and lipids, regulating the balance between cellular anabolism and catabolism. Large ion concentration gradients exist across endomembranes: Ca2+ gradients for most endomembrane organelles and H+ gradients for the acidic compartments. Ion (Na+, K+, H+, Ca2+, and Cl-) channels on the organellar membranes control ion flux in response to cellular cues, allowing rapid informational exchange between the cytosol and organelle lumen. Recent advances in organelle proteomics, organellar electrophysiology, and luminal and juxtaorganellar ion imaging have led to molecular identification and functional characterization of about two dozen endomembrane ion channels. For example, whereas IP3R1-3 channels mediate Ca2+ release from the ER in response to neurotransmitter and hormone stimulation, TRPML1-3 and TMEM175 channels mediate lysosomal Ca2+ and H+ release, respectively, in response to nutritional and trafficking cues. This review aims to summarize the current understanding of these endomembrane channels, with a focus on their subcellular localizations, ion permeation properties, gating mechanisms, cell biological functions, and disease relevance.
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Affiliation(s)
- Meiqin Hu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Xinghua Feng
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Qiang Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Siyu Liu
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Fangqian Huang
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Haoxing Xu
- Department of Neurology and Department of Cardiology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- New Cornerstone Science Laboratory, Liangzhu Laboratory and School of Basic Medical Sciences, Zhejiang University, Hangzhou, People's Republic of China
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States
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19
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Lei Y, Klionsky DJ. A delicate decision between repair and degradation of damaged lysosomes. Autophagy 2024; 20:1471-1472. [PMID: 38744436 PMCID: PMC11210907 DOI: 10.1080/15548627.2024.2350738] [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] [Indexed: 05/16/2024] Open
Abstract
The destination of a damaged lysosome is either being repaired if the damage is small or degraded through a lysosome-specific macroautophagy/autophagy pathway named lysophagy when the damage is too extensive to repair. Even though previous studies report lumenal glycan exposure during lysosome damage as a signal to trigger lysophagy, it is possibly beneficial for cells to initiate lysophagy earlier than membrane rupture. In a recently published article, Gahlot et al. determined that SPART/SPG20 senses lipid-packing defects and recruits and activates the ubiquitin ligase ITCH, which labels damaged lysosomes with ubiquitin chains to initiate lysophagy.
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Affiliation(s)
- Yuchen Lei
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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20
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Tan L, Qu J, Wang J. Development of novel lysosome-related signatures and their potential target drugs based on bulk RNA-seq and scRNA-seq for diabetic foot ulcers. Hum Genomics 2024; 18:62. [PMID: 38862997 PMCID: PMC11165785 DOI: 10.1186/s40246-024-00629-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Diabetic foot ulcers (DFU) is the most serious complication of diabetes mellitus, which has become a global health problem due to its high morbidity and disability rates and the poor efficacy of conventional treatments. Thus, it is urgent to identify novel molecular targets to improve the prognosis and reduce disability rate in DFU patients. RESULTS In the present study, bulk RNA-seq and scRNA-seq associated with DFU were downloaded from the GEO database. We identified 1393 DFU-related DEGs by differential analysis and WGCNA analysis together, and GO/KEGG analysis showed that these genes were associated with lysosomal and immune/inflammatory responses. Immediately thereafter, we identified CLU, RABGEF1 and ENPEP as DLGs for DFU using three machine learning algorithms (Randomforest, SVM-RFE and LASSO) and validated their diagnostic performance in a validation cohort independent of this study. Subsequently, we constructed a novel artificial neural network model for molecular diagnosis of DFU based on DLGs, and the diagnostic performance in the training and validation cohorts was sound. In single-cell sequencing, the heterogeneous expression of DLGs also provided favorable evidence for them to be potential diagnostic targets. In addition, the results of immune infiltration analysis showed that the abundance of mainstream immune cells, including B/T cells, was down-regulated in DFUs and significantly correlated with the expression of DLGs. Finally, we found latamoxef, parthenolide, meclofenoxate, and lomustine to be promising anti-DFU drugs by targeting DLGs. CONCLUSIONS CLU, RABGEF1 and ENPEP can be used as novel lysosomal molecular signatures of DFU, and by targeting them, latamoxef, parthenolide, meclofenoxate and lomustine were identified as promising anti-DFU drugs. The present study provides new perspectives for the diagnosis and treatment of DFU and for improving the prognosis of DFU patients.
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Affiliation(s)
- Longhai Tan
- Department of Dermatology, Tianjin Beichen Hospital, Tianjin, 300400, China.
| | - Junjun Qu
- Zhu Xianyi Memorial Hospital of Tianjin Medical University, Tianjin, 300134, China
| | - Junxia Wang
- Department of Dermatology, Tianjin Beichen Hospital, Tianjin, 300400, China
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21
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Wang X, Xu P, Bentley-DeSousa A, Hancock-Cerutti W, Cai S, Johnson BT, Tonelli F, Talaia G, Alessi DR, Ferguson SM, De Camilli P. Lysosome damage triggers acute formation of ER to lysosomes membrane tethers mediated by the bridge-like lipid transport protein VPS13C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.598070. [PMID: 38895395 PMCID: PMC11185796 DOI: 10.1101/2024.06.08.598070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Based on genetic studies, lysosome dysfunction is thought to play a pathogenetic role in Parkinson's disease (PD). Here we show that VPS13C, a bridge-like lipid transport protein and a PD gene, is a sensor of lysosome stress/damage. Upon lysosome membrane perturbation, VPS13C rapidly relocates from the cytosol to the surface of lysosomes where it tethers their membranes to the ER. This recruitment depends on Rab7 and requires release of a brake, most likely an intramolecular interaction within VPS13C, which hinders access of its VAB domain to lysosome-bound Rab7. While another PD protein, LRRK2, is also recruited to stressed/damaged lysosomes, its recruitment occurs at much later stages and by different mechanisms. Given the putative role of VPS13 proteins in bulk lipid transport, these findings suggest lipid delivery to lysosomes by VPS13C is part of an early response to lysosome damage.
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22
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Ajiki M, Yoshikawa M, Miyazaki T, Kawasaki A, Aoki K, Nakatsu F, Tsukiji S. ORP9-PH domain-based fluorescent reporters for visualizing phosphatidylinositol 4-phosphate dynamics in living cells. RSC Chem Biol 2024; 5:544-555. [PMID: 38846081 PMCID: PMC11151866 DOI: 10.1039/d3cb00232b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/15/2024] [Indexed: 06/09/2024] Open
Abstract
Fluorescent reporters that visualize phosphatidylinositol 4-phosphate (PI4P) in living cells are indispensable to elucidate the roles of this fundamental lipid in cell physiology. However, currently available PI4P reporters have limitations, such as Golgi-biased localization and low detection sensitivity. Here, we present a series of fluorescent PI4P reporters based on the pleckstrin homology (PH) domain of oxysterol-binding protein-related protein 9 (ORP9). We show that the green fluorescent protein AcGFP1-tagged ORP9-PH domain can be used as a fluorescent PI4P reporter to detect cellular PI4P across its wide distribution at multiple cellular locations, including the plasma membrane (PM), Golgi, endosomes, and lysosomes with high specificity and contrast. We also developed blue, red, and near-infrared fluorescent PI4P reporters suitable for multicolor fluorescence imaging experiments. Finally, we demonstrate the utility of the ORP9-PH domain-based reporter to visualize dynamic changes in the PI4P distribution and level in living cells upon synthetic ER-PM membrane contact manipulation and GPCR stimulation. This work offers a new set of genetically encoded fluorescent PI4P reporters that are practically useful for the study of PI4P biology.
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Affiliation(s)
- Moeka Ajiki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
| | - Masaru Yoshikawa
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
| | - Tomoki Miyazaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
| | - Asami Kawasaki
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University 1-757 Asahimachi, Chuo-ku Niigata 951-8510 Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji-cho Okazaki Aichi 444-8787 Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji-cho Okazaki Aichi 444-8787 Japan
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (The Graduate University for Advanced Studies) 5-1 Higashiyama, Myodaiji-cho Okazaki Aichi 444-8787 Japan
| | - Fubito Nakatsu
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University 1-757 Asahimachi, Chuo-ku Niigata 951-8510 Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology Gokiso-cho, Showa-ku Nagoya 466-8555 Japan
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23
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Li YE, Norris DM, Xiao FN, Pandzic E, Whan RM, Fok S, Zhou M, Du G, Liu Y, Du X, Yang H. Phosphatidylserine regulates plasma membrane repair through tetraspanin-enriched macrodomains. J Cell Biol 2024; 223:e202307041. [PMID: 38530252 PMCID: PMC10964951 DOI: 10.1083/jcb.202307041] [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: 07/12/2023] [Revised: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
The integrity of the plasma membrane is critical to cell function and survival. Cells have developed multiple mechanisms to repair damaged plasma membranes. A key process during plasma membrane repair is to limit the size of the damage, which is facilitated by the presence of tetraspanin-enriched rings surrounding damage sites. Here, we identify phosphatidylserine-enriched rings surrounding damaged sites of the plasma membrane, resembling tetraspanin-enriched rings. Importantly, the formation of both the phosphatidylserine- and tetraspanin-enriched rings requires phosphatidylserine and its transfer proteins ORP5 and ORP9. Interestingly, ORP9, but not ORP5, is recruited to the damage sites, suggesting cells acquire phosphatidylserine from multiple sources upon plasma membrane damage. We further demonstrate that ORP9 contributes to efficient plasma membrane repair. Our results thus unveil a role for phosphatidylserine and its transfer proteins in facilitating the formation of tetraspanin-enriched macrodomains and plasma membrane repair.
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Affiliation(s)
- Yang E. Li
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Dougall M. Norris
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Fanqian N. Xiao
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Elvis Pandzic
- Katerina Gaus Light Microscopy Facility, Mark Wainwright Analytical Center, University of New South Wales, Sydney, Australia
| | - Renee M. Whan
- Katerina Gaus Light Microscopy Facility, Mark Wainwright Analytical Center, University of New South Wales, Sydney, Australia
| | - Sandra Fok
- Katerina Gaus Light Microscopy Facility, Mark Wainwright Analytical Center, University of New South Wales, Sydney, Australia
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Guangwei Du
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yang Liu
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ximing Du
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
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24
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Bao L, Liu Q, Wang J, Shi L, Pang Y, Niu Y, Zhang R. The interactions of subcellular organelles in pulmonary fibrosis induced by carbon black nanoparticles: a comprehensive review. Arch Toxicol 2024; 98:1629-1643. [PMID: 38536500 DOI: 10.1007/s00204-024-03719-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 05/21/2024]
Abstract
Owing to the widespread use and improper emissions of carbon black nanoparticles (CBNPs), the adverse effects of CBNPs on human health have attracted much attention. In toxicological research, carbon black is frequently utilized as a negative control because of its low toxicity and poor solubility. However, recent studies have indicated that inhalation exposure to CBNPs could be a risk factor for severe and prolonged pulmonary inflammation and fibrosis. At present, the pathogenesis of pulmonary fibrosis induced by CBNPs is still not fully elucidated, but it is known that with small particle size and large surface area, CBNPs are more easily ingested by cells, leading to organelle damage and abnormal interactions between organelles. Damaged organelle and abnormal organelles interactions lead to cell structure and function disorders, which is one of the important factors in the development and occurrence of various diseases, including pulmonary fibrosis. This review offers a comprehensive analysis of organelle structure, function, and interaction mechanisms, while also summarizing the research advancements in organelles and organelle interactions in CBNPs-induced pulmonary fibrosis.
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Affiliation(s)
- Lei Bao
- Department of Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang, 050017, China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Qingping Liu
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China
| | - Jingyuan Wang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China
| | - Lili Shi
- Department of Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang, 050017, China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Yaxian Pang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China
| | - Yujie Niu
- Department of Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang, 050017, China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Rong Zhang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China.
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China.
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25
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Chou CC, Vest R, Prado MA, Wilson-Grady J, Paulo JA, Shibuya Y, Moran-Losada P, Lee TT, Luo J, Gygi SP, Kelly JW, Finley D, Wernig M, Wyss-Coray T, Frydman J. Human tNeurons reveal aging-linked proteostasis deficits driving Alzheimer's phenotypes. RESEARCH SQUARE 2024:rs.3.rs-4407236. [PMID: 38853828 PMCID: PMC11160905 DOI: 10.21203/rs.3.rs-4407236/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Aging is a prominent risk factor for Alzheimer's disease (AD), but the cellular mechanisms underlying neuronal phenotypes remain elusive. Both accumulation of amyloid plaques and neurofibrillary tangles in the brain1 and age-linked organelle deficits2-7 are proposed as causes of AD phenotypes but the relationship between these events is unclear. Here, we address this question using a transdifferentiated neuron (tNeuron) model directly from human dermal fibroblasts. Patient-derived tNeurons retain aging hallmarks and exhibit AD-linked deficits. Quantitative tNeuron proteomic analyses identify aging and AD-linked deficits in proteostasis and organelle homeostasis, particularly affecting endosome-lysosomal components. The proteostasis and lysosomal homeostasis deficits in aged tNeurons are exacerbated in sporadic and familial AD tNeurons, promoting constitutive lysosomal damage and defects in ESCRT-mediated repair. We find deficits in neuronal lysosomal homeostasis lead to inflammatory cytokine secretion, cell death and spontaneous development of Aß and phospho-Tau deposits. These proteotoxic inclusions co-localize with lysosomes and damage markers and resemble inclusions in brain tissue from AD patients and APP-transgenic mice. Supporting the centrality of lysosomal deficits driving AD phenotypes, lysosome-function enhancing compounds reduce AD-associated cytokine secretion and Aβ deposits. We conclude that proteostasis and organelle deficits are upstream initiating factors leading to neuronal aging and AD phenotypes.
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Affiliation(s)
- Ching-Chieh Chou
- Department of Biology, Stanford University, Stanford, California, USA
| | - Ryan Vest
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California, USA
- Qinotto, Inc. San Carlos, California, USA
| | - Miguel A. Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Joshua Wilson-Grady
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Yohei Shibuya
- Departments of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Patricia Moran-Losada
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California, USA
| | - Ting-Ting Lee
- Department of Biology, Stanford University, Stanford, California, USA
| | - Jian Luo
- Palo Alto Veterans Institute for Research, Inc. (PAVIR), Palo Alto, California, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marius Wernig
- Departments of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, California, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, California, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Lead contact
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Chen W, Motsinger MM, Li J, Bohannon KP, Hanson PI. Ca 2+-sensor ALG-2 engages ESCRTs to enhance lysosomal membrane resilience to osmotic stress. Proc Natl Acad Sci U S A 2024; 121:e2318412121. [PMID: 38781205 PMCID: PMC11145288 DOI: 10.1073/pnas.2318412121] [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: 10/24/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024] Open
Abstract
Lysosomes are central players in cellular catabolism, signaling, and metabolic regulation. Cellular and environmental stresses that damage lysosomal membranes can compromise their function and release toxic content into the cytoplasm. Here, we examine how cells respond to osmotic stress within lysosomes. Using sensitive assays of lysosomal leakage and rupture, we examine acute effects of the osmotic disruptant glycyl-L-phenylalanine 2-naphthylamide (GPN). Our findings reveal that low concentrations of GPN rupture a small fraction of lysosomes, but surprisingly trigger Ca2+ release from nearly all. Chelating cytoplasmic Ca2+ makes lysosomes more sensitive to GPN-induced rupture, suggesting a role for Ca2+ in lysosomal membrane resilience. GPN-elicited Ca2+ release causes the Ca2+-sensor Apoptosis Linked Gene-2 (ALG-2), along with Endosomal Sorting Complex Required for Transport (ESCRT) proteins it interacts with, to redistribute onto lysosomes. Functionally, ALG-2, but not its ESCRT binding-disabled ΔGF122 splice variant, increases lysosomal resilience to osmotic stress. Importantly, elevating juxta-lysosomal Ca2+ without membrane damage by activating TRPML1 also recruits ALG-2 and ESCRTs, protecting lysosomes from subsequent osmotic rupture. These findings reveal that Ca2+, through ALG-2, helps bring ESCRTs to lysosomes to enhance their resilience and maintain organelle integrity in the face of osmotic stress.
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Affiliation(s)
- Wei Chen
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI48109
| | - Madeline M. Motsinger
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI48109
| | - Jiaqian Li
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI48109
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI48109
| | - Kevin P. Bohannon
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI48109
| | - Phyllis I. Hanson
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI48109
- Department of Cell and Developmental Biology, University of Michigan School of Medicine, Ann Arbor, MI48109
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Rose K, Jepson T, Shukla S, Maya-Romero A, Kampmann M, Xu K, Hurley JH. Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes. Proc Natl Acad Sci U S A 2024; 121:e2315690121. [PMID: 38781206 PMCID: PMC11145263 DOI: 10.1073/pnas.2315690121] [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: 09/09/2023] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes and neurons, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification, and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Live cell imaging and STORM superresolution microscopy further show that the nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.
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Affiliation(s)
- Kevin Rose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Tyler Jepson
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
| | - Sankalp Shukla
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Alex Maya-Romero
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94158
| | - Ke Xu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA94720
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He Y, Fan Y, Ahmadpoor X, Wang Y, Li ZA, Zhu W, Lin H. Targeting lysosomal quality control as a therapeutic strategy against aging and diseases. Med Res Rev 2024. [PMID: 38711187 DOI: 10.1002/med.22047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 04/04/2024] [Accepted: 04/21/2024] [Indexed: 05/08/2024]
Abstract
Previously, lysosomes were primarily referred to as the digestive organelles and recycling centers within cells. Recent discoveries have expanded the lysosomal functional scope and revealed their critical roles in nutrient sensing, epigenetic regulation, plasma membrane repair, lipid transport, ion homeostasis, and cellular stress response. Lysosomal dysfunction is also found to be associated with aging and several diseases. Therefore, function of macroautophagy, a lysosome-dependent intracellular degradation system, has been identified as one of the updated twelve hallmarks of aging. In this review, we begin by introducing the concept of lysosomal quality control (LQC), which is a cellular machinery that maintains the number, morphology, and function of lysosomes through different processes such as lysosomal biogenesis, reformation, fission, fusion, turnover, lysophagy, exocytosis, and membrane permeabilization and repair. Next, we summarize the results from studies reporting the association between LQC dysregulation and aging/various disorders. Subsequently, we explore the emerging therapeutic strategies that target distinct aspects of LQC for treating diseases and combatting aging. Lastly, we underscore the existing knowledge gap and propose potential avenues for future research.
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Affiliation(s)
- Yuchen He
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yishu Fan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xenab Ahmadpoor
- Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yumin Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhong Alan Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Shatin, NT, Hong Kong SAR, China
| | - Weihong Zhu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Department of Orthopaedic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Hang Lin
- Department of Orthopaedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Bioengineering, University of Pittsburgh Swanson School of Engineering, Pittsburgh, Pennsylvania, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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29
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Mulligan RJ, Magaj MM, Digilio L, Redemann S, Yap CC, Winckler B. Collapse of late endosomal pH elicits a rapid Rab7 response via the V-ATPase and RILP. J Cell Sci 2024; 137:jcs261765. [PMID: 38578235 PMCID: PMC11166203 DOI: 10.1242/jcs.261765] [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: 11/02/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Endosomal-lysosomal trafficking is accompanied by the acidification of endosomal compartments by the H+-V-ATPase to reach low lysosomal pH. Disruption of the correct pH impairs lysosomal function and the balance of protein synthesis and degradation (proteostasis). Here, we treated mammalian cells with the small dipeptide LLOMe, which is known to permeabilize lysosomal membranes, and find that LLOMe also impacts late endosomes (LEs) by neutralizing their pH without causing membrane permeabilization. We show that LLOMe leads to hyperactivation of Rab7 (herein referring to Rab7a), and disruption of tubulation and mannose-6-phosphate receptor (CI-M6PR; also known as IGF2R) recycling on pH-neutralized LEs. pH neutralization (NH4Cl) and expression of Rab7 hyperactive mutants alone can both phenocopy the alterations in tubulation and CI-M6PR trafficking. Mechanistically, pH neutralization increases the assembly of the V1G1 subunit (encoded by ATP6V1G1) of the V-ATPase on endosomal membranes, which stabilizes GTP-bound Rab7 via RILP, a known interactor of Rab7 and V1G1. We propose a novel pathway by which V-ATPase and RILP modulate LE pH and Rab7 activation in concert. This pathway might broadly contribute to pH control during physiologic endosomal maturation or starvation and during pathologic pH neutralization, which occurs via lysosomotropic compounds and in disease states.
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Affiliation(s)
- Ryan J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Magdalena M. Magaj
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Laura Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Stefanie Redemann
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Chan Choo Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
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30
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Li D, Rocha-Roa C, Schilling MA, Reinisch KM, Vanni S. Lipid scrambling is a general feature of protein insertases. Proc Natl Acad Sci U S A 2024; 121:e2319476121. [PMID: 38621120 PMCID: PMC11047089 DOI: 10.1073/pnas.2319476121] [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: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 04/17/2024] Open
Abstract
Glycerophospholipids are synthesized primarily in the cytosolic leaflet of the endoplasmic reticulum (ER) membrane and must be equilibrated between bilayer leaflets to allow the ER and membranes derived from it to grow. Lipid equilibration is facilitated by integral membrane proteins called "scramblases." These proteins feature a hydrophilic groove allowing the polar heads of lipids to traverse the hydrophobic membrane interior, similar to a credit card moving through a reader. Nevertheless, despite their fundamental role in membrane expansion and dynamics, the identity of most scramblases has remained elusive. Here, combining biochemical reconstitution and molecular dynamics simulations, we show that lipid scrambling is a general feature of protein insertases, integral membrane proteins which insert polypeptide chains into membranes of the ER and organelles disconnected from vesicle trafficking. Our data indicate that lipid scrambling occurs in the same hydrophilic channel through which protein insertion takes place and that scrambling is abolished in the presence of nascent polypeptide chains. We propose that protein insertases could have a so-far-overlooked role in membrane dynamics as scramblases.
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Affiliation(s)
- Dazhi Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Cristian Rocha-Roa
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
| | - Matthew A. Schilling
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06520
| | - Stefano Vanni
- Department of Biology, University of Fribourg, FribourgCH-1700, Switzerland
- Swiss National Center for Competence in Research Bio-Inspired Materials, University of Fribourg, FribourgCH-1700, Switzerland
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31
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Hollingsworth LR, Veeraraghavan P, Paulo JA, Harper JW, Rauch I. Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590338. [PMID: 38659763 PMCID: PMC11042255 DOI: 10.1101/2024.04.19.590338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at: https://harperlab.connect.hms.harvard.edu/inflame/. We will display anonymous peer review for this manuscript on pubpub.org (https://harperlab.pubpub.org/pub/nlrp3/) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
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Affiliation(s)
- L. Robert Hollingsworth
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Isabella Rauch
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University
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32
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Gahlot P, Kravic B, Rota G, van den Boom J, Levantovsky S, Schulze N, Maspero E, Polo S, Behrends C, Meyer H. Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH. Mol Cell 2024; 84:1556-1569.e10. [PMID: 38503285 DOI: 10.1016/j.molcel.2024.02.029] [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: 10/25/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Cells respond to lysosomal membrane permeabilization by membrane repair or selective macroautophagy of damaged lysosomes, termed lysophagy, but it is not fully understood how this decision is made. Here, we uncover a pathway in human cells that detects lipid bilayer perturbations in the limiting membrane of compromised lysosomes, which fail to be repaired, and then initiates ubiquitin-triggered lysophagy. We find that SPG20 binds the repair factor IST1 on damaged lysosomes and, importantly, integrates that with the detection of damage-associated lipid-packing defects of the lysosomal membrane. Detection occurs via sensory amphipathic helices in SPG20 before rupture of the membrane. If lipid-packing defects are extensive, such as during lipid peroxidation, SPG20 recruits and activates ITCH, which marks the damaged lysosome with lysine-63-linked ubiquitin chains to initiate lysophagy and thus triages the lysosome for destruction. With SPG20 being linked to neurodegeneration, these findings highlight the relevance of a coordinated lysosomal damage response for cellular homeostasis.
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Affiliation(s)
- Pinki Gahlot
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Bojana Kravic
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Giulia Rota
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Johannes van den Boom
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Sophie Levantovsky
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Nina Schulze
- Imaging Center Campus Essen, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Hemmo Meyer
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
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Bonet-Ponce L, Tegicho T, Beilina A, Kluss JH, Li Y, Cookson MR. Opposing actions of JIP4 and RILPL1 provide antagonistic motor force to dynamically regulate membrane reformation during lysosomal tubulation/sorting driven by LRRK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587808. [PMID: 38903076 PMCID: PMC11188082 DOI: 10.1101/2024.04.02.587808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Lysosomes are dynamic cellular structures that adaptively remodel their membrane in response to stimuli, including membrane damage. We previously uncovered a process we term LYTL (LYsosomal Tubulation/sorting driven by Leucine-Rich Repeat Kinase 2 [LRRK2]), wherein damaged lysosomes generate tubules sorted into mobile vesicles. LYTL is orchestrated by the Parkinson's disease-associated kinase LRRK2 that recruits the motor adaptor protein and RHD family member JIP4 to lysosomes via phosphorylated RAB proteins. To identify new players involved in LYTL, we performed unbiased proteomics on isolated lysosomes after LRRK2 kinase inhibition. Our results demonstrate that there is recruitment of RILPL1 to ruptured lysosomes via LRRK2 activity to promote phosphorylation of RAB proteins at the lysosomal surface. RILPL1, which is also a member of the RHD family, enhances the clustering of LRRK2-positive lysosomes in the perinuclear area and causes retraction of LYTL tubules, in contrast to JIP4 which promotes LYTL tubule extension. Mechanistically, RILPL1 binds to p150Glued, a dynactin subunit, facilitating the transport of lysosomes and tubules to the minus end of microtubules. Further characterization of the tubulation process revealed that LYTL tubules move along tyrosinated microtubules, with tubulin tyrosination proving essential for tubule elongation. In summary, our findings emphasize the dynamic regulation of LYTL tubules by two distinct RHD proteins and pRAB effectors, serving as opposing motor adaptor proteins: JIP4, promoting tubulation via kinesin, and RILPL1, facilitating tubule retraction through dynein/dynactin. We infer that the two opposing processes generate a metastable lysosomal membrane deformation that facilitates dynamic tubulation events.
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Affiliation(s)
- Luis Bonet-Ponce
- Department of Neurology, Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Tsion Tegicho
- Department of Neurology, Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Alexandra Beilina
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Jillian H. Kluss
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Yan Li
- Proteomic Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Mark R. Cookson
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
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Duran J, Poolsup S, Allers L, Lemus MR, Cheng Q, Pu J, Salemi M, Phinney B, Jia J. A mechanism that transduces lysosomal damage signals to stress granule formation for cell survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587368. [PMID: 38617306 PMCID: PMC11014484 DOI: 10.1101/2024.03.29.587368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Lysosomal damage poses a significant threat to cell survival. Our previous work has reported that lysosomal damage induces stress granule (SG) formation. However, the importance of SG formation in determining cell fate and the precise mechanisms through which lysosomal damage triggers SG formation remains unclear. Here, we show that SG formation is initiated via a novel calcium-dependent pathway and plays a protective role in promoting cell survival in response to lysosomal damage. Mechanistically, we demonstrate that during lysosomal damage, ALIX, a calcium-activated protein, transduces lysosomal damage signals by sensing calcium leakage to induce SG formation by controlling the phosphorylation of eIF2α. ALIX modulates eIF2α phosphorylation by regulating the association between PKR and its activator PACT, with galectin-3 exerting a negative effect on this process. We also found this regulatory event of SG formation occur on damaged lysosomes. Collectively, these investigations reveal novel insights into the precise regulation of SG formation triggered by lysosomal damage, and shed light on the interaction between damaged lysosomes and SGs. Importantly, SG formation is significant for promoting cell survival in the physiological context of lysosomal damage inflicted by SARS-CoV-2 ORF3a, adenovirus infection, Malaria hemozoin, proteopathic tau as well as environmental hazard silica.
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Affiliation(s)
- Jacob Duran
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
| | - Suttinee Poolsup
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
| | - Lee Allers
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Monica Rosas Lemus
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Qiuying Cheng
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Jing Pu
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Brett Phinney
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Jingyue Jia
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM 87106, USA
- Lead Contact
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35
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Sun X, Wu L, Du L, Xu W, Han M. Targeting the organelle for radiosensitization in cancer radiotherapy. Asian J Pharm Sci 2024; 19:100903. [PMID: 38590796 PMCID: PMC10999375 DOI: 10.1016/j.ajps.2024.100903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 01/16/2024] [Indexed: 04/10/2024] Open
Abstract
Radiotherapy is a well-established cytotoxic therapy for local solid cancers, utilizing high-energy ionizing radiation to destroy cancer cells. However, this method has several limitations, including low radiation energy deposition, severe damage to surrounding normal cells, and high tumor resistance to radiation. Among various radiotherapy methods, boron neutron capture therapy (BNCT) has emerged as a principal approach to improve the therapeutic ratio of malignancies and reduce lethality to surrounding normal tissue, but it remains deficient in terms of insufficient boron accumulation as well as short retention time, which limits the curative effect. Recently, a series of radiosensitizers that can selectively accumulate in specific organelles of cancer cells have been developed to precisely target radiotherapy, thereby reducing side effects of normal tissue damage, overcoming radioresistance, and improving radiosensitivity. In this review, we mainly focus on the field of nanomedicine-based cancer radiotherapy and discuss the organelle-targeted radiosensitizers, specifically including nucleus, mitochondria, endoplasmic reticulum and lysosomes. Furthermore, the organelle-targeted boron carriers used in BNCT are particularly presented. Through demonstrating recent developments in organelle-targeted radiosensitization, we hope to provide insight into the design of organelle-targeted radiosensitizers for clinical cancer treatment.
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Affiliation(s)
- Xiaoyan Sun
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Linjie Wu
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Lina Du
- Department of Pharmaceutical Sciences, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Wenhong Xu
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Intervention, The Second Afliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Min Han
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Radiation Oncology, Key Laboratory of Cancer Prevention and Intervention, The Second Afliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310058, China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou 310058, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
- National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
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Liu Y, Yang H. WIPI4 loss linked to ferroptosis. Nat Cell Biol 2024; 26:506-507. [PMID: 38454049 DOI: 10.1038/s41556-024-01359-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Affiliation(s)
- Yang Liu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
- Molecular and Translational Biology Program, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
| | - Hongyuan Yang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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Theodore CJ, Wagner LH, Campellone KG. Autophagosome turnover requires Arp2/3 complex-mediated maintenance of lysosomal integrity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584718. [PMID: 38559247 PMCID: PMC10980047 DOI: 10.1101/2024.03.12.584718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Autophagy is an intracellular degradation process that maintains homeostasis, responds to stress, and plays key roles in the prevention of aging and disease. Autophagosome biogenesis, vesicle rocketing, and autolysosome tubulation are controlled by multiple actin nucleation factors, but the impact of actin assembly on completion of the autophagic pathway is not well understood. Here we studied autophagosome and lysosome remodeling in fibroblasts harboring an inducible knockout (iKO) of the Arp2/3 complex, an essential actin nucleator. Arp2/3 complex ablation resulted in increased basal levels of autophagy receptors and lipidated membrane proteins from the LC3 and GABARAP families. Under both steady-state and starvation conditions, Arp2/3 iKO cells accumulated abnormally high numbers of autolysosomes, suggesting a defect in autophagic flux. The inability of Arp2/3 complex-deficient cells to complete autolysosome degradation and turnover is explained by the presence of damaged, leaky lysosomes. In cells treated with an acute lysosomal membrane-damaging agent, the Arp2/3-activating protein WHAMM is recruited to lysosomes, where Arp2/3 complex-dependent actin assembly is crucial for restoring intact lysosomal structure. These results establish the Arp2/3 complex as a central player late in the canonical autophagy pathway and reveal a new role for the actin nucleation machinery in maintaining lysosomal integrity.
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Affiliation(s)
- Corey J. Theodore
- Department of Molecular and Cell Biology; University of Connecticut, Storrs CT, USA
- Institute for Systems Genomics; University of Connecticut, Storrs CT, USA
| | - Lianna H. Wagner
- Department of Molecular and Cell Biology; University of Connecticut, Storrs CT, USA
- Institute for Systems Genomics; University of Connecticut, Storrs CT, USA
| | - Kenneth G. Campellone
- Department of Molecular and Cell Biology; University of Connecticut, Storrs CT, USA
- Institute for Systems Genomics; University of Connecticut, Storrs CT, USA
- Center on Aging, UConn Health; University of Connecticut, Storrs CT, USA
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38
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Fuggetta N, Rigolli N, Magdeleine M, Hamaï A, Seminara A, Drin G. Reconstitution of ORP-mediated lipid exchange coupled to PI4P metabolism. Proc Natl Acad Sci U S A 2024; 121:e2315493121. [PMID: 38408242 PMCID: PMC10927502 DOI: 10.1073/pnas.2315493121] [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: 09/13/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Oxysterol-binding protein-related proteins (ORPs) play key roles in the distribution of lipids in eukaryotic cells by exchanging sterol or phosphatidylserine for PI4P between the endoplasmic reticulum (ER) and other cell regions. However, it is unclear how their exchange capacity is coupled to PI4P metabolism. To address this question quantitatively, we analyze the activity of a representative ORP, Osh4p, in an ER/Golgi interface reconstituted with ER- and Golgi-mimetic membranes functionalized with PI4P phosphatase Sac1p and phosphatidylinositol (PI) 4-kinase, respectively. Using real-time assays, we demonstrate that upon adenosine triphosphate (ATP) addition, Osh4p creates a sterol gradient between these membranes, relying on the spatially distant synthesis and hydrolysis of PI4P, and quantify how much PI4P is needed for this process. Then, we develop a quantitatively accurate kinetic model, validated by our data, and extrapolate this to estimate to what extent PI4P metabolism can drive ORP-mediated sterol transfer in cells. Finally, we show that Sec14p can support PI4P metabolism and Osh4p activity by transferring PI between membranes. This study establishes that PI4P synthesis drives ORP-mediated lipid exchange and that ATP energy is needed to generate intermembrane lipid gradients. Furthermore, it defines to what extent ORPs can distribute lipids in the cell and reassesses the role of PI-transfer proteins in PI4P metabolism.
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Affiliation(s)
- Nicolas Fuggetta
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
| | - Nicola Rigolli
- Department of Physics, École Normale Supérieure (LPENS), Paris75005, France
| | - Maud Magdeleine
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
| | - Amazigh Hamaï
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
| | - Agnese Seminara
- Malga, Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genoa16145, Italy
| | - Guillaume Drin
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
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Lolicato F, Nickel W, Haucke V, Ebner M. Phosphoinositide switches in cell physiology - From molecular mechanisms to disease. J Biol Chem 2024; 300:105757. [PMID: 38364889 PMCID: PMC10944118 DOI: 10.1016/j.jbc.2024.105757] [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: 11/28/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Phosphoinositides are amphipathic lipid molecules derived from phosphatidylinositol that represent low abundance components of biological membranes. Rather than serving as mere structural elements of lipid bilayers, they represent molecular switches for a broad range of biological processes, including cell signaling, membrane dynamics and remodeling, and many other functions. Here, we focus on the molecular mechanisms that turn phosphoinositides into molecular switches and how the dysregulation of these processes can lead to disease.
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Affiliation(s)
- Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany; Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Ebner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
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Settembre C, Perera RM. Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology. Nat Rev Mol Cell Biol 2024; 25:223-245. [PMID: 38001393 DOI: 10.1038/s41580-023-00676-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 11/26/2023]
Abstract
Every cell must satisfy basic requirements for nutrient sensing, utilization and recycling through macromolecular breakdown to coordinate programmes for growth, repair and stress adaptation. The lysosome orchestrates these key functions through the synchronised interplay between hydrolytic enzymes, nutrient transporters and signalling factors, which together enable metabolic coordination with other organelles and regulation of specific gene expression programmes. In this Review, we discuss recent findings on lysosome-dependent signalling pathways, focusing on how the lysosome senses nutrient availability through its physical and functional association with mechanistic target of rapamycin complex 1 (mTORC1) and how, in response, the microphthalmia/transcription factor E (MiT/TFE) transcription factors exert feedback regulation on lysosome biogenesis. We also highlight the emerging interactions of lysosomes with other organelles, which contribute to cellular homeostasis. Lastly, we discuss how lysosome dysfunction contributes to diverse disease pathologies and how inherited mutations that compromise lysosomal hydrolysis, transport or signalling components lead to multi-organ disorders with severe metabolic and neurological impact. A deeper comprehension of lysosomal composition and function, at both the cellular and organismal level, may uncover fundamental insights into human physiology and disease.
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Affiliation(s)
- Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.
| | - Rushika M Perera
- Department of Anatomy, University of California at San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California at San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
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Chauhan N, Patro BS. Emerging roles of lysosome homeostasis (repair, lysophagy and biogenesis) in cancer progression and therapy. Cancer Lett 2024; 584:216599. [PMID: 38135207 DOI: 10.1016/j.canlet.2023.216599] [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: 09/28/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
In the era of personalized therapy, precise targeting of subcellular organelles holds great promise for cancer modality. Taking into consideration that lysosome represents the intersection site in numerous endosomal trafficking pathways and their modulation in cancer growth, progression, and resistance against cancer therapies, the lysosome is proposed as an attractive therapeutic target for cancer treatment. Based on the recent advances, the current review provides a comprehensive understanding of molecular mechanisms of lysosome homeostasis under 3R responses: Repair, Removal (lysophagy) and Regeneration of lysosomes. These arms of 3R responses have distinct role in lysosome homeostasis although their interdependency along with switching between the pathways still remain elusive. Recent advances underpinning the crucial role of (1) ESCRT complex dependent/independent repair of lysosome, (2) various Galectins-based sensing and ubiquitination in lysophagy and (3) TFEB/TFE proteins in lysosome regeneration/biogenesis of lysosome are outlined. Later, we also emphasised how these recent advancements may aid in development of phytochemicals and pharmacological agents for targeting lysosomes for efficient cancer therapy. Some of these lysosome targeting agents, which are now at various stages of clinical trials and patents, are also highlighted in this review.
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Affiliation(s)
- Nitish Chauhan
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra, 400094, India
| | - Birija Sankar Patro
- Bio-Organic Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra, 400094, India.
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Shariq M, Khan MF, Raj R, Ahsan N, Kumar P. PRKAA2, MTOR, and TFEB in the regulation of lysosomal damage response and autophagy. J Mol Med (Berl) 2024; 102:287-311. [PMID: 38183492 DOI: 10.1007/s00109-023-02411-7] [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: 05/08/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024]
Abstract
Lysosomes function as critical signaling hubs that govern essential enzyme complexes. LGALS proteins (LGALS3, LGALS8, and LGALS9) are integral to the endomembrane damage response. If ESCRT fails to rectify damage, LGALS-mediated ubiquitination occurs, recruiting autophagy receptors (CALCOCO2, TRIM16, and SQSTM1) and VCP/p97 complex containing UBXN6, PLAA, and YOD1, initiating selective autophagy. Lysosome replenishment through biogenesis is regulated by TFEB. LGALS3 interacts with TFRC and TRIM16, aiding ESCRT-mediated repair and autophagy-mediated removal of damaged lysosomes. LGALS8 inhibits MTOR and activates TFEB for ATG and lysosomal gene transcription. LGALS9 inhibits USP9X, activates PRKAA2, MAP3K7, ubiquitination, and autophagy. Conjugation of ATG8 to single membranes (CASM) initiates damage repair mediated by ATP6V1A, ATG16L1, ATG12, ATG5, ATG3, and TECPR1. ATG8ylation or CASM activates the MERIT system (ESCRT-mediated repair, autophagy-mediated clearance, MCOLN1 activation, Ca2+ release, RRAG-GTPase regulation, MTOR modulation, TFEB activation, and activation of GTPase IRGM). Annexins ANAX1 and ANAX2 aid damage repair. Stress granules stabilize damaged membranes, recruiting FLCN-FNIP1/2, G3BP1, and NUFIP1 to inhibit MTOR and activate TFEB. Lysosomes coordinate the synergistic response to endomembrane damage and are vital for innate and adaptive immunity. Future research should unveil the collaborative actions of ATG proteins, LGALSs, TRIMs, autophagy receptors, and lysosomal proteins in lysosomal damage response.
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Affiliation(s)
- Mohd Shariq
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE.
| | - Mohammad Firoz Khan
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE.
| | - Reshmi Raj
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE
| | - Nuzhat Ahsan
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE
| | - Pramod Kumar
- Quantlase Imaging Laboratory, Quantlase Lab LLC, Unit 1-8, Masdar City, Abu Dhabi, UAE
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Shukla S, Chen W, Rao S, Yang S, Ou C, Larsen KP, Hummer G, Hanson PI, Hurley JH. Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca 2+-sensor ALG-2. Proc Natl Acad Sci U S A 2024; 121:e2318046121. [PMID: 38386713 PMCID: PMC10907313 DOI: 10.1073/pnas.2318046121] [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: 10/17/2023] [Accepted: 01/17/2024] [Indexed: 02/24/2024] Open
Abstract
Apoptosis linked Gene-2 (ALG-2) is a multifunctional intracellular Ca2+ sensor and the archetypal member of the penta-EF hand protein family. ALG-2 functions in the repair of damage to both the plasma and lysosome membranes and in COPII-dependent budding at endoplasmic reticulum exit sites (ERES). In the presence of Ca2+, ALG-2 binds to ESCRT-I and ALIX in membrane repair and to SEC31A at ERES. ALG-2 also binds directly to acidic membranes in the presence of Ca2+ by a combination of electrostatic and hydrophobic interactions. By combining giant unilamellar vesicle-based experiments and molecular dynamics simulations, we show that charge-reversed mutants of ALG-2 at these locations disrupt membrane recruitment. ALG-2 membrane binding mutants have reduced or abrogated ERES localization in response to Thapsigargin-induced Ca2+ release but still localize to lysosomes following lysosomal Ca2+ release. In vitro reconstitution shows that the ALG-2 membrane-binding defect can be rescued by binding to ESCRT-I. These data thus reveal the nature of direct Ca2+-dependent membrane binding and its interplay with Ca2+-dependent protein binding in the cellular functions of ALG-2.
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Affiliation(s)
- Sankalp Shukla
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Wei Chen
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI48109
| | - Shanlin Rao
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main60438, Germany
| | - Serim Yang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Chenxi Ou
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Kevin P. Larsen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main60438, Germany
- Institute of Biophysics, Goethe UniversityFrankfurt, Frankfurt am Main60438, Germany
| | - Phyllis I. Hanson
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI48109
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA94720
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Dong X, Wang L, Wang D, Yu M, Yang XJ, Cai H. Proteomic study on nintedanib in gastric cancer cells. PeerJ 2024; 12:e16771. [PMID: 38406279 PMCID: PMC10893871 DOI: 10.7717/peerj.16771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/18/2023] [Indexed: 02/27/2024] Open
Abstract
Background Gastric cancer is a very common gastrointestinal tumor with a high mortality rate. Nintedanib has been shown to significantly reduce tumor cell proliferation and increase apoptosis in gastric cancer cells in vitro. However, its systemic action mechanism on gastric cancer cells remains unclear. A high-throughput proteomic approach should help identify the potential mechanisms and targets of nintedanib on gastric cancer cells. Methods The effects of nintedanib on the biological behavior of gastric cancer cells were evaluated. A cytotoxic proliferation assay was performed to estimate the half maximal inhibitory concentration (IC50). AGS cells were divided into control, and nintedanib-treated groups (5 µM, 48 h), and differential protein expression was investigated using tandem mass tags (TMT) proteomics. The molecular mechanisms of these differentially expressed proteins and their network interactions were then analyzed using bioinformatics, and potential nintedanib targets were identified. Results This study identified 845 differentially expressed proteins in the nintedanib-treated group (compared to the control group), comprising 526 up-regulated and 319 down-regulated proteins. Bioinformatics analysis revealed that the differentially expressed proteins were primarily enriched in biological pathways for branched-chain amino acid metabolism, steroid biosynthesis, propionate metabolism, fatty acid metabolism, lysosome, peroxisome, and ferroptosis. Key driver analysis revealed that proteins, such as enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH), isocitrate dehydrogenase 1 (IDH1), acyl-CoA oxidase 1 (ACOX1), acyl-CoA oxidase 2 (ACOX2), acyl-CoA oxidase 3 (ACOX3), and acetyl-CoA acyltransferase 1 (ACAA1) could be linked with nintedanib action. Conclusion Nintedanib inhibits the proliferation, invasion, and metastasis of gastric cancer cells. The crossover pathways and protein networks predicted by proteomics should provide more detailed molecular information enabling the use of nintedanib against gastric cancer.
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Affiliation(s)
- Xiaohua Dong
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
| | - Liuli Wang
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
| | - Da Wang
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
| | - Miao Yu
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
| | - Xiao jun Yang
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
| | - Hui Cai
- The First School of Clinical Medicine, Lanzhou University, LanZhou, China
- Department of General Surgery, Gansu Provincial Hospital, LanZhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province and NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, LanZhou, China
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Mulligan R, Magaj M, Digilio L, Redemann S, Yap C, Winckler B. Collapse of late endosomal pH elicits a rapid Rab7 response via V-ATPase and RILP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.24.563658. [PMID: 37961579 PMCID: PMC10634777 DOI: 10.1101/2023.10.24.563658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Endosomal-lysosomal trafficking is accompanied by the acidification of endosomal compartments by the H+-V-ATPase to reach low lysosomal pH. Disruption of proper pH impairs lysosomal function and the balance of protein synthesis and degradation (proteostasis). We used the small dipeptide LLOMe, which is known to permeabilize lysosomal membranes, and find that LLOMe also impacts late endosomes (LEs) by neutralizing their pH without causing membrane permeabilization. We show that LLOMe leads to hyper-activation of Rab7 and disruption of tubulation and mannose-6-phosphate receptor (CI-M6PR) recycling on pH-neutralized LEs. Either pH neutralization (NH4Cl) or Rab7 hyper-active mutants alone can phenocopy the alterations in tubulation and CI-M6PR trafficking. Mechanistically, pH neutralization increases the assembly of the V1G1 subunit of the V-ATPase on endosomal membranes, which stabilizes GTP-bound Rab7 via RILP, a known interactor of Rab7 and V1G1. We propose a novel pathway by which V-ATPase and RILP modulate LE pH and Rab7 activation in concert. This pathway might broadly contribute to pH control during physiologic endosomal maturation or starvation and during pathologic pH neutralization, which occurs via lysosomotropic compounds or in disease states.
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Affiliation(s)
- R.J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA
| | - M.M. Magaj
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville VA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA
| | - L. Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, VA
| | - S. Redemann
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville VA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA
| | - C.C. Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA
| | - B Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA
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Omi J, Kato T, Yoshihama Y, Sawada K, Kono N, Aoki J. Phosphatidylserine synthesis controls oncogenic B cell receptor signaling in B cell lymphoma. J Cell Biol 2024; 223:e202212074. [PMID: 38048228 PMCID: PMC10694799 DOI: 10.1083/jcb.202212074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 09/13/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Cancer cells harness lipid metabolism to promote their own survival. We screened 47 cancer cell lines for survival dependency on phosphatidylserine (PS) synthesis using a PS synthase 1 (PTDSS1) inhibitor and found that B cell lymphoma is highly dependent on PS. Inhibition of PTDSS1 in B cell lymphoma cells caused a reduction of PS and phosphatidylethanolamine levels and an increase of phosphoinositide levels. The resulting imbalance of the membrane phospholipidome lowered the activation threshold for B cell receptor (BCR), a B cell-specific survival mechanism. BCR hyperactivation led to aberrant elevation of downstream Ca2+ signaling and subsequent apoptotic cell death. In a mouse xenograft model, PTDSS1 inhibition efficiently suppressed tumor growth and prolonged survival. Our findings suggest that PS synthesis may be a critical vulnerability of malignant B cell lymphomas that can be targeted pharmacologically.
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Affiliation(s)
- Jumpei Omi
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Koki Sawada
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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Chen W, Motsinger MM, Li J, Bohannon KP, Hanson PI. Ca 2+ -sensor ALG-2 engages ESCRTs to enhance lysosomal membrane resilience to osmotic stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578682. [PMID: 38352356 PMCID: PMC10862787 DOI: 10.1101/2024.02.04.578682] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Lysosomes are central players in cellular catabolism, signaling, and metabolic regulation. Cellular and environmental stresses that damage lysosomal membranes can compromise their function and release toxic content into the cytoplasm. Here, we examine how cells respond to osmotic stress within lysosomes. Using sensitive assays of lysosomal leakage and rupture, we examine acute effects of the cathepsin C-metabolized osmotic disruptant glycyl-L-phenylalanine 2-naphthylamide (GPN). Our findings reveal that widely used concentrations of GPN rupture only a small fraction of lysosomes, but surprisingly trigger Ca 2+ release from nearly all. Chelating cytoplasmic Ca 2+ using BAPTA makes lysosomes more likely to rupture under GPN-induced stress, suggesting that Ca 2+ plays a role in protecting or rapidly repairing lysosomal membranes. Mechanistically, we establish that GPN causes the Ca 2+ -sensitive protein Apoptosis Linked Gene-2 (ALG-2) and interacting ESCRT proteins to redistribute onto lysosomes, improving their resistance to membrane stress created by GPN as well as the lysosomotropic drug chlorpromazine. Furthermore, we show that activating the cation channel TRPML1, with or without blocking the endoplasmic reticulum Ca 2+ pump, creates local Ca 2+ signals that protect lysosomes from rupture by recruiting ALG-2 and ESCRTs without any membrane damage. These findings reveal that Ca 2+ , through ALG-2, helps bring ESCRTs to lysosomes to enhance their resilience and maintain organelle integrity in the face of osmotic stress. SIGNIFICANCE As the degradative hub of the cell, lysosomes are full of toxic content that can spill into the cytoplasm. There has been much recent interest in how cells sense and repair lysosomal membrane damage using ESCRTs and cholesterol to rapidly fix "nanoscale damage". Here, we extend understanding of how ESCRTs contribute by uncovering a preventative role of the ESCRT machinery. We show that ESCRTs, when recruited by the Ca 2+ -sensor ALG-2, play a critical role in stabilizing the lysosomal membrane against osmotically-induced rupture. This finding suggests that cells have mechanisms not just for repairing but also for actively protecting lysosomes from stress-induced membrane damage.
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Sun S, Zhao G, Jia M, Jiang Q, Li S, Wang H, Li W, Wang Y, Bian X, Zhao YG, Huang X, Yang G, Cai H, Pastor-Pareja JC, Ge L, Zhang C, Hu J. Stay in touch with the endoplasmic reticulum. SCIENCE CHINA. LIFE SCIENCES 2024; 67:230-257. [PMID: 38212460 DOI: 10.1007/s11427-023-2443-9] [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: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024]
Abstract
The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.
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Affiliation(s)
- Sha Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gan Zhao
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjing Li
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yan G Zhao
- Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ge Yang
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jose C Pastor-Pareja
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Neurosciences, Consejo Superior de Investigaciones Cientfflcas-Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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49
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Hu C, Yan Y, Jin Y, Yang J, Xi Y, Zhong Z. Decoding the Cellular Trafficking of Prion-like Proteins in Neurodegenerative Diseases. Neurosci Bull 2024; 40:241-254. [PMID: 37755677 PMCID: PMC10838874 DOI: 10.1007/s12264-023-01115-9] [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: 12/20/2022] [Accepted: 07/02/2023] [Indexed: 09/28/2023] Open
Abstract
The accumulation and spread of prion-like proteins is a key feature of neurodegenerative diseases (NDs) such as Alzheimer's disease, Parkinson's disease, or Amyotrophic Lateral Sclerosis. In a process known as 'seeding', prion-like proteins such as amyloid beta, microtubule-associated protein tau, α-synuclein, silence superoxide dismutase 1, or transactive response DNA-binding protein 43 kDa, propagate their misfolded conformations by transforming their respective soluble monomers into fibrils. Cellular and molecular evidence of prion-like propagation in NDs, the clinical relevance of their 'seeding' capacities, and their levels of contribution towards disease progression have been intensively studied over recent years. This review unpacks the cyclic prion-like propagation in cells including factors of aggregate internalization, endo-lysosomal leaking, aggregate degradation, and secretion. Debates on the importance of the role of prion-like protein aggregates in NDs, whether causal or consequent, are also discussed. Applications lead to a greater understanding of ND pathogenesis and increased potential for therapeutic strategies.
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Affiliation(s)
- Chenjun Hu
- Department of Neurology of the Second Affiliated Hospital and Department of Human Anatomy, Histology and Embryology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yiqun Yan
- Department of Neurology of the Second Affiliated Hospital and Department of Human Anatomy, Histology and Embryology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yanhong Jin
- Department of Neurology of the Second Affiliated Hospital and Department of Human Anatomy, Histology and Embryology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jun Yang
- Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yongmei Xi
- Division of Human Reproduction and Developmental Genetics, Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Zhen Zhong
- Department of Neurology of the Second Affiliated Hospital and Department of Human Anatomy, Histology and Embryology, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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50
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Xun J, Zhang Z, Lv B, Lu D, Yang H, Shang G, Tan JX. A conserved ion channel function of STING mediates noncanonical autophagy and cell death. EMBO Rep 2024; 25:544-569. [PMID: 38177926 PMCID: PMC10897221 DOI: 10.1038/s44319-023-00045-x] [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: 09/26/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
The cGAS/STING pathway triggers inflammation upon diverse cellular stresses such as infection, cellular damage, aging, and diseases. STING also triggers noncanonical autophagy, involving LC3 lipidation on STING vesicles through the V-ATPase-ATG16L1 axis, as well as induces cell death. Although the proton pump V-ATPase senses organelle deacidification in other contexts, it is unclear how STING activates V-ATPase for noncanonical autophagy. Here we report a conserved channel function of STING in proton efflux and vesicle deacidification. STING activation induces an electron-sparse pore in its transmembrane domain, which mediates proton flux in vitro and the deacidification of post-Golgi STING vesicles in cells. A chemical ligand of STING, C53, which binds to and blocks its channel, strongly inhibits STING-mediated proton flux in vitro. C53 fully blocks STING trafficking from the ER to the Golgi, but adding C53 after STING arrives at the Golgi allows for selective inhibition of STING-dependent vesicle deacidification, LC3 lipidation, and cell death, without affecting trafficking. The discovery of STING as a channel opens new opportunities for selective targeting of canonical and noncanonical STING functions.
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Affiliation(s)
- Jinrui Xun
- Xiangya School of Medicine, Central South University, Changsha, China
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Zhichao Zhang
- College of Life Sciences, Shanxi Agricultural University, Taiyuan, China
| | - Bo Lv
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Defen Lu
- College of Life Sciences, Shanxi Agricultural University, Taiyuan, China
| | - Haoxiang Yang
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Guijun Shang
- College of Life Sciences, Shanxi Agricultural University, Taiyuan, China.
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China.
- Shanxi Provincial Key Laboratory of Protein Structure Determination, SAARI, Taiyuan, China.
| | - Jay Xiaojun Tan
- Aging Institute, University of Pittsburgh School of Medicine/University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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