1
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Xu G, Chen H, Cong Z, Zhou L, Zhao N, Yang Y, Li T, Liu X, Wang Y, Li B. TFE3-mediated lysosomal biogenesis and homeostasis alleviates arsenic-induced lysosomal and immune dysfunction in macrophages. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2025; 299:118374. [PMID: 40409189 DOI: 10.1016/j.ecoenv.2025.118374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 03/21/2025] [Accepted: 05/18/2025] [Indexed: 05/25/2025]
Abstract
Arsenic is a prevalent environmental toxin associated with cancer that disrupts the immune surveillance and defense functions of macrophages. The MiT/TFE family plays a crucial role in maintaining lysosomal biogenesis and homeostasis, with TFE3 being ubiquitously expressed across most immune cell types, however, its specific role in immune function remains largely unexplored and controversial. In this study, arsenic decreased the cellular phagocytic and adhesion abilities and co-stimulatory molecules CD80, CD86 and pro-inflammatory cytokines TNF-α, IL-6 and IL-1β of cultured J774A.1 macrophages. We also observed that arsenic exposure decreased mRNA expression of LYSET and lysosomal hydrolases Ctsd and Ctss, impaired OVA degradation, reduced Lyso-Tracker Red and Lyso-Sensor Green fluorescence intensity, caused abnormal lysosomal pH, as well as blocked the autophagic flux process in macrophages. Co-treatment with arsenic and CQ further enhanced these arsenic-induced immune responses. More importantly, TFE3 knockdown significantly reduced lysosomal cathepsins levels of CTSB and CTSD, decreased lysosomal abundance, disrupted the lysosomal acidic environment and membrane permeabilization. Further TFE3 knockdown enhanced the decrease in phagocytosis, cellular adhesion, and Icam-1 mRNA expression in macrophages. In addition, the co-stimulatory molecules and pro-inflammatory cytokines were further reduced. By contrast, TFE3 overexpression partially alleviated the above lysosomal impairment and macrophage dysfunction induced by arsenic exposure. Collectively, arsenic exposure impairs macrophages immune function and lysosomal homeostasis. TFE3 regulates lysosomal biogenesis and homeostasis, alleviates arsenic-induced lysosomal and immune dysfunction in macrophages. Targeting the MiT/TFE family may provide new strategies for modulating lysosomal homeostasis and immune function.
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Affiliation(s)
- Guowei Xu
- Key Laboratory of Environmental Stress and Chronic Disease Control and Prevention, Ministry of Education (China Medical University), Shenyang, Liaoning, PR China; Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China
| | - Haiyang Chen
- Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China; Disease Control and Prevention Center of Liaoning Province, Shenyang, Liaoning, PR China
| | - Zheng Cong
- Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China; Disease Control and Prevention Center of Liaoning Province, Shenyang, Liaoning, PR China
| | - Ling Zhou
- Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China
| | - Ning Zhao
- Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China
| | - Yuqing Yang
- Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China
| | - Ting Li
- Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China; Health Committee of Baotou, Baotou, Inner Mongolia, PR China
| | - Xuping Liu
- Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China; Urban Vocational College of Sichuan, Chengdu, Sichuan, PR China
| | - Yi Wang
- Key Laboratory of Environmental Stress and Chronic Disease Control and Prevention, Ministry of Education (China Medical University), Shenyang, Liaoning, PR China; Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China.
| | - Bing Li
- Key Laboratory of Environmental Stress and Chronic Disease Control and Prevention, Ministry of Education (China Medical University), Shenyang, Liaoning, PR China; Environment and Non-Communicable Disease Research Center, Key Laboratory of Arsenic-related Biological Effects and Prevention and Treatment in Liaoning Province, School of Public Health, China Medical University, Shenyang, Liaoning, PR China.
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2
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Aviles-Huerta D, Del Pizzo R, Kowar A, Baig AH, Palazzo G, Stepanova E, Amaya Ramirez CC, D'Agostino S, Ratto E, Pechincha C, Siefert N, Engel H, Du S, Cadenas-De Miguel S, Miao B, Cruz-Vilchez VM, Müller-Decker K, Elia I, Sun C, Palm W, Loayza-Puch F. Dual Ribosome Profiling reveals metabolic limitations of cancer and stromal cells in the tumor microenvironment. Nat Commun 2025; 16:4652. [PMID: 40389477 PMCID: PMC12089342 DOI: 10.1038/s41467-025-59986-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Accepted: 05/09/2025] [Indexed: 05/21/2025] Open
Abstract
The tumor microenvironment (TME) influences cancer cell metabolism and survival. However, how immune and stromal cells respond to metabolic stress in vivo, and how nutrient limitations affect therapy, remains poorly understood. Here, we introduce Dual Ribosome Profiling (DualRP) to simultaneously monitor translation and ribosome stalling in multiple tumor cell populations. DualRP reveals that cancer-fibroblast interactions trigger an inflammatory program that reduces amino acid shortages during glucose starvation. In immunocompetent mice, we show that serine and glycine are essential for optimal T cell function and that their deficiency impairs T cell fitness. Importantly, immune checkpoint blockade therapy imposes amino acid restrictions specifically in T cells, demonstrating that therapies create distinct metabolic demands across TME cell types. By mapping codon-resolved ribosome stalling in a cell‑type‑specific manner, DualRP uncovers metabolic crosstalk that shapes translational programs. DualRP thus offers a powerful, innovative approach for dissecting tumor cell metabolic interplay and guiding combined metabolic-immunotherapeutic strategies.
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Affiliation(s)
- Daniela Aviles-Huerta
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Rossella Del Pizzo
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Alexander Kowar
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Ali Hyder Baig
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Giuliana Palazzo
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Ekaterina Stepanova
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Cinthia Claudia Amaya Ramirez
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Sara D'Agostino
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Edoardo Ratto
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Catarina Pechincha
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Nora Siefert
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Helena Engel
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Immune Regulation in Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Shangce Du
- Immune Regulation in Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | | | - Beiping Miao
- Immune Regulation in Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Victor M Cruz-Vilchez
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Karin Müller-Decker
- Core Facility Tumor Models, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Ilaria Elia
- Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Chong Sun
- Immune Regulation in Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Wilhelm Palm
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany.
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3
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Hermann J, Borteçen T, Kalis R, Kowar A, Pechincha C, Vogt V, Schneider M, Helm D, Krijgsveld J, Loayza-Puch F, Zuber J, Palm W. mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery. Nat Commun 2025; 16:4201. [PMID: 40328729 PMCID: PMC12056009 DOI: 10.1038/s41467-025-59185-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/14/2025] [Indexed: 05/08/2025] Open
Abstract
Synthesizing the cellular proteome is a demanding process that is regulated by numerous signaling pathways and RNA modifications. How precisely these mechanisms control the protein synthesis machinery to generate specific proteome subsets remains unclear. Here, through genome-wide CRISPR screens we identify genes that enable mammalian cells to adapt to inactivation of the kinase mechanistic target of rapamycin complex 1 (mTORC1), the central driver of protein synthesis. When mTORC1 is inactive, enzymes that modify tRNAs at wobble uridines (U34-enzymes), Elongator and Ctu1/2, become critically essential for cell growth in vitro and in tumors. By integrating quantitative nascent proteomics, steady-state proteomics and ribosome profiling, we demonstrate that the loss of U34-enzymes particularly impairs the synthesis of ribosomal proteins. However, when mTORC1 is active, this biosynthetic defect only mildly affects steady-state protein abundance. By contrast, simultaneous suppression of mTORC1 and U34-enzymes depletes cells of ribosomal proteins, globally inhibiting translation. Thus, mTORC1 cooperates with tRNA U34-enzymes to sustain the protein synthesis machinery and support the high translational requirements of cell growth.
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Affiliation(s)
- Julia Hermann
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Toman Borteçen
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Kalis
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Kowar
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
- Translational Control and Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Catarina Pechincha
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Vivien Vogt
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Wilhelm Palm
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.
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4
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Bullington AV, Micallo I, Bajaj B, Kumar P, Schlamowitz N, Silva A, Hendrix S, Zelcer N, Kober DL. Structural basis for substrate selectivity by site-one protease revealed by studies with a small-molecule inhibitor. Proc Natl Acad Sci U S A 2025; 122:e2426931122. [PMID: 40299693 PMCID: PMC12067269 DOI: 10.1073/pnas.2426931122] [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: 12/23/2024] [Accepted: 03/31/2025] [Indexed: 05/01/2025] Open
Abstract
Site-one protease (S1P) carries out the first proteolytic step to activate membrane-bound effector proteins in the Golgi. S1P matures through an autocatalytic process that begins in the endoplasmic reticulum (ER) and culminates with the displacement of its inhibitory pro-domain by its cofactor, sterol regulatory element binding protein-regulating gene (SPRING). Spatial control of S1P activity and substrate localization underpins signaling pathways governing, among others, lipogenesis, ER stress, and lysosome biogenesis. The factors governing these pathways are activated by S1P-mediated proteolysis upon their regulated transport from the ER to the Golgi. S1P cleaves substrates with the recognition sequence RX(L/I/V)Z, where X is any residue other than Cys or Pro and Z is preferably Leu or Lys. However, the structural basis for substrate recognition by S1P has remained unknown. Here, we used the small molecule PF-429242, a competitive inhibitor of S1P, to investigate substrate recognition by the S1P/SPRING complex. We determined the structure of S1P/SPRING bound to PF-429242 and found that PF-429242 binds S1P in the same pocket that recognizes the substrate's conserved P4 Arg. Further structural analysis suggests that S1P requires a conformation change to accommodate the substrate's P2 (L/I/V) residue. We designed an S1P mutation (I308A) to reduce the steric clash at the P2 position and generated an S1P that was resistant to PF-429242 in biochemical and cell culture assays. Our findings reveal selectivity in the recognition of substrates by S1P and provide a roadmap for the rational design of improved S1P inhibitors.
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Affiliation(s)
- Ashley V. Bullington
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Ilaria Micallo
- Department of Medical Biochemistry, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam1105AZ, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam1105AZ, the Netherlands
- Amsterdam Cardiovascular Sciences Institute, Amsterdam University Medical Centers, Amsterdam1105AZ, the Netherlands
| | - Bilkish Bajaj
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Pankaj Kumar
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Netanya Schlamowitz
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Aurora Silva
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Sebastian Hendrix
- Department of Medical Biochemistry, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam1105AZ, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam1105AZ, the Netherlands
- Amsterdam Cardiovascular Sciences Institute, Amsterdam University Medical Centers, Amsterdam1105AZ, the Netherlands
| | - Noam Zelcer
- Department of Medical Biochemistry, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam1105AZ, the Netherlands
- Amsterdam Gastroenterology, Endocrinology, and Metabolism Institute, Amsterdam University Medical Centers, Amsterdam1105AZ, the Netherlands
- Amsterdam Cardiovascular Sciences Institute, Amsterdam University Medical Centers, Amsterdam1105AZ, the Netherlands
| | - Daniel L. Kober
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX75390
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5
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Bird LE, Xu B, Hobbs AD, Ziegler AR, Scott NE, Newton P, Thomas DR, Edgington-Mitchell LE, Newton HJ. Coxiella burnetii manipulates the lysosomal protease cathepsin B to facilitate intracellular success. Nat Commun 2025; 16:3844. [PMID: 40274809 PMCID: PMC12022341 DOI: 10.1038/s41467-025-59283-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 04/15/2025] [Indexed: 04/26/2025] Open
Abstract
The obligate intracellular bacterium Coxiella burnetii establishes an intracellular replicative niche termed the Coxiella-containing vacuole (CCV), which has been characterised as a bacterially modified phagolysosome. How C. burnetii withstands the acidic and degradative properties of this compartment is not well understood. We demonstrate that the key lysosomal protease cathepsin B is actively and selectively removed from C. burnetii-infected cells through a mechanism involving the Dot/Icm type IV-B secretion system effector CvpB. Overexpression of cathepsin B leads to defects in CCV biogenesis and bacterial replication, indicating that removal of this protein represents a strategy to reduce the hostility of the intracellular niche. In addition, we show that C. burnetii infection of mammalian cells induces the secretion of a wider cohort of lysosomal proteins, including cathepsin B, to the extracellular milieu via a mechanism dependent on retrograde traffic. This study reveals that C. burnetii is actively modulating the hydrolase cohort of its replicative niche to promote intracellular success and demonstrates that infection incites the secretory pathway to maintain lysosomal homoeostasis.
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Affiliation(s)
- Lauren E Bird
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Bangyan Xu
- Department of Biochemistry and Pharmacology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew D Hobbs
- Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Alexander R Ziegler
- Department of Biochemistry and Pharmacology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Patrice Newton
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - David R Thomas
- Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Pharmacology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| | - Hayley J Newton
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
- Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia.
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6
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Doray B, Jennings BC, Yang X, Liu L, Venkatarangan V, Kornfeld S, Li M. LYSET facilitates integration of both the N- and C-terminal transmembrane helices/cytoplasmic domains of GlcNAc-1-phosphotransferase. Mol Biol Cell 2025; 36:br12. [PMID: 39937677 PMCID: PMC12005095 DOI: 10.1091/mbc.e24-08-0349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 01/06/2025] [Accepted: 02/07/2025] [Indexed: 02/14/2025] Open
Abstract
LYSET is a recently identified Golgi transmembrane (TM) protein, and inactivating mutations in the LYSET gene phenocopy mucolipidosis II (MLII), the lysosomal storage disease caused by loss of function of GlcNAc-1-phosphotransferase αβ (GNPTαβ), which tags lysosomal hydrolases with the mannose 6-phosphate (M6P) tag for delivery to lysosomes. It is conceivable that LYSET facilitates integration of both hydrophilic TM helices (TMHs) of GNPTαβ and retain the latter in the Golgi, although this has only been directly demonstrated for the N-terminal TMH wherein a membrane-stabilized GNPTαβ variant restores lysosomal function in cells lacking LYSET. Here we show that the C-terminal TMH of GNPTαβ also contributes to LYSET-mediated Golgi retention. In addition, disease-causing patient mutations in the N-terminal TMH of GNPTαβ, which increase the hydrophilicity of the helix, are partly rescued by overexpression of LYSET. Finally, we show that a membrane-stabilized GNPTαβ variant, despite overcoming the requirement for LYSET, still requires COPI-mediated recycling via the N-terminal cytosolic domain (CD) for GNPTαβ retention and function in the Golgi.
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Affiliation(s)
- Baraj Doray
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Benjamin C. Jennings
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Lin Liu
- M6P Therapeutics, St. Louis, MO 63108
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Stuart Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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7
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Jain A, Heremans I, Rademaker G, Detomasi TC, Rohweder P, Anderson D, Zhang J, Hernandez GA, Gupta S, von Linde T, Lange M, Spacci M, Luo J, Citron YR, Olzmann JA, Dawson DW, Craik CS, Bommer G, Perera RM, Zoncu R. Leucine aminopeptidase LyLAP enables lysosomal degradation of membrane proteins. Science 2025; 387:eadq8331. [PMID: 40146846 DOI: 10.1126/science.adq8331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 11/25/2024] [Accepted: 01/13/2025] [Indexed: 03/29/2025]
Abstract
Breakdown of every transmembrane protein trafficked to lysosomes requires proteolysis of their hydrophobic helical transmembrane domains. Combining lysosomal proteomics with functional genomic datasets, we identified lysosomal leucine aminopeptidase (LyLAP; formerly phospholipase B domain-containing 1) as the hydrolase most tightly associated with elevated endocytosis. Untargeted metabolomics and biochemical reconstitution demonstrated that LyLAP is a processive monoaminopeptidase with preference for amino-terminal leucine. This activity was necessary and sufficient for the breakdown of hydrophobic transmembrane domains. LyLAP was up-regulated in pancreatic ductal adenocarcinoma (PDA), which relies on macropinocytosis for nutrient uptake. In PDA cells, LyLAP ablation led to the buildup of undigested hydrophobic peptides, lysosomal membrane damage, and growth inhibition. Thus, LyLAP enables lysosomal degradation of membrane proteins and protects lysosomal integrity in highly endocytic cancer cells.
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Affiliation(s)
- Aakriti Jain
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Isaac Heremans
- Metabolic Research Group, de Duve Institute and WELBIO, Universite Catholique de Louvain, Brussels, Belgium
| | - Gilles Rademaker
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler C Detomasi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Peter Rohweder
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Dashiell Anderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Justin Zhang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Grace A Hernandez
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Suprit Gupta
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Teresa von Linde
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Mike Lange
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Martina Spacci
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jiayi Luo
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Y Rose Citron
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - James A Olzmann
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - David W Dawson
- Department of Pathology and Laboratory Medicine and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Guido Bommer
- Metabolic Research Group, de Duve Institute and WELBIO, Universite Catholique de Louvain, Brussels, Belgium
| | - Rushika M Perera
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
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8
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Ramezani M, Weisbart E, Bauman J, Singh A, Yong J, Lozada M, Way GP, Kavari SL, Diaz C, Leardini E, Jetley G, Pagnotta J, Haghighi M, Batista TM, Pérez-Schindler J, Claussnitzer M, Singh S, Cimini BA, Blainey PC, Carpenter AE, Jan CH, Neal JT. A genome-wide atlas of human cell morphology. Nat Methods 2025; 22:621-633. [PMID: 39870862 PMCID: PMC11903339 DOI: 10.1038/s41592-024-02537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/25/2024] [Indexed: 01/29/2025]
Abstract
A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-wide genotype-phenotype maps comprising CRISPR-Cas9-based knockouts of >20,000 genes in >30 million cells. Our optical pooled cell profiling platform (PERISCOPE) combines a destainable high-dimensional phenotyping panel (based on Cell Painting) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This perturbation atlas comprises high-dimensional phenotypic profiles of individual cells with sufficient resolution to cluster thousands of human genes, reconstruct known pathways and protein-protein interaction networks, interrogate subcellular processes and identify culture media-specific responses. Using this atlas, we identify the poorly characterized disease-associated TMEM251/LYSET as a Golgi-resident transmembrane protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes. In sum, this perturbation atlas and screening platform represents a rich and accessible resource for connecting genes to cellular functions at scale.
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Affiliation(s)
- Meraj Ramezani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Weisbart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Bauman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford University, Stanford, CA, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech Department of Cellular and Tissue Genomics, South San Francisco, CA, USA
| | - John Yong
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Maria Lozada
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory P Way
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sanam L Kavari
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Celeste Diaz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford University, Stanford, CA, USA
| | - Eddy Leardini
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gunjan Jetley
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jenlu Pagnotta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Thiago M Batista
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
| | - Joaquín Pérez-Schindler
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
| | - Melina Claussnitzer
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Research, MIT, Cambridge, MA, USA
| | | | - Calvin H Jan
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - James T Neal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute, Cambridge, MA, USA.
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9
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Akaaboune SR, Javed A, Bui S, Wierenga A, Wang Y. GRASP55 regulates sorting and maturation of the lysosomal enzyme β-hexosaminidase A. Mol Biol Cell 2025; 36:ar30. [PMID: 39841559 PMCID: PMC11974951 DOI: 10.1091/mbc.e24-10-0452] [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: 10/16/2024] [Revised: 01/13/2025] [Accepted: 01/15/2025] [Indexed: 01/24/2025] Open
Abstract
The Golgi apparatus plays a crucial role in the delivery of lysosomal enzymes. Golgi reassembly stacking proteins, GRASP55 and GRASP65, are vital for maintaining Golgi structure and function. GRASP55 depletion results in the missorting and secretion of the lysosomal enzyme cathepsin D, though the mechanisms remain unclear. In this study, we conducted secretomic analyses of GRASP55 knockout cells and found a significant increase in lysosome-associated proteins in the extracellular medium. Using the lysosomal beta-hexosaminidase subunit alpha (HEXA) as a model, we found that GRASP55 depletion disrupted normal trafficking and processing of HEXA, resulting in increased secretion of the immature (pro-form) HEXA into the extracellular milieu, along with decreased levels of the mature form and enzymatic activity within the cell. GRASP55 depletion significantly reduced the complex formation between HEXA and mannose 6-phosphate (M6P) receptors (MPR), despite no overall change in MPR expression. Finally, we found there was a notable reduction in the expression of GNPTAB, leading to a reduction in M6P modification of HEXA, hindering its efficient targeting to lysosomes. These findings reveal the role of GRASP55 in regulating lysosomal enzyme dynamics, emphasizing its role in the sorting and trafficking of lysosomal proteins.
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Affiliation(s)
- Sarah Reem Akaaboune
- Department of Molecular, Cellular and Developmental Biology, the University of Michigan, Ann Arbor, MI 48109
| | - Aadil Javed
- Department of Molecular, Cellular and Developmental Biology, the University of Michigan, Ann Arbor, MI 48109
| | - Sarah Bui
- Department of Molecular, Cellular and Developmental Biology, the University of Michigan, Ann Arbor, MI 48109
| | - Alissa Wierenga
- Department of Molecular, Cellular and Developmental Biology, the University of Michigan, Ann Arbor, MI 48109
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, the University of Michigan, Ann Arbor, MI 48109
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518107, China
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10
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Zuber J, Palm W. Modelling and deciphering tumour metabolism in CRISPR screens. Nat Rev Cancer 2025; 25:1-2. [PMID: 39354071 DOI: 10.1038/s41568-024-00758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Affiliation(s)
- Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Wilhelm Palm
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.
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11
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Jain A, Heremans I, Rademaker G, Detomasi TC, Hernandez GA, Zhang J, Gupta S, von Linde T, Lange M, Spacci M, Rohweder P, Anderson D, Citron YR, Olzmann JA, Dawson DW, Craik CS, Bommer G, Perera RM, Zoncu R. Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.13.628212. [PMID: 39713462 PMCID: PMC11661280 DOI: 10.1101/2024.12.13.628212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Proteolysis of hydrophobic helices is required for complete breakdown of every transmembrane protein trafficked to the lysosome and sustains high rates of endocytosis. However, the lysosomal mechanisms for degrading hydrophobic domains remain unknown. Combining lysosomal proteomics with functional genomic data mining, we identify Lysosomal Leucine Aminopeptidase (LyLAP; formerly Phospholipase B Domain-Containing 1) as the hydrolase most tightly associated with elevated endocytic activity. Untargeted metabolomics and biochemical reconstitution demonstrate that LyLAP is not a phospholipase, but a processive monoaminopeptidase with strong preference for N-terminal leucine - an activity necessary and sufficient for breakdown of hydrophobic transmembrane domains. LyLAP is upregulated in pancreatic ductal adenocarcinoma (PDA), which relies on macropinocytosis for nutrient uptake, and its ablation led to buildup of undigested hydrophobic peptides, which compromised lysosomal membrane integrity and inhibited PDA cell growth. Thus, LyLAP enables lysosomal degradation of membrane proteins, and may represent a vulnerability in highly endocytic cancer cells. One sentence summary LyLAP degrades transmembrane proteins to sustain high endocytosis and lysosomal membrane stability in pancreatic cancer.
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12
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Yang X, Doray B, Venkatarangan V, Jennings BC, Henn D, Liang J, Zhao H, Zhang W, Zhang B, Yu L, Chen L, Kornfeld S, Li M. Molecular Insights into the Regulation of GNPTAB by TMEM251. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.05.627003. [PMID: 39677738 PMCID: PMC11643035 DOI: 10.1101/2024.12.05.627003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
In vertebrates, newly synthesized lysosomal enzymes traffick to lysosomes through the mannose-6-phosphate (M6P) pathway. The Golgi membrane protein TMEM251 was recently discovered to regulate lysosome biogenesis by controlling the level of GlcNAc-1-phosphotransferase (GNPT). However, its precise function remained unclear. In this study, we demonstrate that TMEM251 is a two-transmembrane protein indispensable for GNPT stability, cleavage by Site-1-Protease (S1P), and enzymatic activity. We reconcile conflicting models by showing that TMEM251 enhances GNPT cleavage and prevents its mislocalization to lysosomes for degradation. We further establish that TMEM251 achieves this by interacting with GOLPH3 and retromer complexes to anchor the TMEM251-GNPT complex at the Golgi. Alanine mutagenesis identified F4XXR7 motif in TMEM251's N-tail for GOLPH3 binding. Together, our findings uncover TMEM251's multi-faceted role in stabilizing GNPT, retaining it at the Golgi, and ensuring the fidelity of the M6P pathway, thereby providing insights into its molecular function.
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Affiliation(s)
- Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Current address: Department of Biological Sciences, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA
| | - Balraj Doray
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Mo 63110, USA
| | - Varsha Venkatarangan
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Benjamin C. Jennings
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Mo 63110, USA
| | - Danielle Henn
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiaxuan Liang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haikun Zhao
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weichao Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bokai Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Linchen Yu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liang Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stuart Kornfeld
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Mo 63110, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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13
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Zubkov N, Munro S. New players and targets in mannose 6-phosphate-dependent lysosomal sorting. EMBO J 2024; 43:6233-6235. [PMID: 39587298 PMCID: PMC11649812 DOI: 10.1038/s44318-024-00310-2] [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: 11/07/2024] [Accepted: 11/07/2024] [Indexed: 11/27/2024] Open
Abstract
A new study shows how a Golgi-resident protein is sent to the lysosome for degradation.
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Affiliation(s)
- Nikita Zubkov
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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14
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Brauer BK, Chen Z, Beirow F, Li J, Meisinger D, Capriotti E, Schweizer M, Wagner L, Wienberg J, Hobohm L, Blume L, Qiao W, Narimatsu Y, Carette JE, Clausen H, Winter D, Braulke T, Jabs S, Voss M. GOLPH3 and GOLPH3L maintain Golgi localization of LYSET and a functional mannose 6-phosphate transport pathway. EMBO J 2024; 43:6264-6290. [PMID: 39587297 PMCID: PMC11649813 DOI: 10.1038/s44318-024-00305-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 10/17/2024] [Accepted: 10/21/2024] [Indexed: 11/27/2024] Open
Abstract
Glycosylation, which plays an important role in modifying lipids and sorting of proteins, is regulated by asymmetric intra-Golgi distribution and SPPL3-mediated cleavage of Golgi enzymes. We found that cells lacking LYSET/TMEM251, a retention factor for Golgi N-acetylglucosamine-1-phosphotransferase (GNPT), display SPPL3-dependent hypersecretion of the Golgi membrane protein B4GALT5. We demonstrate that in wild-type cells B4GALT5 is tagged with mannose 6-phosphate (M6P), a sorting tag typical of soluble lysosomal hydrolases. Hence, M6P-tagging of B4GALT5 may represent a novel degradative lysosomal pathway. We also observed B4GALT5 hypersecretion and prominent destabilization of LYSET-GNPT complexes, impaired M6P-tagging, and disturbed maturation and trafficking of lysosomal enzymes in multiple human cell lines lacking the COPI adaptors GOLPH3 and GOLPH3L. Mechanistically, we identified LYSET as a novel, atypical client of GOLPH3/GOLPH3L. Thus, by ensuring the cis-Golgi localization of the LYSET-GNPT complex and maintaining its Golgi polarity, GOLPH3/GOLPH3L is essential for the integrity of the M6P-tagging machinery and homeostasis of lysosomes.
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Affiliation(s)
- Berit K Brauer
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Zilei Chen
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Felix Beirow
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Jiaran Li
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | | | - Emanuela Capriotti
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michaela Schweizer
- Morphology and Electron Microscopy, University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology (ZMNH), Hamburg, Germany
| | - Lea Wagner
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | | | - Laura Hobohm
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | - Lukas Blume
- Institute of Biochemistry, Kiel University, Kiel, Germany
- Institute of Cellular and Integrative Physiology, University Medical Center Hamburg Eppendorf, Hamburg, Germany
| | - Wenjie Qiao
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yoshiki Narimatsu
- Faculty of Health Sciences, Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Henrik Clausen
- Faculty of Health Sciences, Centre for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Thomas Braulke
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sabrina Jabs
- Institute of Clinical Molecular Biology, Kiel University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Matthias Voss
- Institute of Biochemistry, Kiel University, Kiel, Germany.
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15
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Tang YH, Liu YS, Fujita M. Production of Domain 9 from the cation-independent mannose-6-phosphate receptor fused with an Fc domain. Glycoconj J 2024; 41:395-405. [PMID: 39382616 PMCID: PMC11735522 DOI: 10.1007/s10719-024-10169-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 09/13/2024] [Accepted: 10/01/2024] [Indexed: 10/10/2024]
Abstract
Lysosomal storage diseases (LSDs) are genetic disorders caused by mutations in lysosomal enzymes, lysosomal membrane proteins or genes related to intracellular transport that result in impaired lysosomal function. Currently, the primary treatment for several LSDs is enzyme replacement therapy (ERT), which involves intravenous administration of the deficient lysosomal enzymes to ameliorate symptoms. The efficacy of ERT largely depends on the mannose-6-phosphate (M6P) modification of the N-glycans associated with the enzyme, as M6P is a marker for the recognition and trafficking of lysosomal enzymes. In cells, N-glycan processing and M6P modification occur in the endoplasmic reticulum and Golgi apparatus. This is a complex process involving multiple enzymes. In the trans-Golgi network (TGN), M6P-modified enzymes are recognized by the cation-independent mannose-6-phosphate receptor (CIMPR) and transported to the lysosome to exert their activities. In this study, we used the 9th domain of CIMPR, which exhibits a high affinity for M6P binding, and fused it with the Fc domain of human immunoglobulin G1 (IgG1). The resulting fusion protein specifically binds to M6P-modified proteins. This provides a tool for the rapid detection and concentration of M6P-containing recombinant enzymes to assess the effectiveness of ERT. The advantages of this approach include its high specificity and sensitivity and may lead to the development of new treatments for LSDs.
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Affiliation(s)
- Yu-He Tang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yi-Shi Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, 501-1193, Japan.
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16
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Zhang H, Liu J, Yuan W, Zhang Q, Luo X, Li Y, Peng Y, Feng J, Liu X, Chen J, Zhou Y, Lv J, Zhou N, Ma J, Tang K, Huang B. Ammonia-induced lysosomal and mitochondrial damage causes cell death of effector CD8 + T cells. Nat Cell Biol 2024; 26:1892-1902. [PMID: 39261719 DOI: 10.1038/s41556-024-01503-x] [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: 01/07/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024]
Abstract
Ammonia is thought to be a cytotoxin and its increase in the blood impairs cell function. However, whether and how this toxin triggers cell death under pathophysiological conditions remains unclear. Here we show that ammonia induces a distinct form of cell death in effector T cells. We found that rapidly proliferating T cells use glutaminolysis to release ammonia in the mitochondria, which is then translocated to and stored in the lysosomes. Excessive ammonia accumulation increases lysosomal pH and results in the termination of lysosomal ammonia storage and ammonia reflux into mitochondria, leading to mitochondrial damage and cell death, which is characterized by lysosomal alkalization, mitochondrial swelling and impaired autophagic flux. Inhibition of glutaminolysis or blocking lysosomal alkalization prevents ammonia-induced T cell death and improves T cell-based antitumour immunotherapy. These findings identify a distinct form of cell death that differs from previously known mechanisms.
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Affiliation(s)
- Huafeng Zhang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China
| | - Jincheng Liu
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wu Yuan
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qian Zhang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao Luo
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yonggang Li
- Hubei Provincial Key Laboratory for Applied Toxicology, Hubei Provincial Center for Disease Control and Prevention, Wuhan, China
| | - Yue'e Peng
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, China
| | - Jingyu Feng
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Liu
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Chen
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yabo Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiadi Lv
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nannan Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingwei Ma
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Tang
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Huang
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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17
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Akaaboune SR, Javed A, Bui S, Wierenga A, Wang Y. GRASP55 Regulates Sorting and Maturation of the Lysosomal Enzyme β-Hexosaminidase A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.16.618769. [PMID: 39464054 PMCID: PMC11507844 DOI: 10.1101/2024.10.16.618769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
The Golgi apparatus plays a crucial role in the delivery of lysosomal enzymes. Golgi Reassembly Stacking Proteins, GRASP55 and GRASP65, are vital for maintaining Golgi structure and function. GRASP55 depletion results in the missorting and secretion of the lysosomal enzyme Cathepsin D (Xiang et al ., 2013), though the mechanisms remain unclear. In this study, we conducted secretomic analyses of GRASP55 knockout (KO) cells and found a significant increase in lysosome-associated proteins in the extracellular medium. Using the lysosomal beta-hexosaminidase subunit alpha (HEXA) as a model, we found that GRASP55 depletion disrupted normal trafficking and processing of HEXA, resulting in increased secretion of the immature (pro-form) HEXA into the extracellular milieu, along with decreased levels of the mature form and enzymatic activity within the cell. GRASP55 depletion significantly reduced the complex formation between HEXA and mannose-6-phosphate (M6P) receptors (MPR), despite no overall change in MPR expression. And finally, we found there was a notable reduction in the expression of GNPTAB, leading to a reduction in M6P modification of HEXA, hindering its efficient targeting to lysosomes. These findings reveal the role of GRASP55 in regulating lysosomal enzyme dynamics, emphasizing its role in the sorting and trafficking of lysosomal proteins.
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18
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Stanley P. Genetics of glycosylation in mammalian development and disease. Nat Rev Genet 2024; 25:715-729. [PMID: 38724711 DOI: 10.1038/s41576-024-00725-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 09/19/2024]
Abstract
Glycosylation of proteins and lipids in mammals is essential for embryogenesis and the development of all tissues. Analyses of glycosylation mutants in cultured mammalian cells and model organisms have been key to defining glycosylation pathways and the biological functions of glycans. More recently, applications of genome sequencing have revealed the breadth of rare congenital disorders of glycosylation in humans and the influence of genetics on the synthesis of glycans relevant to infectious diseases, cancer progression and diseases of the immune system. This improved understanding of glycan synthesis and functions is paving the way for advances in the diagnosis and treatment of glycosylation-related diseases, including the development of glycoprotein therapeutics through glycosylation engineering.
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Affiliation(s)
- Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
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19
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Groessl S, Palm W. Nutrient Levels and Nutrient Sources in Pancreatic Tumors. Cancer Res 2024; 84:2947-2949. [PMID: 39279381 DOI: 10.1158/0008-5472.can-24-2447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 09/18/2024]
Abstract
It has been known that poor tumor perfusion and dysregulated cancer cell metabolism give rise to tumor microenvironments with unphysiologic nutrient levels, but the precise alterations in metabolite abundance are not well defined. In a 2015 study in Cancer Research, Kamphorst and colleagues published a detailed comparison of the metabolome from human pancreatic tumors and benign tissues. Tumors were depleted in glucose and various nonessential amino acids but, surprisingly, enriched in essential amino acids. The authors attributed these nutrient imbalances to macropinocytosis of extracellular proteins, a RAS-driven amino acid acquisition pathway that was found to be increased in human tumors and supports pancreatic cancer cell growth during amino acid starvation. These findings substantially contributed to the understanding of altered nutrient levels in tumors and extracellular proteins as noncanonical nutrients. Intratumoral nutrient levels in different cancer contexts and signaling pathways that regulate nutrient acquisition by cancer cells remain a focus of current research. See related article by Kamphorst and colleagues, Cancer Res 2015;75:544-53.
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Affiliation(s)
- Sven Groessl
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Wilhelm Palm
- Division of Cell Signaling and Metabolism, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
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20
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Bhat M, Nambiar A, Edakkandiyil L, Abraham IM, Sen R, Negi M, Manjithaya R. A genetically-encoded fluorescence-based reporter to spatiotemporally investigate mannose-6-phosphate pathway. Mol Biol Cell 2024; 35:mr6. [PMID: 38888935 PMCID: PMC11321044 DOI: 10.1091/mbc.e23-09-0344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 06/04/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Maintenance of a pool of active lysosomes with acidic pH and degradative hydrolases is crucial for cell health. Abnormalities in lysosomal function are closely linked to diseases, such as lysosomal storage disorders, neurodegeneration, intracellular infections, and cancer among others. Emerging body of research suggests the malfunction of lysosomal hydrolase trafficking pathway to be a common denominator of several disease pathologies. However, available conventional tools to assess lysosomal hydrolase trafficking are insufficient and fail to provide a comprehensive picture about the trafficking flux and location of lysosomal hydrolases. To address some of the shortcomings, we designed a genetically-encoded fluorescent reporter containing a lysosomal hydrolase tandemly tagged with pH sensitive and insensitive fluorescent proteins, which can spatiotemporally trace the trafficking of lysosomal hydrolases. As a proof of principle, we demonstrate that the reporter can detect perturbations in hydrolase trafficking, that are induced by pharmacological manipulations and pathophysiological conditions like intracellular protein aggregates. This reporter can effectively serve as a probe for mapping the mechanistic intricacies of hydrolase trafficking pathway in health and disease and is a utilitarian tool to identify genetic and pharmacological modulators of this pathway, with potential therapeutic implications.
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Affiliation(s)
- Mallika Bhat
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Akshaya Nambiar
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | | | - Irine Maria Abraham
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Ritoprova Sen
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Mamta Negi
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
- Professor and chair, Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
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21
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Köse SG, Güleç Taşkıran AE. Mechanisms of drug resistance in nutrient-depleted colorectal cancer cells: insights into lysosomal and mitochondrial drug sequestration. Biol Open 2024; 13:bio060448. [PMID: 39445740 PMCID: PMC11554266 DOI: 10.1242/bio.060448] [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: 10/25/2024] Open
Abstract
This Review delves into the mechanisms behind drug resistance in colorectal cancer (CRC), particularly examining the role of nutrient depletion and its contribution to multidrug resistance (MDR). The study highlights metabolic adaptations of cancer cells as well as metabolic adaptations of cancer cells under low nutrient availability, including shifts in glycolysis and lipid metabolism. It emphasizes the significance of MDR1 and its encoded efflux transporter, P-glycoprotein (P-gp/B1), in mediating drug resistance and how pathways such as HIF1α, AKT, and mTOR influence the expression of P-gp/B1 under limited nutrient availability. Additionally, the Review explores the dual roles of autophagy in drug sensitivity and resistance under nutrient limited conditions. It further investigates the involvement of lysosomes and mitochondria, focusing on their roles in drug sequestration and the challenges posed by lysosomal entrapment facilitated by non-enzymatic processes and ABC transporters like P-gp/B1. Finally, the Review underscores the importance of understanding the interplay between drug sequestration, lysosomal functions, nutrient depletion, and MDR1 gene modulation. It suggests innovative strategies, including structural modifications and nanotechnology, as promising approaches to overcoming drug resistance in cancer therapy.
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Affiliation(s)
- Serra Gülse Köse
- Molecular Biology and Genetics Department, Baskent University, Ankara 06790, Turkey
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22
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Arab M, Chen T, Lowe M. Mechanisms governing vesicle traffic at the Golgi apparatus. Curr Opin Cell Biol 2024; 88:102365. [PMID: 38705050 DOI: 10.1016/j.ceb.2024.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
Vesicle transport at the Golgi apparatus is a well-described process, and the major protein components involved have been identified. This includes the coat proteins that function in cargo sorting and vesicle formation, and the proteins that mediate the downstream events of vesicle tethering and membrane fusion. However, despite this knowledge, there remain significant gaps in our mechanistic understanding of these processes which includes how they are coordinated in space and time. In this review we discuss recent advances that have provided new insights into the mechanisms of Golgi trafficking, focussing on vesicle formation and cargo sorting, and vesicle tethering and fusion. These studies point to a high degree of spatial organisation of trafficking components at the Golgi and indicate an inherent plasticity of trafficking. Going forward, further advancements in technology and more sophisticated functional assays are expected to yield greater understanding of the mechanisms that govern Golgi trafficking events.
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Affiliation(s)
- Maryam Arab
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Tong Chen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Martin Lowe
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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23
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Rainero E. Macropinocytosis at the crossroad between nutrient scavenging and metabolism in cancer. Curr Opin Cell Biol 2024; 88:102359. [PMID: 38626703 DOI: 10.1016/j.ceb.2024.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
Macropinocytosis (MP), the actin-dependent bulk uptake of extracellular fluids, plays a central role in nutrient scavenging, allowing cancer cells to sustain their growth in the hypoxic and nutrient-deprived microenvironment often found in solid tumours. The lack of soluble nutrients and several oncogenic signalling pathways, with RAS being the most studied, push MP-dependent internalisation of extracellular proteins, which are then digested in the lysosomes, replenishing the intracellular nutrient pools. This review will highlight recent advances in understanding how MP is regulated in hypoxic cancers, how it impinges on chemoresistance, and how different MP cargos facilitate tumour growth. Finally, I will highlight the crosstalk between MP and extracellular matrix receptors.
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Affiliation(s)
- Elena Rainero
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
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24
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Li C, Fu J, Shao S, Luo ZQ. Legionella pneumophila exploits the endo-lysosomal network for phagosome biogenesis by co-opting SUMOylated Rab7. PLoS Pathog 2024; 20:e1011783. [PMID: 38739652 PMCID: PMC11115209 DOI: 10.1371/journal.ppat.1011783] [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: 10/30/2023] [Revised: 05/23/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Legionella pneumophila strains harboring wild-type rpsL such as Lp02rpsLWT cannot replicate in mouse bone marrow-derived macrophages (BMDMs) due to induction of extensive lysosome damage and apoptosis. The bacterial factor directly responsible for inducing such cell death and the host factor involved in initiating the signaling cascade that leads to lysosome damage remain unknown. Similarly, host factors that may alleviate cell death induced by these bacterial strains have not yet been investigated. Using a genome-wide CRISPR/Cas9 screening, we identified Hmg20a and Nol9 as host factors important for restricting strain Lp02rpsLWT in BMDMs. Depletion of Hmg20a protects macrophages from infection-induced lysosomal damage and apoptosis, allowing productive bacterial replication. The restriction imposed by Hmg20a was mediated by repressing the expression of several endo-lysosomal proteins, including the small GTPase Rab7. We found that SUMOylated Rab7 is recruited to the bacterial phagosome via SulF, a Dot/Icm effector that harbors a SUMO-interacting motif (SIM). Moreover, overexpression of Rab7 rescues intracellular growth of strain Lp02rpsLWT in BMDMs. Our results establish that L. pneumophila exploits the lysosomal network for the biogenesis of its phagosome in BMDMs.
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Affiliation(s)
- Chuang Li
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Jiaqi Fu
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Shuai Shao
- College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Zhao-Qing Luo
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
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25
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Bin P, Wang C, Zhang H, Yan Y, Ren W. Targeting methionine metabolism in cancer: opportunities and challenges. Trends Pharmacol Sci 2024; 45:395-405. [PMID: 38580603 DOI: 10.1016/j.tips.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
Reprogramming of methionine metabolism is a conserved hallmark of tumorigenesis. Recent studies have revealed mechanisms regulating methionine metabolism within the tumor microenvironment (TME) that drive both cancer development and antitumor immunity evasion. In this review article we summarize advancements in our understanding of tumor regulation of methionine metabolism and therapies in development that target tumor methionine metabolism. We also delineate the challenges of methionine blockade therapies in cancer and discuss emerging strategies to address them.
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Affiliation(s)
- Peng Bin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Chuanlong Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hangchao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yuqi Yan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wenkai Ren
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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26
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Frustaci A, Verardo R, Galea N, Alfarano M, Magnocavallo M, Marchitelli L, Sansone L, Belli M, Cristina M, Frustaci E, Russo MA, Chimenti C. Long-Term Clinical-Pathologic Results of Enzyme Replacement Therapy in Prehypertrophic Fabry Disease Cardiomyopathy. J Am Heart Assoc 2024; 13:e032734. [PMID: 38563373 PMCID: PMC11262509 DOI: 10.1161/jaha.123.032734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/04/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND The limited ability of enzyme replacement therapy (ERT) in removing globotriaosylceramide from cardiomyocytes is recognized for advanced Fabry disease cardiomyopathy (FDCM). Prehypertrophic FDCM is believed to be cured or stabilized by ERT. However, no pathologic confirmation is available. We report here on the long-term clinical-pathologic impact of ERT on prehypertrophic FDCM. METHODS AND RESULTS Fifteen patients with Fabry disease with left ventricular maximal wall thickness ≤10.5 mm at cardiac magnetic resonance required endomyocardial biopsy because of angina and ventricular arrhythmias. Endomyocardial biopsy showed coronary small-vessel disease in the angina cohort, and vacuoles in smooth muscle cells and cardiomyocytes ≈20% of the cell surface containing myelin bodies at electron microscopy. Patients received α-agalsidase in 8 cases, and β-agalsidase in 7 cases. Both groups experienced symptom improvement except 1 patients treated with α-agalsidase and 1 treated with β-agalsidase. After ERT administration ranging from 4 to 20 years, all patients had control cardiac magnetic resonance and left ventricular endomyocardial biopsy because of persistence of symptoms or patient inquiry on disease resolution. In 13 asymptomatic patients with FDCM, left ventricular maximal wall thickness and left ventricular mass, cardiomyocyte diameter, vacuole surface/cell surface ratio, and vessels remained unchanged or minimally increased (left ventricular mass increased by <2%) even after 20 years of observation, and storage material was still present at electron microscopy. In 2 symptomatic patients, FDCM progressed, with larger and more engulfed by globotriaosylceramide myocytes being associated with myocardial virus-negative lymphocytic inflammation. CONCLUSIONS ERT stabilizes storage deposits and myocyte dimensions in 87% of patients with prehypertrophic FDCM. Globotriaosylceramide is never completely removed even after long-term treatment. Immune-mediated myocardial inflammation can overlap, limiting ERT activity.
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Affiliation(s)
- Andrea Frustaci
- Cellular and Molecular Cardiology LabIRCCS L. SpallanzaniRomeItaly
| | - Romina Verardo
- Cellular and Molecular Cardiology LabIRCCS L. SpallanzaniRomeItaly
| | - Nicola Galea
- Department of Clinical, Internal, Anesthesiology and Cardiovascular SciencesSapienza University of RomeRomeItaly
| | - Maria Alfarano
- Department of Clinical, Internal, Anesthesiology and Cardiovascular SciencesSapienza University of RomeRomeItaly
| | | | - Livia Marchitelli
- Department of Radiological, Oncological, and Pathological Anatomy SciencesSapienza University of RomeRomeItaly
| | - Luigi Sansone
- Department of Human Sciences and Promotion of the Quality of LifeSan Raffaele Roma Open UniversityRomeItaly
- Laboratory of Molecular and Cellular PathologyIRCCS San Raffaele RomaRomeItaly
| | - Manuel Belli
- Department of Human Sciences and Promotion of the Quality of LifeSan Raffaele Roma Open UniversityRomeItaly
- Laboratory of Molecular and Cellular PathologyIRCCS San Raffaele RomaRomeItaly
| | - Mario Cristina
- Department of Molecular MedicineSapienza University of RomeRomeItaly
- MEBIC Consortium and IRCCS San Raffaele RomaRomeItaly
| | - Emanuela Frustaci
- Department of Molecular MedicineSapienza University of RomeRomeItaly
- Technoscience, Parco Scientifico e Tecnologico PontinoLatinaItaly
- MEBIC Consortium and IRCCS San Raffaele RomaRomeItaly
| | | | - Cristina Chimenti
- Department of Clinical, Internal, Anesthesiology and Cardiovascular SciencesSapienza University of RomeRomeItaly
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27
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Kiriyama K, Fujioka K, Kawai K, Mizuno T, Shinohara Y, Itoh K. Novel synthetic biological study on intracellular distribution of human GlcNAc-1-phosphotransferase expressed in insect cells. J Biochem 2024; 175:265-274. [PMID: 37948633 DOI: 10.1093/jb/mvad090] [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: 06/25/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Many lysosomal enzymes contain N-glycans carrying mannose 6-phosphate (M6P) residues. Modifying lysosomal enzymes by M6P residues requires a two-step process in the Golgi apparatus. Then the lysosomal enzymes with M6P residues are transported from the trans-Golgi network to endosomes and lysosomes by M6P receptors. In insect cells, M6P residues are not added to N-glycans. Therefore, many insect lysosomal enzymes are transported to lysosomes by the M6P-independent pathway. The expression and subcellular distribution of M6P-modifying enzymes were examined by amplifying DNA fragments of M6P-modifying enzymes, generating the corresponding plasmid constructs, and transfection each construct into Sf9 cells, an insect cell line. The human GlcNac-1-phosphotransferase α/β subunit, one of the M6P-modifying enzymes, was found to differ in maturation and localization between mammalian and insect cells. In mammalian cells, newly biosynthesized α/β subunit localized in the cis-Golgi. In Sf9 cells, most of the α/β subunit was localized in the endoplasmic reticulum, and few mature forms of α/β subunit were observed. However, by the co-expression of the human site-1 protease, the mature forms were observed significantly and co-localization with each protein. Our study indicates new insights into regulating the intracellular distribution of the human GlcNac-1-phosphotransferase α/β subunit in insect cells.
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Affiliation(s)
- Kei Kiriyama
- Institute for Genome Research, Tokushima University, 3-18-15, Kuramotocho, Tokushima-shi, Tokushima 770-8503, Japan
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
| | - Keisuke Fujioka
- Department of Medicinal Biotechnology, Faculty of Pharmaceutical Sciences, Tokushima University,1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
| | - Kaito Kawai
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
| | - Teru Mizuno
- Institute for Genome Research, Tokushima University, 3-18-15, Kuramotocho, Tokushima-shi, Tokushima 770-8503, Japan
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
| | - Yasuo Shinohara
- Institute for Genome Research, Tokushima University, 3-18-15, Kuramotocho, Tokushima-shi, Tokushima 770-8503, Japan
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
- Department of Medicinal Biotechnology, Faculty of Pharmaceutical Sciences, Tokushima University,1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
| | - Kohji Itoh
- Department of Medicinal Biotechnology, Institute for Medicinal Research, Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
- Department of Medicinal Biotechnology, Faculty of Pharmaceutical Sciences, Tokushima University,1-78-1, Shoumachi, Tokushima-shi, Tokushima 770-8505, Japan
- Department of Pediatrics, Jichi Medical University School of Medicine, 3311-1, Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan
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28
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Braulke T, Carette JE, Palm W. Lysosomal enzyme trafficking: from molecular mechanisms to human diseases. Trends Cell Biol 2024; 34:198-210. [PMID: 37474375 DOI: 10.1016/j.tcb.2023.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
Lysosomes degrade and recycle macromolecules that are delivered through the biosynthetic, endocytic, and autophagic routes. Hydrolysis of the different classes of macromolecules is catalyzed by about 70 soluble enzymes that are transported from the Golgi apparatus to lysosomes in a mannose 6-phosphate (M6P)-dependent process. The molecular machinery that generates M6P tags for receptor-mediated targeting of lysosomal enzymes was thought to be understood in detail. However, recent studies on the M6P pathway have identified a previously uncharacterized core component, yielded structural insights in known components, and uncovered functions in various human diseases. Here we review molecular mechanisms of lysosomal enzyme trafficking and discuss its relevance for rare lysosomal disorders, cancer, and viral infection.
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Affiliation(s)
- Thomas Braulke
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wilhelm Palm
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
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29
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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: 65] [Impact Index Per Article: 65.0] [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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30
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Liu Q, Wang W, Xu L, Zhang Q, Wang H. The host mannose-6-phosphate pathway and viral infection. Front Cell Infect Microbiol 2024; 14:1349221. [PMID: 38357444 PMCID: PMC10865371 DOI: 10.3389/fcimb.2024.1349221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Viruses, despite their simple structural composition, engage in intricate and complex interactions with their hosts due to their parasitic nature. A notable demonstration of viral behavior lies in their exploitation of lysosomes, specialized organelles responsible for the breakdown of biomolecules and clearance of foreign substances, to bolster their own replication. The man-nose-6-phosphate (M6P) pathway, crucial for facilitating the proper transport of hydrolases into lysosomes and promoting lysosome maturation, is frequently exploited for viral manipulation in support of replication. Recently, the discovery of lysosomal enzyme trafficking factor (LYSET) as a pivotal regulator within the lysosomal M6P pathway has introduced a fresh perspective on the intricate interplay between viral entry and host factors. This groundbreaking revelation illuminates unexplored dimensions of these interactions. In this review, we endeavor to provide a thorough overview of the M6P pathway and its intricate interplay with viral factors during infection. By consolidating the current understanding in this field, our objective is to establish a valuable reference for the development of antiviral drugs that selectively target the M6P pathway.
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Affiliation(s)
- Qincheng Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
| | - Weiqi Wang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
| | - Liwei Xu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
| | - Qisheng Zhang
- Shanghai Sino Organoid Lifesciences Co., Ltd., Shanghai, China
| | - Hongna Wang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
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31
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Li F, Wang W, Lai G, Lan S, Lv L, Wang S, Liu X, Zheng J. Development and validation of a novel lysosome-related LncRNA signature for predicting prognosis and the immune landscape features in colon cancer. Sci Rep 2024; 14:622. [PMID: 38182713 PMCID: PMC10770065 DOI: 10.1038/s41598-023-51126-9] [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: 10/11/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024] Open
Abstract
Lysosomes are essential components for managing tumor microenvironment and regulating tumor growth. Moreover, recent studies have also demonstrated that long non-coding RNAs could be used as a clinical biomarker for diagnosis and treatment of colorectal cancer. However, the influence of lysosome-related lncRNA (LRLs) on the progression of colon cancer is still unclear. This study aimed to identify a prognostic LRL signature in colon cancer and elucidated potential biological function. Herein, 10 differential expressed lysosome-related genes were obtained by the TCGA database and ultimately 4 prognostic LRLs for conducting a risk model were identified by the co-expression, univariate cox, least absolute shrinkage and selection operator analyses. Kaplan-Meier analysis, principal-component analysis, functional enrichment annotation, and nomogram were used to verify the risk model. Besides, the association between the prognostic model and immune infiltration, chemotherapeutic drugs sensitivity were also discussed in this study. This risk model based on the LRLs may be promising for potential clinical prognosis and immunotherapeutic responses related indicator in colon cancer patients.
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Affiliation(s)
- Fengming Li
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Wenyi Wang
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen, China
| | - Guanbiao Lai
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Shiqian Lan
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Liyan Lv
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China
| | - Shengjie Wang
- Department of Thyroid and Breast Surgery, Xiamen Humanity Hospital Fujian Medical University, Xiamen, Fujian, China.
| | - Xinli Liu
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
| | - Juqin Zheng
- Center of Digestive Endoscopy, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, China.
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Wang T, Zhang Y, Liu Y, Huang Y, Wang W. Amino Acid-Starved Cancer Cells Utilize Macropinocytosis and Ubiquitin-Proteasome System for Nutrient Acquisition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304791. [PMID: 37983609 PMCID: PMC10767443 DOI: 10.1002/advs.202304791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/06/2023] [Indexed: 11/22/2023]
Abstract
To grow in nutrient-deprived tumor microenvironment, cancer cells often internalize and degrade extracellular proteins to refuel intracellular amino acids. However, the nutrient acquisition routes reported by previous studies are mainly restricted in autophagy-lysosomal pathway. It remains largely unknown if other protein degradation systems also contribute to the utilization of extracellular nutrients. Herein, it is demonstrated that under amino acid starvation, extracellular protein internalization through macropinocytosis and protein degradation through ubiquitin-proteasome system are activated as a nutrient supply route, sensitizing cancer cells to proteasome inhibition. By inhibiting both macropinocytosis and ubiquitin-proteasome system, an innovative approach to intensify amino acid starvation for cancer therapy is presented. To maximize therapeutic efficacy and minimize systemic side effects, a pH-responsive polymersome nanocarrier is developed to deliver therapeutic agents specifically to tumor tissues. This nanoparticle system provides an approach to exacerbate amino acid starvation for cancer therapy, which represents a promising strategy for cancer treatment.
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Affiliation(s)
- Tianyi Wang
- State Key Laboratory of Pharmaceutical BiotechnologyThe University of Hong KongHong KongChina
- Department of Pharmacology and PharmacyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Dr. Li Dak‐Sum Research CentreThe University of Hong KongHong KongChina
| | - Yaming Zhang
- State Key Laboratory of Pharmaceutical BiotechnologyThe University of Hong KongHong KongChina
- Department of Pharmacology and PharmacyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Dr. Li Dak‐Sum Research CentreThe University of Hong KongHong KongChina
| | - Yuwei Liu
- State Key Laboratory of Pharmaceutical BiotechnologyThe University of Hong KongHong KongChina
- Department of Pharmacology and PharmacyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Dr. Li Dak‐Sum Research CentreThe University of Hong KongHong KongChina
| | - Yi Huang
- State Key Laboratory of Pharmaceutical BiotechnologyThe University of Hong KongHong KongChina
- Department of Pharmacology and PharmacyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Dr. Li Dak‐Sum Research CentreThe University of Hong KongHong KongChina
| | - Weiping Wang
- State Key Laboratory of Pharmaceutical BiotechnologyThe University of Hong KongHong KongChina
- Department of Pharmacology and PharmacyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Dr. Li Dak‐Sum Research CentreThe University of Hong KongHong KongChina
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Chen Y, He J, Jin T, Zhang Y, Ou Y. Functional enrichment analysis of LYSET and identification of related hub gene signatures as novel biomarkers to predict prognosis and immune infiltration status of clear cell renal cell carcinoma. J Cancer Res Clin Oncol 2023; 149:16905-16929. [PMID: 37740762 PMCID: PMC10645642 DOI: 10.1007/s00432-023-05280-2] [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: 07/04/2023] [Accepted: 08/10/2023] [Indexed: 09/25/2023]
Abstract
PURPOSE The latest research shows that the lysosomal enzyme trafficking factor (LYSET) encoded by TMEM251 is a key regulator of the amino acid metabolism reprogramming (AAMR) and related pathways significantly correlate with the progression of some tumors. The purpose of this study was to explore the potential pathways of the TMEM251 in clear cell renal cell carcinoma (ccRCC) and establish related predictive models based on the hub genes in these pathways for prognosis and tumor immune microenvironment (TIME). METHODS We obtained mRNA expression data and clinical information of ccRCC samples from The Cancer Genome Atlas (TCGA), E-MATE-1980, and immunotherapy cohorts. Single-cell sequencing data (GSE152938) were downloaded from the Gene Expression Omnibus (GEO) database. We explored biological pathways of the LYSET by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of TMEM251-coexpression genes. The correlation of LYSET-related pathways with the prognosis was conducted by Gene Set Variation Analysis (GSVA) and unsupervised cluster analysis. The least absolute shrinkage and selection operator (LASSO) and Cox regression were used to identify hub prognostic genes and construct the risk score. Immune infiltration analysis was conducted by CIBERSORTx and Tumor Immune Estimation Resource (TIMER) databases. The predictive value of the risk score and hub prognostic genes on immunotherapy responsiveness was analyzed through the tumor mutation burden (TMB) score, immune checkpoint expression, and survival analysis. Immunohistochemistry (IHC) was finally used to verify the expressions of hub prognostic genes. RESULTS The TMEM251 was found to be significantly correlated with some AAMR pathways. AAGAB, ENTR1, SCYL2, and WDR72 in LYSET-related pathways were finally identified to construct a risk score model. Immune infiltration analysis showed that LYSET-related gene signatures significantly influenced the infiltration of some vital immune cells such as CD4 + cells, NK cells, M2 macrophages, and so on. In addition, the constructed risk score was found to be positively correlated with TMB and some common immune checkpoint expressions. Different predictive values of these signatures for Nivolumab therapy responsiveness were also uncovered in immunotherapy cohorts. Finally, based on single-cell sequencing analysis, the TMEM251 and the hub gene signatures were found to be expressed in tumor cells and some immune cells. Interestingly, IHC verification showed a potential dual role of four hub genes in ccRCC progression. CONCLUSION The novel predictive biomarkers we built may benefit clinical decision-making for ccRCC. Our study may provide some evidence that LYSET-related gene signatures could be novel potential targets for treating ccRCC and improving immunotherapy efficacy. Our nomogram might be beneficial to clinical choices, but the results need more experimental verifications in the future.
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Affiliation(s)
- Yuxing Chen
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Jinhang He
- First Clinical Medical College, Chongqing Medical University, Chongqing, China
| | - Tian Jin
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ye Zhang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China
| | - Yunsheng Ou
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
- Orthopedic Laboratory of Chongqing Medical University, Chongqing, China.
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Tan JX, Finkel T. Lysosomes in senescence and aging. EMBO Rep 2023; 24:e57265. [PMID: 37811693 PMCID: PMC10626421 DOI: 10.15252/embr.202357265] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/08/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
Dysfunction of lysosomes, the primary hydrolytic organelles in animal cells, is frequently associated with aging and age-related diseases. At the cellular level, lysosomal dysfunction is strongly linked to cellular senescence or the induction of cell death pathways. However, the precise mechanisms by which lysosomal dysfunction participates in these various cellular or organismal phenotypes have remained elusive. The ability of lysosomes to degrade diverse macromolecules including damaged proteins and organelles puts lysosomes at the center of multiple cellular stress responses. Lysosomal activity is tightly regulated by many coordinated cellular processes including pathways that function inside and outside of the organelle. Here, we collectively classify these coordinated pathways as the lysosomal processing and adaptation system (LYPAS). We review evidence that the LYPAS is upregulated by diverse cellular stresses, its adaptability regulates senescence and cell death decisions, and it can form the basis for therapeutic manipulation for a wide range of age-related diseases and potentially for aging itself.
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Affiliation(s)
- Jay Xiaojun Tan
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPAUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Toren Finkel
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPAUSA
- Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPAUSA
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Li C, Fu J, Shao S, Luo ZQ. Legionella pneumophila exploits the endo-lysosomal network for phagosome biogenesis by co-opting SUMOylated Rab7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564884. [PMID: 37961430 PMCID: PMC10634985 DOI: 10.1101/2023.10.31.564884] [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
L. pneumophila strains harboring wild-type rpsL such as Lp02rpsLWT cannot replicate in mouse bone marrow-derived macrophages (BMDMs) due to induction of extensive lysosome damage and apoptosis. The mechanism of this unique infection-induced cell death remains unknown. Using a genome-wide CRISPR/Cas9 screening, we identified Hmg20a and Nol9 as host factors important for restricting strain Lp02rpsLWT in BMDMs. Depletion of Hmg20a protects macrophages from infection-induced lysosomal damage and apoptosis, allowing productive bacterial replication. The restriction imposed by Hmg20a was mediated by repressing the expression of several endo-lysosomal proteins, including the small GTPase Rab7. We found that SUMOylated Rab7 is recruited to the bacterial phagosome via SulF, a Dot/Icm effector that harbors a SUMO-interacting motif (SIM). Moreover, overexpression of Rab7 rescues intracellular growth of strain Lp02rpsLWT in BMDMs. Our results establish that L. pneumophila exploits the lysosomal network for the biogenesis of its phagosome in BMDMs.
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Affiliation(s)
- Chuang Li
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
| | - Jiaqi Fu
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
| | - Shuai Shao
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Zhao-Qing Luo
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Department of Biological Sciences, Purdue University, West Lafayette, IN 47906, USA
- Lead Contact
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Ahn G, Riley NM, Kamber RA, Wisnovsky S, Moncayo von Hase S, Bassik MC, Banik SM, Bertozzi CR. Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras. Science 2023; 382:eadf6249. [PMID: 37856615 PMCID: PMC10766146 DOI: 10.1126/science.adf6249] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Targeted protein degradation can provide advantages over inhibition approaches in the development of therapeutic strategies. Lysosome-targeting chimeras (LYTACs) harness receptors, such as the cation-independent mannose 6-phosphate receptor (CI-M6PR), to direct extracellular proteins to lysosomes. In this work, we used a genome-wide CRISPR knockout approach to identify modulators of LYTAC-mediated membrane protein degradation in human cells. We found that disrupting retromer genes improved target degradation by reducing LYTAC recycling to the plasma membrane. Neddylated cullin-3 facilitated LYTAC-complex lysosomal maturation and was a predictive marker for LYTAC efficacy. A substantial fraction of cell surface CI-M6PR remains occupied by endogenous M6P-modified glycoproteins. Thus, inhibition of M6P biosynthesis increased the internalization of LYTAC-target complexes. Our findings inform design strategies for next-generation LYTACs and elucidate aspects of cell surface receptor occupancy and trafficking.
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Affiliation(s)
- Green Ahn
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Nicholas M. Riley
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Roarke A. Kamber
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Simon Wisnovsky
- Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Salvador Moncayo von Hase
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Steven M. Banik
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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Ji S, Huang L, Chang S, Sun X, Liu H, Li A, Jin Y, Fei H. Albumin pre-opsonized membrane-active iPep nanomedicine potentiates chemo to immunotherapy of cancer. Biomaterials 2023; 301:122269. [PMID: 37573840 DOI: 10.1016/j.biomaterials.2023.122269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/27/2023] [Accepted: 08/06/2023] [Indexed: 08/15/2023]
Abstract
Chemotherapy-conjugated immunotherapy in clinical oncology conceptually resembles the combined effects of cytoreduction and immunostimulation in membrane targeted cell killings mediated by pore-forming proteins or host defense peptides. Of the similar concept, targeting cancer cell membrane using membrane active peptides is a hopeful therapeutic modality but had long been hindered from in vivo application. Here we report an enabling strategy of pre-opsonizing a membrane penetrating Ir-complexed octa-arginine peptide (iPep) with serum albumin via intrinsic amphipathicity-driven bimodal interactions into nanoparticles (NP). We found that NP triggered stress-mediated 4T1 cell oncosis which induced potent immunological activation, surpassing several well-known immunogenic medicines. Vested with albumin-enhanced in vivo tumor targeting specificity and pharmacokinetic properties, NP showed combined chemo to immunotherapies of s. c. tumors in mice, with decreased percentages of MDSC, Treg, M2-like macrophage and improved infiltration of CTLs in tumor site, caused complete regression of 4T1 and CT26 tumors, outperforming clinical medicines. In a challenging orthotopic breast cancer model, boost i. v. injections of NP acted as in situ tumor vaccine that drastically enhanced 4T1-specific cellular and humoral immunities to reverse disease progression. Thus, with combined effects of direct cytoreduction, immune activation and tumor vaccine, iPep-NP presents the promise and potential of a new modality of cancer medicine.
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Affiliation(s)
- Shuangshuang Ji
- Nanobiomedicine Division, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China; Key Laboratory of Nano-Bio Interface, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Liu Huang
- Nanobiomedicine Division, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China; School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China
| | - Shiwei Chang
- Nanobiomedicine Division, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China; Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, 215123, China
| | - Xingwei Sun
- Intervention Department, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Hanjie Liu
- Nanobiomedicine Division, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China; School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China
| | - Ang Li
- Nanobiomedicine Division, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China; School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China
| | - Yong Jin
- Intervention Department, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Hao Fei
- Nanobiomedicine Division, Suzhou Institute of Nano-Tech & Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China; Key Laboratory of Nano-Bio Interface, Chinese Academy of Sciences, Suzhou, 215123, China.
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Nicastro R, Brohée L, Alba J, Nüchel J, Figlia G, Kipschull S, Gollwitzer P, Romero-Pozuelo J, Fernandes SA, Lamprakis A, Vanni S, Teleman AA, De Virgilio C, Demetriades C. Malonyl-CoA is a conserved endogenous ATP-competitive mTORC1 inhibitor. Nat Cell Biol 2023; 25:1303-1318. [PMID: 37563253 PMCID: PMC10495264 DOI: 10.1038/s41556-023-01198-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023]
Abstract
Cell growth is regulated by the mammalian/mechanistic target of rapamycin complex 1 (mTORC1), which functions both as a nutrient sensor and a master controller of virtually all biosynthetic pathways. This ensures that cells are metabolically active only when conditions are optimal for growth. Notably, although mTORC1 is known to regulate fatty acid biosynthesis, how and whether the cellular lipid biosynthetic capacity signals back to fine-tune mTORC1 activity remains poorly understood. Here we show that mTORC1 senses the capacity of a cell to synthesise fatty acids by detecting the levels of malonyl-CoA, an intermediate of this biosynthetic pathway. We find that, in both yeast and mammalian cells, this regulation is direct, with malonyl-CoA binding to the mTOR catalytic pocket and acting as a specific ATP-competitive inhibitor. When fatty acid synthase (FASN) is downregulated/inhibited, elevated malonyl-CoA levels are channelled to proximal mTOR molecules that form direct protein-protein interactions with acetyl-CoA carboxylase 1 (ACC1) and FASN. Our findings represent a conserved and unique homeostatic mechanism whereby impaired fatty acid biogenesis leads to reduced mTORC1 activity to coordinately link this metabolic pathway to the overall cellular biosynthetic output. Moreover, they reveal the existence of a physiological metabolite that directly inhibits the activity of a signalling kinase in mammalian cells by competing with ATP for binding.
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Affiliation(s)
- Raffaele Nicastro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Laura Brohée
- Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne, Germany
| | - Josephine Alba
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Julian Nüchel
- Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne, Germany
| | - Gianluca Figlia
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | | | - Peter Gollwitzer
- Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne, Germany
| | - Jesus Romero-Pozuelo
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
- Unidad de Investigación Biomedica, Universidad Alfonso X El Sabio (UAX), Madrid, Spain
| | | | - Andreas Lamprakis
- Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne, Germany
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Heidelberg University, Heidelberg, Germany.
| | | | - Constantinos Demetriades
- Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne, Germany.
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany.
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Ramezani M, Bauman J, Singh A, Weisbart E, Yong J, Lozada M, Way GP, Kavari SL, Diaz C, Haghighi M, Batista TM, Pérez-Schindler J, Claussnitzer M, Singh S, Cimini BA, Blainey PC, Carpenter AE, Jan CH, Neal JT. A genome-wide atlas of human cell morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552164. [PMID: 37609130 PMCID: PMC10441312 DOI: 10.1101/2023.08.06.552164] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
A key challenge of the modern genomics era is developing data-driven representations of gene function. Here, we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-scale genotype-phenotype maps comprising >20,000 single-gene CRISPR-Cas9-based knockout experiments in >30 million cells. Our optical pooled cell profiling approach (PERISCOPE) combines a de-stainable high-dimensional phenotyping panel (based on Cell Painting1,2) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This approach provides high-dimensional phenotypic profiles of individual cells, while simultaneously enabling interrogation of subcellular processes. Our atlas reconstructs known pathways and protein-protein interaction networks, identifies culture media-specific responses to gene knockout, and clusters thousands of human genes by phenotypic similarity. Using this atlas, we identify the poorly-characterized disease-associated transmembrane protein TMEM251/LYSET as a Golgi-resident protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes, showing the power of these representations. In sum, our atlas and screening technology represent a rich and accessible resource for connecting genes to cellular functions at scale.
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Affiliation(s)
- Meraj Ramezani
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Bauman
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Stanford University, Stanford, CA, USA
| | - Avtar Singh
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Genentech Department of Cellular and Tissue Genomics, South San Francisco, CA, USA
| | - Erin Weisbart
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - John Yong
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Maria Lozada
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory P Way
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Sanam L Kavari
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: University of Pennsylvania, Philadelphia, PA, USA
| | - Celeste Diaz
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Stanford University, Stanford, CA, USA
| | | | - Thiago M Batista
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
| | - Joaquín Pérez-Schindler
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
| | - Melina Claussnitzer
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Beth A Cimini
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- MIT Department of Biological Engineering, Cambridge, MA, USA
- Koch Institute for Integrative Research at MIT, Cambridge, MA, USA
| | | | - Calvin H Jan
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - James T Neal
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
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40
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Ling Z, Han K, Liu W, Hua X, Jia S. Volumetric live-cell autofluorescence imaging using Fourier light-field microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:4237-4245. [PMID: 37799690 PMCID: PMC10549745 DOI: 10.1364/boe.495506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/07/2023]
Abstract
This study introduces a rapid, volumetric live-cell imaging technique for visualizing autofluorescent sub-cellular structures and their dynamics by employing high-resolution Fourier light-field microscopy. We demonstrated this method by capturing lysosomal autofluorescence in fibroblasts and HeLa cells. Additionally, we conducted multicolor imaging to simultaneously observe lysosomal autofluorescence and fluorescently-labeled organelles such as lysosomes and mitochondria. We further analyzed the data to quantify the interactions between lysosomes and mitochondria. This research lays the foundation for future exploration of native cellular states and functions in three-dimensional environments, effectively reducing photodamage and eliminating the necessity for exogenous labels.
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Affiliation(s)
- Zhi Ling
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Keyi Han
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Wenhao Liu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Xuanwen Hua
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Shu Jia
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Calcagni' A, Staiano L, Zampelli N, Minopoli N, Herz NJ, Di Tullio G, Huynh T, Monfregola J, Esposito A, Cirillo C, Bajic A, Zahabiyon M, Curnock R, Polishchuk E, Parkitny L, Medina DL, Pastore N, Cullen PJ, Parenti G, De Matteis MA, Grumati P, Ballabio A. Loss of the batten disease protein CLN3 leads to mis-trafficking of M6PR and defective autophagic-lysosomal reformation. Nat Commun 2023; 14:3911. [PMID: 37400440 DOI: 10.1038/s41467-023-39643-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Batten disease, one of the most devastating types of neurodegenerative lysosomal storage disorders, is caused by mutations in CLN3. Here, we show that CLN3 is a vesicular trafficking hub connecting the Golgi and lysosome compartments. Proteomic analysis reveals that CLN3 interacts with several endo-lysosomal trafficking proteins, including the cation-independent mannose 6 phosphate receptor (CI-M6PR), which coordinates the targeting of lysosomal enzymes to lysosomes. CLN3 depletion results in mis-trafficking of CI-M6PR, mis-sorting of lysosomal enzymes, and defective autophagic lysosomal reformation. Conversely, CLN3 overexpression promotes the formation of multiple lysosomal tubules, which are autophagy and CI-M6PR-dependent, generating newly formed proto-lysosomes. Together, our findings reveal that CLN3 functions as a link between the M6P-dependent trafficking of lysosomal enzymes and lysosomal reformation pathway, explaining the global impairment of lysosomal function in Batten disease.
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Affiliation(s)
- Alessia Calcagni'
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Institute for Genetic and Biomedical Research, National Research Council (CNR), Milan, Italy
| | | | - Nadia Minopoli
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Niculin J Herz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Tuong Huynh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Alessandra Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- SSM School for Advanced Studies, Federico II University, Naples, Italy
| | - Carmine Cirillo
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Mahla Zahabiyon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Rachel Curnock
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Luke Parkitny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Diego Luis Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Nunzia Pastore
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Giancarlo Parenti
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy.
- SSM School for Advanced Studies, Federico II University, Naples, Italy.
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Qiao W, Richards CM, Jabs S. LYSET/TMEM251- a novel key component of the mannose 6-phosphate pathway. Autophagy 2023; 19:2143-2145. [PMID: 36633450 PMCID: PMC10283412 DOI: 10.1080/15548627.2023.2167376] [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: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Degradation of macromolecules delivered to lysosomes by processes such as autophagy or endocytosis is crucial for cellular function. Lysosomes require more than 60 soluble hydrolases in order to catabolize such macromolecules. These soluble hydrolases are tagged with mannose6-phosphate (M6P) moieties in sequential reactions by the Golgi-resident GlcNAc-1-phosphotransferase complex and NAGPA/UCE/uncovering enzyme (N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase), which allows their delivery to endosomal/lysosomal compartments through trafficking mediated by cation-dependent and -independent mannose 6-phosphate receptors (MPRs). We and others recently identified TMEM251 as a novel regulator of the M6P pathway via independent genome-wide genetic screening strategies. We renamed TMEM251 to LYSET (lysosomal enzyme trafficking factor) to establish nomenclature reflective to this gene's function. LYSET is a Golgi-localized transmembrane protein important for the retention of the GlcNAc-1-phosphotransferase complex in the Golgi-apparatus. The current understanding of LYSET's importance regarding human biology is 3-fold: 1) highly pathogenic viruses that depend on lysosomal hydrolase activity require LYSET for infection. 2) The presence of LYSET is critical for cancer cell proliferation in nutrient-deprived environments in which extracellular proteins must be catabolized. 3) Inherited pathogenic alleles of LYSET can cause a severe inherited disease which resembles GlcNAc-1-phosphotransferase deficiency (i.e., mucolipidosis type II).Abbreviations: GlcNAc-1-PT: GlcNAc-1-phosphotransferase; KO: knockout; LSD: lysosomal storage disorder; LYSET: lysosomal enzyme trafficking factor; M6P: mannose 6-phosphate; MPRs: mannose-6-phosphate receptors, cation-dependent or -independent; MBTPS1/site-1 protease: membrane bound transcription factor peptidase, site 1; MLII: mucolipidosis type II; WT: wild-type.
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Affiliation(s)
- Wenjie Qiao
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher M. Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sabrina Jabs
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Schleswig-Holstein, Germany
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Bird LE, Edgington-Mitchell LE, Newton HJ. Eat, prey, love: Pathogen-mediated subversion of lysosomal biology. Curr Opin Immunol 2023; 83:102344. [PMID: 37245414 DOI: 10.1016/j.coi.2023.102344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/23/2023] [Accepted: 04/30/2023] [Indexed: 05/30/2023]
Abstract
The mammalian lysosome is classically considered the 'garbage can' of the cell, contributing to clearance of infection through its primary function as a degradative organelle. Intracellular pathogens have evolved several strategies to evade contact with this harsh environment through subversion of endolysosomal trafficking or escape into the cytosol. Pathogens can also manipulate pathways that lead to lysosomal biogenesis or alter the abundance or activity of lysosomal content. This pathogen-driven subversion of lysosomal biology is highly dynamic and depends on a range of factors, including cell type, stage of infection, intracellular niche and pathogen load. The growing body of literature in this field highlights the nuanced and complex relationship between intracellular pathogens and the host lysosome, which is critical for our understanding of infection biology.
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Affiliation(s)
- Lauren E Bird
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia; Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, VIC 3800, Australia
| | | | - Hayley J Newton
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia; Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, VIC 3800, Australia.
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44
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Zhang B, Yang X, Li M. LYSET/TMEM251/GCAF is critical for autophagy and lysosomal function by regulating the mannose-6-phosphate (M6P) pathway. Autophagy 2023; 19:1596-1598. [PMID: 36633445 PMCID: PMC10240974 DOI: 10.1080/15548627.2023.2167375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/06/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Vertebrate cells rely on mannose-6-phosphate (M6P) modifications to deliver most lumenal hydrolases to the lysosome. As a critical trafficking signal for lysosomal enzymes, the M6P biosynthetic pathway has been thoroughly investigated. However, its regulatory mechanism is largely unknown. Here, we summarize three recent studies that independently discovered LYSET/TMEM251/GCAF as a key regulator of the M6P pathway. LYSET/TMEM251 directly interacts with GNPT, the enzyme that catalyzes the transfer of M6P, and is critical for its activity and stability. Deleting LYSET/TMEM251 impairs the GNPT function and M6P modifications. Consequently, lysosomal enzymes are mistargeted for secretion. Defective lysosomes fail to degrade cargoes such as endocytic vesicles and autophagosomes, leading to a newly identified lysosomal storage disease in humans. These discoveries open up a new direction in the regulation of the M6P biosynthetic pathway.Abbreviations: ER: endoplasmic reticulum; GNPT: GlcNAc-1-phosphotransferase; KO: knockout; LMP: lysosome membrane protein; LYSET: lysosomal enzyme trafficking factor; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; M6P: mannose-6-phosphate; MBTPS1/S1P: membrane-bound transcription factor peptidase, site 1; MPR: mannose-6-phosphate receptor; SQSTM1: sequestosome 1; TEM: transmission electron microscopy; TGN: trans-Golgi network.
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Affiliation(s)
- Bokai Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xi Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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45
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Jain V, Singh MP, Amaravadi RK. Recent advances in targeting autophagy in cancer. Trends Pharmacol Sci 2023; 44:290-302. [PMID: 36931971 PMCID: PMC10106406 DOI: 10.1016/j.tips.2023.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/20/2023] [Accepted: 02/20/2023] [Indexed: 03/17/2023]
Abstract
Autophagy is a cellular homeostasis mechanism that fuels the proliferation and survival of advanced cancers by degrading and recycling organelles and proteins. Preclinical studies have identified that within an established tumor, tumor cell autophagy and host cell autophagy conspire to support tumor growth. A growing body of evidence suggests that autophagy inhibition can augment the efficacy of chemotherapy, targeted therapy, or immunotherapy to enhance tumor shrinkage. First-generation autophagy inhibition trials in cancer using the lysosomal inhibitor hydroxychloroquine (HCQ) have produced mixed results but have guided the way for the development of more potent and specific autophagy inhibitors in clinical trials. In this review, we will discuss the role of autophagy in cancer, newly discovered molecular mechanisms of the autophagy pathway, the effects of autophagy modulation in cancer and host cells, and novel autophagy inhibitors that are entering clinical trials.
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Affiliation(s)
- Vaibhav Jain
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mahendra Pal Singh
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi K Amaravadi
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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46
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Wang L, Shen HM. TMEM251, a new player in lysosomal enzyme trafficking. LIFE METABOLISM 2023; 2:loac039. [PMID: 39872736 PMCID: PMC11749558 DOI: 10.1093/lifemeta/loac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 01/30/2025]
Affiliation(s)
- Liming Wang
- School of Biomedical Sciences, Hunan University, Changsha, Hunan 410082, China
| | - Han-Ming Shen
- Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China
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47
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Zhou Z, Bonds MM, Edil BH, Houchen CW, Liu Z, Li M. Lysosomes Promote Cancer Metastasis via Exosome in PTEN-Deficient Tumors. Gastroenterology 2023; 164:329-331. [PMID: 36608713 DOI: 10.1053/j.gastro.2022.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Affiliation(s)
- Zhijun Zhou
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Morgan M Bonds
- Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Barish H Edil
- Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Courtney W Houchen
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Min Li
- Department of Medicine and, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.
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48
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Hao X, Chen J, Li Y, Liu X, Li Y, Wang B, Cao J, Gu Y, Ma W, Ma L. Molecular Defense Response of Bursaphelenchus xylophilus to the Nematophagous Fungus Arthrobotrys robusta. Cells 2023; 12:cells12040543. [PMID: 36831210 PMCID: PMC9953903 DOI: 10.3390/cells12040543] [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: 11/23/2022] [Revised: 01/14/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Bursaphelenchus xylophilus causes pine wilt disease, which poses a serious threat to forestry ecology around the world. Microorganisms are environmentally friendly alternatives to the use of chemical nematicides to control B. xylophilus in a sustainable way. In this study, we isolated a nematophagous fungus-Arthrobotrys robusta-from the xylem of diseased Pinus massoniana. The nematophagous activity of A. robusta against the PWNs was observed after just 6 h. We found that B. xylophilus entered the trap of A. robusta at 24 h, and the nervous system and immunological response of B. xylophilus were stimulated by metabolites that A. robusta produced. At 30 h of exposure to A. robusta, B. xylophilus exhibited significant constriction, and we were able to identify xenobiotics. Bursaphelenchus xylophilus activated xenobiotic metabolism, which expelled the xenobiotics from their bodies, by providing energy through lipid metabolism. When PWNs were exposed to A. robusta for 36 h, lysosomal and autophagy-related genes were activated, and the bodies of the nematodes underwent disintegration. Moreover, a gene co-expression pattern network was constructed by WGCNA and Cytoscape. The gene co-expression pattern network suggested that metabolic processes, developmental processes, detoxification, biological regulation, and signaling were influential when the B. xylophilus specimens were exposed to A. robusta. Additionally, bZIP transcription factors, ankyrin, ATPases, innexin, major facilitator, and cytochrome P450 played critical roles in the network. This study proposes a model in which mobility improved whenever B. xylophilus entered the traps of A. robusta. The model will provide a solid foundation with which to understand the molecular and evolutionary mechanisms underlying interactions between nematodes and nematophagous fungi. Taken together, these findings contribute in several ways to our understanding of B. xylophilus exposed to microorganisms and provide a basis for establishing an environmentally friendly prevention and control strategy.
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Affiliation(s)
- Xin Hao
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jie Chen
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yongxia Li
- Key Laboratory of Forest Protection, National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Xuefeng Liu
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yang Li
- School of Forestry, Northeast Forestry University, Harbin 150040, China
- China Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bowen Wang
- School of Art and Archaeology, Zhejiang University, Hangzhou 310028, China
| | - Jingxin Cao
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yaru Gu
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Wei Ma
- College of Pharmaceutical Sciences, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Ling Ma
- School of Forestry, Northeast Forestry University, Harbin 150040, China
- Correspondence:
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Chen Y, Lu Y, Huang C, Wu J, Shao Y, Wang Z, Zhang H, Fu Z. Subtypes analysis and prognostic model construction based on lysosome-related genes in colon adenocarcinoma. Front Genet 2023; 14:1149995. [PMID: 37168510 PMCID: PMC10166181 DOI: 10.3389/fgene.2023.1149995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 05/13/2023] Open
Abstract
Background: Lysosomes are essential for the development and recurrence of cancer. The relationship between a single lysosome-related gene and cancer has previously been studied, but the relationship between the lysosome-related genes (LRGs) and colon adenocarcinoma (COAD) remains unknown. This research examined the role of lysosome-related genes in colon adenocarcinoma. Methods: 28 lysosome-related genes associated with prognosis (PLRGs) were found by fusing the gene set that is differently expressed between tumor and non-tumor in colon adenocarcinoma with the gene set that is related to lysosomes. Using consensus unsupervised clustering of PLRGs, the colon adenocarcinoma cohort was divided into two subtypes. Prognostic and tumor microenvironment (TME) comparisons between the two subtypes were then made. The PLRGs_score was constructed using the least absolute shrinkage and selection operator regression (LASSO) method to quantify each patient's prognosis and provide advice for treatment. Lastly, Western Blot and immunohistochemistry (IHC) were used to identify MOGS expression at the protein level in colon adenocarcinoma tissues. Results: PLRGs had more somatic mutations and changes in genetic level, and the outcomes of the two subtypes differed significantly in terms of prognosis, tumor microenvironment, and enrichment pathways. Then, PLRGs_score was established based on two clusters of differential genes in the cancer genome atlas (TCGA) database, and external verification was performed using the gene expression omnibus (GEO) database. Then, we developed a highly accurate nomogram to enhance the clinical applicability of the PLRGs_score. Finally, a higher PLRGs_score was associated with a poorer overall survival (OS), a lower tumor mutation burden (TMB), a lower cancer stem cell (CSC) index, more microsatellite stability (MSS), and a higher clinical stage. MOGS was substantially elevated at the protein level in colon adenocarcinoma as additional confirmation. Conclusion: Overall, based on PLRGs, we identified two subtypes that varied significantly in terms of prognosis and tumor microenvironment. Then, in order to forecast patient prognosis and make treatment suggestions, we developed a diagnostic model with major significance for prognosis, clinical relevance, and immunotherapy. Moreover, we were the first to demonstrate that MOGS is highly expressed in colon adenocarcinoma.
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Affiliation(s)
- Yang Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Lu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changzhi Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jingyu Wu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Shao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenling Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongqiang Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- The First College of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Zan Fu,
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50
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Huang J, Zhao C, Zhang X, Zhao Q, Zhang Y, Chen L, Dai G. Hepatitis B virus pathogenesis relevant immunosignals uncovering amino acids utilization related risk factors guide artificial intelligence-based precision medicine. Front Pharmacol 2022; 13:1079566. [PMID: 36569318 PMCID: PMC9780394 DOI: 10.3389/fphar.2022.1079566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Background: Although immune microenvironment-related chemokines, extracellular matrix (ECM), and intrahepatic immune cells are reported to be highly involved in hepatitis B virus (HBV)-related diseases, their roles in diagnosis, prognosis, and drug sensitivity evaluation remain unclear. Here, we aimed to study their clinical use to provide a basis for precision medicine in hepatocellular carcinoma (HCC) via the amalgamation of artificial intelligence. Methods: High-throughput liver transcriptomes from Gene Expression Omnibus (GEO), NODE (https://www.bio.sino.org/node), the Cancer Genome Atlas (TCGA), and our in-house hepatocellular carcinoma patients were collected in this study. Core immunosignals that participated in the entire diseases course of hepatitis B were explored using the "Gene set variation analysis" R package. Using ROC curve analysis, the impact of core immunosignals and amino acid utilization related gene on hepatocellular carcinoma patient's clinical outcome were calculated. The utility of core immunosignals as a classifier for hepatocellular carcinoma tumor tissue was evaluated using explainable machine-learning methods. A novel deep residual neural network model based on immunosignals was constructed for the long-term overall survival (LS) analysis. In vivo drug sensitivity was calculated by the "oncoPredict" R package. Results: We identified nine genes comprising chemokines and ECM related to hepatitis B virus-induced inflammation and fibrosis as CLST signals. Moreover, CLST was co-enriched with activated CD4+ T cells bearing harmful factors (aCD4) during all stages of hepatitis B virus pathogenesis, which was also verified by our hepatocellular carcinoma data. Unexpectedly, we found that hepatitis B virus-hepatocellular carcinoma patients in the CLSThighaCD4high subgroup had the shortest overall survival (OS) and were characterized by a risk gene signature associated with amino acids utilization. Importantly, characteristic genes specific to CLST/aCD4 showed promising clinical relevance in identifying patients with early-stage hepatocellular carcinoma via explainable machine learning. In addition, the 5-year long-term overall survival of hepatocellular carcinoma patients can be effectively classified by CLST/aCD4 based GeneSet-ResNet model. Subgroups defined by CLST and aCD4 were significantly involved in the sensitivity of hepatitis B virus-hepatocellular carcinoma patients to chemotherapy treatments. Conclusion: CLST and aCD4 are hepatitis B virus pathogenesis-relevant immunosignals that are highly involved in hepatitis B virus-induced inflammation, fibrosis, and hepatocellular carcinoma. Gene set variation analysis derived immunogenomic signatures enabled efficient diagnostic and prognostic model construction. The clinical application of CLST and aCD4 as indicators would be beneficial for the precision management of hepatocellular carcinoma.
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Affiliation(s)
- Jun Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunbei Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xinhe Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qiaohui Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanting Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Liping Chen
- Key Laboratory of Gastroenterology and Hepatology, State Key Laboratory for Oncogenes and Related Genes, Department of Gastroenterology and Hepatology, Ministry of Health, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Guifu Dai
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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