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Hu Y, Liu Y, Zhu Q, Chen Y, Zeng Y. Identification of Novel Biomarkers Related to Vesicle Trafficking in Alzheimer's Disease Using Bioinformatics Approaches. Neurochem Res 2025; 50:157. [PMID: 40338387 DOI: 10.1007/s11064-025-04410-1] [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: 03/15/2025] [Revised: 04/23/2025] [Accepted: 04/28/2025] [Indexed: 05/09/2025]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder with complex pathogenesis. Vesicle trafficking abnormalities are closely associated with AD, making the identification of related biomarkers crucial. Chip data of AD were downloaded from the GEO database as training and test sets. Differentially expressed vesicle trafficking-related genes were analyzed, followed by construction of protein-protein interaction (PPI) networks, machine learning for important biomarkers identification, and various analyses including ROC curve analysis, and construction of regulatory networks. A total of 149 differentially expressed vesicle trafficking-related genes were identified. Through multiple analyses, 5 key genes (KIF22, ACTR10, TUBB2A, TUBA3C, and DCTN1) were obtained. Additionally, potential miRNA regulatory networks and candidate drugs were predicted, and AD subtypes were characterized.This study successfully identified novel biomarkers related to vesicle trafficking in AD, and these findings provide new insights into the role of intracellular transport dysfunction in AD pathogenesis.
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Affiliation(s)
- Yirong Hu
- Department of Neurology, Yichun People's Hospital, No. 1061 Jinxiu Avenue, Yiyang New District, Yichun, Jiangxi, 336000, China
| | - Yi Liu
- Cardiothoracic surgery, Yichun People's Hospital, Yichun, Jiangxi, 336000, China
| | - Qiuyan Zhu
- Department of Neurology, Yichun People's Hospital, No. 1061 Jinxiu Avenue, Yiyang New District, Yichun, Jiangxi, 336000, China
| | - Yong Chen
- Department of Neurology, Yichun People's Hospital, No. 1061 Jinxiu Avenue, Yiyang New District, Yichun, Jiangxi, 336000, China
| | - Ying Zeng
- Department of Neurology, Yichun People's Hospital, No. 1061 Jinxiu Avenue, Yiyang New District, Yichun, Jiangxi, 336000, China.
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2
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Zhang W, Zhou R, Lei X, Wang M, Duan Q, Miao Y, Zhang T, Li X, Zutong Z, Wang L, Jones OD, Xu M, Bryant J, Ma J, Liu Y, Xu X. Molecular mechanism on autophagy associated cardiovascular dysfunction in Drosophila melanogaster. Front Cell Dev Biol 2025; 13:1512341. [PMID: 40099194 PMCID: PMC11911378 DOI: 10.3389/fcell.2025.1512341] [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: 10/16/2024] [Accepted: 01/10/2025] [Indexed: 03/19/2025] Open
Abstract
As a highly conserved cellular process, autophagy has been the focus of extensive research due to its critical role in maintaining cellular homeostasis and its implications in cardiovascular pathogenesis. The decline in muscular function, along with the neuronal system, and increased sensitivity to stress have been recognized in multiple animal models. Autophagic defects in cardiovascular architecture and cellular dysfunction have been linked to both physiological and pathological conditions of the heart in mammals and Drosophila. In this review, we systematically analyze the autophagy-associated pathways in the hearts of fruit flies and aim to provide a comprehensive understanding for developing potential treatments for patients and effective strategies for agricultural applications. This analysis elucidates the molecular mechanisms of autophagy in cardiovascular function under both physiological and pathological conditions in Drosophila, offering significant insights into the development of cardiovascular diseases. The loss of key autophagy-associated proteins, including the transmembrane protein Atg9 and its partners Atg2 or Atg18, along with DmSestrin, leads to cardiac hypertrophy and structural abnormalities in Drosophila, resembling the age-dependent deterioration of cardiac function. Members of the autophagy-related (Atg) gene family, cellular or nuclear skeletal lamins, and the mechanistic or mammalian target of rapamycin (mTOR) signaling pathways are critically influential in heart function in Drosophila, with autophagy activation shown to suppress cardiac laminopathy. The mTORC1/C2 complexes, along with axis of Atg2-AMPK/Sirt1/PGC-1α pathway, are essential in the hearts of both mammals and fruit flies, governing cardiac development, growth, maturation, and the maintenance of cardiac homeostasis. The beneficial effects of several interventions that enhance cardiac function, including exercise and cold stress, can influence autophagy-dependent TOR activity of the serine/threonine protein kinase signaling in both mammals and Drosophila. Exercise has been shown to increase autophagy when it is deficient and to inhibit it when it is excessive, highlighting the dual role of autophagy in cardiac health. This review evaluates the functional significance of autophagy in the heart, particularly in the context of Drosophila, in relation to mTORC-associated autophagy and the axis of Atg2-AMPK/Sirt1/PGC-1α pathways. It systematically contrasts the molecular mechanisms underlying autophagy-related cardiovascular physiological and pathological conditions in both fruit flies and mammals. The evolutionary conservation of autophagy underscores the value of Drosophila as a model for understanding broader mechanisms of autophagy across species. This study not only deepens our understanding of autophagy's role in cardiovascular function but also provides a theoretical foundation for the potential application of autophagy in agricultural pest control.
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Affiliation(s)
- Wei Zhang
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Rong Zhou
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Xinjuan Lei
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Mofei Wang
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Qinchun Duan
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Yuanlin Miao
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Tingting Zhang
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Xinjie Li
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Zhang Zutong
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Liyang Wang
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
| | - Odell D Jones
- University Laboratory Animal Resources (ULAR), University of Pennsylvania School of Medicine, Philadelphia, PA, United States
| | - Mengmeng Xu
- Department of Pediatrics, Morgan Stanley Children's Hospital, Columbia University, New York, NY, United States
| | - Joseph Bryant
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jianjie Ma
- Division of Surgical Sciences, Department of Surgery, University of Virginia Medical School, Charlottesville, VA, United States
| | - Yingli Liu
- Department of Internal Medicine, University Hospital Shaanxi Normal University, Xi'an, China
| | - Xuehong Xu
- Laboratory of Cell Biology, Genetics and Developmental Biology, Shaanxi Normal University College of Life Sciences, Xi'an, China
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3
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Gavrilova A, Boström A, Korabel N, Fedotov S, Poulin GB, Allan VJ. The role of kinesin-1 in neuronal dense core vesicle transport, locomotion and lifespan regulation in C. elegans. J Cell Sci 2024; 137:jcs262148. [PMID: 39171448 PMCID: PMC11423817 DOI: 10.1242/jcs.262148] [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: 03/25/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024] Open
Abstract
Fast axonal transport is crucial for neuronal function and is driven by kinesins and cytoplasmic dynein. Here, we investigated the role of kinesin-1 in dense core vesicle (DCV) transport in C. elegans, using mutants in the kinesin light chains (klc-1 and klc-2) and the motor subunit (unc-116) expressing an ida-1::gfp transgene that labels DCVs. DCV transport in both directions was greatly impaired in an unc-116 mutant and had reduced velocity in a klc-2 mutant. In contrast, the speed of retrograde DCV transport was increased in a klc-1 mutant whereas anterograde transport was unaffected. We identified striking differences between the klc mutants in their effects on worm locomotion and responses to drugs affecting neuromuscular junction activity. We also determined lifespan, finding that unc-116 mutant was short-lived whereas the klc single mutant lifespan was wild type. The ida-1::gfp transgenic strain was also short-lived, but surprisingly, klc-1 and klc-2 extended the ida-1::gfp lifespan beyond that of wild type. Our findings suggest that kinesin-1 not only influences anterograde and retrograde DCV transport but is also involved in regulating lifespan and locomotion, with the two kinesin light chains playing distinct roles.
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Affiliation(s)
- Anna Gavrilova
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Rumford St, Manchester M13 9PT, UK
- Department of Mathematics, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Astrid Boström
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Rumford St, Manchester M13 9PT, UK
| | - Nickolay Korabel
- Department of Mathematics, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Sergei Fedotov
- Department of Mathematics, Faculty of Science and Engineering, The University of Manchester, Manchester M13 9PL, UK
| | - Gino B Poulin
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Rumford St, Manchester M13 9PT, UK
| | - Victoria J Allan
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, The Michael Smith Building, Rumford St, Manchester M13 9PT, UK
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Yeo JC, Tay FP, Bennion R, Loss O, Maignel J, Pons L, Foster K, Beard M, Bard F. Botulinum toxin intoxication requires retrograde transport and membrane translocation at the ER in RenVM neurons. eLife 2024; 12:RP92806. [PMID: 39196607 DOI: 10.7554/elife.92806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
Botulinum neurotoxin A (BoNT/A) is a highly potent proteolytic toxin specific for neurons with numerous clinical and cosmetic uses. After uptake at the synapse, the protein is proposed to translocate from synaptic vesicles to the cytosol through a self-formed channel. Surprisingly, we found that after intoxication proteolysis of a fluorescent reporter occurs in the neuron soma first and then centrifugally in neurites. To investigate the molecular mechanisms at play, we use a genome-wide siRNA screen in genetically engineered neurons and identify over three hundred genes. An organelle-specific split-mNG complementation indicates BoNT/A traffic from the synapse to the soma-localized Golgi in a retromer-dependent fashion. The toxin then moves to the ER and appears to require the Sec61 complex for retro-translocation to the cytosol. Our study identifies genes and trafficking processes hijacked by the toxin, revealing a new pathway mediating BoNT/A cellular toxicity.
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Affiliation(s)
- Jeremy C Yeo
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Felicia P Tay
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Rebecca Bennion
- Centre de Recherche en Cancérologie de Marseille, Aix Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes, Equipe Leader Fondation ARC 2021, Marseille, France
| | - Omar Loss
- Ipsen Bioinnovation, London, United Kingdom
| | | | | | | | | | - Frederic Bard
- Institute of Molecular and Cell Biology, Singapore, Singapore
- Centre de Recherche en Cancérologie de Marseille, Aix Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes, Equipe Leader Fondation ARC 2021, Marseille, France
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5
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Vicidomini R, Choudhury SD, Han TH, Nguyen TH, Nguyen P, Opazo F, Serpe M. Versatile nanobody-based approach to image, track and reconstitute functional Neurexin-1 in vivo. Nat Commun 2024; 15:6068. [PMID: 39025931 PMCID: PMC11258300 DOI: 10.1038/s41467-024-50462-2] [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: 11/22/2022] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Neurexins are key adhesion proteins that coordinate extracellular and intracellular synaptic components. Nonetheless, the low abundance of these multidomain proteins has complicated any localization and structure-function studies. Here we combine an ALFA tag (AT)/nanobody (NbALFA) tool with classic genetics, cell biology and electrophysiology to examine the distribution and function of the Drosophila Nrx-1 in vivo. We generate full-length and ΔPDZ ALFA-tagged Nrx-1 variants and find that the PDZ binding motif is key to Nrx-1 surface expression. A PDZ binding motif provided in trans, via genetically encoded cytosolic NbALFA-PDZ chimera, fully restores the synaptic localization and function of NrxΔPDZ-AT. Using cytosolic NbALFA-mScarlet intrabody, we achieve compartment-specific detection of endogenous Nrx-1, track live Nrx-1 transport along the motor neuron axons, and demonstrate that Nrx-1 co-migrates with Rab2-positive vesicles. Our findings illustrate the versatility of the ALFA system and pave the way towards dissecting functional domains of complex proteins in vivo.
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Affiliation(s)
- Rosario Vicidomini
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Saumitra Dey Choudhury
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
- Centralized Core Research Facility-Microscopy, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Tae Hee Han
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Tho Huu Nguyen
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Peter Nguyen
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Felipe Opazo
- Department of Neuro and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- NanoTag Biotechnologies GmbH, Göttingen, Germany
| | - Mihaela Serpe
- Section on Cellular Communication, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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Xiong GJ, Sheng ZH. Presynaptic perspective: Axonal transport defects in neurodevelopmental disorders. J Cell Biol 2024; 223:e202401145. [PMID: 38568173 PMCID: PMC10988239 DOI: 10.1083/jcb.202401145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Disruption of synapse assembly and maturation leads to a broad spectrum of neurodevelopmental disorders. Presynaptic proteins are largely synthesized in the soma, where they are packaged into precursor vesicles and transported into distal axons to ensure precise assembly and maintenance of presynapses. Due to their morphological features, neurons face challenges in the delivery of presynaptic cargos to nascent boutons. Thus, targeted axonal transport is vital to build functional synapses. A growing number of mutations in genes encoding the transport machinery have been linked to neurodevelopmental disorders. Emerging lines of evidence have started to uncover presynaptic mechanisms underlying axonal transport defects, thus broadening the view of neurodevelopmental disorders beyond postsynaptic mechanisms. In this review, we discuss presynaptic perspectives of neurodevelopmental disorders by focusing on impaired axonal transport and disturbed assembly and maintenance of presynapses. We also discuss potential strategies for restoring axonal transport as an early therapeutic intervention.
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Affiliation(s)
- Gui-Jing Xiong
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Zu-Hang Sheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
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7
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Zhu Y, Hui Q, Zhang Z, Fu H, Qin Y, Zhao Q, Li Q, Zhang J, Guo L, He W, Han C. Advancements in the study of synaptic plasticity and mitochondrial autophagy relationship. J Neurosci Res 2024; 102:e25309. [PMID: 38400573 DOI: 10.1002/jnr.25309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Synapses serve as the points of communication between neurons, consisting primarily of three components: the presynaptic membrane, synaptic cleft, and postsynaptic membrane. They transmit signals through the release and reception of neurotransmitters. Synaptic plasticity, the ability of synapses to undergo structural and functional changes, is influenced by proteins such as growth-associated proteins, synaptic vesicle proteins, postsynaptic density proteins, and neurotrophic growth factors. Furthermore, maintaining synaptic plasticity consumes more than half of the brain's energy, with a significant portion of this energy originating from ATP generated through mitochondrial energy metabolism. Consequently, the quantity, distribution, transport, and function of mitochondria impact the stability of brain energy metabolism, thereby participating in the regulation of fundamental processes in synaptic plasticity, including neuronal differentiation, neurite outgrowth, synapse formation, and neurotransmitter release. This article provides a comprehensive overview of the proteins associated with presynaptic plasticity, postsynaptic plasticity, and common factors between the two, as well as the relationship between mitochondrial energy metabolism and synaptic plasticity.
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Affiliation(s)
- Yousong Zhu
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
| | - Qinlong Hui
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
| | - Zheng Zhang
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
| | - Hao Fu
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
| | - Yali Qin
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
| | - Qiong Zhao
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
| | - Qinqing Li
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
| | - Junlong Zhang
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
| | - Lei Guo
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
| | - Wenbin He
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
| | - Cheng Han
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, Jinzhong, China
- National International Joint Research Center for Molecular Traditional Chinese Medicine, Jinzhong, China
- Basic Medical College of Shanxi University of Chinese Medicine, Jinzhong, China
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8
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Iannuccelli M, Vitriolo A, Licata L, Lo Surdo P, Contino S, Cheroni C, Capocefalo D, Castagnoli L, Testa G, Cesareni G, Perfetto L. Curation of causal interactions mediated by genes associated with autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders. Mol Psychiatry 2024; 29:186-196. [PMID: 38102483 PMCID: PMC11078740 DOI: 10.1038/s41380-023-02317-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 10/14/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
Autism spectrum disorder (ASD) comprises a large group of neurodevelopmental conditions featuring, over a wide range of severity and combinations, a core set of manifestations (restricted sociality, stereotyped behavior and language impairment) alongside various comorbidities. Common and rare variants in several hundreds of genes and regulatory regions have been implicated in the molecular pathogenesis of ASD along a range of causation evidence strength. Despite significant progress in elucidating the impact of few paradigmatic individual loci, such sheer complexity in the genetic architecture underlying ASD as a whole has hampered the identification of convergent actionable hubs hypothesized to relay between the vastness of risk alleles and the core phenotypes. In turn this has limited the development of strategies that can revert or ameliorate this condition, calling for a systems-level approach to probe the cross-talk of cooperating genes in terms of causal interaction networks in order to make convergences experimentally tractable and reveal their clinical actionability. As a first step in this direction, we have captured from the scientific literature information on the causal links between the genes whose variants have been associated with ASD and the whole human proteome. This information has been annotated in a computer readable format in the SIGNOR database and is made freely available in the resource website. To link this information to cell functions and phenotypes, we have developed graph algorithms that estimate the functional distance of any protein in the SIGNOR causal interactome to phenotypes and pathways. The main novelty of our approach resides in the possibility to explore the mechanistic links connecting the suggested gene-phenotype relations.
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Affiliation(s)
- Marta Iannuccelli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Vitriolo
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Prisca Lo Surdo
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Silvia Contino
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Cristina Cheroni
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Daniele Capocefalo
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy
| | - Giuseppe Testa
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122, Milan, Italy.
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy.
| | - Livia Perfetto
- Computational Biology Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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9
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Mulligan RJ, Winckler B. Regulation of Endosomal Trafficking by Rab7 and Its Effectors in Neurons: Clues from Charcot-Marie-Tooth 2B Disease. Biomolecules 2023; 13:1399. [PMID: 37759799 PMCID: PMC10527268 DOI: 10.3390/biom13091399] [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: 08/27/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Intracellular endosomal trafficking controls the balance between protein degradation and synthesis, i.e., proteostasis, but also many of the cellular signaling pathways that emanate from activated growth factor receptors after endocytosis. Endosomal trafficking, sorting, and motility are coordinated by the activity of small GTPases, including Rab proteins, whose function as molecular switches direct activity at endosomal membranes through effector proteins. Rab7 is particularly important in the coordination of the degradative functions of the pathway. Rab7 effectors control endosomal maturation and the properties of late endosomal and lysosomal compartments, such as coordination of recycling, motility, and fusion with downstream compartments. The spatiotemporal regulation of endosomal receptor trafficking is particularly challenging in neurons because of their enormous size, their distinct intracellular domains with unique requirements (dendrites vs. axons), and their long lifespans as postmitotic, differentiated cells. In Charcot-Marie-Tooth 2B disease (CMT2B), familial missense mutations in Rab7 cause alterations in GTPase cycling and trafficking, leading to an ulcero-mutilating peripheral neuropathy. The prevailing hypothesis to account for CMT2B pathologies is that CMT2B-associated Rab7 alleles alter endocytic trafficking of the neurotrophin NGF and its receptor TrkA and, thereby, disrupt normal trophic signaling in the peripheral nervous system, but other Rab7-dependent pathways are also impacted. Here, using TrkA as a prototypical endocytic cargo, we review physiologic Rab7 effector interactions and control in neurons. Since neurons are among the largest cells in the body, we place particular emphasis on the temporal and spatial regulation of endosomal sorting and trafficking in neuronal processes. We further discuss the current findings in CMT2B mutant Rab7 models, the impact of mutations on effector interactions or balance, and how this dysregulation may confer disease.
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Affiliation(s)
- Ryan J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, USA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA 22903, USA
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, USA
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10
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Petzoldt AG. Presynaptic Precursor Vesicles-Cargo, Biogenesis, and Kinesin-Based Transport across Species. Cells 2023; 12:2248. [PMID: 37759474 PMCID: PMC10527734 DOI: 10.3390/cells12182248] [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: 07/06/2023] [Revised: 08/11/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The faithful formation and, consequently, function of a synapse requires continuous and tightly controlled delivery of synaptic material. At the presynapse, a variety of proteins with unequal molecular properties are indispensable to compose and control the molecular machinery concerting neurotransmitter release through synaptic vesicle fusion with the presynaptic membrane. As presynaptic proteins are produced mainly in the neuronal soma, they are obliged to traffic along microtubules through the axon to reach the consuming presynapse. This anterograde transport is performed by highly specialised and diverse presynaptic precursor vesicles, membranous organelles able to transport as different proteins such as synaptic vesicle membrane and membrane-associated proteins, cytosolic active zone proteins, ion-channels, and presynaptic membrane proteins, coordinating synaptic vesicle exo- and endocytosis. This review aims to summarise and categorise the diverse and numerous findings describing presynaptic precursor cargo, mode of trafficking, kinesin-based axonal transport and the molecular mechanisms of presynaptic precursor vesicles biogenesis in both vertebrate and invertebrate model systems.
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Affiliation(s)
- Astrid G Petzoldt
- Institute for Biology and Genetics, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
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11
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Szinyákovics J, Keresztes F, Kiss EA, Falcsik G, Vellai T, Kovács T. Potent New Targets for Autophagy Enhancement to Delay Neuronal Ageing. Cells 2023; 12:1753. [PMID: 37443788 PMCID: PMC10341134 DOI: 10.3390/cells12131753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Autophagy is a lysosomal-dependent degradation process of eukaryotic cells responsible for breaking down unnecessary and damaged intracellular components. Autophagic activity gradually declines with age due to genetic control, and this change contributes to the accumulation of cellular damage at advanced ages, thereby causing cells to lose their functionality and viability. This could be particularly problematic in post-mitotic cells including neurons, the mass destruction of which leads to various neurodegenerative diseases. Here, we aim to uncover new regulatory points where autophagy could be specifically activated and test these potential drug targets in neurodegenerative disease models of Drosophila melanogaster. One possible way to activate autophagy is by enhancing autophagosome-lysosome fusion that creates the autolysosome in which the enzymatic degradation happens. The HOPS (homotypic fusion and protein sorting) and SNARE (Snap receptor) protein complexes regulate the fusion process. The HOPS complex forms a bridge between the lysosome and autophagosome with the assistance of small GTPase proteins. Thus, small GTPases are essential for autolysosome maturation, and among these proteins, Rab2 (Ras-associated binding 2), Rab7, and Arl8 (Arf-like 8) are required to degrade the autophagic cargo. For our experiments, we used Drosophila melanogaster as a model organism. Nerve-specific small GTPases were silenced and overexpressed. We examined the effects of these genetic interventions on lifespan, climbing ability, and autophagy. Finally, we also studied the activation of small GTPases in a Parkinson's disease model. Our results revealed that GTP-locked, constitutively active Rab2 (Rab2-CA) and Arl8 (Arl8-CA) expression reduces the levels of the autophagic substrate p62/Ref(2)P in neurons, extends lifespan, and improves the climbing ability of animals during ageing. However, Rab7-CA expression dramatically shortens lifespan and inhibits autophagy. Rab2-CA expression also increases lifespan in a Parkinson's disease model fly strain overexpressing human mutant (A53T) α-synuclein protein. Data provided by this study suggests that Rab2 and Arl8 serve as potential targets for autophagy enhancement in the Drosophila nervous system. In the future, it might be interesting to assess the effect of Rab2 and Arl8 coactivation on autophagy, and it would also be worthwhile to validate these findings in a mammalian model and human cell lines. Molecules that specifically inhibit Rab2 or Arl8 serve as potent drug candidates to modulate the activity of the autophagic process in treating neurodegenerative pathologies. In the future, it would be reasonable to investigate which GAP enzyme can inhibit Rab2 or Arl8 specifically, but not affect Rab7, with similar medical purposes.
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Affiliation(s)
- Janka Szinyákovics
- Department of Genetics, Eötvös Loránd University (ELTE), H-1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University (ELTE), Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
- ELKH-ELTE Genetic Research Group, H-1117 Budapest, Hungary
| | - Fanni Keresztes
- Department of Genetics, Eötvös Loránd University (ELTE), H-1117 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University (ELTE), Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Eszter Anna Kiss
- Department of Genetics, Eötvös Loránd University (ELTE), H-1117 Budapest, Hungary
| | - Gergő Falcsik
- Department of Genetics, Eötvös Loránd University (ELTE), H-1117 Budapest, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University (ELTE), H-1117 Budapest, Hungary
- ELKH-ELTE Genetic Research Group, H-1117 Budapest, Hungary
| | - Tibor Kovács
- Department of Genetics, Eötvös Loránd University (ELTE), H-1117 Budapest, Hungary
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12
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Kato Y, Shirai R, Ohbuchi K, Oizumi H, Yamamoto M, Miyata W, Iguchi T, Mimaki Y, Miyamoto Y, Yamauchi J. Hesperetin Ameliorates Inhibition of Neuronal and Oligodendroglial Cell Differentiation Phenotypes Induced by Knockdown of Rab2b, an Autism Spectrum Disorder-Associated Gene Product. Neurol Int 2023; 15:371-391. [PMID: 36976668 PMCID: PMC10057161 DOI: 10.3390/neurolint15010025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Autism spectrum disorder (ASD) is a central nervous system (CNS) neurodevelopmental disorder that includes autism, pervasive developmental disorder, and Asperger’s syndrome. ASD is characterized by repetitive behaviors and social communication deficits. ASD is thought to be a multifactorial disorder with a range of genetic and environmental factors/candidates. Among such factors is the rab2b gene, although it remains unclear how Rab2b itself is related to the CNS neuronal and glial developmental disorganization observed in ASD patients. Rab2 subfamily members regulate intracellular vesicle transport between the endoplasmic reticulum and the Golgi body. To the best of our knowledge, we are the first to report that Rab2b positively regulates neuronal and glial cell morphological differentiation. Knockdown of Rab2b inhibited morphological changes in N1E-115 cells, which are often used as the neuronal cell differentiation model. These changes were accomplished with decreased expression levels of marker proteins in neuronal cells. Similar results were obtained for FBD-102b cells, which are used as the model of oligodendroglial cell morphological differentiation. In contrast, knockdown of Rab2a, which is another Rab2 family member not known to be associated with ASD, affected only oligodendroglial and not neuronal morphological changes. In contrast, treatment with hesperetin, a citrus flavonoid with various cellular protective effects, in cells recovered the defective morphological changes induced by Rab2b knockdown. These results suggest that knockdown of Rab2b inhibits differentiation in neuronal and glial cells and may be associated with pathological cellular phenotypes in ASD and that hesperetin can recover their phenotypes at the in vitro level at least.
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Affiliation(s)
- Yukino Kato
- Department of Molecular Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Tokyo, Japan; (Y.K.); (W.M.); (Y.M.)
| | - Remina Shirai
- Department of Molecular Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Tokyo, Japan; (Y.K.); (W.M.); (Y.M.)
| | - Katsuya Ohbuchi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki 200-1192, Ibaraki, Japan; (K.O.); (H.O.); (M.Y.)
| | - Hiroaki Oizumi
- Tsumura Research Laboratories, Tsumura & Co., Inashiki 200-1192, Ibaraki, Japan; (K.O.); (H.O.); (M.Y.)
| | - Masahiro Yamamoto
- Tsumura Research Laboratories, Tsumura & Co., Inashiki 200-1192, Ibaraki, Japan; (K.O.); (H.O.); (M.Y.)
| | - Wakana Miyata
- Department of Molecular Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Tokyo, Japan; (Y.K.); (W.M.); (Y.M.)
| | - Tomoki Iguchi
- Department of Medicinal Pharmacognosy, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Tokyo, Japan; (T.I.); (Y.M.)
| | - Yoshihiro Mimaki
- Department of Medicinal Pharmacognosy, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Tokyo, Japan; (T.I.); (Y.M.)
| | - Yuki Miyamoto
- Department of Molecular Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Tokyo, Japan; (Y.K.); (W.M.); (Y.M.)
- Department of Pharmacology, National Research Institute for Child Health and Development, Setagaya 157-8535, Tokyo, Japan
| | - Junji Yamauchi
- Department of Molecular Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Tokyo, Japan; (Y.K.); (W.M.); (Y.M.)
- Department of Pharmacology, National Research Institute for Child Health and Development, Setagaya 157-8535, Tokyo, Japan
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Setagaya 156-8506, Tokyo, Japan
- Correspondence: ; Tel.: +81-42-676-7164; Fax: +81-42-676-8841
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13
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Liu Y, Shuai K, Sun Y, Zhu L, Wu XM. Advances in the study of axon-associated vesicles. Front Mol Neurosci 2022; 15:1045778. [PMID: 36545123 PMCID: PMC9760877 DOI: 10.3389/fnmol.2022.1045778] [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: 09/16/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
The central nervous system is the most important and difficult to study system in the human body and is known for its complex functions, components, and mechanisms. Neurons are the basic cellular units realizing neural functions. In neurons, vesicles are one of the critical pathways for intracellular material transport, linking information exchanges inside and outside cells. The axon is a vital part of neuron since electrical and molecular signals must be conducted through axons. Here, we describe and explore the formation, trafficking, and sorting of cellular vesicles within axons, as well as related-diseases and practical implications. Furthermore, with deepening of understanding and the development of new approaches, accumulating evidence proves that besides signal transmission between synapses, the material exchange and vesicular transmission between axons and extracellular environment are involved in physiological processes, and consequently to neural pathology. Recent studies have also paid attention to axonal vesicles and their physiological roles and pathological effects on axons themselves. Therefore, this review mainly focuses on these two key nodes to explain the role of intracellular vesicles and extracellular vesicles migrated from cells on axons and neurons, providing innovative strategy for future researches.
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Affiliation(s)
- Yanling Liu
- Institute of Special Environmental Medicine, Nantong University, Nantong, Jiangsu, China
| | - Ke Shuai
- Institute of Special Environmental Medicine, Nantong University, Nantong, Jiangsu, China
| | - Yiyan Sun
- Institute of Special Environmental Medicine, Nantong University, Nantong, Jiangsu, China
| | - Li Zhu
- Institute of Special Environmental Medicine, Nantong University, Nantong, Jiangsu, China,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China
| | - Xiao-Mei Wu
- Institute of Special Environmental Medicine, Nantong University, Nantong, Jiangsu, China,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, China,*Correspondence: Xiao-Mei Wu,
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14
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Sung H, Lloyd TE. Defective axonal transport of endo-lysosomes and dense core vesicles in a Drosophila model of C9-ALS/FTD. Traffic 2022; 23:430-441. [PMID: 35908282 DOI: 10.1111/tra.12861] [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: 02/10/2022] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 10/16/2022]
Abstract
A GGGGCC (G4 C2 ) repeat expansion in the C9orf72 gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although disruptions in axonal transport are implicated in the pathogenesis of multiple neurodegenerative diseases, the underlying mechanisms causing these defects remain unclear. Here, we performed live imaging of Drosophila motor neurons expressing expanded G4 C2 repeats in third-instar larvae and investigated the axonal transport of multiple organelles in vivo. Expression of expanded G4 C2 repeats causes an increase in static axonal lysosomes, while it impairs trafficking of late endosomes (LEs) and dense core vesicles (DCVs). Surprisingly, however, axonal transport of mitochondria is unaffected in motor axons expressing expanded G4 C2 repeats. Thus, our data indicate that expanded G4 C2 repeat expression differentially impacts axonal transport of vesicular organelles and mitochondria in Drosophila models of C9orf72-associated ALS/FTD. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hyun Sung
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD.,Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Thomas E Lloyd
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD.,Solomon H. Snyder Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD
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15
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Liu Y, Lu Y, Tang Z, Cao Y, Huang D, Wu F, Zhang Y, Li C, Chen G, Wang Q. Single-particle fluorescence tracking combined with TrackMate assay reveals highly heterogeneous and discontinuous lysosomal transport in freely orientated axons. Biotechnol J 2022; 17:e2200006. [PMID: 35765726 DOI: 10.1002/biot.202200006] [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: 01/04/2022] [Revised: 06/11/2022] [Accepted: 06/22/2022] [Indexed: 11/12/2022]
Abstract
Axonal transport plays a significant role in the establishment of neuronal polarity, axon growth, and synapse formation during neuronal development. The axon of a naturally growing neuron is a highly complex and multifurcated structure with a large number of bends and branches. Nowadays, the study of dynamic axonal transport in morphologically complex neurons is greatly limited by the technological barrier. Here, a sparse gene transfection strategy was developed to locate fluorescent mCherry in the lysosome of primary neurons, thus enabling us to track the lysosome-based axonal transport with a single-particle resolution. Thereby, several axonal transport models were observed, including the forward or backward transport model, stop-and-go model, repeated back-and-forth transport model, and cross-branch transport model. Then, the accurate single-particle velocity quantification by TrackMate revealed a highly heterogeneous and discontinuous transportation process of lysosome-based axonal transport in freely orientated axons. And, multiple physical factors, such as the axonal structure and the size of particles, were disclosed to affect the velocity of particle transporting in freely orientated axons. The combined single-particle fluorescence tracking and TrackMate assay can be served as a facile tool for evaluating axonal transport in neuronal development and axonal transport-related diseases.
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Affiliation(s)
- Yongyang Liu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Yaxin Lu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Zhiyong Tang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Yuheng Cao
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China.,School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Dehua Huang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Feng Wu
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Yejun Zhang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
| | - Chunyan Li
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Guangcun Chen
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Qiangbin Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China.,School of Physical Science and Technology, ShanghaiTech University, Shanghai, China.,College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, China
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16
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Selective motor activation in organelle transport along axons. Nat Rev Mol Cell Biol 2022; 23:699-714. [DOI: 10.1038/s41580-022-00491-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 12/17/2022]
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17
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Barral DC, Staiano L, Guimas Almeida C, Cutler DF, Eden ER, Futter CE, Galione A, Marques ARA, Medina DL, Napolitano G, Settembre C, Vieira OV, Aerts JMFG, Atakpa‐Adaji P, Bruno G, Capuozzo A, De Leonibus E, Di Malta C, Escrevente C, Esposito A, Grumati P, Hall MJ, Teodoro RO, Lopes SS, Luzio JP, Monfregola J, Montefusco S, Platt FM, Polishchuck R, De Risi M, Sambri I, Soldati C, Seabra MC. Current methods to analyze lysosome morphology, positioning, motility and function. Traffic 2022; 23:238-269. [PMID: 35343629 PMCID: PMC9323414 DOI: 10.1111/tra.12839] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of lysosomes more than 70 years ago, much has been learned about the functions of these organelles. Lysosomes were regarded as exclusively degradative organelles, but more recent research has shown that they play essential roles in several other cellular functions, such as nutrient sensing, intracellular signalling and metabolism. Methodological advances played a key part in generating our current knowledge about the biology of this multifaceted organelle. In this review, we cover current methods used to analyze lysosome morphology, positioning, motility and function. We highlight the principles behind these methods, the methodological strategies and their advantages and limitations. To extract accurate information and avoid misinterpretations, we discuss the best strategies to identify lysosomes and assess their characteristics and functions. With this review, we aim to stimulate an increase in the quantity and quality of research on lysosomes and further ground-breaking discoveries on an organelle that continues to surprise and excite cell biologists.
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Affiliation(s)
- Duarte C. Barral
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute for Genetic and Biomedical ResearchNational Research Council (CNR)MilanItaly
| | | | - Dan F. Cutler
- MRC Laboratory for Molecular Cell BiologyUniversity College LondonLondonUK
| | - Emily R. Eden
- University College London (UCL) Institute of OphthalmologyLondonUK
| | - Clare E. Futter
- University College London (UCL) Institute of OphthalmologyLondonUK
| | | | | | - Diego Luis Medina
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Clinical Medicine and Surgery DepartmentFederico II UniversityNaplesItaly
| | - Otília V. Vieira
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | | | | | - Gemma Bruno
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Elvira De Leonibus
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Institute of Biochemistry and Cell Biology, CNRRomeItaly
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | | | | | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Michael J. Hall
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Rita O. Teodoro
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - Susana S. Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
| | - J. Paul Luzio
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | | | | | | | | | - Maria De Risi
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Irene Sambri
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Chiara Soldati
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Miguel C. Seabra
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de LisboaLisbonPortugal
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18
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The biogenesis and secretion of exosomes and multivesicular bodies (MVBs): Intercellular shuttles and implications in human diseases. Genes Dis 2022. [PMID: 37492712 PMCID: PMC10363595 DOI: 10.1016/j.gendis.2022.03.021] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Exosomes carry and transmit signaling molecules used for intercellular communication. The generation and secretion of exosomes is a multistep interlocking process that allows simultaneous control of multiple regulatory sites. Protein molecules, mainly RAB GTPases, cytoskeletal proteins and soluble N-ethylmaleimide-sensitive fusion attachment protein receptor (SNARE), are specifically regulated in response to pathological conditions such as altered cellular microenvironment, stimulation by pathogenic factors, or gene mutation. This interferes with the smooth functioning of endocytosis, translocation, degradation, docking and fusion processes, leading to changes in the secretion of exosomes. Large numbers of secreted exosomes are disseminated by the flow of body fluids and absorbed by the recipient cells. By transmitting characteristic functional proteins and genetic information produced under disease conditions, exosomes can change the physiological state of the recipient cells and their microenvironment. The microenvironment, in turn, affects the occurrence and development of disease. Therefore, this review will discuss the mechanism by which exosome secretion is regulated in cells following the formation of mature secretory multivesicular bodies (MVBs). The overall aim is to find ways to eliminate disease-derived exosomes at their source, thereby providing an important new basis for the clinical treatment of disease.
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19
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Keren-Kaplan T, Sarić A, Ghosh S, Williamson CD, Jia R, Li Y, Bonifacino JS. RUFY3 and RUFY4 are ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin. Nat Commun 2022; 13:1506. [PMID: 35314674 PMCID: PMC8938451 DOI: 10.1038/s41467-022-28952-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
The small GTPase ARL8 associates with endolysosomes, leading to the recruitment of several effectors that couple endolysosomes to kinesins for anterograde transport along microtubules, and to tethering factors for eventual fusion with other organelles. Herein we report the identification of the RUN- and FYVE-domain-containing proteins RUFY3 and RUFY4 as ARL8 effectors that promote coupling of endolysosomes to dynein-dynactin for retrograde transport along microtubules. Using various methodologies, we find that RUFY3 and RUFY4 interact with both GTP-bound ARL8 and dynein-dynactin. In addition, we show that RUFY3 and RUFY4 promote concentration of endolysosomes in the juxtanuclear area of non-neuronal cells, and drive redistribution of endolysosomes from the axon to the soma in hippocampal neurons. The function of RUFY3 in retrograde transport contributes to the juxtanuclear redistribution of endolysosomes upon cytosol alkalinization. These studies thus identify RUFY3 and RUFY4 as ARL8-dependent, dynein-dynactin adaptors or regulators, and highlight the role of ARL8 in the control of both anterograde and retrograde endolysosome transport.
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Affiliation(s)
- Tal Keren-Kaplan
- 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
| | - Amra Sarić
- 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
| | - Saikat Ghosh
- 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
| | - Rui Jia
- 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
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, 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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20
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Ghosh S, Leng W, Wilsch-Bräuninger M, Barrera-Velázquez M, Léopold P, Eaton S. A local insulin reservoir in Drosophila alpha cell homologs ensures developmental progression under nutrient shortage. Curr Biol 2022; 32:1788-1797.e5. [PMID: 35316653 DOI: 10.1016/j.cub.2022.02.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/21/2021] [Accepted: 02/23/2022] [Indexed: 12/19/2022]
Abstract
Insulin/insulin-like growth factor (IGF) signaling (IIS) controls many aspects of development and physiology. In Drosophila, a conserved family of insulin-like peptides called Dilps is produced by brain neurosecretory cells, and it regulates organismal growth and developmental timing. To accomplish these systemic functions, the Dilps are secreted into the general circulation, and they signal to peripheral tissues in an endocrine fashion. Here, we describe the local uptake and storage of Dilps in the corpora cardiaca (CC), an endocrine organ composed of alpha cell homologs known to produce the glucagon-like adipokinetic hormone (AKH). We show that Dilp uptake by the CC relies on the expression of an IGF-binding protein called ImpL2. Following their uptake, immunogold staining demonstrates that Dilps are co-packaged with AKH in dense-core vesicles for secretion. In response to nutrient shortage, this specific Dilp reservoir is released and activates IIS in a paracrine manner in the prothoracic gland. This stimulates the production of the steroid hormone ecdysone and initiates entry into pupal development. We therefore uncover a sparing mechanism whereby insulin stores in CC serve to locally activate IIS and the production of ecdysone in the PG, accelerating developmental progression in adverse food conditions.
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Affiliation(s)
- Suhrid Ghosh
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany; Biotechnologisches Zentrum, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.
| | - Weihua Leng
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Michaela Wilsch-Bräuninger
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Mariana Barrera-Velázquez
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany; Undergraduate Program on Genomic Sciences, Centro de Ciencias Genómicas, UNAM, Cuernavaca, Morelos 62210, Mexico
| | - Pierre Léopold
- Institut Curie, PSL Research University, CNRS UMR3215, Inserm U934, 26 Rue d'Ulm, 75005 Paris, France.
| | - Suzanne Eaton
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany; Biotechnologisches Zentrum, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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21
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Roney JC, Cheng XT, Sheng ZH. Neuronal endolysosomal transport and lysosomal functionality in maintaining axonostasis. J Cell Biol 2022; 221:213000. [PMID: 35142819 PMCID: PMC8932522 DOI: 10.1083/jcb.202111077] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 02/08/2023] Open
Abstract
Lysosomes serve as degradation hubs for the turnover of endocytic and autophagic cargos, which is essential for neuron function and survival. Deficits in lysosome function result in progressive neurodegeneration in most lysosomal storage disorders and contribute to the pathogenesis of aging-related neurodegenerative diseases. Given their size and highly polarized morphology, neurons face exceptional challenges in maintaining cellular homeostasis in regions far removed from the cell body where mature lysosomes are enriched. Neurons therefore require coordinated bidirectional intracellular transport to sustain efficient clearance capacity in distal axonal regions. Emerging lines of evidence have started to uncover mechanisms and signaling pathways regulating endolysosome transport and maturation to maintain axonal homeostasis, or “axonostasis,” that is relevant to a range of neurologic disorders. In this review, we discuss recent advances in how axonal endolysosomal trafficking, distribution, and lysosomal functionality support neuronal health and become disrupted in several neurodegenerative diseases.
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Affiliation(s)
- Joseph C Roney
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Xiu-Tang Cheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Zu-Hang Sheng
- Synaptic Function Section, The Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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22
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Nassal JP, Murphy FH, Toonen RF, Verhage M. Differential axonal trafficking of Neuropeptide Y-, LAMP1-, and RAB7-tagged organelles in vivo. eLife 2022; 11:81721. [PMID: 36459486 PMCID: PMC9718525 DOI: 10.7554/elife.81721] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
Different organelles traveling through neurons exhibit distinct properties in vitro, but this has not been investigated in the intact mammalian brain. We established simultaneous dual color two-photon microscopy to visualize the trafficking of Neuropeptide Y (NPY)-, LAMP1-, and RAB7-tagged organelles in thalamocortical axons imaged in mouse cortex in vivo. This revealed that LAMP1- and RAB7-tagged organelles move significantly faster than NPY-tagged organelles in both anterograde and retrograde direction. NPY traveled more selectively in anterograde direction than LAMP1 and RAB7. By using a synapse marker and a calcium sensor, we further investigated the transport dynamics of NPY-tagged organelles. We found that these organelles slow down and pause at synapses. In contrast to previous in vitro studies, a significant increase of transport speed was observed after spontaneous activity and elevated calcium levels in vivo as well as electrically stimulated activity in acute brain slices. Together, we show a remarkable diversity in speeds and properties of three axonal organelle marker in vivo that differ from properties previously observed in vitro.
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Affiliation(s)
- Joris P Nassal
- Departments of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and VU University Medical CenterAmsterdamNetherlands
| | - Fiona H Murphy
- Departments of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and VU University Medical CenterAmsterdamNetherlands
| | - Ruud F Toonen
- Departments of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and VU University Medical CenterAmsterdamNetherlands
| | - Matthijs Verhage
- Departments of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research (CNCR), VU University Amsterdam and VU University Medical CenterAmsterdamNetherlands
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23
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Pinto C, Pérez V, Mella J, Albistur M, Caprile T, Bronfman FC, Henríquez JP. Transport and Secretion of the Wnt3 Ligand by Motor Neuron-like Cells and Developing Motor Neurons. Biomolecules 2021; 11:biom11121898. [PMID: 34944540 PMCID: PMC8699186 DOI: 10.3390/biom11121898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
The vertebrate neuromuscular junction (NMJ) is formed by a presynaptic motor nerve terminal and a postsynaptic muscle specialization. Cumulative evidence reveals that Wnt ligands secreted by the nerve terminal control crucial steps of NMJ synaptogenesis. For instance, the Wnt3 ligand is expressed by motor neurons at the time of NMJ formation and induces postsynaptic differentiation in recently formed muscle fibers. However, the behavior of presynaptic-derived Wnt ligands at the vertebrate NMJ has not been deeply analyzed. Here, we conducted overexpression experiments to study the expression, distribution, secretion, and function of Wnt3 by transfection of the motor neuron-like NSC-34 cell line and by in ovo electroporation of chick motor neurons. Our findings reveal that Wnt3 is transported along motor axons in vivo following a vesicular-like pattern and reaches the NMJ area. In vitro, we found that endogenous Wnt3 expression increases as the differentiation of NSC-34 cells proceeds. Although NSC-34 cells overexpressing Wnt3 do not modify their morphological differentiation towards a neuronal phenotype, they effectively induce acetylcholine receptor clustering on co-cultured myotubes. These findings support the notion that presynaptic Wnt3 is transported and secreted by motor neurons to induce postsynaptic differentiation in nascent NMJs.
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Affiliation(s)
- Cristina Pinto
- Neuromuscular Studies Laboratory (NeSt Lab), CMA Bio-Bio, Group for the Study of Developmental Processes (GDeP), Department of Cell Biology, Universidad de Concepción, Concepción 4070112, Chile; (C.P.); (V.P.); (J.M.); (M.A.)
| | - Viviana Pérez
- Neuromuscular Studies Laboratory (NeSt Lab), CMA Bio-Bio, Group for the Study of Developmental Processes (GDeP), Department of Cell Biology, Universidad de Concepción, Concepción 4070112, Chile; (C.P.); (V.P.); (J.M.); (M.A.)
| | - Jessica Mella
- Neuromuscular Studies Laboratory (NeSt Lab), CMA Bio-Bio, Group for the Study of Developmental Processes (GDeP), Department of Cell Biology, Universidad de Concepción, Concepción 4070112, Chile; (C.P.); (V.P.); (J.M.); (M.A.)
| | - Miguel Albistur
- Neuromuscular Studies Laboratory (NeSt Lab), CMA Bio-Bio, Group for the Study of Developmental Processes (GDeP), Department of Cell Biology, Universidad de Concepción, Concepción 4070112, Chile; (C.P.); (V.P.); (J.M.); (M.A.)
| | - Teresa Caprile
- Axon Guidance Laboratory, Group for the Study of Developmental Processes (GDeP), Department of Cell Biology, Universidad de Concepción, Concepción 4070112, Chile;
| | - Francisca C. Bronfman
- Institute of Biomedical Sciences (ICB), Faculty of Medicine and Faculty of Life Science, Universidad Andres Bello, Santiago 8320000, Chile;
- CARE Biomedical Research Center, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
| | - Juan Pablo Henríquez
- Neuromuscular Studies Laboratory (NeSt Lab), CMA Bio-Bio, Group for the Study of Developmental Processes (GDeP), Department of Cell Biology, Universidad de Concepción, Concepción 4070112, Chile; (C.P.); (V.P.); (J.M.); (M.A.)
- Correspondence: ; Tel.: +56-41-220-3492
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