1
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Pan H, Li S, Ning Y, Hu Z. Apelin-13 exerts protective effects against acute kidney injury by lysosomal function regulation. Ren Fail 2025; 47:2480243. [PMID: 40125924 PMCID: PMC11934166 DOI: 10.1080/0886022x.2025.2480243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Revised: 02/08/2025] [Accepted: 03/11/2025] [Indexed: 03/25/2025] Open
Abstract
BACKGROUND Recent studies suggest that the loss of lysosomal function is associated with acute kidney injury (AKI), potentially leading to impaired autophagy. Apelin has been known to regulate autophagy processes in cardiovascular and pulmonary diseases. We sought to explore its potential contribution in lysosomal function and autophagy modulation during AKI. METHODS Apelin-13 (30 μg/kg) or a vehicle control was administered to mice intraperitoneally 24 h prior to and at 0 h, 24 h, and 48 h following renal ischemia-reperfusion (I/R) injury or a sham procedure. Kidney and serum samples were collected for analysis 24 or 72 h postoperatively. RESULTS Our findings indicate that apelin-13 significantly mitigated renal damage and inhibited apoptosis post-AKI. Flow cytometry analysis revealed that apelin-13 treatment modulates the macrophages polarization within the kidney from M1 to M2 phenotype. Additionally, apelin-13 was found to reduce the expression of the (pro)renin receptor, restore lysosomal membrane permeability, augment lysosomal biogenesis, and enhance autophagic flux in the kidney following AKI. CONCLUSIONS Our study elucidates novel mechanisms underlying the protective effects of apelin in AKI through modulating lysosomal function and autophagy.
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Affiliation(s)
- Hao Pan
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Shuangshuang Li
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Yong Ning
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Zhizhi Hu
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
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2
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Wang R, Baehrecke EH. Atg9 is a conserved regulator of lysosome repair. J Cell Biol 2025; 224:e202504129. [PMID: 40358357 PMCID: PMC12071192 DOI: 10.1083/jcb.202504129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025] Open
Abstract
The ATG9 transmembrane protein scrambles lipids to regulate phagophore formation during autophagy. Two recent studies from Peng et al. (https://doi.org/10.1083/jcb.202411092) and De Tito et al. (https://doi.org/10.1101/2024.07.23.604321) identify ATG9 as a conserved regulator of lysosome repair in Caenorhabditis elegans and human cells, but differences in repair mechanisms exist between these taxa.
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Affiliation(s)
- Ruoxi Wang
- Department of Neuroscience, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Eric H. Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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3
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Peng K, Zhao G, Zhao H, Noda NN, Zhang H. The autophagy protein ATG-9 regulates lysosome function and integrity. J Cell Biol 2025; 224:e202411092. [PMID: 40202485 PMCID: PMC11980680 DOI: 10.1083/jcb.202411092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 03/05/2025] [Accepted: 03/11/2025] [Indexed: 04/10/2025] Open
Abstract
The transmembrane autophagy protein ATG9 has multiple functions essential for autophagosome formation. Here, we uncovered a novel function of ATG-9 in regulating lysosome biogenesis and integrity in Caenorhabditis elegans. Through a genetic screen, we identified that mutations attenuating the lipid scrambling activity of ATG-9 suppress the autophagy defect in epg-5 mutants, in which non-degradative autolysosomes accumulate. The scramblase-attenuated ATG-9 mutants promote lysosome biogenesis and delivery of lysosome-localized hydrolases and also facilitate the maintenance of lysosome integrity. Through manipulation of phospholipid levels, we found that a reduction in phosphatidylethanolamine (PE) also suppresses the autophagy defects and lysosome damage associated with impaired lysosomal degradation. Our results reveal that modulation of phospholipid composition and distribution, e.g., by attenuating the scramblase activity of ATG-9 or reducing the PE level, regulates lysosome function and integrity.
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Affiliation(s)
- Kangfu Peng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Guoxiu Zhao
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hongyu Zhao
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
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4
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Fei M, Luo S, Gao C, Huang X, Wang L, Jin T, Liu M, Zhou M, Wang H. OSBP Participates in Neural Damage Repair by Regulating Lysosome Transport Under Oxidative Stress. Mol Neurobiol 2025; 62:7557-7575. [PMID: 39915357 DOI: 10.1007/s12035-025-04698-8] [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: 07/08/2024] [Accepted: 01/10/2025] [Indexed: 05/15/2025]
Abstract
Oxidative stress is a major pathological factor in acute brain injury, such as traumatic brain injury (TBI). As highly branched cells, the transport of lysosomes plays a crucial role in neuronal homeostasis. However, the effects and mechanisms of oxidative damage on axonal lysosome transport remain unknown. In this study, we demonstrated that the downregulation of the membrane lipid orchestrator oxysterol-binding protein (OSBP) induced by oxidative stress alters the subcellular distribution of lysosomes in neurons through regulating lysosomal phosphatidylinositol-4-monophosphate (PI(4)P)/phosphatidylinositol-3-monophosphate (PI(3)P) contents, thus disrupting lysosomal transport. The results of the cell experiments confirmed the occurrence of an autophagic pressure burst, disordered anterograde lysosome transport, and an imbalance in the PI(4)P/PI(3)P ratio in neurons after H2O2 treatment. Mechanistically, oxidative damage reduced neuronal OSBP protein levels, thus contributing to lysosomal PI(4)P storage. Furthermore, a protein‒liposome binding assay revealed that compared with liposomes containing PI(4)P, liposomes containing PI(3)P or cholesterol presented decreased coprecipitation of Arl8. The overexpression of OSBP restored the PI(4)P/PI(3)P content, improved the binding ability of Arl8 to bind to lysosomes, increased lysosome localization in neurites, and promoted axonal injury repair. Finally, overexpression of neuronal OSBP through adeno-associated virus intervention in vivo alleviated dendritic damage and improved the neurological function of mice with TBI. Taken together, these findings suggest that disturbance of OSBP induced by oxidative stress results in abnormal lysosomal distribution and contributes to neuronal malfunction in TBI, and OSBP could be a potential target to promote neuronal repair and regeneration by regulating lysosomal lipid composition and axonal localization.
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Affiliation(s)
- Maoxing Fei
- Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Shiqiao Luo
- Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Chaochao Gao
- Department of Neurosurgery, The Affiliated Jinling Hospital of Nanjing Medical University, Nanjing, China
| | - Xiwen Huang
- Department of Neurosurgery, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Lan Wang
- Department of Neurosurgery, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Tianle Jin
- Department of Neurosurgery, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Mingda Liu
- Department of Core Laboratory, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Mengliang Zhou
- Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
| | - Handong Wang
- Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Department of Neurosurgery, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China.
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5
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Murley A, Popovici AC, Hu XS, Lund A, Wickham K, Durieux J, Joe L, Koronyo E, Zhang H, Genuth NR, Dillin A. Quiescent cell re-entry is limited by macroautophagy-induced lysosomal damage. Cell 2025; 188:2670-2686.e14. [PMID: 40203825 DOI: 10.1016/j.cell.2025.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 01/14/2025] [Accepted: 03/06/2025] [Indexed: 04/11/2025]
Abstract
To maintain tissue homeostasis, many cells reside in a quiescent state until prompted to divide. The reactivation of quiescent cells is perturbed with aging and may underlie declining tissue homeostasis and resiliency. The unfolded protein response regulators IRE-1 and XBP-1 are required for the reactivation of quiescent cells in developmentally L1-arrested C. elegans. Utilizing a forward genetic screen in C. elegans, we discovered that macroautophagy targets protein aggregates to lysosomes in quiescent cells, leading to lysosome damage. Genetic inhibition of macroautophagy and stimulation of lysosomes via the overexpression of HLH-30 (TFEB/TFE3) synergistically reduces lysosome damage. Damaged lysosomes require IRE-1/XBP-1 for their repair following prolonged L1 arrest. Protein aggregates are also targeted to lysosomes by macroautophagy in quiescent cultured mammalian cells and are associated with lysosome damage. Thus, lysosome damage is a hallmark of quiescent cells, and limiting lysosome damage by restraining macroautophagy can stimulate their reactivation.
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Affiliation(s)
- Andrew Murley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ann Catherine Popovici
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Xiwen Sophie Hu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anina Lund
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kevin Wickham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jenni Durieux
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Larry Joe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Etai Koronyo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hanlin Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Naomi R Genuth
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew Dillin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
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6
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Zhang R, Vooijs MA, Keulers TG. Key Mechanisms in Lysosome Stability, Degradation and Repair. Mol Cell Biol 2025; 45:212-224. [PMID: 40340648 DOI: 10.1080/10985549.2025.2494762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 04/10/2025] [Accepted: 04/10/2025] [Indexed: 05/10/2025] Open
Abstract
Lysosomes are organelles that play pivotal roles in macromolecule digestion, signal transduction, autophagy, and cellular homeostasis. Lysosome instability, including the inhibition of lysosomal intracellular activity and the leakage of their contents, is associated with various pathologies, including cancer, neurodegenerative diseases, inflammatory diseases and infections. These lysosomal-related pathologies highlight the significance of factors contributing to lysosomal dysfunction. The vulnerability of the lysosomal membrane and its components to internal and external stimuli make lysosomes particularly susceptible to damage. Cells are equipped with mechanisms to repair or degrade damaged lysosomes to prevent cell death. Understanding the factors influencing lysosome stabilization and damage repair is essential for developing effective therapeutic interventions for diseases. This review explores the factors affecting lysosome acidification, membrane integrity, and functional homeostasis and examines the underlying mechanisms of lysosomal damage repair. In addition, we summarize how various risk factors impact lysosomal activity and cell fate.
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Affiliation(s)
- Rui Zhang
- Department of Radiation Oncology (MAASTRO)/GROW Research Institute for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marc A Vooijs
- Department of Radiation Oncology (MAASTRO)/GROW Research Institute for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Tom Gh Keulers
- Department of Radiation Oncology (MAASTRO)/GROW Research Institute for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
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7
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Wang X, Xu P, Bentley-DeSousa A, Hancock-Cerutti W, Cai S, Johnson BT, Tonelli F, Shao L, Talaia G, Alessi DR, Ferguson SM, De Camilli P. The bridge-like lipid transport protein VPS13C/PARK23 mediates ER-lysosome contacts following lysosome damage. Nat Cell Biol 2025; 27:776-789. [PMID: 40211074 DOI: 10.1038/s41556-025-01653-6] [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: 05/24/2024] [Accepted: 03/06/2025] [Indexed: 04/12/2025]
Abstract
Based on genetic studies, lysosome dysfunction is thought to play a pathogenetic role in Parkinson's disease. Here we show that VPS13C, a bridge-like lipid-transport protein and a Parkinson's disease gene, is a sensor of lysosome stress or damage. Following lysosome membrane perturbation, VPS13C rapidly relocates from the cytosol to the surface of lysosomes where it tethers their membranes to the ER. This recruitment depends on Rab7 and requires a signal at the damaged lysosome surface that releases an inhibited state of VPS13C, which hinders access of its VAB domain to lysosome-bound Rab7. Although another Parkinson's disease protein, LRRK2, is also recruited to stressed or damaged lysosomes, its recruitment occurs at much later stages and by different mechanisms. Given the role of VPS13 proteins in bulk lipid transport, these findings suggest that lipid delivery to lysosomes by VPS13C is part of an early protective response to lysosome damage.
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Affiliation(s)
- Xinbo Wang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Peng Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Amanda Bentley-DeSousa
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - William Hancock-Cerutti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Shujun Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Benjamin T Johnson
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Francesca Tonelli
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lin Shao
- Center for Neurodevelopment and Plasticity, Wu Tsai Institute, Yale University, New Haven, CT, USA
| | - Gabriel Talaia
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Shawn M Ferguson
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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8
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Xun J, Tan JX. Lysosomal Repair in Health and Disease. J Cell Physiol 2025; 240:e70044. [PMID: 40349217 PMCID: PMC12066097 DOI: 10.1002/jcp.70044] [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: 03/15/2025] [Revised: 04/17/2025] [Accepted: 04/21/2025] [Indexed: 05/14/2025]
Abstract
Lysosomes are essential organelles degrading a wide range of substrates, maintaining cellular homeostasis, and regulating cell growth through nutrient and metabolic signaling. A key vulnerability of lysosomes is their membrane permeabilization (LMP), a process tightly linked to diseases including aging, neurodegeneration, lysosomal storage disorders, and cardiovascular disease. Research progress in the past few years has greatly improved our understanding of lysosomal repair mechanisms. Upon LMP, cells activate multiple membrane remodeling processes to restore lysosomal integrity, such as membrane invagination, tubulation, lipid patching, and membrane stabilization. These repair pathways are critical in preserving cellular stress tolerance and preventing deleterious inflammation and cell death triggered by lysosomal damage. This review focuses on the expanding mechanistic insights of lysosomal repair, highlighting its crucial role in maintaining cellular health and the implications for disease pathogenesis and therapeutic strategies.
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Affiliation(s)
- Jinrui Xun
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
| | - Jay Xiaojun Tan
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPennsylvaniaUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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9
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Balla T. Phosphatidylinositol 4-phosphate; A minor lipid with multiple personalities. Biochim Biophys Acta Mol Cell Biol Lipids 2025; 1870:159615. [PMID: 40262701 DOI: 10.1016/j.bbalip.2025.159615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 04/08/2025] [Accepted: 04/18/2025] [Indexed: 04/24/2025]
Abstract
Phosphorylated products of phosphatidylinositol (PI), named Diphosphoinositide (DPI) and triphosphoinositide (TPI) were identified long time ago and found to exhibit high turnover rates based on their rapid 32P-phosphate labeling. The PI kinase activities that were responsible for their production were subsequently identified and found to be associated with different organelle membranes, including the plasma membrane. These activities were then linked with a certain group of cell surface receptors that activated phospholipase C enzymes to hydrolyze PI and used calcium or cGMP as a second messenger. This visionary concept was introduced in the seminal BBA review written by Robert Michell, exactly 50 years ago. The enzymology and functional diversity of PI 4-phosphate (PI4P) (the term that has replaced DPI) has since underwent an expansion that could not have been foreseen. In this review I will attempt to revisit this expansion with some historical reflections celebrating the 50th anniversary of the Michell review.
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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10
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Hanna MG, Rodriguez Cruz HO, Fujise K, Wu Y, Xu CS, Pang S, Li Z, Monetti M, De Camilli P. BLTP3A is associated with membranes of the late endocytic pathway and is an effector of CASM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.09.28.615015. [PMID: 39386594 PMCID: PMC11463362 DOI: 10.1101/2024.09.28.615015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Recent studies have identified a family of rod-shaped proteins thought to mediate lipid transfer at intracellular membrane contacts by a bridge-like mechanism. We show one such protein, bridge-like lipid transfer protein 3A (BLTP3A)/UHRF1BP1 binds VAMP7 vesicles via its C-terminal region and anchors them to lysosomes via its chorein domain containing N-terminal region to Rab7. Upon lysosome damage, BLTP3A-positive vesicles rapidly (within minutes) dissociate from lysosomes. Lysosome damage is known to activate the CASM (Conjugation of ATG8 to Single Membranes) pathway leading to lipidation and recruitment to lysosomes of mammalian ATG8 (mATG8) proteins. We find that this process drives the reassociation of BLTP3A with damaged lysosomes via an interaction of its LIR motif with mATG8 which coincides with a dissociation from the vesicles. Our findings reveal that BLTP3A is an effector of CASM, potentially as part of a mechanism to help repair or minimize lysosome damage.
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Affiliation(s)
- Michael G. Hanna
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Hely O. Rodriguez Cruz
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Kenshiro Fujise
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - Yumei Wu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
| | - C. Shan Xu
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT
| | - Song Pang
- Yale University School of Medicine, New Haven, CT
| | - Zhuonging Li
- Proteomics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mara Monetti
- Proteomics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD
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11
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Bentley-DeSousa A, Clegg D, Ferguson SM. LRRK2, lysosome damage, and Parkinson's disease. Curr Opin Cell Biol 2025; 93:102482. [PMID: 39983584 DOI: 10.1016/j.ceb.2025.102482] [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: 12/22/2024] [Revised: 01/27/2025] [Accepted: 01/28/2025] [Indexed: 02/23/2025]
Abstract
Limited understanding of regulatory mechanisms controlling LRRK2 kinase activity has hindered insights into both its normal biology and how its dysregulation contributes to Parkinson's disease. Fortunately, recent years have yielded an increased understanding of how LRRK2 kinase activity is dynamically regulated by recruitment to endolysosomal membranes. Notably, multiple small GTPases from the Rab family act as both activators and substrates of LRRK2. Additionally, it was recently discovered that LRRK2 is recruited to, and activated at, stressed or damaged lysosomes through an interaction with GABARAP via the CASM (conjugation of ATG8 to single membranes) pathway. These discoveries position LRRK2 within the rapidly growing field of lysosomal damage and repair mechanisms, offering important insights into lysosome biology and the pathogenesis of Parkinson's disease.
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Affiliation(s)
- Amanda Bentley-DeSousa
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Devin Clegg
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Shawn M Ferguson
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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12
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Lu TW, Frost A, Moss FR. Organelle homeostasis requires ESCRTs. Curr Opin Cell Biol 2025; 93:102481. [PMID: 39954309 DOI: 10.1016/j.ceb.2025.102481] [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: 12/04/2024] [Accepted: 01/22/2025] [Indexed: 02/17/2025]
Abstract
The endosomal sorting complexes required for transport (ESCRT) catalyze membrane shape transformations throughout the cell. Canonical functions of the ESCRTs include endosomal multivesicular body biogenesis, enveloped virus budding, and abscission of daughter cell plasma membranes. The ESCRT machinery is also required for membranous organelle homeostasis generally, including by facilitating lipid transport at membrane contact sites, repairing membrane damage, driving lysosomal catabolism, and maintaining nuclear envelope integrity, among other roles. Here, we review a subset of recent discoveries and highlight opportunities to better understand how ESCRT activities support cell health.
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Affiliation(s)
- Tsan-Wen Lu
- Bay Area Institute of Science, Altos Labs, Redwood City, CA 94065, USA
| | - Adam Frost
- Bay Area Institute of Science, Altos Labs, Redwood City, CA 94065, USA
| | - Frank R Moss
- Bay Area Institute of Science, Altos Labs, Redwood City, CA 94065, USA.
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13
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Ebner M, Fröhlich F, Haucke V. Mechanisms and functions of lysosomal lipid homeostasis. Cell Chem Biol 2025; 32:392-407. [PMID: 40054455 DOI: 10.1016/j.chembiol.2025.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 01/30/2025] [Accepted: 02/11/2025] [Indexed: 03/23/2025]
Abstract
Lysosomes are the central degradative organelle of mammalian cells and have emerged as major intersections of cellular metabolite flux. Macromolecules derived from dietary and intracellular sources are delivered to the acidic lysosomal lumen where they are subjected to degradation by acid hydrolases. Lipids derived from lipoproteins, autophagy cargo, or autophagosomal membranes themselves constitute major lysosomal substrates. Dysregulation of lysosomal lipid processing, defective export of lipid catabolites, and lysosomal membrane permeabilization underly diseases ranging from neurodegeneration to metabolic syndromes and lysosomal storage disorders. Mammalian cells are equipped with sophisticated homeostatic control mechanisms that protect the lysosomal limiting membrane from excessive damage, prevent the spillage of luminal hydrolases into the cytoplasm, and preserve the lysosomal membrane composition in the face of constant fusion with heterotypic organelles such as endosomes and autophagosomes. In this review we discuss the molecular mechanisms that govern lysosomal lipid homeostasis and, thereby, lysosome function in health and disease.
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Affiliation(s)
- Michael Ebner
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Florian Fröhlich
- Bioanalytical Chemistry Section, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany; Center of Cellular Nanoanalytics Osnabrück (CellNanOs), 49076 Osnabrück, Germany
| | - Volker Haucke
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany.
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14
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Wang Q, Wang R, Hu H, Huo X, Wang F. Lysosomes' fallback strategies: more than just survival or death. Front Cell Dev Biol 2025; 13:1559504. [PMID: 40134576 PMCID: PMC11933002 DOI: 10.3389/fcell.2025.1559504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Accepted: 02/18/2025] [Indexed: 03/27/2025] Open
Abstract
Lysosomes are heterogeneous, acidic organelles whose proper functionality is critically dependent on maintaining the integrity of their membranes and the acidity within their lumen. When subjected to stress, the lysosomal membrane can become permeabilized, posing a significant risk to the organelle's survival and necessitating prompt repair. Although numerous mechanisms for lysosomal repair have been identified in recent years, the progression of lysosome-related diseases is more closely linked to the organelle's alternative strategies when repair mechanisms fail, particularly in the contexts of aging and pathogen infection. This review explores lysosomal responses to damage, including the secretion of lysosomal contents and the interactions with lysosome-associated organelles in the endolysosomal system. Furthermore, it examines the role of organelles outside this system, such as the endoplasmic reticulum (ER) and Golgi apparatus, as auxiliary organelles of the endolysosomal system. These alternative strategies are crucial to understanding disease progression. For instance, the secretion and spread of misfolded proteins play key roles in neurodegenerative disease advancement, while pathogen escape via lysosomal secretion and lysosomotropic drug expulsion underlie cancer treatment resistance. Reexamining these lysosomal fallback strategies could provide new perspectives on lysosomal biology and their contribution to disease progression.
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Affiliation(s)
- Quan Wang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Ruolin Wang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Haihui Hu
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Xiaoqing Huo
- Huaian Maternity and Child Healthcare Hospital of JiangSu Province, Huaian, China
| | - Fulong Wang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
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15
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Gdovinova I, Descoteaux A. VAPA mediates lipid exchange between Leishmania amazonensis and host macrophages. PLoS Pathog 2025; 21:e1012636. [PMID: 40163521 PMCID: PMC11981147 DOI: 10.1371/journal.ppat.1012636] [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: 10/01/2024] [Revised: 04/09/2025] [Accepted: 03/03/2025] [Indexed: 04/02/2025] Open
Abstract
Leishmania is a vacuolar pathogen that replicates within parasitophorous vacuoles inside host phagocytes. To promote its replication, Leishmania relies on a panoply of strategies to acquire macromolecules such as lipids from host macrophages. In this study, we have evaluated the role of VAPA, an endoplasmic reticulum-resident membrane protein involved in inter-organellar lipid transport, in macrophages infected with L. amazonensis. Following infection of bone marrow-derived macrophages with L. amazonensis metacyclic promastigotes, we observed that VAPA gradually associates with communal parasitophorous vacuoles. Knockdown of VAPA prevented the replication of L. amazonensis, which was accompanied by an impaired parasitophorous vacuole expansion. Using fluorescent ceramide, we established that VAPA is required for the transport of sphingolipids to the parasitophorous vacuoles and for its acquisition by L. amazonensis amastigotes. Proximity-ligation assays revealed that L. amazonensis hijacks VAPA by disrupting its interactions with the host cell lipid transfer proteins CERT and ORP1L. Finally, we found that VAPA is essential for the transfer of the Leishmania virulence glycolipid lipophosphoglycan from the parasitophorous vacuoles to the host cell endoplasmic reticulum. We propose that VAPA contributes to the ability of L. amazonensis to colonize macrophages by mediating bi-directional transfer of lipids essential for parasite replication and virulence between the parasitophorous vacuoles and the host cell endoplasmic reticulum.
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Affiliation(s)
- Ilona Gdovinova
- INRS- Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Infectiopôle INRS, Laval, Québec, Canada
| | - Albert Descoteaux
- INRS- Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Infectiopôle INRS, Laval, Québec, Canada
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16
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Wang X, Xu P, Bentley-DeSousa A, Hancock-Cerutti W, Cai S, Johnson BT, Tonelli F, Shao L, Talaia G, Alessi DR, Ferguson SM, De Camilli P. Lysosome damage triggers acute formation of ER to lysosomes membrane tethers mediated by the bridge-like lipid transport protein VPS13C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.06.08.598070. [PMID: 38895395 PMCID: PMC11185796 DOI: 10.1101/2024.06.08.598070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Based on genetic studies, lysosome dysfunction is thought to play a pathogenetic role in Parkinson's disease (PD). Here we show that VPS13C, a bridge-like lipid transport protein and a PD gene, is a sensor of lysosome stress/damage. Upon lysosome membrane perturbation, VPS13C rapidly relocates from the cytosol to the surface of lysosomes where it tethers their membranes to the ER. This recruitment depends on Rab7 and requires a signal at the damaged lysosome surface that releases an inhibited state of VPS13C which hinders access of its VAB domain to lysosome-bound Rab7. While another PD protein, LRRK2, is also recruited to stressed/damaged lysosomes, its recruitment occurs at much later stages and by different mechanisms. Given the role of VPS13 proteins in bulk lipid transport, these findings suggest that lipid delivery to lysosomes by VPS13C is part of an early protective response to lysosome damage.
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17
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Henn D, Yang X, Li M. Lysosomal quality control Review. Autophagy 2025:1-20. [PMID: 39968899 DOI: 10.1080/15548627.2025.2469206] [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: 10/20/2024] [Revised: 02/10/2025] [Accepted: 02/14/2025] [Indexed: 02/20/2025] Open
Abstract
Healthy cells need functional lysosomes to degrade cargo delivered by autophagy and endocytosis. Defective lysosomes can lead to severe conditions such as lysosomal storage diseases (LSDs) and neurodegeneration. To maintain lysosome integrity and functionality, cells have evolved multiple quality control pathways corresponding to different types of stress and damage. These can be divided into five levels: regulation, reformation, repair, removal, and replacement. The different levels of lysosome quality control often work together to maintain the integrity of the lysosomal network. This review summarizes the different quality control pathways and discusses the less-studied area of lysosome membrane protein regulation and degradation, highlighting key unanswered questions in the field.Abbreviation: ALR: autophagic lysosome reformation; CASM: conjugation of ATG8 to single membranes: ER: endoplasmic reticulum; ESCRT: endosomal sorting complexes required for transport; ILF: intralumenal fragment; LSD: lysosomal storage disease; LYTL: lysosomal tubulation/sorting driven by LRRK2; PITT: phosphoinositide-initiated membrane tethering and lipid transport; PE: phosphatidylethanolamine; PLR: phagocytic lysosome reformation; PS: phosphatidylserine; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns4P: phosphatidylinositol-4-phosphate; PtdIns(4,5)P2: phosphatidylinositol-4,5-bisphosphate; V-ATPase: vacuolar-type H+-translocating ATPase.
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Affiliation(s)
- Danielle Henn
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xi Yang
- Department of Biological Sciences, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Ming Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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18
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Wang J, Wang M, Zeng X, Li Y, Lei L, Chen C, Lin X, Fang P, Guo Y, Jiang X, Wang Y, Chen L, Long J. Targeting membrane contact sites to mediate lipid dynamics: innovative cancer therapies. Cell Commun Signal 2025; 23:89. [PMID: 39955542 PMCID: PMC11830217 DOI: 10.1186/s12964-025-02089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 02/06/2025] [Indexed: 02/17/2025] Open
Abstract
Membrane contact sites (MCS) are specialized regions where organelles are closely interconnected through membrane structures, facilitating the transfer and exchange of ions, lipids, and other molecules. This proximity enables a synergistic regulation of cellular homeostasis and functions. The formation and maintenance of these contact sites are governed by specific proteins that bring organelle membranes into close apposition, thereby enabling functional crosstalk between cellular compartments. In eukaryotic cells, lipids are primarily synthesized and metabolized within distinct organelles and must be transported through MCS to ensure proper cellular function. Consequently, MCS act as pivotal platforms for lipid synthesis and trafficking, particularly in cancer cells and immune cells within the tumor microenvironment, where dynamic alterations are critical for maintaining lipid homeostasis. This article provides a comprehensive analysis of how these cells exploit membrane contact sites to modulate lipid synthesis, metabolism, and transport, with a specific focus on how MCS-mediated lipid dynamics influence tumor progression. We also examine the differences in MCS and associated molecules across various cancer types, exploring novel therapeutic strategies targeting MCS-related lipid metabolism for the development of anticancer drugs, while also addressing the challenges involved.
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Affiliation(s)
- Jie Wang
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China.
| | - Meifeng Wang
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China
| | - Xueni Zeng
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China
| | - Yanhan Li
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China
| | - Lingzhi Lei
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China
| | - Changan Chen
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China
| | - Xi Lin
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China
| | - Peiyuan Fang
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China
| | - Yuxuan Guo
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University, Changsha, Hunan, 410013, China
| | - Xianjie Jiang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Yian Wang
- Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Department of Pathophysiology, School of Medicine, Engineering Research Center of Reproduction and Translational Medicine of Hunan Province, Hunan Normal University, Changsha, Hunan, 410013, China
| | - Lihong Chen
- Department of Pathology and Institute of Oncology, The School of Basic Medical Sciences & Diagnostic Pathology Center, Fujian Medical University, University Town, Fuzhou, Fujian, 350122, China.
- Department of Pathology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, Fujian, 350028, China.
| | - Jun Long
- Shenzhen Geim Graphene Center, Tsinghua-Berkeley Shenzhen Institute & Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, 518055, China.
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19
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Kurhaluk N. Palm oil as part of a high-fat diet: advances and challenges, or possible risks of pathology? Nutr Rev 2025; 83:e547-e573. [PMID: 38699959 DOI: 10.1093/nutrit/nuae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024] Open
Abstract
Nutritional status disorders have the most significant impact on the development of cardiovascular and oncologic diseases; therefore, the interest in the study of palm oil as among the leading components of nutrition has been increasing. The data examined in this review were sourced from the Scopus, SCIE (Web of Science), PubMed and PubMed Central, MEDLINE, CAPlus/SciFinder, and Embase databases; experts in the field; bibliographies; and abstracts from review analyses from the past 15 years. This review summarizes recent research data focusing on the quantitative and qualitative composition of nutrition of modern humans; concepts of the relationship between high-fat diets and disorders of insulin functioning and transport and metabolism of fatty acids; analyses of data regarding the palmitic acid (16:0) to oleic acid (18:1) ratio; and the effect of diet based on palm oil consumption on cardiovascular risk factors and lipid and lipoprotein levels. Several studies suggest a potential vector contributing to the transmission of maternal, high-fat-diet-induced, addictive-like behaviors and obesogenic phenotypes across generations. The relationship between cholesterol accumulation in lysosomes that may lead to lysosome dysfunction and inhibition of the autophagy process is analyzed, as is the progression of inflammatory diseases, atherosclerosis, nonalcoholic liver inflammation, and obesity with associated complications. Data are discussed from analyses of differences between rodent models and human population studies in the investigated different effects of palm oil consumption as a high-fat diet component. A conclusion is reached that the results cannot be generalized in human population studies because no similar effects were observed. Although there are numerous published reports, more studies are necessary to elucidate the complex regulatory mechanisms in digestive and nutrition processes, because there are great differences in lipoprotein profiles between rodents and humans, which makes it difficult to reproduce the pathology of many diseases caused by different types of the high-fat diet.
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Affiliation(s)
- Natalia Kurhaluk
- Department of Animal Physiology, Institute of Biology, Pomeranian University in Słupsk, Słupsk, Poland
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20
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Raj D, Nair AV, Singh A, Basu S, Sarkar K, Sharma J, Sharma S, Sharma S, Rathore M, Singh S, Prakash S, Simran, Sahu S, Kaushik AC, Siddiqi MI, Ghoshal UC, Chandra T, Bhosale V, Dasgupta A, Gupta SK, Verma S, Guha R, Chakravortty D, Ammanathan V, Lahiri A. Salmonella Typhimurium effector SseI regulates host peroxisomal dynamics to acquire lysosomal cholesterol. EMBO Rep 2025; 26:656-689. [PMID: 39695325 PMCID: PMC11811301 DOI: 10.1038/s44319-024-00328-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 10/16/2024] [Accepted: 10/25/2024] [Indexed: 12/20/2024] Open
Abstract
Salmonella enterica serotype Typhimurium (Salmonella) resides and multiplies intracellularly in cholesterol-rich compartments called Salmonella-containing vacuoles (SCVs) with actin-rich tubular extensions known as Salmonella-induced filaments (SIFs). SCV maturation depends on host-derived cholesterol, but the transport mechanism of low-density lipoprotein (LDL)-derived cholesterol to SCVs remains unclear. Here we find that peroxisomes are recruited to SCVs and function as pro-bacterial organelle. The Salmonella effector protein SseI is required for the interaction between peroxisomes and the SCV. SseI contains a variant of the PTS1 peroxisome-targeting sequence, GKM, localizes to the peroxisomes and activates the host Ras GTPase, ADP-ribosylation factor-1 (ARF-1). Activation of ARF-1 leads to the recruitment of phosphatidylinsolitol-5-phosphate-4 kinase and the generation of phosphatidylinsolitol-4-5-bisphosphate on peroxisomes. This enhances the interaction of peroxisomes with lysosomes and allows for the transfer of lysosomal cholesterol to SCVs using peroxisomes as a bridge. Salmonella infection of peroxisome-depleted cells leads to the depletion of cholesterol on the SCVs, resulting in reduced SIF formation and bacterial proliferation. Taken together, our work identified peroxisomes as a target of Salmonella secretory effectors, and as conveyance of host cholesterol to enhance SCV stability, SIF integrity, and intracellular bacterial growth.
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Affiliation(s)
- Desh Raj
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhilash Vijay Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Anmol Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Swarnali Basu
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Kabita Sarkar
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Jyotsna Sharma
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shiva Sharma
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanmi Sharma
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Manisha Rathore
- Laboratory Animal Facility Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shriya Singh
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shakti Prakash
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Simran
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Neuroscience & Ageing Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shikha Sahu
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medicine, Lucknow, India
| | - Aman Chandra Kaushik
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Uday C Ghoshal
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medicine, Lucknow, India
| | - Tulika Chandra
- Department of Transfusion Medicine, King Georges' Medical University, Lucknow, India
| | - Vivek Bhosale
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Toxicology and Experimental Medicine Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Arunava Dasgupta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shashi Kumar Gupta
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sonia Verma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Neuroscience & Ageing Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Rajdeep Guha
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory Animal Facility Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.
| | - Veena Ammanathan
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India.
| | - Amit Lahiri
- Pharmacology Division, CSIR-Central Drug Research Institute, Lucknow, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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21
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Kiraly S, Stanley J, Eden ER. Lysosome-Mitochondrial Crosstalk in Cellular Stress and Disease. Antioxidants (Basel) 2025; 14:125. [PMID: 40002312 PMCID: PMC11852311 DOI: 10.3390/antiox14020125] [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: 11/26/2024] [Revised: 12/23/2024] [Accepted: 01/11/2025] [Indexed: 02/27/2025] Open
Abstract
The perception of lysosomes and mitochondria as entirely separate and independent entities that degrade material and produce ATP, respectively, has been challenged in recent years as not only more complex roles for both organelles, but also an unanticipated level of interdependence are being uncovered. Coupled lysosome and mitochondrial function and dysfunction involve complex crosstalk between the two organelles which goes beyond mitochondrial quality control and lysosome-mediated clearance of damaged mitochondria through mitophagy. Our understanding of crosstalk between these two essential metabolic organelles has been transformed by major advances in the field of membrane contact sites biology. We now know that membrane contact sites between lysosomes and mitochondria play central roles in inter-organelle communication. This importance of mitochondria-lysosome contacts (MLCs) in cellular homeostasis, evinced by the growing number of diseases that have been associated with their dysregulation, is starting to be appreciated. How MLCs are regulated and how their coordination with other pathways of lysosome-mitochondria crosstalk is achieved are the subjects of ongoing scrutiny, but this review explores the current understanding of the complex crosstalk governing the function of the two organelles and its impact on cellular stress and disease.
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Affiliation(s)
| | | | - Emily R. Eden
- UCL Institute of Ophthalmology, London EC1V 9EL, UK; (S.K.); (J.S.)
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22
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Bond C, Hugelier S, Xing J, Sorokina EM, Lakadamyali M. Heterogeneity of late endosome/lysosomes shown by multiplexed DNA-PAINT imaging. J Cell Biol 2025; 224:e202403116. [PMID: 39485275 PMCID: PMC11533445 DOI: 10.1083/jcb.202403116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 08/20/2024] [Accepted: 10/08/2024] [Indexed: 11/03/2024] Open
Abstract
Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins; however, whether these proteins are uniformly present on each LEL, or if there are cell-type-dependent LEL subpopulations with unique protein compositions is unclear. We employed quantitative, multiplexed DNA-PAINT super-resolution imaging to examine the distribution of seven key LEL proteins (LAMP1, LAMP2, CD63, Cathepsin D, TMEM192, NPC1, and LAMTOR4). While LAMP1, LAMP2, and Cathepsin D were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type-specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts.
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Affiliation(s)
- Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Siewert Hugelier
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiazheng Xing
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elena M. Sorokina
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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23
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Cheetham-Wilkinson IJ, Sivalingam B, Flitton C, Flottmann F, Vehling L, Drechsler M, Stojchevska M, Raimondi A, Paululat A, Fröhlich F, Swan LE, Stagi M. RpH-ILV: Probe for lysosomal pH and acute LLOMe-induced membrane permeabilization in cell lines and Drosophila. SCIENCE ADVANCES 2025; 11:eadr7325. [PMID: 39752501 PMCID: PMC11698090 DOI: 10.1126/sciadv.adr7325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 12/02/2024] [Indexed: 01/06/2025]
Abstract
Lysosomal pH dysregulation is a critical element of the pathophysiology of neurodegenerative diseases, cancers, and lysosomal storage disorders (LSDs). To study the role of lysosomes in pathophysiology, probes to analyze lysosomal size, positioning, and pH are indispensable tools. Here, we developed and characterized a ratiometric genetically encoded lysosomal pH probe, RpH-ILV, targeted to a subpopulation of lysosomal intraluminal vesicles. This subpopulation behaves similarly to the general population of LAMP1-positive vesicles in terms of pH response to pharmacological stresses. In addition, RpH-ILV, which is trafficked to the lysosome via a different cytosolic motif than our previous ratiometric sensor, RpH-LAMP1, is well tolerated by the model organism Drosophila melanogaster, exhibits minimal plasma membrane fluorescence, and reveals sensitivity to the lysosomal damaging agent LLOMe, adding a valuable tool to our repertoire of lysosomal pH sensors.
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Affiliation(s)
- Izaak J. Cheetham-Wilkinson
- Department of Biochemistry Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Bhavya Sivalingam
- Division of Molecular Membrane Biology, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Chloe Flitton
- Department of Biochemistry Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Franziska Flottmann
- Department of Zoology & Developmental Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Luisa Vehling
- Department of Zoology & Developmental Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Maik Drechsler
- Department of Zoology & Developmental Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Marija Stojchevska
- Department of Biochemistry Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
- Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Achim Paululat
- Department of Zoology & Developmental Biology, Osnabrück University, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics Osnabrück – CellNanOs, Osnabrück University, 49076 Osnabrück, Germany
| | - Florian Fröhlich
- Division of Molecular Membrane Biology, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
- Center of Cellular Nanoanalytics Osnabrück – CellNanOs, Osnabrück University, 49076 Osnabrück, Germany
| | - Laura E. Swan
- Department of Biochemistry Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Massimiliano Stagi
- Department of Biochemistry Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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24
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Sasaki K, Toide M, Adachi T, Morishita F, Watanabe Y, Sakurai HT, Wakabayashi S, Kusumi S, Yamaji T, Sakurai K, Koga D, Hanada K, Yohda M, Yoshida H. Dysregulation of PI4P in the trans Golgi regions activates the mammalian Golgi stress response. J Biol Chem 2025; 301:108075. [PMID: 39675715 PMCID: PMC11770552 DOI: 10.1016/j.jbc.2024.108075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 11/17/2024] [Accepted: 12/02/2024] [Indexed: 12/17/2024] Open
Abstract
The Golgi stress response is an important cytoprotective system that enhances Golgi function in response to cellular demand, while cells damaged by prolonged Golgi stress undergo cell death. OSW-1, a natural compound with anticancer activity, potently inhibits OSBP that transports cholesterol and phosphatidylinositol-4-phosphate (PI4P) at contact sites between the endoplasmic reticulum and the Golgi apparatus. Previously, we reported that OSW-1 induces the Golgi stress response, resulting in Golgi stress-induced transcription and cell death. However, the underlying molecular mechanism has been unknown. To reveal the mechanism of a novel pathway of the Golgi stress response regulating transcriptional induction and cell death (the PI4P pathway), we performed a genome-wide KO screen and found that transcriptional induction as well as cell death induced by OSW-1 was repressed by the loss of regulators of PI4P synthesis, such as PITPNB and PI4KB. Our data indicate that OSW-1 induces Golgi stress-dependent transcriptional induction and cell death through dysregulation of the PI4P metabolism in the Golgi.
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Affiliation(s)
- Kanae Sasaki
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan.
| | - Marika Toide
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan
| | - Takuya Adachi
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan
| | - Fumi Morishita
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan
| | - Yuto Watanabe
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan
| | - Hajime Tajima Sakurai
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan
| | - Sadao Wakabayashi
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan
| | - Satoshi Kusumi
- Division of Morphological Sciences, Kagoshima University Graduate School of Medicine and Dental Sciences, Kagoshima, Kagoshima, Japan
| | - Toshiyuki Yamaji
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan; Faculty of Pharmacy, Department of Microbiology and Immunology, Juntendo University, Urayasu, Chiba, Japan
| | - Kaori Sakurai
- Faculty of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Daisuke Koga
- Department of Microscopic Anatomy and Cell Biology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Kentaro Hanada
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan; Center for Quality Management Systems, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Masafumi Yohda
- Faculty of Engineering, Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Hiderou Yoshida
- Department of Molecular Biochemistry, Graduate School of Science, University of Hyogo, Ako, Hyogo, Japan.
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25
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Sho T, Li Y, Jiao H, Yu L. Migratory autolysosome disposal mitigates lysosome damage. J Cell Biol 2024; 223:e202403195. [PMID: 39347717 PMCID: PMC11457477 DOI: 10.1083/jcb.202403195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/26/2024] [Accepted: 08/14/2024] [Indexed: 10/01/2024] Open
Abstract
Lysosomes, essential for intracellular degradation and recycling, employ damage-control strategies such as lysophagy and membrane repair mechanisms to maintain functionality and cellular homeostasis. Our study unveils migratory autolysosome disposal (MAD), a response to lysosomal damage where cells expel LAMP1-LC3 positive structures via autolysosome exocytosis, requiring autophagy machinery, SNARE proteins, and cell migration. This mechanism, crucial for mitigating lysosomal damage, underscores the role of cell migration in lysosome damage control and facilitates the release of small extracellular vesicles, highlighting the intricate relationship between cell migration, organelle quality control, and extracellular vesicle release.
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Affiliation(s)
- Takami Sho
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ying Li
- Cryo-EM Facility of Tsinghua University, Branch of National Protein Science Facility, Tsinghua University, Beijing, China
| | - Haifeng Jiao
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
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26
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Scrima S, Lambrughi M, Favaro L, Maeda K, Jäättelä M, Papaleo E. Acidic sphingomyelinase interactions with lysosomal membranes and cation amphiphilic drugs: A molecular dynamics investigation. Comput Struct Biotechnol J 2024; 23:2516-2533. [PMID: 38974886 PMCID: PMC11226985 DOI: 10.1016/j.csbj.2024.05.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 07/09/2024] Open
Abstract
Lysosomes are pivotal in cellular functions and disease, influencing cancer progression and therapy resistance with Acid Sphingomyelinase (ASM) governing their membrane integrity. Moreover, cation amphiphilic drugs (CADs) are known as ASM inhibitors and have anti-cancer activity, but the structural mechanisms of their interactions with the lysosomal membrane and ASM are poorly explored. Our study, leveraging all-atom explicit solvent molecular dynamics simulations, delves into the interaction of glycosylated ASM with the lysosomal membrane and the effects of CAD representatives, i.e., ebastine, hydroxyebastine and loratadine, on the membrane and ASM. Our results confirm the ASM association to the membrane through the saposin domain, previously only shown with coarse-grained models. Furthermore, we elucidated the role of specific residues and ASM-induced membrane curvature in lipid recruitment and orientation. CADs also interfere with the association of ASM with the membrane at the level of a loop in the catalytic domain engaging in membrane interactions. Our computational approach, applicable to various CADs or membrane compositions, provides insights into ASM and CAD interaction with the membrane, offering a valuable tool for future studies.
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Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen 2100, Denmark
- Cancer System Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby 2800, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen 2100, Denmark
| | - Lorenzo Favaro
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen 2100, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen 2100, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen 2100, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, Copenhagen 2100, Denmark
- Cancer System Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby 2800, Denmark
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27
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Duran J, Salinas JE, Wheaton RP, Poolsup S, Allers L, Rosas-Lemus M, Chen L, Cheng Q, Pu J, Salemi M, Phinney B, Ivanov P, Lystad AH, Bhaskar K, Rajaiya J, Perkins DJ, Jia J. Calcium signaling from damaged lysosomes induces cytoprotective stress granules. EMBO J 2024; 43:6410-6443. [PMID: 39533058 PMCID: PMC11649789 DOI: 10.1038/s44318-024-00292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 09/18/2024] [Accepted: 10/11/2024] [Indexed: 11/16/2024] Open
Abstract
Lysosomal damage induces stress granule (SG) formation. However, the importance of SGs in determining cell fate and the precise mechanisms that mediate SG formation in response to lysosomal damage remain unclear. Here, we describe a novel calcium-dependent pathway controlling SG formation, which promotes cell survival during lysosomal damage. Mechanistically, the calcium-activated protein ALIX transduces lysosomal damage signals to SG formation by controlling eIF2α phosphorylation after sensing calcium leakage. ALIX enhances eIF2α phosphorylation by promoting the association between PKR and its activator PACT, with galectin-3 inhibiting this interaction; these regulatory events occur on damaged lysosomes. We further find that SG formation plays a crucial role in promoting cell survival upon lysosomal damage caused by factors such as SARS-CoV-2ORF3a, adenovirus, malarial pigment, proteopathic tau, or environmental hazards. Collectively, these data provide insights into the mechanism of SG formation upon lysosomal damage and implicate it in diseases associated with damaged lysosomes and SGs.
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Affiliation(s)
- Jacob Duran
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA
| | - Jay E Salinas
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA
| | - Rui Ping Wheaton
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA
| | - Suttinee Poolsup
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA
| | - Lee Allers
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Monica Rosas-Lemus
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Li Chen
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Qiuying Cheng
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Jing Pu
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, CA, 95616, USA
| | - Brett Phinney
- Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, CA, 95616, USA
| | - Pavel Ivanov
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School; HMS Initiative for RNA Medicine, Boston, MA, 02115, USA
| | - Alf Håkon Lystad
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo; Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Kiran Bhaskar
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
- Department of Neurology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Jaya Rajaiya
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Douglas J Perkins
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA
| | - Jingyue Jia
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87106, USA.
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM, 87106, USA.
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28
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Tengberg JF, Russo F, Benned-Jensen T, Nielsen J. LRRK2 and RAB8A regulate cell death after lysosomal damage in macrophages through cholesterol-related pathways. Neurobiol Dis 2024; 202:106728. [PMID: 39521098 DOI: 10.1016/j.nbd.2024.106728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 10/23/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024] Open
Abstract
Activating mutations in Leucine Rich Repeat Kinase 2 (LRRK2) are among the most common genetic causes of Parkinson's disease (PD). The mechanistic path from LRRK2 mutations to PD is not established, but several lines of data suggest that LRRK2 modulation of lysosomal function is involved. It has previously been shown that LRRK2 is recruited to lysosomes upon lysosomal damage leading to increased phosphorylation of its RAB GTPase substrates in macrophage-derived RAW 264.7 cells. Here, we find that LRRK2 kinase inhibition reduces cell death induced by the lysosomotropic compound LLOMe in RAW 264.7 cells showing that lysosomal damage and LRRK2 functionally interacts in both directions: lysosomal damage can lead to activation of LRRK2 signaling and LRRK2 inhibition can attenuate LLOMe-induced cell death. The effect is lysosome specific, as only lysosomal stressors and not a variety of other cell death inducers could be modulated by LRRK2 kinase inhibition. We show with timing and Lysotracker experiments that LRRK2 inhibition does not affect the immediate lysosomal permeabilization induced by LLOMe, but rather modulates the subsequent cellular response to lysosomal damage. siRNA-mediated knockdown of LRRK2 and its main substrates, the RAB GTPases, showed that LRRK2 and RAB8A knockdown could attenuate LLOMe-induced cell death, but not other RAB GTPases tested. An RNA sequencing study was done to identify downstream pathways modulated by LLOMe and LRRK2 inhibition. The most striking finding was that almost all cholesterol biosynthesis genes were strongly downregulated by LLOMe and upregulated with LRRK2 inhibition in combination with LLOMe treatment. To explore the functional relevance of the transcriptional changes, we pretreated cells with the NPC1 inhibitor U18666A that can lead to accumulation of lysosomal cholesterol. U18666A-treated cells were less sensitive to LLOMe-induced cell death, but the attenuation of cell death by LRRK2 inhibition was strongly reduced suggesting that LRRK2 inhibition and lysosomal cholesterol reduces cell death by overlapping mechanisms. Thus, our data demonstrates a LRRK2- and RAB8A-mediated attenuation of RAW 264.7 cell death induced by lysosomal damage that is modulated by lysosomal cholesterol.
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Affiliation(s)
- Josefine Fussing Tengberg
- Neuroscience, Molecular and Single Cell Pharmacology, H. Lundbeck A/S, Valby, 2500 Copenhagen, Denmark; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Francesco Russo
- Bioinformatics, H. Lundbeck A/S, Valby, 2500 Copenhagen, Denmark
| | - Tau Benned-Jensen
- Neuroscience, Molecular and Single Cell Pharmacology, H. Lundbeck A/S, Valby, 2500 Copenhagen, Denmark
| | - Jacob Nielsen
- Neuroscience, Molecular and Single Cell Pharmacology, H. Lundbeck A/S, Valby, 2500 Copenhagen, Denmark.
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29
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Wang H, Jiang Y, Zhu M, Li H, Chen H, Wang H, Zhang S, Guo Q, Hui H. LW-213, a derivative of wogonin, triggers reticulophagy-mediated cell death in NSCLC via lysosomal damage combined with NPC1 inhibition. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 134:155958. [PMID: 39241385 DOI: 10.1016/j.phymed.2024.155958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/31/2024] [Accepted: 08/14/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Maintaining intracellular equilibrium is essential for the viability of tumor cells, which tend to be particularly vulnerable to environmental stressors. Consequently, targeting the disruption of this homeostasis offers a promising approach for oncological treatments. LW-213, a novel derivative of wogonin, effectively induces apoptosis in cancer cells by initiating endoplasmic reticulum (ER) stress, although the precise molecular pathways involved remain intricate and multifaceted. PURPOSE This research aimed to explore how LW-213 prompts apoptosis in non-small cell lung cancer (NSCLC) cells and to clarify the detailed mechanisms that govern this process. METHODS Various NSCLC cell lines were utilized to delineate the apoptotic effects induced by LW-213. Advanced methodologies, including RNA sequencing (RNA-seq), Western blotting (WB), immunofluorescence (IF), immunoprecipitation (IP), flow cytometry (Fc), real-time quantitative polymerase chain reaction (RT-qPCR), and electron microscopy, were employed to investigate the underlying molecular interactions. The efficacy and mechanistic action of LW-213 were also assessed in a xenograft model using nude mice. RESULTS We demonstrated that LW-213, a small molecule cationic amphiphilic drug (CAD), inhibited Niemann-Pick C1 (NPC1) function and induced lysosomal membrane damage, thereby activating the phosphoinositide-initiated membrane tethering and lipid transport (PITT) pathway. This activation promoted cholesterol transport from the ER to the lysosome, perpetuating a cholesterol-deficient state in the ER, including massive exocytosis of Ca2+ and activation of FAM134B-mediated reticulophagy. Ultimately, excessive reticulophagy induced lethal ER stress. CONCLUSIONS In summary, our study elucidates an organelle domino reaction initiated by lysosome damage and a series of self-rescue mechanisms that eventually lead to irreversible lethal effects, revealing a potential drug intervention strategy.
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Affiliation(s)
- Hongzheng Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Yuexin Jiang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Mengyuan Zhu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Hui Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Hongyu Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Haidi Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Shuai Zhang
- The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing 21009, PR China
| | - Qinglong Guo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Hui Hui
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
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30
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Hao M, Sebag SC, Qian Q, Yang L. Lysosomal physiology and pancreatic lysosomal stress in diabetes mellitus. EGASTROENTEROLOGY 2024; 2:e100096. [PMID: 39512752 PMCID: PMC11542681 DOI: 10.1136/egastro-2024-100096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
Endocrine and exocrine functions of the pancreas control nutritional absorption, utilisation and systemic metabolic homeostasis. Under basal conditions, the lysosome is pivotal in regulating intracellular organelles and metabolite turnover. In response to acute or chronic stress, the lysosome senses metabolic flux and inflammatory challenges, thereby initiating the adaptive programme to re-establish cellular homeostasis. A growing body of evidence has demonstrated the pathophysiological relevance of the lysosomal stress response in metabolic diseases in diverse sets of tissues/organs, such as the liver and the heart. In this review, we discuss the pathological relevance of pancreatic lysosome stress in diabetes mellitus. We begin by summarising lysosomal biology, followed by exploring the immune and metabolic functions of lysosomes and finally discussing the interplay between lysosomal stress and the pathogenesis of pancreatic diseases. Ultimately, our review aims to enhance our understanding of lysosomal stress in disease pathogenesis, which could potentially lead to the discovery of innovative treatment methods for these conditions.
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Affiliation(s)
- Meihua Hao
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Sara C Sebag
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Qingwen Qian
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Ling Yang
- Department of Anatomy and Cell Biology, Fraternal Order of Eagles Diabetes Research Center, Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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31
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Wang X, Geng J, Rimal S, Sui Y, Pan J, Qin Z, Lu B. The p53 target DRAM1 modulates calcium homeostasis and ER stress by promoting contact between lysosomes and the ER through STIM1. Proc Natl Acad Sci U S A 2024; 121:e2400531121. [PMID: 39292746 PMCID: PMC11441506 DOI: 10.1073/pnas.2400531121] [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: 01/11/2024] [Accepted: 07/27/2024] [Indexed: 09/20/2024] Open
Abstract
It is well established that DNA Damage Regulated Autophagy Modulator 1 (DRAM1), a lysosomal protein and a target of p53, participates in autophagy. The cellular functions of DRAM1 beyond autophagy remain elusive. Here, we show p53-dependent upregulation of DRAM1 in mitochondrial damage-induced Parkinson's disease (PD) models and exacerbation of disease phenotypes by DRAM1. We find that the lysosomal location of DRAM1 relies on its intact structure including the cytosol-facing C-terminal domain. Excess DRAM1 disrupts endoplasmic reticulum (ER) structure, triggers ER stress, and induces protective ER-phagy. Mechanistically, DRAM1 interacts with stromal interacting molecule 1 (STIM1) to tether lysosomes to the ER and perturb STIM1 function in maintaining intracellular calcium homeostasis. STIM1 overexpression promotes cellular health by restoring calcium homeostasis, ER stress response, ER-phagy, and AMP-activated protein kinase (AMPK)-Unc-51 like autophagy activating kinase 1 (ULK1) signaling in cells with excess DRAM1. Thus, by promoting organelle contact between lysosomes and the ER, DRAM1 modulates ER structure and function and cell survival under stress. Our results suggest that DRAM1 as a lysosomal protein performs diverse roles in cellular homeostasis and stress response. These findings may have significant implications for our understanding of the role of the p53/DRAM1 axis in human diseases, from cancer to neurodegenerative diseases.
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Affiliation(s)
- Xiying Wang
- Department of Psychiatry, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing210029, China
| | - Ji Geng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Suman Rimal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Yuxiu Sui
- Department of Psychiatry, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing210029, China
| | - Jie Pan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Zhenghong Qin
- Institute of Health Technology, Global Institute of Software Technology, Suzhou215163, China
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, School of Pharmaceutical Sciences, Soochow University, Suzhou215123, China
| | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
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Feng T, Zheng H, Zhang Z, Fan P, Yang X. Mechanism and therapeutic targets of the involvement of a novel lysosomal proton channel TMEM175 in Parkinson's disease. Ageing Res Rev 2024; 100:102373. [PMID: 38960046 DOI: 10.1016/j.arr.2024.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
Parkinson's disease (PD), recognized as the second most prevalent neurodegenerative disease in the aging population, presents a significant challenge due to the current lack of effective treatment methods to mitigate its progression. Many pathogenesis of PD are related to lysosomal dysfunction. Moreover, extensive genetic studies have shown a significant correlation between the lysosomal membrane protein TMEM175 and the risk of developing PD. Building on this discovery, TMEM175 has been identified as a novel potassium ion channel. Intriguingly, further investigations have found that potassium ion channels gradually close and transform into hydrion "excretion" channels in the microenvironment of lysosomes. This finding was further substantiated by studies on TMEM175 knockout mice, which exhibited pronounced motor dysfunction in pole climbing and suspension tests, alongside a notable reduction in dopamine neurons within the substantia nigra compacta. Despite these advancements, the current research landscape is not without its controversies. In light of this, the present review endeavors to methodically examine and consolidate a vast array of recent literature on TMEM175. This comprehensive analysis spans from the foundational research on the structure and function of TMEM175 to expansive population genetics studies and mechanism research utilizing cellular and animal models.A thorough understanding of the structure and function of TMEM175, coupled with insights into the intricate mechanisms underpinning lysosomal dysfunction in PD dopaminergic neurons, is imperative. Such knowledge is crucial for pinpointing precise intervention targets, thereby paving the way for novel therapeutic strategies that could potentially alter the neurodegenerative trajectory of PD.
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Affiliation(s)
- Tingting Feng
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China; Xinjiang Medical University, Urumqi 830017, China
| | | | - Zhan Zhang
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China
| | - Peidong Fan
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China
| | - Xinling Yang
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China; Xinjiang Medical University, Urumqi 830017, China.
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Bonet-Ponce L, Kluss JH, Cookson MR. Mechanisms of lysosomal tubulation and sorting driven by LRRK2. Biochem Soc Trans 2024; 52:1909-1919. [PMID: 39083004 PMCID: PMC11668303 DOI: 10.1042/bst20240087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/29/2024]
Abstract
Lysosomes are dynamic cellular structures that adaptively remodel their membrane in response to stimuli, including membrane damage. Lysosomal dysfunction plays a central role in the pathobiology of Parkinson's disease (PD). Gain-of-function mutations in Leucine-rich repeat kinase 2 (LRRK2) cause familial PD and genetic variations in its locus increase the risk of developing the sporadic form of the disease. We previously uncovered a process we term LYTL (LYsosomal Tubulation/sorting driven by LRRK2), wherein membrane-damaged lysosomes generate tubules sorted into mobile vesicles. Subsequently, these vesicles interact with healthy lysosomes. LYTL is orchestrated by LRRK2 kinase activity, via the recruitment and phosphorylation of a subset of RAB GTPases. Here, we summarize the current understanding of LYTL and its regulation, as well as the unknown aspects of this process.
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Affiliation(s)
- Luis Bonet-Ponce
- Department of Neurology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, U.S.A
| | | | - Mark R. Cookson
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, U.S.A
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Cabukusta B, Borst Pauwels S, Akkermans JJLL, Blomberg N, Mulder AA, Koning RI, Giera M, Neefjes J. The ORP9-ORP11 dimer promotes sphingomyelin synthesis. eLife 2024; 12:RP91345. [PMID: 39106189 PMCID: PMC11302984 DOI: 10.7554/elife.91345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024] Open
Abstract
Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by the loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans-Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.
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Affiliation(s)
- Birol Cabukusta
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Shalom Borst Pauwels
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Jimmy JLL Akkermans
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Niek Blomberg
- Centre for Proteomics and Metabolomics, Leiden University Medical CenterLeidenNetherlands
| | - Aat A Mulder
- Electron Microscopy Facility, Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Roman I Koning
- Electron Microscopy Facility, Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Martin Giera
- Centre for Proteomics and Metabolomics, Leiden University Medical CenterLeidenNetherlands
| | - Jacques Neefjes
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
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Alessi DR, Pfeffer SR. Leucine-Rich Repeat Kinases. Annu Rev Biochem 2024; 93:261-287. [PMID: 38621236 DOI: 10.1146/annurev-biochem-030122-051144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Activating mutations in leucine-rich repeat kinase 2 (LRRK2) represent the most common cause of monogenic Parkinson's disease. LRRK2 is a large multidomain protein kinase that phosphorylates a specific subset of the ∼65 human Rab GTPases, which are master regulators of the secretory and endocytic pathways. After phosphorylation by LRRK2, Rabs lose the capacity to bind cognate effector proteins and guanine nucleotide exchange factors. Moreover, the phosphorylated Rabs cannot interact with their cognate prenyl-binding retrieval proteins (also known as guanine nucleotide dissociation inhibitors) and, thus, they become trapped on membrane surfaces. Instead, they gain the capacity to bind phospho-Rab-specific effector proteins, such as RILPL1, with resulting pathological consequences. Rab proteins also act upstream of LRRK2 by controlling its activation and recruitment onto membranes. LRRK2 signaling is counteracted by the phosphoprotein phosphatase PPM1H, which selectively dephosphorylates phospho-Rab proteins. We present here our current understanding of the structure, biochemical properties, and cell biology of LRRK2 and its related paralog LRRK1 and discuss how this information guides the generation of LRRK2 inhibitors for the potential benefit of patients.
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Affiliation(s)
- Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, United Kingdom;
| | - Suzanne R Pfeffer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Bandyopadhyay S, Adebayo D, Obaseki E, Hariri H. Lysosomal membrane contact sites: Integrative hubs for cellular communication and homeostasis. CURRENT TOPICS IN MEMBRANES 2024; 93:85-116. [PMID: 39181579 DOI: 10.1016/bs.ctm.2024.07.001] [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] [Indexed: 08/27/2024]
Abstract
Lysosomes are more than just cellular recycling bins; they play a crucial role in regulating key cellular functions. Proper lysosomal function is essential for growth pathway regulation, cell proliferation, and metabolic homeostasis. Impaired lysosomal function is associated with lipid storage disorders and neurodegenerative diseases. Lysosomes form extensive and dynamic close contacts with the membranes of other organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and lipid droplets. These membrane contacts sites (MCSs) are vital for many lysosomal functions. In this chapter, we will explore lysosomal MCSs focusing on the machinery that mediates these contacts, how they are regulated, and their functional implications on physiology and pathology.
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Affiliation(s)
- Sumit Bandyopadhyay
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Daniel Adebayo
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Eseiwi Obaseki
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Hanaa Hariri
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States.
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Guallar-Garrido S, Soldati T. Exploring host-pathogen interactions in the Dictyostelium discoideum-Mycobacterium marinum infection model of tuberculosis. Dis Model Mech 2024; 17:dmm050698. [PMID: 39037280 PMCID: PMC11552500 DOI: 10.1242/dmm.050698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Mycobacterium tuberculosis is a pathogenic mycobacterium that causes tuberculosis. Tuberculosis is a significant global health concern that poses numerous clinical challenges, particularly in terms of finding effective treatments for patients. Throughout evolution, host immune cells have developed cell-autonomous defence strategies to restrain and eliminate mycobacteria. Concurrently, mycobacteria have evolved an array of virulence factors to counteract these host defences, resulting in a dynamic interaction between host and pathogen. Here, we review recent findings, including those arising from the use of the amoeba Dictyostelium discoideum as a model to investigate key mycobacterial infection pathways. D. discoideum serves as a scalable and genetically tractable model for human phagocytes, providing valuable insights into the intricate mechanisms of host-pathogen interactions. We also highlight certain similarities between M. tuberculosis and Mycobacterium marinum, and the use of M. marinum to more safely investigate mycobacteria in D. discoideum.
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Affiliation(s)
- Sandra Guallar-Garrido
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Science II, 1211 Geneva-4, Switzerland
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, Science II, 1211 Geneva-4, Switzerland
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Liu R, Hong W, Hou D, Huang H, Duan C. Decoding Organelle Interactions: Unveiling Molecular Mechanisms and Disease Therapies. Adv Biol (Weinh) 2024; 8:e2300288. [PMID: 38717793 DOI: 10.1002/adbi.202300288] [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: 07/06/2023] [Revised: 01/05/2024] [Indexed: 07/13/2024]
Abstract
Organelles, substructures in the cytoplasm with specific morphological structures and functions, interact with each other via membrane fusion, membrane transport, and protein interactions, collectively termed organelle interaction. Organelle interaction is a complex biological process involving the interaction and regulation of several organelles, including the interaction between mitochondria-endoplasmic reticulum, endoplasmic reticulum-Golgi, mitochondria-lysosomes, and endoplasmic reticulum-peroxisomes. This interaction enables intracellular substance transport, metabolism, and signal transmission, and is closely related to the occurrence, development, and treatment of many diseases, such as cancer, neurodegenerative diseases, and metabolic diseases. Herein, the mechanisms and regulation of organelle interactions are reviewed, which are critical for understanding basic principles of cell biology and disease development mechanisms. The findings will help to facilitate the development of novel strategies for disease prevention, diagnosis, and treatment opportunities.
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Affiliation(s)
- Ruixue Liu
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P. R. China
| | - Weilong Hong
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P. R. China
| | - Dongyao Hou
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P. R. China
| | - He Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P. R. China
| | - Chenyang Duan
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P. R. China
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Yaya-Candela AP, Ravagnani FG, Dietrich N, Sousa R, Baptista MS. Specific photodamage on HT-29 cancer cells leads to endolysosomal failure and autophagy blockage by cathepsin depletion. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 255:112919. [PMID: 38677261 DOI: 10.1016/j.jphotobiol.2024.112919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
Endolysosomes perform a wide range of cellular functions, including nutrient sensing, macromolecule digestion and recycling, as well as plasma membrane repair. Because of their high activity in cancerous cells, endolysosomes are attractive targets for the development of novel cancer treatments. Light-activated compounds termed photosensitizers (PS) can catalyze the oxidation of specific biomolecules and intracellular organelles. To selectively damage endosomes and lysosomes, HT-29 colorectal cancer cells were incubated with nanomolar concentrations of meso-tetraphenylporphine disulfonate (TPPS2a), an amphiphilic PS taken up via endocytosis and activated by green light (522 nm, 2.1 J.cm-1). Several cellular responses were characterized by a combination of immunofluorescence and immunoblotting assays. We showed that TPPS2a photosensitization blocked autophagic flux without extensive endolysosomal membrane rupture. Nevertheless, there was a severe functional failure of endolysosomes due to a decrease in CTSD (cathepsin D, 55%) and CTSB (cathepsin B, 52%) maturation. PSAP (prosaposin) processing (into saposins) was also considerably impaired, a fact that could be detrimental to glycosphingolipid homeostasis. Therefore, photosensitization of HT-29 cells previously incubated with a low concentration of TPPS2a promotes endolysosomal dysfunction, an effect that can be used to improve cancer therapies.
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Affiliation(s)
| | | | - Natasha Dietrich
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Rafaela Sousa
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
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40
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Bao L, Liu Q, Wang J, Shi L, Pang Y, Niu Y, Zhang R. The interactions of subcellular organelles in pulmonary fibrosis induced by carbon black nanoparticles: a comprehensive review. Arch Toxicol 2024; 98:1629-1643. [PMID: 38536500 DOI: 10.1007/s00204-024-03719-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/29/2024] [Indexed: 05/21/2024]
Abstract
Owing to the widespread use and improper emissions of carbon black nanoparticles (CBNPs), the adverse effects of CBNPs on human health have attracted much attention. In toxicological research, carbon black is frequently utilized as a negative control because of its low toxicity and poor solubility. However, recent studies have indicated that inhalation exposure to CBNPs could be a risk factor for severe and prolonged pulmonary inflammation and fibrosis. At present, the pathogenesis of pulmonary fibrosis induced by CBNPs is still not fully elucidated, but it is known that with small particle size and large surface area, CBNPs are more easily ingested by cells, leading to organelle damage and abnormal interactions between organelles. Damaged organelle and abnormal organelles interactions lead to cell structure and function disorders, which is one of the important factors in the development and occurrence of various diseases, including pulmonary fibrosis. This review offers a comprehensive analysis of organelle structure, function, and interaction mechanisms, while also summarizing the research advancements in organelles and organelle interactions in CBNPs-induced pulmonary fibrosis.
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Affiliation(s)
- Lei Bao
- Department of Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang, 050017, China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Qingping Liu
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China
| | - Jingyuan Wang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China
| | - Lili Shi
- Department of Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang, 050017, China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Yaxian Pang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China
| | - Yujie Niu
- Department of Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang, 050017, China
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China
| | - Rong Zhang
- Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, 050017, China.
- Department of Toxicology, Hebei Medical University, 361 Zhongshan East Rd, Shijiazhuang, 050017, Hebei, China.
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Rose K, Jepson T, Shukla S, Maya-Romero A, Kampmann M, Xu K, Hurley JH. Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes. Proc Natl Acad Sci U S A 2024; 121:e2315690121. [PMID: 38781206 PMCID: PMC11145263 DOI: 10.1073/pnas.2315690121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes and neurons, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification, and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Live cell imaging and STORM superresolution microscopy further show that the nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.
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Affiliation(s)
- Kevin Rose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Tyler Jepson
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
| | - Sankalp Shukla
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Alex Maya-Romero
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94158
| | - Ke Xu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA94720
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Mulligan RJ, Magaj MM, Digilio L, Redemann S, Yap CC, Winckler B. Collapse of late endosomal pH elicits a rapid Rab7 response via the V-ATPase and RILP. J Cell Sci 2024; 137:jcs261765. [PMID: 38578235 PMCID: PMC11166203 DOI: 10.1242/jcs.261765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Endosomal-lysosomal trafficking is accompanied by the acidification of endosomal compartments by the H+-V-ATPase to reach low lysosomal pH. Disruption of the correct pH impairs lysosomal function and the balance of protein synthesis and degradation (proteostasis). Here, we treated mammalian cells with the small dipeptide LLOMe, which is known to permeabilize lysosomal membranes, and find that LLOMe also impacts late endosomes (LEs) by neutralizing their pH without causing membrane permeabilization. We show that LLOMe leads to hyperactivation of Rab7 (herein referring to Rab7a), and disruption of tubulation and mannose-6-phosphate receptor (CI-M6PR; also known as IGF2R) recycling on pH-neutralized LEs. pH neutralization (NH4Cl) and expression of Rab7 hyperactive mutants alone can both phenocopy the alterations in tubulation and CI-M6PR trafficking. Mechanistically, pH neutralization increases the assembly of the V1G1 subunit (encoded by ATP6V1G1) of the V-ATPase on endosomal membranes, which stabilizes GTP-bound Rab7 via RILP, a known interactor of Rab7 and V1G1. We propose a novel pathway by which V-ATPase and RILP modulate LE pH and Rab7 activation in concert. This pathway might broadly contribute to pH control during physiologic endosomal maturation or starvation and during pathologic pH neutralization, which occurs via lysosomotropic compounds and in disease states.
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Affiliation(s)
- Ryan J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Magdalena M. Magaj
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Laura Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Stefanie Redemann
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Chan Choo Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
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43
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Lin F, Xiang L, Wu L, Liu Y, Jiang Q, Deng L, Cui W. Positioning regulation of organelle network via Chinese microneedle. SCIENCE ADVANCES 2024; 10:eadl3063. [PMID: 38640234 PMCID: PMC11029808 DOI: 10.1126/sciadv.adl3063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
The organelle network is a key factor in the repair and regeneration of lesion. However, effectively intervening in the organelle network which has complex interaction mechanisms is challenging. In this study, on the basis of electromagnetic laws, we constructed a biomaterial-based physical/chemical restraint device. This device was designed to jointly constrain electrical and biological factors in a conductive screw-threaded microneedle (ST-needle) system, identifying dual positioning regulation of the organelle network. The unique physical properties of this system could accurately locate the lesion and restrict the current path to the lesion cells through electromagnetic laws, and dynamic Van der Waals forces were activated to release functionalized hydrogel microspheres. Subsequently, the mitochondria-endoplasmic reticulum (ER) complex was synergistically targeted by increasing mitochondrial ATP supply to the ER via electrical stimulation and by blocking calcium current from the ER to the mitochondria using microspheres, and then the life activity of the lesion cells was effectively restored.
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Affiliation(s)
| | | | - Longxi Wu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
| | - Yupu Liu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
| | - Qinzhe Jiang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
| | - Lianfu Deng
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
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Gahlot P, Kravic B, Rota G, van den Boom J, Levantovsky S, Schulze N, Maspero E, Polo S, Behrends C, Meyer H. Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH. Mol Cell 2024; 84:1556-1569.e10. [PMID: 38503285 DOI: 10.1016/j.molcel.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Cells respond to lysosomal membrane permeabilization by membrane repair or selective macroautophagy of damaged lysosomes, termed lysophagy, but it is not fully understood how this decision is made. Here, we uncover a pathway in human cells that detects lipid bilayer perturbations in the limiting membrane of compromised lysosomes, which fail to be repaired, and then initiates ubiquitin-triggered lysophagy. We find that SPG20 binds the repair factor IST1 on damaged lysosomes and, importantly, integrates that with the detection of damage-associated lipid-packing defects of the lysosomal membrane. Detection occurs via sensory amphipathic helices in SPG20 before rupture of the membrane. If lipid-packing defects are extensive, such as during lipid peroxidation, SPG20 recruits and activates ITCH, which marks the damaged lysosome with lysine-63-linked ubiquitin chains to initiate lysophagy and thus triages the lysosome for destruction. With SPG20 being linked to neurodegeneration, these findings highlight the relevance of a coordinated lysosomal damage response for cellular homeostasis.
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Affiliation(s)
- Pinki Gahlot
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Bojana Kravic
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Giulia Rota
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Johannes van den Boom
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Sophie Levantovsky
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Nina Schulze
- Imaging Center Campus Essen, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Elena Maspero
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Simona Polo
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical Faculty, Ludwig-Maximilians-University München, Munich, Germany
| | - Hemmo Meyer
- Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
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Bonet-Ponce L, Tegicho T, Beilina A, Kluss JH, Li Y, Cookson MR. Opposing actions of JIP4 and RILPL1 provide antagonistic motor force to dynamically regulate membrane reformation during lysosomal tubulation/sorting driven by LRRK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587808. [PMID: 38903076 PMCID: PMC11188082 DOI: 10.1101/2024.04.02.587808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Lysosomes are dynamic cellular structures that adaptively remodel their membrane in response to stimuli, including membrane damage. We previously uncovered a process we term LYTL (LYsosomal Tubulation/sorting driven by Leucine-Rich Repeat Kinase 2 [LRRK2]), wherein damaged lysosomes generate tubules sorted into mobile vesicles. LYTL is orchestrated by the Parkinson's disease-associated kinase LRRK2 that recruits the motor adaptor protein and RHD family member JIP4 to lysosomes via phosphorylated RAB proteins. To identify new players involved in LYTL, we performed unbiased proteomics on isolated lysosomes after LRRK2 kinase inhibition. Our results demonstrate that there is recruitment of RILPL1 to ruptured lysosomes via LRRK2 activity to promote phosphorylation of RAB proteins at the lysosomal surface. RILPL1, which is also a member of the RHD family, enhances the clustering of LRRK2-positive lysosomes in the perinuclear area and causes retraction of LYTL tubules, in contrast to JIP4 which promotes LYTL tubule extension. Mechanistically, RILPL1 binds to p150Glued, a dynactin subunit, facilitating the transport of lysosomes and tubules to the minus end of microtubules. Further characterization of the tubulation process revealed that LYTL tubules move along tyrosinated microtubules, with tubulin tyrosination proving essential for tubule elongation. In summary, our findings emphasize the dynamic regulation of LYTL tubules by two distinct RHD proteins and pRAB effectors, serving as opposing motor adaptor proteins: JIP4, promoting tubulation via kinesin, and RILPL1, facilitating tubule retraction through dynein/dynactin. We infer that the two opposing processes generate a metastable lysosomal membrane deformation that facilitates dynamic tubulation events.
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Affiliation(s)
- Luis Bonet-Ponce
- Department of Neurology, Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Tsion Tegicho
- Department of Neurology, Wexner Medical Center, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Alexandra Beilina
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Jillian H. Kluss
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Yan Li
- Proteomic Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Mark R. Cookson
- Cell Biology and Gene Expression Section, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, 20892, USA
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Bond C, Hugelier S, Xing J, Sorokina EM, Lakadamyali M. Multiplexed DNA-PAINT Imaging of the Heterogeneity of Late Endosome/Lysosome Protein Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585634. [PMID: 38562776 PMCID: PMC10983937 DOI: 10.1101/2024.03.18.585634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins, however, whether these proteins are uniformly present on each LEL, or if there are cell-type dependent LEL sub-populations with unique protein compositions is unclear. We employed a quantitative, multiplexed DNA-PAINT super-resolution approach to examine the distribution of six key LEL proteins (LAMP1, LAMP2, CD63, TMEM192, NPC1 and LAMTOR4) on individual LELs. While LAMP1 and LAMP2 were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts. Summary This study develops a multiplexed and quantitative DNA-PAINT super-resolution imaging pipeline to investigate the distribution of late endosomal/lysosomal (LEL) proteins across individual LELs, revealing cell-type specific LEL sub-populations with unique protein compositions, offering insights into organelle heterogeneity at single-organelle resolution.
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Theodore CJ, Wagner LH, Campellone KG. Autophagosome turnover requires Arp2/3 complex-mediated maintenance of lysosomal integrity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584718. [PMID: 38559247 PMCID: PMC10980047 DOI: 10.1101/2024.03.12.584718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Autophagy is an intracellular degradation process that maintains homeostasis, responds to stress, and plays key roles in the prevention of aging and disease. Autophagosome biogenesis, vesicle rocketing, and autolysosome tubulation are controlled by multiple actin nucleation factors, but the impact of actin assembly on completion of the autophagic pathway is not well understood. Here we studied autophagosome and lysosome remodeling in fibroblasts harboring an inducible knockout (iKO) of the Arp2/3 complex, an essential actin nucleator. Arp2/3 complex ablation resulted in increased basal levels of autophagy receptors and lipidated membrane proteins from the LC3 and GABARAP families. Under both steady-state and starvation conditions, Arp2/3 iKO cells accumulated abnormally high numbers of autolysosomes, suggesting a defect in autophagic flux. The inability of Arp2/3 complex-deficient cells to complete autolysosome degradation and turnover is explained by the presence of damaged, leaky lysosomes. In cells treated with an acute lysosomal membrane-damaging agent, the Arp2/3-activating protein WHAMM is recruited to lysosomes, where Arp2/3 complex-dependent actin assembly is crucial for restoring intact lysosomal structure. These results establish the Arp2/3 complex as a central player late in the canonical autophagy pathway and reveal a new role for the actin nucleation machinery in maintaining lysosomal integrity.
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Affiliation(s)
- Corey J. Theodore
- Department of Molecular and Cell Biology; University of Connecticut, Storrs CT, USA
- Institute for Systems Genomics; University of Connecticut, Storrs CT, USA
| | - Lianna H. Wagner
- Department of Molecular and Cell Biology; University of Connecticut, Storrs CT, USA
- Institute for Systems Genomics; University of Connecticut, Storrs CT, USA
| | - Kenneth G. Campellone
- Department of Molecular and Cell Biology; University of Connecticut, Storrs CT, USA
- Institute for Systems Genomics; University of Connecticut, Storrs CT, USA
- Center on Aging, UConn Health; University of Connecticut, Storrs CT, USA
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Fuggetta N, Rigolli N, Magdeleine M, Hamaï A, Seminara A, Drin G. Reconstitution of ORP-mediated lipid exchange coupled to PI4P metabolism. Proc Natl Acad Sci U S A 2024; 121:e2315493121. [PMID: 38408242 PMCID: PMC10927502 DOI: 10.1073/pnas.2315493121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Oxysterol-binding protein-related proteins (ORPs) play key roles in the distribution of lipids in eukaryotic cells by exchanging sterol or phosphatidylserine for PI4P between the endoplasmic reticulum (ER) and other cell regions. However, it is unclear how their exchange capacity is coupled to PI4P metabolism. To address this question quantitatively, we analyze the activity of a representative ORP, Osh4p, in an ER/Golgi interface reconstituted with ER- and Golgi-mimetic membranes functionalized with PI4P phosphatase Sac1p and phosphatidylinositol (PI) 4-kinase, respectively. Using real-time assays, we demonstrate that upon adenosine triphosphate (ATP) addition, Osh4p creates a sterol gradient between these membranes, relying on the spatially distant synthesis and hydrolysis of PI4P, and quantify how much PI4P is needed for this process. Then, we develop a quantitatively accurate kinetic model, validated by our data, and extrapolate this to estimate to what extent PI4P metabolism can drive ORP-mediated sterol transfer in cells. Finally, we show that Sec14p can support PI4P metabolism and Osh4p activity by transferring PI between membranes. This study establishes that PI4P synthesis drives ORP-mediated lipid exchange and that ATP energy is needed to generate intermembrane lipid gradients. Furthermore, it defines to what extent ORPs can distribute lipids in the cell and reassesses the role of PI-transfer proteins in PI4P metabolism.
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Affiliation(s)
- Nicolas Fuggetta
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
| | - Nicola Rigolli
- Department of Physics, École Normale Supérieure (LPENS), Paris75005, France
| | - Maud Magdeleine
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
| | - Amazigh Hamaï
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
| | - Agnese Seminara
- Malga, Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genoa16145, Italy
| | - Guillaume Drin
- Université Côte d’Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne06560, France
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49
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Lolicato F, Nickel W, Haucke V, Ebner M. Phosphoinositide switches in cell physiology - From molecular mechanisms to disease. J Biol Chem 2024; 300:105757. [PMID: 38364889 PMCID: PMC10944118 DOI: 10.1016/j.jbc.2024.105757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
Phosphoinositides are amphipathic lipid molecules derived from phosphatidylinositol that represent low abundance components of biological membranes. Rather than serving as mere structural elements of lipid bilayers, they represent molecular switches for a broad range of biological processes, including cell signaling, membrane dynamics and remodeling, and many other functions. Here, we focus on the molecular mechanisms that turn phosphoinositides into molecular switches and how the dysregulation of these processes can lead to disease.
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Affiliation(s)
- Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany; Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Ebner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
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50
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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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