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Cao T, Xu Z, Dong W, Ma H, Fan Z, Liu Y. A ratiometric fluorescent probe with dual-targeting capability for heat shock imaging. Talanta 2024; 276:126213. [PMID: 38718652 DOI: 10.1016/j.talanta.2024.126213] [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: 03/04/2024] [Revised: 04/29/2024] [Accepted: 05/05/2024] [Indexed: 06/14/2024]
Abstract
HSO3- is an important reactive sulfur species that maintains the normal physiological activities of living organisms and participates in a variety of redox homeostatic processes. It has been found that changes in HSO3- levels is closely related to the heat stroke phenomenon of the organism. Heat stroke causes damage to normal cells, which in turn causes damage to the body and even death. It is crucial to accurately monitor and track the physiological behavior of HSO3- during heat stroke. Herein, a ratiometric multifunctional fluorescent probe DRM-SO2 with dual-targeting ability to rapidly and precisely recognize HSO3- being constructed based on the FRET mechanism. DRM-SO2 has extra Large Stokes shift (216 nm), very high sensitivity (DL = 12.2 nM), fast response time and good specificity. When DRM-SO2 undergoes Michael addition with HSO3-, the fluorescence emission peak was blue-shifted from 616 nm to 472 nm, and a clear ratiometric signal appeared. The interaction between lysosomes and mitochondria in maintaining cellular homeostasis was investigated by the dual-targeting ability of the probe using HSO3- as a mediator. DRM-SO2 achieved successful targeting and real-time monitoring of exogenous and endogenous HSO3- in the cells. More importantly, imaging experiments in heat stroke mice revealed high HSO3- expression in intestinal tissues. This provides new ideas and research tools for early prevention of heat stroke-induced diseases such as intestinal injuries. In addition, the semi-quantitative monitoring experiments for paper-based visualization of HSO3- make the probe promising for the design of portable detectors.
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Affiliation(s)
- Ting Cao
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials Ministry of Education, The School of Chemical and Material Science, Shanxi Normal University, Taiyuan 030031, China
| | - Zhongsheng Xu
- Department of Radiology, Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Wenhua Dong
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials Ministry of Education, The School of Chemical and Material Science, Shanxi Normal University, Taiyuan 030031, China
| | - Hong Ma
- College of Chemistry and Materials, Taiyuan Normal University, Jinzhong 030619, China
| | - Zhefeng Fan
- Key Laboratory of Magnetic Molecules & Magnetic Information Materials Ministry of Education, The School of Chemical and Material Science, Shanxi Normal University, Taiyuan 030031, China.
| | - Yun Liu
- Department of Radiology, Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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2
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Wang Z, Tang R, Wang H, Li X, Liu Z, Li W, Peng G, Zhou H. Bioinformatics analysis of the role of lysosome-related genes in breast cancer. Comput Methods Biomech Biomed Engin 2024:1-20. [PMID: 39054687 DOI: 10.1080/10255842.2024.2379936] [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: 03/12/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
This study aimed to investigate the roles of lysosome-related genes in BC prognosis and immunity. Transcriptome data from TCGA and MSigDB, along with lysosome-related gene sets, underwent NMF cluster analysis, resulting in two subtypes. Using lasso regression and univariate/multivariate Cox regression analysis, an 11-gene signature was successfully identified and verified. High- and low-risk populations were dominated by HR+ sample types. There were differences in pathway enrichment, immune cell infiltration, and immune scores. Sensitive drugs targeting model genes were screened using GDSC and CCLE. This study constructed a reliable prognostic model with lysosome-related genes, providing valuable insights for BC clinical immunotherapy.
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Affiliation(s)
- Zhongming Wang
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
| | - Ruiyao Tang
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
| | - Huazhong Wang
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
| | - Xizhang Li
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
| | - Zhenbang Liu
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
| | - Wenjie Li
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
| | - Gui Peng
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
| | - Huaiying Zhou
- Department of Breast Oncology, The Third People's Hospital of Yongzhou, Yongzhou City, Hunan Province, China
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3
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Seo D, Yue Y, Yamazaki S, Verhey KJ, Gammon DB. Poxvirus A51R Proteins Negatively Regulate Microtubule-Dependent Transport by Kinesin-1. Int J Mol Sci 2024; 25:7825. [PMID: 39063067 PMCID: PMC11277487 DOI: 10.3390/ijms25147825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Microtubule (MT)-dependent transport is a critical means of intracellular movement of cellular cargo by kinesin and dynein motors. MT-dependent transport is tightly regulated by cellular MT-associated proteins (MAPs) that directly bind to MTs and either promote or impede motor protein function. Viruses have been widely shown to usurp MT-dependent transport to facilitate their virion movement to sites of replication and/or for exit from the cell. However, it is unclear if viruses also negatively regulate MT-dependent transport. Using single-molecule motility and cellular transport assays, we show that the vaccinia virus (VV)-encoded MAP, A51R, inhibits kinesin-1-dependent transport along MTs in vitro and in cells. This inhibition is selective as the function of kinesin-3 is largely unaffected by VV A51R. Interestingly, we show that A51R promotes the perinuclear accumulation of cellular cargo transported by kinesin-1 such as lysosomes and mitochondria during infection. Moreover, A51R also regulates the release of specialized VV virions that exit the cell using kinesin-1-dependent movement. Using a fluorescently tagged rigor mutant of kinesin-1, we show that these motors accumulate on A51R-stabilized MTs, suggesting these stabilized MTs may form a "kinesin-1 sink" to regulate MT-dependent transport in the cell. Collectively, our findings uncover a new mechanism by which viruses regulate host cytoskeletal processes.
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Affiliation(s)
- Dahee Seo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Shin Yamazaki
- Department of Neuroscience and Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Don B. Gammon
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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Tinker J, Anees P, Krishnan Y. Quantitative Chemical Imaging of Organelles. Acc Chem Res 2024; 57:1906-1917. [PMID: 38916405 DOI: 10.1021/acs.accounts.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
ConspectusDNA nanodevices are nanoscale assemblies, formed from a collection of synthetic DNA strands, that may perform artificial functions. The pioneering developments of a DNA cube by Nadrian Seeman in 1991 and a DNA nanomachine by Turberfield and Yurke in 2000 spawned an entire generation of DNA nanodevices ranging from minimalist to rococo architectures. Since our first demonstration in 2009 that a DNA nanodevice can function autonomously inside a living cell, it became clear that this molecular scaffold was well-placed to probe living systems. Its water solubility, biocompatibility, and engineerability to yield molecularly identical assemblies predisposed it to probe and program biology.Since DNA is a modular scaffold, one can integrate independent or interdependent functionalities onto a single assembly. Work from our group has established a new class of organelle-targeted, DNA-based fluorescent reporters. These reporters comprise three to four oligonucleotides that each display a specific motif or module with a specific function. Given the 1:1 stoichiometry of Watson-Crick-Franklin base pairing, all modules are present in a fixed ratio in every DNA nanodevice. These modules include an ion-sensitive dye or a detection module and a normalizing dye for ratiometry that along with detection module forms a "measuring module". The third module is an organelle-targeting module that engages a cognate protein so that the whole assembly is trafficked to the lumen of a target organelle. Together, these modules allow us to measure free ion concentrations with accuracies that were previously unattainable, in subcellular locations that were previously inaccessible, and at single organelle resolution. By revealing that organelles exist in different chemical states, DNA nanodevices are providing new insights into organelle biology. Further, the ability to deliver molecules with cell-type and organelle level precision in animal models is leading to biomedical applications.This Account outlines the development of DNA nanodevices as fluorescent reporters for chemically mapping or modulating organelle function in real time in living systems. We discuss the technical challenges of measuring ions within endomembrane organelles and show how the unique properties of DNA nanodevices enable organelle targeting and chemical mapping. Starting from the pioneering finding that an autonomous DNA nanodevice could map endolysosomal pH in cells, we chart the development of strategies to target organelles beyond the endolysosomal pathway and expanding chemical maps to include all the major ions in physiology, reactive species, enzyme activity, and voltage. We present a series of vignettes highlighting the new biology unlocked with each development, from the discovery of chemical heterogeneity in lysosomes to identifying the first protein importer of Ca2+ into lysosomes. Finally, we discuss the broader applicability of targeting DNA nanodevices organelle-specifically beyond just reporting ions, namely using DNA nanodevices to modulate organelle state, and thereby cell state, with potential therapeutic applications.
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Affiliation(s)
- JoAnn Tinker
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Palapuravan Anees
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517619, India
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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Lee S, Ju IG, Eo H, Kim JH, Choi Y, Oh MS. Rhei Undulati Rhizoma attenuates memory decline and reduces amyloid-β induced neuritic dystrophy in 5xFAD mouse. Chin Med 2024; 19:95. [PMID: 38965625 PMCID: PMC11223309 DOI: 10.1186/s13020-024-00966-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/22/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a common type of dementia characterized by amyloid-β (Aβ) accumulation, lysosomal dysfunction, and tau hyperphosphorylation, leading to neurite dystrophy and memory loss. This study aimed to investigate whether Rhei Undulati Rhizoma (RUR), which has been reported to have anti-neuroinflammatory effect, attenuates Aβ-induced memory impairment, neuritic dystrophy, and tau hyperphosphorylation, and to reveal its mode of action. METHODS Five-month-old 5xFAD mice received RUR (50 mg/kg) orally for 2 months. The Y-maze test was used to assess working memory. After behavioral testing, brain tissue was analyzed using thioflavin S staining, western blotting, and immunofluorescence staining to investigate the mode of action of RUR. To confirm whether RUR directly reduces Aβ aggregation, a thioflavin T assay and dot blot were performed after incubating Aβ with RUR. RESULTS RUR administration attenuated the Aβ-induced memory impairment in 5xFAD mice. Furthermore, decreased accumulation of Aβ was observed in the hippocampus of the RUR-treated 5xFAD group compare to the vehicle-treated 5xFAD group. Moreover, RUR reduced the dystrophic neurites (DNs) that accumulate impaired endolysosomal organelles around Aβ. In particular, RUR treatment downregulated the expression of β-site amyloid precursor protein cleaving enzyme 1 and the hyperphosphorylation of tau within DNs. Additionally, RUR directly suppressed the aggregation of Aβ, and eliminated Aβ oligomers in vitro. CONCLUSIONS This study showed that RUR could attenuate Aβ-induced pathology and directly regulate the aggregation of Aβ. These results suggest that RUR could be an efficient material for AD treatment through Aβ regulation.
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Affiliation(s)
- Seungmin Lee
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea
| | - In Gyoung Ju
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea
| | - Hyeyoon Eo
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea
| | - Jin Hee Kim
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea
| | - Yujin Choi
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea
| | - Myung Sook Oh
- Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea.
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea.
- Department of Integrated Drug Development and Natural Products, Graduate School, Kyung Hee University, 26, Kyungheedae-Ro, Dongdaemun-Gu, Seoul, 02447, Republic of Korea.
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Yin P, Wang H, Xue T, Yu X, Meng X, Mi Q, Song S, Xiong B, Bi Y, Yu L. Four-Dimensional Label-Free Quantitative Proteomics of Ginsenoside Rg 2 Ameliorated Scopolamine-Induced Memory Impairment in Mice through the Lysosomal Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14640-14652. [PMID: 38885433 DOI: 10.1021/acs.jafc.4c00181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease. Ginsenoside Rg2 has shown potential in treating AD, but the underlying protein regulatory mechanisms associated with ginsenoside Rg2 treatment for AD remain unclear. This study utilized scopolamine to induce memory impairment in mice, and proteomics methods were employed to investigate the potential molecular mechanism of ginsenoside Rg2 in treating AD model mice. The Morris water maze, hematoxylin and eosin staining, and Nissl staining results indicated that ginsenoside Rg2 enhanced cognitive ability and decreased neuronal damage in AD mice. Proteomics, western blot, and immunofluorescence results showed that ginsenoside Rg2 primarily improved AD mice by downregulating the expression of LGMN, LAMP1, and PSAP proteins through the regulation of the lysosomal pathway. Transmission electron microscopy and network pharmacology prediction results showed a potential connection between the mechanism of ginsenoside Rg2 treatment for AD mice and lysosomes. The comprehensive results indicated that ginsenoside Rg2 may improve AD by downregulating LGMN, LAMP1, and PSAP through the regulation of the lysosomal pathway.
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Affiliation(s)
- Pei Yin
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Heyu Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Tingfang Xue
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Xiaoran Yu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Xingjian Meng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Qianwen Mi
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Shixin Song
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Boyu Xiong
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Yunfeng Bi
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
| | - Lei Yu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, People's Republic of China
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7
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Jiang T, Ma C, Chen H. Unraveling the ultrastructure and dynamics of autophagic vesicles: Insights from advanced imaging techniques. FASEB Bioadv 2024; 6:189-199. [PMID: 38974114 PMCID: PMC11226998 DOI: 10.1096/fba.2024-00035] [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: 03/01/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 07/09/2024] Open
Abstract
Autophagy, an intracellular self-degradation process, is governed by a complex interplay of signaling pathways and interactions between proteins and organelles. Its fundamental purpose is to efficiently clear and recycle cellular components that are damaged or redundant. Central to this process are autophagic vesicles, specialized structures that encapsulate targeted cellular elements, playing a pivotal role in autophagy. Despite growing interest in the molecular components of autophagic machinery and their regulatory mechanisms, capturing the detailed ultrastructural dynamics of autophagosome formation continues to present significant challenges. However, recent advancements in microscopy, particularly in electron microscopy, have begun to illuminate the dynamic regulatory processes underpinning autophagy. This review endeavors to provide an exhaustive overview of contemporary research on the ultrastructure of autophagic processes. By synthesizing observations from diverse technological methodologies, this review seeks to deepen our understanding of the genesis of autophagic vesicles, their membrane origins, and the dynamic alterations that transpire during the autophagy process. The aim is to bridge gaps in current knowledge and foster a more comprehensive comprehension of this crucial cellular mechanism.
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Affiliation(s)
- Ting Jiang
- Institute of Reproductive MedicineMedical School of Nantong UniversityNantongPR China
| | - Chaoye Ma
- Institute of Reproductive MedicineMedical School of Nantong UniversityNantongPR China
| | - Hao Chen
- Institute of Reproductive MedicineMedical School of Nantong UniversityNantongPR China
- Guangzhou Women and Children’s Medical Center, GMU‐GIBH Joint School of Life ScienceGuangzhou Medical UniversityGuangzhouChina
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8
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Goldman C, Kareva T, Sarrafha L, Schuldt BR, Sahasrabudhe A, Ahfeldt T, Blanchard JW. Genetically Encoded and Modular SubCellular Organelle Probes (GEM-SCOPe) reveal lysosomal and mitochondrial dysfunction driven by PRKN knockout. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.594886. [PMID: 38979135 PMCID: PMC11230217 DOI: 10.1101/2024.05.21.594886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Cellular processes including lysosomal and mitochondrial dysfunction are implicated in the development of many diseases. Quantitative visualization of mitochondria and lysosoesl is crucial to understand how these organelles are dysregulated during disease. To address a gap in live-imaging tools, we developed GEM-SCOPe (Genetically Encoded and Modular SubCellular Organelle Probes), a modular toolbox of fluorescent markers designed to inform on localization, distribution, turnover, and oxidative stress of specific organelles. We expressed GEM-SCOPe in differentiated astrocytes and neurons from a human pluripotent stem cell PRKN-knockout model of Parkinson's disease and identified disease-associated changes in proliferation, lysosomal distribution, mitochondrial transport and turnover, and reactive oxygen species. We demonstrate GEM-SCOPe is a powerful panel that provide critical insight into the subcellular mechanisms underlying Parkinson's disease in human cells. GEM-SCOPe can be expanded upon and applied to a diversity of cellular models to glean an understanding of the mechanisms that promote disease onset and progression.
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Affiliation(s)
- Camille Goldman
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Tatyana Kareva
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Braxton R. Schuldt
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Abhishek Sahasrabudhe
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
| | - Joel W. Blanchard
- Icahn School of Medicine, Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Mount Sinai, New York, NY USA
- Black Family Stem Cell Institute, Mount Sinai, New York, NY, USA
- Lead Contact
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9
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Ayagama T, Charles PD, Bose SJ, Boland B, Priestman DA, Aston D, Berridge G, Fischer R, Cribbs AP, Song Q, Mirams GR, Amponsah K, Heather L, Galione A, Herring N, Kramer H, Capel RA, Platt FM, Schotten U, Verheule S, Burton RA. Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation. iScience 2024; 27:109609. [PMID: 38827406 PMCID: PMC11141153 DOI: 10.1016/j.isci.2024.109609] [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: 08/30/2023] [Revised: 02/07/2024] [Accepted: 03/25/2024] [Indexed: 06/04/2024] Open
Abstract
Endolysosomes (EL) are known for their role in regulating both intracellular trafficking and proteostasis. EL facilitate the elimination of damaged membranes, protein aggregates, membranous organelles and play an important role in calcium signaling. The specific role of EL in cardiac atrial fibrillation (AF) is not well understood. We isolated atrial EL organelles from AF goat biopsies and conducted a comprehensive integrated omics analysis to study the EL-specific proteins and pathways. We also performed electron tomography, protein and enzyme assays on these biopsies. Our results revealed the upregulation of the AMPK pathway and the expression of EL-specific proteins that were not found in whole tissue lysates, including GAA, DYNLRB1, CLTB, SIRT3, CCT2, and muscle-specific HSPB2. We also observed structural anomalies, such as autophagic-vacuole formation, irregularly shaped mitochondria, and glycogen deposition. Our results provide molecular information suggesting EL play a role in AF disease process over extended time frames.
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Affiliation(s)
- Thamali Ayagama
- Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Samuel J. Bose
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Barry Boland
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | | | - Daniel Aston
- Department of Anaesthesia and Critical Care, Royal Papworth Hospital NHS Foundation Trust, Papworth Road, Cambridge CB2 0AY, UK
| | | | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Adam P. Cribbs
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Headington OX3 7LD, UK
| | - Qianqian Song
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Gary R. Mirams
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kwabena Amponsah
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Lisa Heather
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Neil Herring
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Holger Kramer
- Mass spectrometry Facility, The MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | - Ulrich Schotten
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Sander Verheule
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Rebecca A.B. Burton
- Department of Pharmacology, University of Oxford, Oxford, UK
- University of Liverpool, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, Liverpool, UK
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10
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Paumier JM, Gowrishankar S. Disruptions in axonal lysosome transport and its contribution to neurological disease. Curr Opin Cell Biol 2024; 89:102382. [PMID: 38905918 DOI: 10.1016/j.ceb.2024.102382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/23/2024]
Abstract
Lysosomes are central to the maintenance of protein and organelle homeostasis in cells. Optimal lysosome function is particularly critical for neurons which are long-lived, non-dividing and highly polarized with specialized compartments such as axons and dendrites with distinct architecture, cargo, and turnover requirements. In recent years, there has been a growing appreciation for the role played by axonal lysosome transport in regulating neuronal development, its maintenance and functioning. Perturbations to optimal axonal lysosome abundance leading to either strong accumulations or dearth of lysosomes are both linked to altered neuronal health and functioning. In this review we highlight how two critical regulators of axonal lysosome transport and abundance, the small GTPase Arl8 and the adaptor protein JIP3, aid in maintaining axonal lysosome homeostasis and how alterations to their levels and activity could contribute to neurodevelopmental and neurodegenerative diseases.
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Affiliation(s)
- Jean-Michel Paumier
- Department of Anatomy and Cell Biology, University of Illinois Chicago, 808 S Wood St, Chicago, IL 60612, USA
| | - Swetha Gowrishankar
- Department of Anatomy and Cell Biology, University of Illinois Chicago, 808 S Wood St, Chicago, IL 60612, USA.
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11
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Cen J, Hu N, Shen J, Gao Y, Lu H. Pathological Functions of Lysosomal Ion Channels in the Central Nervous System. Int J Mol Sci 2024; 25:6565. [PMID: 38928271 PMCID: PMC11203704 DOI: 10.3390/ijms25126565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Lysosomes are highly dynamic organelles that maintain cellular homeostasis and regulate fundamental cellular processes by integrating multiple metabolic pathways. Lysosomal ion channels such as TRPML1-3, TPC1/2, ClC6/7, CLN7, and TMEM175 mediate the flux of Ca2+, Cl-, Na+, H+, and K+ across lysosomal membranes in response to osmotic stimulus, nutrient-dependent signals, and cellular stresses. These ion channels serve as the crucial transducers of cell signals and are essential for the regulation of lysosomal biogenesis, motility, membrane contact site formation, and lysosomal homeostasis. In terms of pathophysiology, genetic variations in these channel genes have been associated with the development of lysosomal storage diseases, neurodegenerative diseases, inflammation, and cancer. This review aims to discuss the current understanding of the role of these ion channels in the central nervous system and to assess their potential as drug targets.
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Affiliation(s)
| | | | | | - Yongjing Gao
- Institute of Pain Medicine and Special Environmental Medicine, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226019, China; (J.C.); (N.H.); (J.S.)
| | - Huanjun Lu
- Institute of Pain Medicine and Special Environmental Medicine, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226019, China; (J.C.); (N.H.); (J.S.)
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12
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Domingues N, Pires J, Milosevic I, Raimundo N. Role of lipids in interorganelle communication. Trends Cell Biol 2024:S0962-8924(24)00095-3. [PMID: 38866684 DOI: 10.1016/j.tcb.2024.04.008] [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: 02/06/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/14/2024]
Abstract
Cell homeostasis and function rely on well-orchestrated communication between different organelles. This communication is ensured by signaling pathways and membrane contact sites between organelles. Many players involved in organelle crosstalk have been identified, predominantly proteins and ions. The role of lipids in interorganelle communication remains poorly understood. With the development and broader availability of methods to quantify lipids, as well as improved spatiotemporal resolution in detecting different lipid species, the contribution of lipids to organelle interactions starts to be evident. However, the specific roles of various lipid molecules in intracellular communication remain to be studied systematically. We summarize new insights in the interorganelle communication field from the perspective of organelles and discuss the roles played by lipids in these complex processes.
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Affiliation(s)
- Neuza Domingues
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Joana Pires
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Ira Milosevic
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nuno Raimundo
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal; Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA; Penn State Cancer Institute, Hershey, PA, USA.
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13
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Li J, Wang H, Lu Q, Han J, Xu H, Sun P, Xu Q, Huang J, Ji J. Lysosome-Related Genes and RNF19B as Prognostic Markers for Survival and Immunotherapy Efficacy in Hepatocellular Carcinoma. Clin Transl Gastroenterol 2024; 15:e1. [PMID: 38546132 PMCID: PMC11196081 DOI: 10.14309/ctg.0000000000000701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/18/2024] [Indexed: 06/26/2024] Open
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) poses a considerable worldwide health concern due to its associated high risk of death. The heterogeneity of HCC poses challenges in developing practical risk stratification tools and identifying prognostic markers for personalized targeted treatments. Recently, lysosomes were shown to be crucial contributors to numerous cellular activities, including tumor initiation and immune response regulation. We aimed to construct a reliable prognostic signature based on lysosome-related genes and determine its association with the immune microenvironment. METHODS We comprehensively analyzed lysosome-related genes in HCC to investigate their influence on patient survival and the tumor immune microenvironment. A prognostic signature comprising 14 genes associated with lysosomes was created to estimate the survival outcomes of individuals with HCC. In addition, we verified the prognostic importance of Ring Finger Protein 19B (RNF19B) in patients with HCC through multiplex immunohistochemistry analysis. RESULTS Our constructed lysosome-related prediction model could significantly discriminate between HCC patients with good and poor survival outcomes ( P < 0.05). We also found that elevated RNF19B expression was linked to unfavorable prognostic outcomes and showed a connection with specific clinicopathological characteristics. Moreover, it was observed that RNF19B could facilitate the transformation of macrophages into M2-polarized macrophages and showed a significant positive correlation with PD-1 and CTLA-4. DISCUSSION In summary, our study proposes that the expression of lysosome-related genes is associated with the immune microenvironment, serving as a predictor for HCC patient survival. Meanwhile, RNF19B was identified as a novel prognostic marker for predicting overall survival and immunotherapy effects in patients with HCC.
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Affiliation(s)
- Jieying Li
- Department of Pathology, Medical School of Nantong University & Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, China
| | - Hui Wang
- Department of Pathology, Medical School of Nantong University & Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, China
| | - Qian Lu
- Department of General Surgery, Tongzhou People's Hospital, Nantong, Jiangsu Province, China
| | - Jiayi Han
- Department of Pathology, Medical School of Nantong University & Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, China
| | - Haiyan Xu
- Department of Pathology, Medical School of Nantong University & Department of Clinical Biobank, Affiliated Hospital of Nantong University, Nantong, China
| | - Pingping Sun
- Department of Clinical Biobank & The Institute of Oncology, the Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Qiang Xu
- Department of Pathology, Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu Province, China
| | - Jianfei Huang
- Department of Clinical Biobank & The Institute of Oncology, the Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Juling Ji
- Department of Pathology, Medical School of Nantong University, Nantong, Jiangsu Province, China
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14
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van der Graaf K, Srivastav S, Nishad R, Stern M, McNew JA. The Drosophila Nesprin-1 homolog MSP300 is required for muscle autophagy and proteostasis. J Cell Sci 2024; 137:jcs262096. [PMID: 38757366 PMCID: PMC11213522 DOI: 10.1242/jcs.262096] [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: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
Nesprin proteins, which are components of the linker of nucleoskeleton and cytoskeleton (LINC) complex, are located within the nuclear envelope and play prominent roles in nuclear architecture. For example, LINC complex proteins interact with both chromatin and the cytoskeleton. Here, we report that the Drosophila Nesprin MSP300 has an additional function in autophagy within larval body wall muscles. RNAi-mediated MSP300 knockdown in larval body wall muscles resulted in defects in the contractile apparatus, muscle degeneration and defective autophagy. In particular, MSP300 knockdown caused accumulation of cytoplasmic aggregates that contained poly-ubiquitylated cargo, as well as the autophagy receptor ref(2)P (the fly homolog of p62 or SQSTM) and Atg8a. Furthermore, MSP300 knockdown larvae expressing an mCherry-GFP-tagged Atg8a transgene exhibited aberrant persistence of the GFP signal within these aggregates, indicating failure of autophagosome maturation. These autophagy deficits were similar to those exhibited by loss of the endoplasmic reticulum (ER) fusion protein Atlastin (Atl), raising the possibility that Atl and MSP300 might function in the same pathway. In support of this possibility, we found that a GFP-tagged MSP300 protein trap exhibited extensive localization to the ER. Alteration of ER-directed MSP300 might abrogate important cytoskeletal contacts necessary for autophagosome completion.
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Affiliation(s)
| | | | - Rajkishor Nishad
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Michael Stern
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - James A. McNew
- Department of BioSciences, Rice University, Houston, TX 77005, USA
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15
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Costanzo M, Cevenini A, Kollipara L, Caterino M, Bianco S, Pirozzi F, Scerra G, D'Agostino M, Pavone LM, Sickmann A, Ruoppolo M. Methylmalonic acidemia triggers lysosomal-autophagy dysfunctions. Cell Biosci 2024; 14:63. [PMID: 38760822 PMCID: PMC11102240 DOI: 10.1186/s13578-024-01245-1] [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: 11/21/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Methylmalonic acidemia (MMA) is a rare inborn error of propionate metabolism caused by deficiency of the mitochondrial methylmalonyl-CoA mutase (MUT) enzyme. As matter of fact, MMA patients manifest impairment of the primary metabolic network with profound damages that involve several cell components, many of which have not been discovered yet. We employed cellular models and patients-derived fibroblasts to refine and uncover new pathologic mechanisms connected with MUT deficiency through the combination of multi-proteomics and bioinformatics approaches. RESULTS Our data show that MUT deficiency is connected with profound proteome dysregulations, revealing molecular actors involved in lysosome and autophagy functioning. To elucidate the effects of defective MUT on lysosomal and autophagy regulation, we analyzed the morphology and functionality of MMA-lysosomes that showed deep alterations, thus corroborating omics data. Lysosomes of MMA cells present as enlarged vacuoles with low degradative capabilities. Notwithstanding, treatment with an anti-propionigenic drug is capable of totally rescuing lysosomal morphology and functional activity in MUT-deficient cells. These results indicate a strict connection between MUT deficiency and lysosomal-autophagy dysfunction, providing promising therapeutic perspectives for MMA. CONCLUSIONS Defective homeostatic mechanisms in the regulation of autophagy and lysosome functions have been demonstrated in MUT-deficient cells. Our data prove that MMA triggers such dysfunctions impacting on autophagosome-lysosome fusion and lysosomal activity.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy.
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy.
| | - Armando Cevenini
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | | | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Sabrina Bianco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Francesca Pirozzi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Gianluca Scerra
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
| | - Massimo D'Agostino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
| | - Luigi Michele Pavone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
- Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, Naples, 80131, Italy.
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy.
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16
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Tempes A, Bogusz K, Brzozowska A, Weslawski J, Macias M, Tkaczyk O, Orzoł K, Lew A, Calka-Kresa M, Bernas T, Szczepankiewicz AA, Mlostek M, Kumari S, Liszewska E, Machnicka K, Bakun M, Rubel T, Malik AR, Jaworski J. Autophagy initiation triggers p150 Glued-AP-2β interaction on the lysosomes and facilitates their transport. Cell Mol Life Sci 2024; 81:218. [PMID: 38758395 PMCID: PMC11101406 DOI: 10.1007/s00018-024-05256-6] [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: 10/01/2023] [Revised: 01/25/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
The endocytic adaptor protein 2 (AP-2) complex binds dynactin as part of its noncanonical function, which is necessary for dynein-driven autophagosome transport along microtubules in neuronal axons. The absence of this AP-2-dependent transport causes neuronal morphology simplification and neurodegeneration. The mechanisms that lead to formation of the AP-2-dynactin complex have not been studied to date. However, the inhibition of mammalian/mechanistic target of rapamycin complex 1 (mTORC1) enhances the transport of newly formed autophagosomes by influencing the biogenesis and protein interactions of Rab-interacting lysosomal protein (RILP), another dynein cargo adaptor. We tested effects of mTORC1 inhibition on interactions between the AP-2 and dynactin complexes, with a focus on their two essential subunits, AP-2β and p150Glued. We found that the mTORC1 inhibitor rapamycin enhanced p150Glued-AP-2β complex formation in both neurons and non-neuronal cells. Additional analysis revealed that the p150Glued-AP-2β interaction was indirect and required integrity of the dynactin complex. In non-neuronal cells rapamycin-driven enhancement of the p150Glued-AP-2β interaction also required the presence of cytoplasmic linker protein 170 (CLIP-170), the activation of autophagy, and an undisturbed endolysosomal system. The rapamycin-dependent p150Glued-AP-2β interaction occurred on lysosomal-associated membrane protein 1 (Lamp-1)-positive organelles but without the need for autolysosome formation. Rapamycin treatment also increased the acidification and number of acidic organelles and increased speed of the long-distance retrograde movement of Lamp-1-positive organelles. Altogether, our results indicate that autophagy regulates the p150Glued-AP-2β interaction, possibly to coordinate sufficient motor-adaptor complex availability for effective lysosome transport.
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Affiliation(s)
- Aleksandra Tempes
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Karolina Bogusz
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Agnieszka Brzozowska
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Jan Weslawski
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Matylda Macias
- Microscopy and Flow Cytometry Core Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Oliver Tkaczyk
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Katarzyna Orzoł
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Aleksandra Lew
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | | | - Tytus Bernas
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Microscopy Facility, Department of Anatomy and Neurology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | | | - Magdalena Mlostek
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Shiwani Kumari
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Ewa Liszewska
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Katarzyna Machnicka
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland
| | - Magdalena Bakun
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tymon Rubel
- Institute of Radioelectronics and Multimedia Technology, Warsaw University of Technology, Warsaw, Poland
| | - Anna R Malik
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland.
- Cellular Neurobiology Research Group, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Miecznikowa St. 1, 02-096, Warsaw, Poland.
| | - Jacek Jaworski
- Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology, Ks. Trojdena St. 4, 02-109, Warsaw, Poland.
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17
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Deng W, Yan Y, Shi C, Sui D. Single-cell and bulk RNAseq unveils the immune infiltration landscape and targeted therapeutic biomarkers of psoriasis. Front Genet 2024; 15:1365273. [PMID: 38699235 PMCID: PMC11063342 DOI: 10.3389/fgene.2024.1365273] [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: 01/04/2024] [Accepted: 04/01/2024] [Indexed: 05/05/2024] Open
Abstract
Background Psoriasis represents a multifaceted and debilitating immune-mediated systemic ailment afflicting millions globally. Despite the continuous discovery of biomarkers associated with psoriasis, identifying lysosomal biomarkers, pivotal as cellular metabolic hubs, remains elusive. Methods We employed a combination of differential expression analysis and weighted gene co-expression network analysis (WGCNA) to initially identify lysosomal genes. Subsequently, to mitigate overfitting and eliminate collinear genes, we applied 12 machine learning algorithms to screen robust lysosomal genes. These genes underwent further refinement through random forest (RF) and Lasso algorithms to ascertain the final hub lysosomal genes. To assess their predictive efficacy, we conducted receiver operating characteristic (ROC) analysis and verified the expression of diagnostic biomarkers at both bulk and single-cell levels. Furthermore, we utilized single-sample gene set enrichment analysis (ssGSEA), CIBERSORT, and Pearson's correlation analysis to elucidate the association between immune phenotypes and hub lysosomal genes in psoriatic samples. Finally, employing the Cellchat algorithm, we explored potential mechanisms underlying the participation of these hub lysosomal genes in cell-cell communication. Results Functional enrichment analyses revealed a close association between psoriasis and lysosomal functions. Subsequent intersection analysis identified 19 key lysosomal genes, derived from DEGs, phenotypic genes of WGCNA, and lysosomal gene sets. Following the exclusion of collinear genes, we identified 11 robust genes, further refined through RF and Lasso, yielding 3 hub lysosomal genes (S100A7, SERPINB13, and PLBD1) closely linked to disease occurrence, with high predictive capability for disease diagnosis. Concurrently, we validated their relative expression in separate bulk datasets and single-cell datasets. A nomogram based on these hub genes may offer clinical advantages for patients. Notably, these three hub genes facilitated patient classification into two subtypes, namely metabolic-immune subtype 1 and signaling subtype 2. CMap analysis suggested butein and arachidonic fasudil as preferred treatment agents for subtype 1 and subtype 2, respectively. Finally, through Cellchat and correlation analysis, we identified PRSS3-F2R as potentially promoting the expression of hub genes in the psoriasis group, thereby enhancing keratinocyte-fibroblast interaction, ultimately driving psoriasis occurrence and progression. Conclusion Our study identifies S100A7, SERPINB13, and PLBD1 as potential diagnostic biomarkers, offering promising prospects for more precisely tailored psoriatic immunotherapy designs.
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Affiliation(s)
- Wenhui Deng
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yijiao Yan
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Chengzhi Shi
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Daoshun Sui
- The First Affiliated Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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18
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Johnson D, Colijn S, Richee J, Yano J, Burns M, Davis AE, Pham VN, Saric A, Jain A, Yin Y, Castranova D, Melani M, Fujita M, Grainger S, Bonifacino JS, Weinstein BM, Stratman AN. Regulation of angiogenesis by endocytic trafficking mediated by cytoplasmic dynein 1 light intermediate chain 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587559. [PMID: 38903077 PMCID: PMC11188074 DOI: 10.1101/2024.04.01.587559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Dynein cytoplasmic 1 light intermediate chain 1 (LIC1, DYNC1LI1) is a core subunit of the dynein motor complex. The LIC1 subunit also interacts with various cargo adaptors to regulate Rab-mediated endosomal recycling and lysosomal degradation. Defects in this gene are predicted to alter dynein motor function, Rab binding capabilities, and cytoplasmic cargo trafficking. Here, we have identified a dync1li1 zebrafish mutant, harboring a premature stop codon at the exon 12/13 splice acceptor site, that displays increased angiogenesis. In vitro, LIC1-deficient human endothelial cells display increases in cell surface levels of the pro-angiogenic receptor VEGFR2, SRC phosphorylation, and Rab11-mediated endosomal recycling. In vivo, endothelial-specific expression of constitutively active Rab11a leads to excessive angiogenesis, similar to the dync1li1 mutants. Increased angiogenesis is also evident in zebrafish harboring mutations in rilpl1/2, the adaptor proteins that promote Rab docking to Lic1 to mediate lysosomal targeting. These findings suggest that LIC1 and the Rab-adaptor proteins RILPL1 and 2 restrict angiogenesis by promoting degradation of VEGFR2-containing recycling endosomes. Disruption of LIC1- and RILPL1/2-mediated lysosomal targeting increases Rab11-mediated recycling endosome activity, promoting excessive SRC signaling and angiogenesis.
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Affiliation(s)
- Dymonn Johnson
- Cell Biology and Physiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Sarah Colijn
- Cell Biology and Physiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Jahmiera Richee
- Cell Biology and Physiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Joseph Yano
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
- Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Margaret Burns
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
| | - Andrew E. Davis
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
| | - Van N. Pham
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
| | - Amra Saric
- Section on Intracellular Protein Trafficking, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
- Neurosciences and Mental Health Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Akansha Jain
- Section on Intracellular Protein Trafficking, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
| | - Ying Yin
- Cell Biology and Physiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
| | - Daniel Castranova
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
| | - Mariana Melani
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Consejo Nacional De Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires, Buenos Aires, Argentina
| | - Misato Fujita
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
- Kanagawa University, Kanagawa, 221-8686, Japan
| | - Stephanie Grainger
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, 49503
| | - Juan S. Bonifacino
- Section on Intracellular Protein Trafficking, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
| | - Brant M. Weinstein
- Section on Vertebrate Organogenesis, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892
| | - Amber N. Stratman
- Cell Biology and Physiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110
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19
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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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20
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Settembre C, Perera RM. Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology. Nat Rev Mol Cell Biol 2024; 25:223-245. [PMID: 38001393 DOI: 10.1038/s41580-023-00676-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 11/26/2023]
Abstract
Every cell must satisfy basic requirements for nutrient sensing, utilization and recycling through macromolecular breakdown to coordinate programmes for growth, repair and stress adaptation. The lysosome orchestrates these key functions through the synchronised interplay between hydrolytic enzymes, nutrient transporters and signalling factors, which together enable metabolic coordination with other organelles and regulation of specific gene expression programmes. In this Review, we discuss recent findings on lysosome-dependent signalling pathways, focusing on how the lysosome senses nutrient availability through its physical and functional association with mechanistic target of rapamycin complex 1 (mTORC1) and how, in response, the microphthalmia/transcription factor E (MiT/TFE) transcription factors exert feedback regulation on lysosome biogenesis. We also highlight the emerging interactions of lysosomes with other organelles, which contribute to cellular homeostasis. Lastly, we discuss how lysosome dysfunction contributes to diverse disease pathologies and how inherited mutations that compromise lysosomal hydrolysis, transport or signalling components lead to multi-organ disorders with severe metabolic and neurological impact. A deeper comprehension of lysosomal composition and function, at both the cellular and organismal level, may uncover fundamental insights into human physiology and disease.
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Affiliation(s)
- Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.
| | - Rushika M Perera
- Department of Anatomy, University of California at San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California at San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
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21
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van der Beek J, de Heus C, Sanza P, Liv N, Klumperman J. Loss of the HOPS complex disrupts early-to-late endosome transition, impairs endosomal recycling and induces accumulation of amphisomes. Mol Biol Cell 2024; 35:ar40. [PMID: 38198575 PMCID: PMC10916860 DOI: 10.1091/mbc.e23-08-0328] [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: 08/29/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024] Open
Abstract
The multisubunit HOPS tethering complex is a well-established regulator of lysosome fusion with late endosomes and autophagosomes. However, the role of the HOPS complex in other stages of endo-lysosomal trafficking is not well understood. To address this, we made HeLa cells knocked out for the HOPS-specific subunits Vps39 or Vps41, or the HOPS-CORVET-core subunits Vps18 or Vps11. In all four knockout cells, we found that endocytosed cargos were trapped in enlarged endosomes that clustered in the perinuclear area. By correlative light-electron microscopy, these endosomes showed a complex ultrastructure and hybrid molecular composition, displaying markers for early (Rab5, PtdIns3P, EEA1) as well as late (Rab7, CD63, LAMP1) endosomes. These "HOPS bodies" were not acidified, contained enzymatically inactive cathepsins and accumulated endocytosed cargo and cation-independent mannose-6-phosphate receptor (CI-MPR). Consequently, CI-MPR was depleted from the TGN, and secretion of lysosomal enzymes to the extracellular space was enhanced. Strikingly, HOPS bodies also contained the autophagy proteins p62 and LC3, defining them as amphisomes. Together, these findings show that depletion of the lysosomal HOPS complex has a profound impact on the functional organization of the entire endosomal system and suggest the existence of a HOPS-independent mechanism for amphisome formation.
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Affiliation(s)
- Jan van der Beek
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Cecilia de Heus
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Paolo Sanza
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, 3584 CX Utrecht, The Netherlands
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22
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Dema A, Charafeddine RA, van Haren J, Rahgozar S, Viola G, Jacobs KA, Kutys ML, Wittmann T. Doublecortin reinforces microtubules to promote growth cone advance in soft environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582626. [PMID: 38464100 PMCID: PMC10925279 DOI: 10.1101/2024.02.28.582626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Doublecortin (DCX) is a microtubule-associated protein critical for brain development. Although most highly expressed in the developing central nervous system, the molecular function of DCX in neuron morphogenesis remains unknown and controversial. We demonstrate that DCX function is intimately linked to its microtubule-binding activity. By using human induced pluripotent stem cell (hiPSC)- derived cortical i 3 Neurons genome engineered to express mEmerald-tagged DCX from the endogenous locus, we find that DCX-MT interactions become highly polarized very early during neuron morphogenesis. DCX becomes enriched only on straight microtubules in advancing growth cones with approximately 120 DCX molecules bound per micrometer of growth cone microtubule. At a similar saturation, microtubule-bound DCX molecules begin to impede lysosome transport, and thus can potentially control growth cone organelle entry. In addition, by comparing control, DCX-mEmerald and knockout DCX -/Y i 3 Neurons, we find that DCX stabilizes microtubules in the growth cone peripheral domain by reducing the microtubule catastrophe frequency and the depolymerization rate. DCX -/Y i 3 Neuron morphogenesis was inhibited in soft microenvironments that mimic the viscoelasticity of brain tissue and DCX -/Y neurites failed to grow toward brain-derived neurotrophic factor (BDNF) gradients. Together with high resolution traction force microscopy data, we propose a model in which DCX-decorated, rigid growth cone microtubules provide intracellular mechanical resistance to actomyosin generated contractile forces in soft physiological environments in which weak and transient adhesion-mediated forces in the growth cone periphery may be insufficient for productive growth cone advance. These data provide a new mechanistic understanding of how DCX mutations cause lissencephaly-spectrum brain malformations by impacting growth cone dynamics during neuron morphogenesis in physiological environments.
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23
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Sun S, Zhao G, Jia M, Jiang Q, Li S, Wang H, Li W, Wang Y, Bian X, Zhao YG, Huang X, Yang G, Cai H, Pastor-Pareja JC, Ge L, Zhang C, Hu J. Stay in touch with the endoplasmic reticulum. SCIENCE CHINA. LIFE SCIENCES 2024; 67:230-257. [PMID: 38212460 DOI: 10.1007/s11427-023-2443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024]
Abstract
The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.
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Affiliation(s)
- Sha Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gan Zhao
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjing Li
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yan G Zhao
- Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ge Yang
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jose C Pastor-Pareja
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Neurosciences, Consejo Superior de Investigaciones Cientfflcas-Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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24
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Kumar R, Khan M, Francis V, Aguila A, Kulasekaran G, Banks E, McPherson PS. DENND6A links Arl8b to a Rab34/RILP/dynein complex, regulating lysosomal positioning and autophagy. Nat Commun 2024; 15:919. [PMID: 38296963 PMCID: PMC10830484 DOI: 10.1038/s41467-024-44957-1] [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: 08/21/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024] Open
Abstract
Lysosomes help maintain cellular proteostasis, and defects in lysosomal positioning and function can cause disease, including neurodegenerative disorders. The spatiotemporal distribution of lysosomes is regulated by small GTPases including Rabs, which are activated by guanine nucleotide exchange factors (GEFs). DENN domain proteins are the largest family of Rab GEFs. Using a cell-based assay, we screened DENND6A, a member of the DENN domain protein family against all known Rabs and identified it as a potential GEF for 20 Rabs, including Rab34. Here, we demonstrate that DENND6A activates Rab34, which recruits a RILP/dynein complex to lysosomes, promoting lysosome retrograde transport. Further, we identify DENND6A as an effector of Arl8b, a major regulatory GTPase on lysosomes. We demonstrate that Arl8b recruits DENND6A to peripheral lysosomes to activate Rab34 and initiate retrograde transport, regulating nutrient-dependent lysosomal juxtanuclear repositioning. Loss of DENND6A impairs autophagic flux. Our findings support a model whereby Arl8b/DENND6A/Rab34-dependent lysosomal retrograde trafficking controls autophagy.
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Affiliation(s)
- Rahul Kumar
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada.
| | - Maleeha Khan
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Vincent Francis
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Adriana Aguila
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Gopinath Kulasekaran
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Emily Banks
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute (the Neuro), McGill University, Montreal, QC, Canada.
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25
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Yu Y, Gao SM, Guan Y, Hu PW, Zhang Q, Liu J, Jing B, Zhao Q, Sabatini DM, Abu-Remaileh M, Jung SY, Wang MC. Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity. eLife 2024; 13:e85214. [PMID: 38240316 PMCID: PMC10876212 DOI: 10.7554/elife.85214] [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: 11/28/2022] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins associated with the lysosome mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked to longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using deep proteomic profiling, we systemically profiled lysosome-associated proteins linked with four different longevity mechanisms. We discovered the lysosomal recruitment of AMP-activated protein kinase and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we further elucidated lysosomal heterogeneity across tissues as well as the increased enrichment of the Ragulator complex on Cystinosin-positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity across multiple scales and provides resources for understanding the contribution of lysosomal protein dynamics to signal transduction, organelle crosstalk, and organism longevity.
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Affiliation(s)
- Yong Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
| | - Shihong M Gao
- Developmental Biology Graduate Program, Baylor College of MedicineHoustonUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Youchen Guan
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Molecular and Cellular Biology Graduate Program, Baylor College of MedicineHoustonUnited States
| | - Pei-Wen Hu
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
| | - Qinghao Zhang
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
| | - Jiaming Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Bentian Jing
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Qian Zhao
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - David M Sabatini
- Institute of Organic Chemistry and BiochemistryPragueCzech Republic
| | - Monther Abu-Remaileh
- Institute for Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford UniversityStanfordUnited States
- Department of Chemical Engineering and Genetics, Stanford UniversityStanfordUnited States
| | - Sung Yun Jung
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
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26
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Jeong E, Willett R, Rissone A, La Spina M, Puertollano R. TMEM55B links autophagy flux, lysosomal repair, and TFE3 activation in response to oxidative stress. Nat Commun 2024; 15:93. [PMID: 38168055 PMCID: PMC10761734 DOI: 10.1038/s41467-023-44316-6] [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: 07/20/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Lysosomes have emerged as critical regulators of cellular homeostasis. Here we show that the lysosomal protein TMEM55B contributes to restore cellular homeostasis in response to oxidative stress by three different mechanisms: (1) TMEM55B mediates NEDD4-dependent PLEKHM1 ubiquitination, causing PLEKHM1 proteasomal degradation and halting autophagosome/lysosome fusion; (2) TMEM55B promotes recruitment of components of the ESCRT machinery to lysosomal membranes to stimulate lysosomal repair; and (3) TMEM55B sequesters the FLCN/FNIP complex to facilitate translocation of the transcription factor TFE3 to the nucleus, allowing expression of transcriptional programs that enable cellular adaptation to stress. Knockout of tmem55 genes in zebrafish embryos increases their susceptibility to oxidative stress, causing early death of tmem55-KO animals in response to arsenite toxicity. Altogether, our work identifies a role for TMEM55B as a molecular sensor that coordinates autophagosome degradation, lysosomal repair, and activation of stress responses.
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Affiliation(s)
- Eutteum Jeong
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rose Willett
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alberto Rissone
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martina La Spina
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rosa Puertollano
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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27
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Caldas LA, Carneiro FA, Augusto I, Corrêa IA, da Costa LJ, Miranda K, Tanuri A, de Souza W. SARS-CoV-2 egress from Vero cells: a morphological approach. Histochem Cell Biol 2024; 161:59-67. [PMID: 37736815 DOI: 10.1007/s00418-023-02239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Despite being extensively studied because of the current coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interactions with mammalian cells are still poorly understood. Furthermore, little is known about this coronavirus cycle within the host cells, particularly the steps that lead to viral egress. This study aimed to shed light on the morphological features of SARS-CoV-2 egress by utilizing transmission and high-resolution scanning electron microscopy, along with serial electron tomography, to describe the route of nascent virions towards the extracellular medium. Electron microscopy revealed that the clusters of viruses in the paracellular space did not seem to result from collective virus release. Instead, virus accumulation was observed on incurved areas of the cell surface, with egress primarily occurring through individual vesicles. Additionally, our findings showed that the emission of long membrane projections, which could facilitate virus surfing in Vero cells infected with SARS-CoV-2, was also observed in non-infected cultures, suggesting that these are constitutive events in this cell lineage.
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Affiliation(s)
- Lucio Ayres Caldas
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil.
- Núcleo Multidisciplinar de Pesquisas em Biologia - NUMPEX-BIO, Campus Duque de Caxias Geraldo Cidade, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Duque de Caxias, RJ, Brazil.
| | - Fabiana Avila Carneiro
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
- Núcleo Multidisciplinar de Pesquisas em Biologia - NUMPEX-BIO, Campus Duque de Caxias Geraldo Cidade, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Duque de Caxias, RJ, Brazil
| | - Ingrid Augusto
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
| | - Isadora Alonso Corrêa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana Jesus da Costa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kildare Miranda
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem (INBEB) and Centro Nacional de Biologia Estutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Prédio CCS, Bloco C, Subsolo, Cidade Universitária, Rio de Janeiro, RJ, CEP:21941902, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem (INBEB) and Centro Nacional de Biologia Estutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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28
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Pramanik S, Sil AK. Cigarette smoke extract induces foam cell formation by impairing machinery involved in lipid droplet degradation. Pflugers Arch 2024; 476:59-74. [PMID: 37910205 DOI: 10.1007/s00424-023-02870-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/03/2023]
Abstract
The formation of foam cells, lipid-loaded macrophages, is the hallmark event of atherosclerosis. Since cigarette smoking is a risk factor for developing atherosclerosis, the current study investigated the effects of cigarette smoke extract (CSE) on different events like expressions of genes involved in lipid influx and efflux, lipophagy, etc., that play vital roles in foam cell formation. The accumulation of lipids after CSE treatment U937 macrophage cells was examined by staining lipids with specific dyes: Oil red O and BODIPY493/503. Results showed an accumulation of lipids in CSE-treated cells, confirming foam cell formation by CSE treatment. To decipher the mechanism, the levels of CD36, an ox-LDL receptor, and ABCA1, an exporter of lipids, were examined in CSE-treated and -untreated U937 cells by real-time PCR and immunofluorescence analysis. Consistent with lipid accumulation, an increased level of CD36 and a reduction in ABCA1 were observed in CSE-treated cells. Moreover, CSE treatment caused inhibition of lipophagy-mediated lipid degradation by blocking lipid droplets (LDs)-lysosome fusion and increasing the lysosomal pH. CSE also impaired mitochondrial lipid oxidation. Thus, the present study demonstrates that CSE treatment affects lipid homeostasis by altering its influx and efflux, lysosomal degradation, and mitochondrial utilization, leading to the formation of lipid-loaded foam cells. Moreover, the current study also showed that the leucine supplement caused a significant reduction of CSE-induced foam cell formation in vitro. Thus, the current study provides insight into CS-induced atherosclerosis and an agent to combat the disease.
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Affiliation(s)
- Soudipta Pramanik
- Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Ballygunge, Kolkata, West Bengal, India, PIN-700019
| | - Alok Kumar Sil
- Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Ballygunge, Kolkata, West Bengal, India, PIN-700019.
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29
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Hippman RS, Snead AM, Petros ZA, Korkmaz-Vaisys MA, Patel S, Sotelo D, Dobria A, Salkovski M, Nguyen TTA, Linares R, Cologna SM, Gowrishankar S, Aldrich LN. Discovery of a Small-Molecule Modulator of the Autophagy-Lysosome Pathway That Targets Lamin A/C and LAMP1, Induces Autophagic Flux, and Affects Lysosome Positioning in Neurons. ACS Chem Neurosci 2023; 14:4363-4382. [PMID: 38069806 PMCID: PMC10739612 DOI: 10.1021/acschemneuro.3c00573] [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: 09/05/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
Autophagy is a major catabolic degradation and recycling process that maintains homeostasis in cells and is especially important in postmitotic neurons. We implemented a high-content phenotypic assay to discover small molecules that promote autophagic flux and completed target identification and validation studies to identify protein targets that modulate the autophagy pathway and promote neuronal health and survival. Efficient syntheses of the prioritized compounds were developed to readily access analogues of the initial hits, enabling initial structure-activity relationship studies to improve potency and preparation of a biotin-tagged pulldown probe that retains activity. This probe facilitated target identification and validation studies through pulldown and competition experiments using both an unbiased proteomics approach and western blotting to reveal Lamin A/C and LAMP1 as the protein targets of compound RH1115. Evaluation of RH1115 in neurons revealed that this compound induces changes to LAMP1 vesicle properties and alters lysosome positioning. Dysfunction of the autophagy-lysosome pathway has been implicated in a variety of neurodegenerative diseases, including Alzheimer's disease, highlighting the value of new strategies for therapeutic modulation and the importance of small-molecule probes to facilitate the study of autophagy regulation in cultured neurons and in vivo.
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Affiliation(s)
- Ryan S. Hippman
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Amanda M. Snead
- Department
of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, 808 S. Wood Street, Chicago, Illinois 60612, United States
| | - Zoe A. Petros
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Melissa A. Korkmaz-Vaisys
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Sruchi Patel
- Department
of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, 808 S. Wood Street, Chicago, Illinois 60612, United States
| | - Daniel Sotelo
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Andrew Dobria
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Maryna Salkovski
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Thu T. A. Nguyen
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Ricardo Linares
- Department
of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, 808 S. Wood Street, Chicago, Illinois 60612, United States
| | - Stephanie M. Cologna
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
| | - Swetha Gowrishankar
- Department
of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, 808 S. Wood Street, Chicago, Illinois 60612, United States
| | - Leslie N. Aldrich
- Department
of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, United States
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Abdelaziz RF, Hussein AM, Kotob MH, Weiss C, Chelminski K, Stojanovic T, Studenik CR, Aufy M. Enhancement of Radiation Sensitivity by Cathepsin L Suppression in Colon Carcinoma Cells. Int J Mol Sci 2023; 24:17106. [PMID: 38069428 PMCID: PMC10707098 DOI: 10.3390/ijms242317106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Cancer is one of the main causes of death globally. Radiotherapy/Radiation therapy (RT) is one of the most common and effective cancer treatments. RT utilizes high-energy radiation to damage the DNA of cancer cells, leading to their death or impairing their proliferation. However, radiation resistance remains a significant challenge in cancer treatment, limiting its efficacy. Emerging evidence suggests that cathepsin L (cath L) contributes to radiation resistance through multiple mechanisms. In this study, we investigated the role of cath L, a member of the cysteine cathepsins (caths) in radiation sensitivity, and the potential reduction in radiation resistance by using the specific cath L inhibitor (Z-FY(tBu)DMK) or by knocking out cath L with CRISPR/Cas9 in colon carcinoma cells (caco-2). Cells were treated with different doses of radiation (2, 4, 6, 8, and 10), dose rate 3 Gy/min. In addition, the study conducted protein expression analysis by western blot and immunofluorescence assay, cytotoxicity MTT, and apoptosis assays. The results demonstrated that cath L was upregulated in response to radiation treatment, compared to non-irradiated cells. In addition, inhibiting or knocking out cath L led to increased radiosensitivity in contrast to the negative control group. This may indicate a reduced ability of cancer cells to recover from radiation-induced DNA damage, resulting in enhanced cell death. These findings highlight the possibility of targeting cath L as a therapeutic strategy to enhance the effectiveness of RT. Further studies are needed to elucidate the underlying molecular mechanisms and to assess the translational implications of cath L knockout in clinical settings. Ultimately, these findings may contribute to the development of novel treatment approaches for improving outcomes of RT in cancer patients.
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Affiliation(s)
- Ramadan F. Abdelaziz
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (R.F.A.); (M.H.K.); (C.W.); (M.A.)
- Division of Human Health, International Atomic Energy Agency, Wagramer Str. 5, 1400 Vienna, Austria;
| | - Ahmed M. Hussein
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (R.F.A.); (M.H.K.); (C.W.); (M.A.)
| | - Mohamed H. Kotob
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (R.F.A.); (M.H.K.); (C.W.); (M.A.)
| | - Christina Weiss
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (R.F.A.); (M.H.K.); (C.W.); (M.A.)
| | - Krzysztof Chelminski
- Division of Human Health, International Atomic Energy Agency, Wagramer Str. 5, 1400 Vienna, Austria;
| | - Tamara Stojanovic
- Programme for Proteomics, Paracelsus Medical University, 5020 Salzburg, Austria;
| | - Christian R. Studenik
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (R.F.A.); (M.H.K.); (C.W.); (M.A.)
| | - Mohammed Aufy
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, 1090 Vienna, Austria; (R.F.A.); (M.H.K.); (C.W.); (M.A.)
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31
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Maji S, Pirozzi M, Ruturaj, Pandey R, Ghosh T, Das S, Gupta A. Copper-independent lysosomal localisation of the Wilson disease protein ATP7B. Traffic 2023; 24:587-609. [PMID: 37846526 DOI: 10.1111/tra.12919] [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: 10/20/2022] [Revised: 09/10/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023]
Abstract
In hepatocytes, the Wilson disease protein ATP7B resides on the trans-Golgi network (TGN) and traffics to peripheral lysosomes to export excess intracellular copper through lysosomal exocytosis. We found that in basal copper or even upon copper chelation, a significant amount of ATP7B persists in the endolysosomal compartment of hepatocytes but not in non-hepatic cells. These ATP7B-harbouring lysosomes lie in close proximity of ~10 nm to the TGN. ATP7B constitutively distributes itself between the sub-domain of the TGN with a lower pH and the TGN-proximal lysosomal compartments. The presence of ATP7B on TGN-lysosome colocalising sites upon Golgi disruption suggested a possible exchange of ATP7B directly between the TGN and its proximal lysosomes. Manipulating lysosomal positioning significantly alters the localisation of ATP7B in the cell. Contrary to previous understanding, we found that upon copper chelation in a copper-replete hepatocyte, ATP7B is not retrieved back to TGN from peripheral lysosomes; rather, ATP7B recycles to these TGN-proximal lysosomes to initiate the next cycle of copper transport. We report a hitherto unknown copper-independent lysosomal localisation of ATP7B and the importance of TGN-proximal lysosomes but not TGN as the terminal acceptor organelle of ATP7B in its retrograde pathway.
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Affiliation(s)
- Saptarshi Maji
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | | | - Ruturaj
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Raviranjan Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Tamal Ghosh
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Santanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Arnab Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
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Sun L, Wang X, Chen L, Gao Z, Xu S, Hu C, Fan G, Wang B, Feng T, Wang W, Ying X. CPT1A mediates chemoresistance in human hypopharyngeal squamous cell carcinoma via ATG16L1-dependent cellular autophagy. CELL INSIGHT 2023; 2:100127. [PMID: 37961047 PMCID: PMC10632670 DOI: 10.1016/j.cellin.2023.100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/04/2023] [Accepted: 10/08/2023] [Indexed: 11/15/2023]
Abstract
Hypopharyngeal squamous cell carcinoma (HSCC) is a highly aggressive malignancy that constitutes approximately 95% of all hypopharyngeal carcinomas, and it carries a poor prognosis. The primary factor influencing the efficacy of anti-cancer drugs for this type of carcinoma is chemoresistance. Carnitine palmitoyltransferase 1A (CPT1A) has been associated with tumor progression in various cancers, including breast, gastric, lung, and prostate cancer. The inhibition or depletion of CPT1A can lead to apoptosis, curbing cancer cell proliferation and chemoresistance. However, the role of CPT1A in HSCC is not yet fully understood. In this study, we discovered that CPT1A is highly expressed in HSCC and is associated with an advanced T-stage and a poor 5-year survival rate among patients. Furthermore, the overexpression of CPT1A contributes to HSCC chemoresistance. Mechanistically, CPT1A can interact with the autophagy-related protein ATG16L1 and stimulate the succinylation of ATG16L1, which in turn drives autophagosome formation and autophagy. We also found that treatment with 3-methyladenine (3-MA) can reduce cisplatin resistance in HSCC cells that overexpress CPT1A. Our findings also showed that a CPT1A inhibitor significantly enhances cisplatin sensitivity both in vitro and in vivo. This study is the first to suggest that CPT1A has a regulatory role in autophagy and is linked to poor prognosis in HSCC patients. It presents novel insights into the roles of CPT1A in tumorigenesis and proposes that CPT1A could be a potential therapeutic target for HSCC treatment.
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Affiliation(s)
- Lianhui Sun
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Xing Wang
- Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Lixiao Chen
- Department of Otolaryngology Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201620, China
| | - Zheng Gao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Songhui Xu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chen Hu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Guangjian Fan
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Baoxin Wang
- Department of Otolaryngology Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201620, China
| | - Tingting Feng
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wang Wang
- School of Cell and Gene Therapy,Shanghai Jiaotong University School of Medicine, Shanghai, 201600, China
| | - Xinjiang Ying
- Department of Otolaryngology Head and Neck Surgery, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 201620, China
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Lee JW, Lee IH, Watanabe H, Liu Y, Sawada K, Maekawa M, Uehara S, Kobayashi Y, Imai Y, Kong SW, Iimura T. Centrosome clustering control in osteoclasts through CCR5-mediated signaling. Sci Rep 2023; 13:20813. [PMID: 38012303 PMCID: PMC10681980 DOI: 10.1038/s41598-023-48140-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
Osteoclasts uniquely resorb calcified bone matrices. To exert their function, mature osteoclasts maintain the cellular polarity and directional vesicle trafficking to and from the resorbing bone surface. However, the regulatory mechanisms and pathophysiological relevance of these processes remain largely unexplored. Bone histomorphometric analyses in Ccr5-deficient mice showed abnormalities in the morphology and functional phenotype of their osteoclasts, compared to wild type mice. We observed disorganized clustering of nuclei, as well as centrosomes that organize the microtubule network, which was concomitant with impaired cathepsin K secretion in cultured Ccr5-deficient osteoclasts. Intriguingly, forced expression of constitutively active Rho or Rac restored these cytoskeletal phenotypes with recovery of cathepsin K secretion. Furthermore, a gene-disease enrichment analysis identified that PLEKHM1, a responsible gene for osteopetrosis, which regulates lysosomal trafficking in osteoclasts, was regulated by CCR5. These experimental results highlighted that CCR5-mediated signaling served as an intracellular organizer for centrosome clustering in osteoclasts, which was involved in the pathophysiology of bone metabolism.
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Affiliation(s)
- Ji-Won Lee
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, 060-8586, Japan.
- Department of Oral Molecular Microbiology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan.
| | - In-Hee Lee
- Computational Health and Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Haruhisa Watanabe
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, 060-8586, Japan
| | - Yunqing Liu
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, 060-8586, Japan
| | - Kazuaki Sawada
- NIKON SOLUTIONS CO., LTD., Oi Plant 6-3, Nishioi 1-Chome, Shinagawa-ku, Tokyo, Japan
| | - Masashi Maekawa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Shunsuke Uehara
- Department of Biochemistry, Matsumoto Dental University, Nagano, Japan
| | - Yasuhiro Kobayashi
- Division of Hard Tissue Research, Institute for Oral Science, Matsumoto Dental University, Nagano, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Sek Won Kong
- Computational Health and Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Tadahiro Iimura
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, 060-8586, Japan.
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34
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Tan JX, Finkel T. Lysosomes in senescence and aging. EMBO Rep 2023; 24:e57265. [PMID: 37811693 PMCID: PMC10626421 DOI: 10.15252/embr.202357265] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/08/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
Dysfunction of lysosomes, the primary hydrolytic organelles in animal cells, is frequently associated with aging and age-related diseases. At the cellular level, lysosomal dysfunction is strongly linked to cellular senescence or the induction of cell death pathways. However, the precise mechanisms by which lysosomal dysfunction participates in these various cellular or organismal phenotypes have remained elusive. The ability of lysosomes to degrade diverse macromolecules including damaged proteins and organelles puts lysosomes at the center of multiple cellular stress responses. Lysosomal activity is tightly regulated by many coordinated cellular processes including pathways that function inside and outside of the organelle. Here, we collectively classify these coordinated pathways as the lysosomal processing and adaptation system (LYPAS). We review evidence that the LYPAS is upregulated by diverse cellular stresses, its adaptability regulates senescence and cell death decisions, and it can form the basis for therapeutic manipulation for a wide range of age-related diseases and potentially for aging itself.
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Affiliation(s)
- Jay Xiaojun Tan
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPAUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Toren Finkel
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPAUSA
- Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPAUSA
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35
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Pierga A, Matusiak R, Cauhapé M, Branchu J, Danglot L, Boutry M, Darios F. Spatacsin regulates directionality of lysosome trafficking by promoting the degradation of its partner AP5Z1. PLoS Biol 2023; 21:e3002337. [PMID: 37871017 PMCID: PMC10621996 DOI: 10.1371/journal.pbio.3002337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 11/02/2023] [Accepted: 09/15/2023] [Indexed: 10/25/2023] Open
Abstract
The endoplasmic reticulum (ER) forms contacts with the lysosomal compartment, regulating lysosome positioning and motility. The movements of lysosomes are controlled by the attachment of molecular motors to their surface. However, the molecular mechanisms by which ER controls lysosome dynamics are still elusive. Here, using mouse brain extracts and mouse embryonic fibroblasts, we demonstrate that spatacsin is an ER-resident protein regulating the formation of tubular lysosomes, which are highly dynamic. Screening for spatacsin partners required for tubular lysosome formation showed spatacsin to act by regulating protein degradation. We demonstrate that spatacsin promotes the degradation of its partner AP5Z1, which regulates the relative amount of spastizin and AP5Z1 at lysosomes. Spastizin and AP5Z1 contribute to regulate tubular lysosome formation, as well as their trafficking by interacting with anterograde and retrograde motor proteins, kinesin KIF13A and dynein/dynactin subunit p150Glued, respectively. Ultimately, investigations in polarized mouse cortical neurons in culture demonstrated that spatacsin-regulated degradation of AP5Z1 controls the directionality of lysosomes trafficking. Collectively, our results identify spatacsin as a protein regulating the directionality of lysosome trafficking.
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Affiliation(s)
- Alexandre Pierga
- Sorbonne Université, Paris, France
- Paris Brain Institute, ICM, Paris, France
- Inserm, U1127, Paris, France
- CNRS, UMR 7225, Paris, France
| | - Raphaël Matusiak
- Sorbonne Université, Paris, France
- Paris Brain Institute, ICM, Paris, France
- Inserm, U1127, Paris, France
- CNRS, UMR 7225, Paris, France
| | - Margaux Cauhapé
- Sorbonne Université, Paris, France
- Paris Brain Institute, ICM, Paris, France
- Inserm, U1127, Paris, France
- CNRS, UMR 7225, Paris, France
| | - Julien Branchu
- Sorbonne Université, Paris, France
- Paris Brain Institute, ICM, Paris, France
- Inserm, U1127, Paris, France
- CNRS, UMR 7225, Paris, France
| | - Lydia Danglot
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Université Paris Cité, Paris, France
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Scientific director of NeurImag facility, Université Paris Cité, Paris, France
| | - Maxime Boutry
- Sorbonne Université, Paris, France
- Paris Brain Institute, ICM, Paris, France
- Inserm, U1127, Paris, France
- CNRS, UMR 7225, Paris, France
| | - Frédéric Darios
- Sorbonne Université, Paris, France
- Paris Brain Institute, ICM, Paris, France
- Inserm, U1127, Paris, France
- CNRS, UMR 7225, Paris, France
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Baumer Y, Singh K, Baez AS, Gutierrez-Huerta CA, Chen L, Igboko M, Turner BS, Yeboah JA, Reger RN, Ortiz-Whittingham LR, Bleck CK, Mitchell VM, Collins BS, Pirooznia M, Dagur PK, Allan DS, Muallem-Schwartz D, Childs RW, Powell-Wiley TM. Social Determinants modulate NK cell activity via obesity, LDL, and DUSP1 signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.556825. [PMID: 37745366 PMCID: PMC10515802 DOI: 10.1101/2023.09.12.556825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Adverse social determinants of health (aSDoH) are associated with obesity and related comorbidities like diabetes, cardiovascular disease, and cancer. Obesity is also associated with natural killer cell (NK) dysregulation, suggesting a potential mechanistic link. Therefore, we measured NK phenotypes and function in a cohort of African-American (AA) women from resource-limited neighborhoods. Obesity was associated with reduced NK cytotoxicity and a shift towards a regulatory phenotype. In vitro, LDL promoted NK dysfunction, implicating hyperlipidemia as a mediator of obesity-related immune dysregulation. Dual specific phosphatase 1 (DUSP1) was induced by LDL and was upregulated in NK cells from subjects with obesity, implicating DUSP1 in obesity-mediated NK dysfunction. In vitro, DUSP1 repressed LAMP1/CD107a, depleting NK cells of functional lysosomes to prevent degranulation and cytokine secretion. Together, these data provide novel mechanistic links between aSDoH, obesity, and immune dysregulation that could be leveraged to improve outcomes in marginalized populations.
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Affiliation(s)
- Yvonne Baumer
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Komudi Singh
- Bioinformatics and Computational Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew S. Baez
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christian A. Gutierrez-Huerta
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Long Chen
- Section of Transplantation Immunotherapy, Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Muna Igboko
- Section of Transplantation Immunotherapy, Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Briana S. Turner
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Josette A. Yeboah
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert N. Reger
- Section of Transplantation Immunotherapy, Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lola R. Ortiz-Whittingham
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher K.E. Bleck
- Electron Microscopy Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Valerie M. Mitchell
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Billy S. Collins
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Pradeep K. Dagur
- Flow Cytometry Core, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - David S.J. Allan
- Section of Transplantation Immunotherapy, Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Richard W. Childs
- Section of Transplantation Immunotherapy, Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tiffany M. Powell-Wiley
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Intramural Research Program, National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
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37
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Mutvei AP, Nagiec MJ, Blenis J. Balancing lysosome abundance in health and disease. Nat Cell Biol 2023; 25:1254-1264. [PMID: 37580388 DOI: 10.1038/s41556-023-01197-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/28/2023] [Indexed: 08/16/2023]
Abstract
Lysosomes are catabolic organelles that govern numerous cellular processes, including macromolecule degradation, nutrient signalling and ion homeostasis. Aberrant changes in lysosome abundance are implicated in human diseases. Here we outline the mechanisms of lysosome biogenesis and turnover, and discuss how changes in the lysosome pool impact physiological and pathophysiological processes.
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Affiliation(s)
- Anders P Mutvei
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Huddinge, Sweden.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| | - Michal J Nagiec
- Meyer Cancer Center and Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA
| | - John Blenis
- Meyer Cancer Center and Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA.
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38
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Dang TT, Kim MJ, Lee YY, Le HT, Kim KH, Nam S, Hyun SH, Kim HL, Chung SW, Chung HT, Jho EH, Yoshida H, Kim K, Park CY, Lee MS, Back SH. Phosphorylation of EIF2S1 (eukaryotic translation initiation factor 2 subunit alpha) is indispensable for nuclear translocation of TFEB and TFE3 during ER stress. Autophagy 2023; 19:2111-2142. [PMID: 36719671 PMCID: PMC10283430 DOI: 10.1080/15548627.2023.2173900] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Abstract
There are diverse links between macroautophagy/autophagy pathways and unfolded protein response (UPR) pathways under endoplasmic reticulum (ER) stress conditions to restore ER homeostasis. Phosphorylation of EIF2S1/eIF2α is an important mechanism that can regulate all three UPR pathways through transcriptional and translational reprogramming to maintain cellular homeostasis and overcome cellular stresses. In this study, to investigate the roles of EIF2S1 phosphorylation in regulation of autophagy during ER stress, we used EIF2S1 phosphorylation-deficient (A/A) cells in which residue 51 was mutated from serine to alanine. A/A cells exhibited defects in several steps of autophagic processes (such as autophagosome and autolysosome formation) that are regulated by the transcriptional activities of the autophagy master transcription factors TFEB and TFE3 under ER stress conditions. EIF2S1 phosphorylation was required for nuclear translocation of TFEB and TFE3 during ER stress. In addition, EIF2AK3/PERK, PPP3/calcineurin-mediated dephosphorylation of TFEB and TFE3, and YWHA/14-3-3 dissociation were required for their nuclear translocation, but were insufficient to induce their nuclear retention during ER stress. Overexpression of the activated ATF6/ATF6α form, XBP1s, and ATF4 differentially rescued defects of TFEB and TFE3 nuclear translocation in A/A cells during ER stress. Consequently, overexpression of the activated ATF6 or TFEB form more efficiently rescued autophagic defects, although XBP1s and ATF4 also displayed an ability to restore autophagy in A/A cells during ER stress. Our results suggest that EIF2S1 phosphorylation is important for autophagy and UPR pathways, to restore ER homeostasis and reveal how EIF2S1 phosphorylation connects UPR pathways to autophagy.Abbreviations: A/A: EIF2S1 phosphorylation-deficient; ACTB: actin beta; Ad-: adenovirus-; ATF6: activating transcription factor 6; ATZ: SERPINA1/α1-antitrypsin with an E342K (Z) mutation; Baf A1: bafilomycin A1; BSA: bovine serum albumin; CDK4: cyclin dependent kinase 4; CDK6: cyclin dependent kinase 6; CHX: cycloheximide; CLEAR: coordinated lysosomal expression and regulation; Co-IP: coimmunoprecipitation; CTSB: cathepsin B; CTSD: cathepsin D; CTSL: cathepsin L; DAPI: 4',6-diamidino-2-phenylindole dihydrochloride; DMEM: Dulbecco's modified Eagle's medium; DMSO: dimethyl sulfoxide; DTT: dithiothreitol; EBSS: Earle's Balanced Salt Solution; EGFP: enhanced green fluorescent protein; EIF2S1/eIF2α: eukaryotic translation initiation factor 2 subunit alpha; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERAD: endoplasmic reticulum-associated degradation; ERN1/IRE1α: endoplasmic reticulum to nucleus signaling 1; FBS: fetal bovine serum; gRNA: guide RNA; GSK3B/GSK3β: glycogen synthase kinase 3 beta; HA: hemagglutinin; Hep: immortalized hepatocyte; IF: immunofluorescence; IRES: internal ribosome entry site; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LMB: leptomycin B; LPS: lipopolysaccharide; MAP1LC3A/B/LC3A/B: microtubule associated protein 1 light chain 3 alpha/beta; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MEFs: mouse embryonic fibroblasts; MFI: mean fluorescence intensity; MTORC1: mechanistic target of rapamycin kinase complex 1; NES: nuclear export signal; NFE2L2/NRF2: NFE2 like bZIP transcription factor 2; OE: overexpression; PBS: phosphate-buffered saline; PLA: proximity ligation assay; PPP3/calcineurin: protein phosphatase 3; PTM: post-translational modification; SDS: sodium dodecyl sulfate; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SEM: standard error of the mean; TEM: transmission electron microscopy; TFE3: transcription factor E3; TFEB: transcription factor EB; TFs: transcription factors; Tg: thapsigargin; Tm: tunicamycin; UPR: unfolded protein response; WB: western blot; WT: wild-type; Xbp1s: spliced Xbp1; XPO1/CRM1: exportin 1.
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Affiliation(s)
- Thao Thi Dang
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
| | - Mi-Jeong Kim
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
| | - Yoon Young Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Korea
| | - Hien Thi Le
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
| | - Kook Hwan Kim
- Severance Biomedical Research Institute, Yonsei University College of Medicine, 03722, Seoul, Korea
| | - Somi Nam
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
| | - Seung Hwa Hyun
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
| | - Hong Lim Kim
- Integrative Research Support Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Su Wol Chung
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
| | - Hun Taeg Chung
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
| | - Eek-Hoon Jho
- Department of Life Science, University of Seoul, Seoul, Korea
| | - Hiderou Yoshida
- Department of Molecular Biochemistry, Graduate School of Life Science, University of Hyogo, 678-1297, Hyogo, Japan
| | - Kyoungmi Kim
- Department of Biomedical Sciences and Department of Physiology, Korea University College of Medicine, 02841, Seoul, Korea
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Korea
| | - Myung-Shik Lee
- Department of Integrated Biomedical Science & Division of Endocrinology, Department of Internal Medicine, SIMS (Soonchunhyang Institute of Medi-bio Science) & Soonchunhyang University Hospital, Soonchunhyang University, 31151, Cheonan, Korea
| | - Sung Hoon Back
- School of Biological Sciences, University of Ulsan, Ulsan, 44610, Korea
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Shariq M, Malik AA, Sheikh JA, Hasnain SE, Ehtesham NZ. Regulation of autophagy by SARS-CoV-2: The multifunctional contributions of ORF3a. J Med Virol 2023; 95:e28959. [PMID: 37485696 DOI: 10.1002/jmv.28959] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-1 (SARS-CoV-2) regulates autophagic flux by blocking the fusion of autophagosomes with lysosomes, causing the accumulation of membranous vesicles for replication. Multiple SARS-CoV-2 proteins regulate autophagy with significant roles attributed to ORF3a. Mechanistically, open reading frame 3a (ORF3a) forms a complex with UV radiation resistance associated, regulating the functions of the PIK3C3-1 and PIK3C3-2 lipid kinase complexes, thereby modulating autophagosome biogenesis. ORF3a sequesters VPS39 onto the late endosome/lysosome, inhibiting assembly of the soluble NSF attachement protein REceptor (SNARE) complex and preventing autolysosome formation. ORF3a promotes the interaction between BECN1 and HMGB1, inducing the assembly of PIK3CA kinases into the ER (endoplasmic reticulum) and activating reticulophagy, proinflammatory responses, and ER stress. ORF3a recruits BORCS6 and ARL8B to lysosomes, initiating the anterograde transport of the virus to the plasma membrane. ORF3a also activates the SNARE complex (STX4-SNAP23-VAMP7), inducing fusion of lysosomes with the plasma membrane for viral egress. These mechanistic details can provide multiple targets for inhibiting SARS-CoV-2 by developing host- or host-pathogen interface-based therapeutics.
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Affiliation(s)
- Mohd Shariq
- Inflammation Biology and Cell Signalling Laboratory, ICMR-National Institute of Pathology, New Delhi, India
| | - Asrar A Malik
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Javaid A Sheikh
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Nasreen Z Ehtesham
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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Shelke GV, Williamson CD, Jarnik M, Bonifacino JS. Inhibition of endolysosome fusion increases exosome secretion. J Cell Biol 2023; 222:e202209084. [PMID: 37213076 PMCID: PMC10202829 DOI: 10.1083/jcb.202209084] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/04/2023] [Accepted: 03/17/2023] [Indexed: 05/23/2023] Open
Abstract
Exosomes are small vesicles that are secreted from cells to dispose of undegraded materials and mediate intercellular communication. A major source of exosomes is intraluminal vesicles within multivesicular endosomes that undergo exocytic fusion with the plasma membrane. An alternative fate of multivesicular endosomes is fusion with lysosomes, resulting in degradation of the intraluminal vesicles. The factors that determine whether multivesicular endosomes fuse with the plasma membrane or with lysosomes are unknown. In this study, we show that impairment of endolysosomal fusion by disruption of a pathway involving the BLOC-one-related complex (BORC), the small GTPase ARL8, and the tethering factor HOPS increases exosome secretion by preventing the delivery of intraluminal vesicles to lysosomes. These findings demonstrate that endolysosomal fusion is a critical determinant of the amount of exosome secretion and suggest that suppression of the BORC-ARL8-HOPS pathway could be used to boost exosome yields in biotechnology applications.
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Affiliation(s)
- Ganesh Vilas Shelke
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D. Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michal Jarnik
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Juan S. Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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41
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McKee CA, Polino AJ, King MW, Musiek ES. Circadian clock protein BMAL1 broadly influences autophagy and endolysosomal function in astrocytes. Proc Natl Acad Sci U S A 2023; 120:e2220551120. [PMID: 37155839 PMCID: PMC10194014 DOI: 10.1073/pnas.2220551120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
An emerging role for the circadian clock in autophagy and lysosome function has opened new avenues for exploration in the field of neurodegeneration. The daily rhythms of circadian clock proteins may coordinate gene expression programs involved not only in daily rhythms but in many cellular processes. In the brain, astrocytes are critical for sensing and responding to extracellular cues to support neurons. The core clock protein BMAL1 serves as the primary positive circadian transcriptional regulator and its depletion in astrocytes not only disrupts circadian function but also leads to a unique cell-autonomous activation phenotype. We report here that astrocyte-specific deletion of Bmal1 influences endolysosome function, autophagy, and protein degradation dynamics. In vitro, Bmal1-deficient astrocytes exhibit increased endocytosis, lysosome-dependent protein cleavage, and accumulation of LAMP1- and RAB7-positive organelles. In vivo, astrocyte-specific Bmal1 knockout (aKO) brains show accumulation of autophagosome-like structures within astrocytes by electron microscopy. Transcriptional analysis of isolated astrocytes from young and aged Bmal1 aKO mice indicates broad dysregulation of pathways involved in lysosome function which occur independently of TFEB activation. Since a clear link has been established between neurodegeneration and endolysosome dysfunction over the course of aging, this work implicates BMAL1 as a key regulator of these crucial astrocyte functions in health and disease.
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Affiliation(s)
- Celia A. McKee
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Alexander J. Polino
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Melvin W. King
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Erik S. Musiek
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
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Grande V, Schuld J, van der Ven PFM, Gruss OJ, Fürst DO. Filamin-A-interacting protein 1 (FILIP1) is a dual compartment protein linking myofibrils and microtubules during myogenic differentiation and upon mechanical stress. Cell Tissue Res 2023:10.1007/s00441-023-03776-4. [PMID: 37178194 DOI: 10.1007/s00441-023-03776-4] [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: 02/02/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
Variations in the gene encoding filamin-A-interacting protein 1 (FILIP1) were identified to be associated with a combination of neurological and muscular symptoms. While FILIP1 was shown to regulate motility of brain ventricular zone cells, a process important for corticogenesis, the function of the protein in muscle cells has been less well characterized. The expression of FILIP1 in regenerating muscle fibres predicted a role in early muscle differentiation. Here we analysed expression and localization of FILIP1 and its binding partners filamin-C (FLNc) and microtubule plus-end-binding protein EB3 in differentiating cultured myotubes and adult skeletal muscle. Prior to the development of cross-striated myofibrils, FILIP1 is associated with microtubules and colocalizes with EB3. During further myofibril maturation its localization changes, and FILIP1 localizes to myofibrillar Z-discs together with the actin-binding protein FLNc. Forced contractions of myotubes by electrical pulse stimulation (EPS) induce focal disruptions in myofibrils and translocation of both proteins from Z-discs to these lesions, suggesting a role in induction and/or repair of these structures. The immediate proximity of tyrosylated, dynamic microtubules and EB3 to lesions implies that also these play a role in these processes. This implication is supported by the fact that in nocodazole-treated myotubes that lack functional microtubules, the number of lesions induced by EPS is significantly reduced. In summary, we here show that FILIP1 is a cytolinker protein that is associated with both microtubules and actin filaments, and might play a role in the assembly of myofibrils and their stabilization upon mechanical stress to protect them from damage.
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Affiliation(s)
- Valentina Grande
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany
| | - Julia Schuld
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany
| | - Peter F M van der Ven
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany
| | - Oliver J Gruss
- Institute of Genetics, University of Bonn, Karlrobert-Kreiten-Str. 13, 53115, Bonn, Germany
| | - Dieter O Fürst
- Institute for Cell Biology, University of Bonn, Ulrich-Haberland-Str. 61a, 53121, Bonn, Germany.
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43
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Herrejon Chavez F, Luo H, Cifani P, Pine A, Chu KL, Joshi S, Barin E, Schurer A, Chan M, Chang K, Han GYQ, Pierson AJ, Xiao M, Yang X, Kuehm LM, Hong Y, Nguyen DTT, Chiosis G, Kentsis A, Leslie C, Vu LP, Kharas MG. RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells. Nat Commun 2023; 14:2290. [PMID: 37085479 PMCID: PMC10121618 DOI: 10.1038/s41467-023-38001-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: 04/23/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Tissue homeostasis is maintained after stress by engaging and activating the hematopoietic stem and progenitor compartments in the blood. Hematopoietic stem cells (HSCs) are essential for long-term repopulation after secondary transplantation. Here, using a conditional knockout mouse model, we revealed that the RNA-binding protein SYNCRIP is required for maintenance of blood homeostasis especially after regenerative stress due to defects in HSCs and progenitors. Mechanistically, we find that SYNCRIP loss results in a failure to maintain proteome homeostasis that is essential for HSC maintenance. SYNCRIP depletion results in increased protein synthesis, a dysregulated epichaperome, an accumulation of misfolded proteins and induces endoplasmic reticulum stress. Additionally, we find that SYNCRIP is required for translation of CDC42 RHO-GTPase, and loss of SYNCRIP results in defects in polarity, asymmetric segregation, and dilution of unfolded proteins. Forced expression of CDC42 recovers polarity and in vitro replating activities of HSCs. Taken together, we uncovered a post-transcriptional regulatory program that safeguards HSC self-renewal capacity and blood homeostasis.
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Affiliation(s)
- Florisela Herrejon Chavez
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hanzhi Luo
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Cifani
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Alli Pine
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen L Chu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell School of Medical Sciences, New York, NY, USA
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ersilia Barin
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Program of the Weill Cornell Graduate School of Medicine Sciences, New York, NY, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mandy Chan
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn Chang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Grace Y Q Han
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aspen J Pierson
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Xiao
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yuning Hong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Diu T T Nguyen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
| | - Christina Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ly P Vu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Kounoupa Z, Tivodar S, Theodorakis K, Kyriakis D, Denaxa M, Karagogeos D. Rac1 and Rac3 GTPases and TPC2 are required for axonal outgrowth and migration of cortical interneurons. J Cell Sci 2023; 136:286920. [PMID: 36744839 DOI: 10.1242/jcs.260373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/31/2023] [Indexed: 02/07/2023] Open
Abstract
Rho GTPases, among them Rac1 and Rac3, are major transducers of extracellular signals and are involved in multiple cellular processes. In cortical interneurons, the neurons that control the balance between excitation and inhibition of cortical circuits, Rac1 and Rac3 are essential for their development. Ablation of both leads to a severe reduction in the numbers of mature interneurons found in the murine cortex, which is partially due to abnormal cell cycle progression of interneuron precursors and defective formation of growth cones in young neurons. Here, we present new evidence that upon Rac1 and Rac3 ablation, centrosome, Golgi complex and lysosome positioning is significantly perturbed, thus affecting both interneuron migration and axon growth. Moreover, for the first time, we provide evidence of altered expression and localization of the two-pore channel 2 (TPC2) voltage-gated ion channel that mediates Ca2+ release. Pharmacological inhibition of TPC2 negatively affected axonal growth and migration of interneurons. Our data, taken together, suggest that TPC2 contributes to the severe phenotype in axon growth initiation, extension and interneuron migration in the absence of Rac1 and Rac3.
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Affiliation(s)
- Zouzana Kounoupa
- Institute of Molecular Biology and Biotechnology (IMBB, FORTH), Heraklion 71110, Greece.,Department of Basic Science, Faculty of Medicine, University of Crete, Heraklion 71110, Greece
| | - Simona Tivodar
- Institute of Molecular Biology and Biotechnology (IMBB, FORTH), Heraklion 71110, Greece.,Department of Basic Science, Faculty of Medicine, University of Crete, Heraklion 71110, Greece
| | - Kostas Theodorakis
- Institute of Molecular Biology and Biotechnology (IMBB, FORTH), Heraklion 71110, Greece.,Department of Basic Science, Faculty of Medicine, University of Crete, Heraklion 71110, Greece
| | - Dimitrios Kyriakis
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Myrto Denaxa
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre 'Al. Fleming', Vari, 16672, Greece
| | - Domna Karagogeos
- Institute of Molecular Biology and Biotechnology (IMBB, FORTH), Heraklion 71110, Greece.,Department of Basic Science, Faculty of Medicine, University of Crete, Heraklion 71110, Greece
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45
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The role of lysosomes in metabolic and autoimmune diseases. Nat Rev Nephrol 2023; 19:366-383. [PMID: 36894628 DOI: 10.1038/s41581-023-00692-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 03/11/2023]
Abstract
Lysosomes are catabolic organelles that contribute to the degradation of intracellular constituents through autophagy and of extracellular components through endocytosis, phagocytosis and macropinocytosis. They also have roles in secretory mechanisms, the generation of extracellular vesicles and certain cell death pathways. These functions make lysosomes central organelles in cell homeostasis, metabolic regulation and responses to environment changes including nutrient stresses, endoplasmic reticulum stress and defects in proteostasis. Lysosomes also have important roles in inflammation, antigen presentation and the maintenance of long-lived immune cells. Their functions are tightly regulated by transcriptional modulation via TFEB and TFE3, as well as by major signalling pathways that lead to activation of mTORC1 and mTORC2, lysosome motility and fusion with other compartments. Lysosome dysfunction and alterations in autophagy processes have been identified in a wide variety of diseases, including autoimmune, metabolic and kidney diseases. Deregulation of autophagy can contribute to inflammation, and lysosomal defects in immune cells and/or kidney cells have been reported in inflammatory and autoimmune pathologies with kidney involvement. Defects in lysosomal activity have also been identified in several pathologies with disturbances in proteostasis, including autoimmune and metabolic diseases such as Parkinson disease, diabetes mellitus and lysosomal storage diseases. Targeting lysosomes is therefore a potential therapeutic strategy to regulate inflammation and metabolism in a variety of pathologies.
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46
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Zheng W, Chen Q, Liu H, Zeng L, Zhou Y, Liu X, Bai Y, Zhang J, Pan Y, Shao C. SDC1-dependent TGM2 determines radiosensitivity in glioblastoma by coordinating EPG5-mediated fusion of autophagosomes with lysosomes. Autophagy 2023; 19:839-857. [PMID: 35913916 PMCID: PMC9980589 DOI: 10.1080/15548627.2022.2105562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common brain malignancy insensitive to radiotherapy (RT). Although macroautophagy/autophagy was reported to be a fundamental factor prolonging the survival of tumors under radiotherapeutic stress, the autophagic biomarkers coordinated to radioresistance of GBM are still lacking in clinical practice. Here we established radioresistant GBM cells and identified their protein profiles using tandem mass tag (TMT) quantitative proteomic analysis. It was found that SDC1 and TGM2 proteins were overexpressed in radioresistant GBM cells and tissues and they contributed to the poor prognosis of RT. Knocking down SDC1 and TGM2 inhibited the fusion of autophagosomes with lysosomes and thus enhanced the radiosensitivity of GBM cells. After irradiation, TGM2 bound with SDC1 and transported it from the cell membrane to lysosomes, and then bound to LC3 through its two LC3-interacting regions (LIRs), coordinating the encounter between autophagosomes and lysosomes, which should be a prerequisite for lysosomal EPG5 to recognize LC3 and subsequently stabilize the STX17-SNAP29-VAMP8 QabcR SNARE complex assembly. Moreover, when combined with RT, cystamine dihydrochloride (a TGM2 inhibitor) extended the lifespan of GBM-bearing mice. Overall, our findings demonstrated the EPG5 tethering mode with SDC1 and TGM2 during the fusion of autophagosomes with lysosomes, providing new insights into the molecular mechanism and therapeutic target underlying radioresistant GBM.Abbreviations: BafA1: bafilomycin A1; CQ: chloroquine; Cys-D: cystamine dihydrochloride; EPG5: ectopic P-granules 5 autophagy tethering factor; GBM: glioblastoma multiforme; GFP: green fluorescent protein; LAMP2: lysosomal associated membrane protein 2; LIRs: LC3-interacting regions; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NC: negative control; RFP: red fluorescent protein; RT: radiotherapy; SDC1: syndecan 1; SNAP29: synaptosome associated protein 29; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TGM2: transglutaminase 2; TMT: tandem mass tag; VAMP8: vesicle associated membrane protein 8; WT: wild type.
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Affiliation(s)
- Wang Zheng
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qianping Chen
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongxia Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liang Zeng
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuchuan Zhou
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinglong Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Bai
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianghong Zhang
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Pan
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, China
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47
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Patra S, Patil S, Klionsky DJ, Bhutia SK. Lysosome signaling in cell survival and programmed cell death for cellular homeostasis. J Cell Physiol 2023; 238:287-305. [PMID: 36502521 DOI: 10.1002/jcp.30928] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/06/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Recent developments in lysosome biology have transformed our view of lysosomes from static garbage disposals that can also act as suicide bags to decidedly dynamic multirole adaptive operators of cellular homeostasis. Lysosome-governed signaling pathways, proteins, and transcription factors equilibrate the rate of catabolism and anabolism (autophagy to lysosomal biogenesis and metabolite pool maintenance) by sensing cellular metabolic status. Lysosomes also interact with other organelles by establishing contact sites through which they exchange cellular contents. Lysosomal function is critically assessed by lysosomal positioning and motility for cellular adaptation. In this setting, mechanistic target of rapamycin kinase (MTOR) is the chief architect of lysosomal signaling to control cellular homeostasis. Notably, lysosomes can orchestrate explicit cell death mechanisms, such as autophagic cell death and lysosomal membrane permeabilization-associated regulated necrotic cell death, to maintain cellular homeostasis. These lines of evidence emphasize that the lysosomes serve as a central signaling hub for cellular homeostasis.
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Affiliation(s)
- Srimanta Patra
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
| | - Shankargouda Patil
- Division of Oral Pathology, Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Daniel J Klionsky
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Sujit K Bhutia
- Cancer and Cell Death Laboratory, Department of Life Science, National Institute of Technology, Rourkela, Odisha, India
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48
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Qin Y, Medina MW. Mechanism of the Regulation of Plasma Cholesterol Levels by PI(4,5)P 2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:89-119. [PMID: 36988878 DOI: 10.1007/978-3-031-21547-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Elevated low-density lipoprotein (LDL) cholesterol (LDLc) is one of the most well-established risk factors for cardiovascular disease, while high levels of high-density lipoprotein (HDL) cholesterol (HDLc) have been associated with protection from cardiovascular disease. Cardiovascular disease remains one of the leading causes of death worldwide; thus it is important to understand mechanisms that impact LDLc and HDLc metabolism. In this chapter, we will discuss molecular processes by which phosphatidylinositol-(4,5)-bisphosphate, PI(4,5)P2, is thought to modulate LDLc or HDLc. Section 1 will provide an overview of cholesterol in the circulation, discussing processes that modulate the various forms of lipoproteins (LDL and HDL) carrying cholesterol. Section 2 will describe how a PI(4,5)P2 phosphatase, transmembrane protein 55B (TMEM55B), impacts circulating LDLc levels through its ability to regulate lysosomal decay of the low-density lipoprotein receptor (LDLR), the primary receptor for hepatic LDL uptake. Section 3 will discuss how PI(4,5)P2 interacts with apolipoprotein A-I (apoA1), the key apolipoprotein on HDL. In addition to direct mechanisms of PI(4,5)P2 action on circulating cholesterol, Sect. 4 will review how PI(4,5)P2 may indirectly impact LDLc and HDLc by affecting insulin action. Last, as cholesterol is controlled through intricate negative feedback loops, Sect. 5 will describe how PI(4,5)P2 is regulated by cholesterol.
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Affiliation(s)
- Yuanyuan Qin
- Department of Pediatrics, Division of Cardiology, University of California, San Francisco, Oakland, CA, USA
| | - Marisa W Medina
- Department of Pediatrics, Division of Cardiology, University of California, San Francisco, Oakland, CA, USA.
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Raas Q, Tawbeh A, Tahri-Joutey M, Gondcaille C, Keime C, Kaiser R, Trompier D, Nasser B, Leoni V, Bellanger E, Boussand M, Hamon Y, Benani A, Di Cara F, Truntzer C, Cherkaoui-Malki M, Andreoletti P, Savary S. Peroxisomal defects in microglial cells induce a disease-associated microglial signature. Front Mol Neurosci 2023; 16:1170313. [PMID: 37138705 PMCID: PMC10149961 DOI: 10.3389/fnmol.2023.1170313] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Microglial cells ensure essential roles in brain homeostasis. In pathological condition, microglia adopt a common signature, called disease-associated microglial (DAM) signature, characterized by the loss of homeostatic genes and the induction of disease-associated genes. In X-linked adrenoleukodystrophy (X-ALD), the most common peroxisomal disease, microglial defect has been shown to precede myelin degradation and may actively contribute to the neurodegenerative process. We previously established BV-2 microglial cell models bearing mutations in peroxisomal genes that recapitulate some of the hallmarks of the peroxisomal β-oxidation defects such as very long-chain fatty acid (VLCFA) accumulation. In these cell lines, we used RNA-sequencing and identified large-scale reprogramming for genes involved in lipid metabolism, immune response, cell signaling, lysosome and autophagy, as well as a DAM-like signature. We highlighted cholesterol accumulation in plasma membranes and observed autophagy patterns in the cell mutants. We confirmed the upregulation or downregulation at the protein level for a few selected genes that mostly corroborated our observations and clearly demonstrated increased expression and secretion of DAM proteins in the BV-2 mutant cells. In conclusion, the peroxisomal defects in microglial cells not only impact on VLCFA metabolism but also force microglial cells to adopt a pathological phenotype likely representing a key contributor to the pathogenesis of peroxisomal disorders.
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Affiliation(s)
- Quentin Raas
- Laboratoire Bio-PeroxIL EA7270, University of Bourgogne, Dijon, France
| | - Ali Tawbeh
- Laboratoire Bio-PeroxIL EA7270, University of Bourgogne, Dijon, France
| | - Mounia Tahri-Joutey
- Laboratoire Bio-PeroxIL EA7270, University of Bourgogne, Dijon, France
- Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Faculty of Sciences and Techniques, University Hassan I, Settat, Morocco
| | | | - Céline Keime
- Plateforme GenomEast, IGBMC, CNRS UMR 7104, Inserm U1258, University of Strasbourg, Illkirch, France
| | - Romain Kaiser
- Plateforme GenomEast, IGBMC, CNRS UMR 7104, Inserm U1258, University of Strasbourg, Illkirch, France
| | - Doriane Trompier
- Laboratoire Bio-PeroxIL EA7270, University of Bourgogne, Dijon, France
| | - Boubker Nasser
- Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Faculty of Sciences and Techniques, University Hassan I, Settat, Morocco
| | - Valerio Leoni
- Laboratory of Clinical Biochemistry, Hospital of Desio, ASST-Brianza and Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Emma Bellanger
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | - Maud Boussand
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | - Yannick Hamon
- Aix Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | - Alexandre Benani
- Centre des Sciences du Goût et de l’Alimentation, CNRS, INRAE, Institut Agro Dijon, University of Bourgogne Franche-Comté, Dijon, France
| | - Francesca Di Cara
- Department of Microbiology and Immunology, IWK Health Centre, Dalhousie University, Halifax, NS, Canada
| | - Caroline Truntzer
- Platform of Transfer in Biological Oncology, Georges François Leclerc Cancer Center–Unicancer, Dijon, France
| | | | | | - Stéphane Savary
- Laboratoire Bio-PeroxIL EA7270, University of Bourgogne, Dijon, France
- *Correspondence: Stéphane Savary,
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50
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Tapia D, Cavieres VA, Burgos PV, Cancino J. Impact of interorganelle coordination between the conventional early secretory pathway and autophagy in cellular homeostasis and stress response. Front Cell Dev Biol 2023; 11:1069256. [PMID: 37152281 PMCID: PMC10160633 DOI: 10.3389/fcell.2023.1069256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 04/07/2023] [Indexed: 05/09/2023] Open
Abstract
The conventional early secretory pathway and autophagy are two essential interconnected cellular processes that are crucial for maintaining cellular homeostasis. The conventional secretory pathway is an anabolic cellular process synthesizing and delivering proteins to distinct locations, including different organelles, the plasma membrane, and the extracellular media. On the other hand, autophagy is a catabolic cellular process that engulfs damaged organelles and aberrant cytosolic constituents into the double autophagosome membrane. After fusion with the lysosome and autolysosome formation, this process triggers digestion and recycling. A growing list of evidence indicates that these anabolic and catabolic processes are mutually regulated. While knowledge about the molecular actors involved in the coordination and functional cooperation between these two processes has increased over time, the mechanisms are still poorly understood. This review article summarized and discussed the most relevant evidence about the key molecular players implicated in the interorganelle crosstalk between the early secretory pathway and autophagy under normal and stressful conditions.
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Affiliation(s)
- Diego Tapia
- Cell Biology of Interorganelle Signaling Laboratory, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Viviana A. Cavieres
- Organelle Phagy Lab, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Patricia V. Burgos
- Organelle Phagy Lab, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Jorge Cancino
- Cell Biology of Interorganelle Signaling Laboratory, Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: Jorge Cancino,
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