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Liao Z, Tong B, Ke W, Yang C, Wu X, Lei M. Extracellular vesicles as carriers for mitochondria: Biological functions and clinical applications. Mitochondrion 2024; 78:101935. [PMID: 39002687 DOI: 10.1016/j.mito.2024.101935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/21/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
In recent years, research has increasingly focused on the biogenesis of extracellular vesicles (EVs) and the sorting mechanisms for their contents. Mitochondria can be selectively loaded into EVs, serving as a way to maintain cellular mitochondrial homeostasis. EV-mediated mitochondrial transfer has also been shown to greatly impact the function of target cells. Based on the mechanism of EV-mediated mitochondrial transfer, therapies can be developed to treat human diseases. This review summarizes the recent advances in the biogenesis and molecular composition of EVs. It also highlights the sorting and trafficking mechanisms of mitochondrial components into EVs. Furthermore, it explores the current role of EV-mediated mitochondrial transfer in the development of human diseases, as well as its diagnostic and therapeutic applications.
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Affiliation(s)
- Zhiwei Liao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bide Tong
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wencan Ke
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xinghuo Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Ming Lei
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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2
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Zanirati G, Dos Santos PG, Alcará AM, Bruzzo F, Ghilardi IM, Wietholter V, Xavier FAC, Gonçalves JIB, Marinowic D, Shetty AK, da Costa JC. Extracellular Vesicles: The Next Generation of Biomarkers and Treatment for Central Nervous System Diseases. Int J Mol Sci 2024; 25:7371. [PMID: 39000479 PMCID: PMC11242541 DOI: 10.3390/ijms25137371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 07/16/2024] Open
Abstract
It has been widely established that the characterization of extracellular vesicles (EVs), particularly small EVs (sEVs), shed by different cell types into biofluids, helps to identify biomarkers and therapeutic targets in neurological and neurodegenerative diseases. Recent studies are also exploring the efficacy of mesenchymal stem cell-derived extracellular vesicles naturally enriched with therapeutic microRNAs and proteins for treating various diseases. In addition, EVs released by various neural cells play a crucial function in the modulation of signal transmission in the brain in physiological conditions. However, in pathological conditions, such EVs can facilitate the spread of pathological proteins from one brain region to the other. On the other hand, the analysis of EVs in biofluids can identify sensitive biomarkers for diagnosis, prognosis, and disease progression. This review discusses the potential therapeutic use of stem cell-derived EVs in several central nervous system diseases. It lists their differences and similarities and confers various studies exploring EVs as biomarkers. Further advances in EV research in the coming years will likely lead to the routine use of EVs in therapeutic settings.
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Affiliation(s)
- Gabriele Zanirati
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Paula Gabrielli Dos Santos
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Allan Marinho Alcará
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Fernanda Bruzzo
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Isadora Machado Ghilardi
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Vinicius Wietholter
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Fernando Antônio Costa Xavier
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - João Ismael Budelon Gonçalves
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Daniel Marinowic
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
| | - Ashok K Shetty
- Institute for Regenerative Medicine, Department of Cell Biology and Genetics, Texas A&M University School of Medicine, College Station, TX 77807, USA
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre 90610-000, RS, Brazil
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Cappe B, Vandenabeele P, Riquet FB. A guide to the expanding field of extracellular vesicles and their release in regulated cell death programs. FEBS J 2024; 291:2068-2090. [PMID: 37872002 DOI: 10.1111/febs.16981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
Homeostasis disruption is visible at the molecular and cellular levels and may often lead to cell death. This vital process allows us to maintain the more extensive system's integrity by keeping the different features (genetic, metabolic, physiologic, and individual) intact. Interestingly, while cells can die in different manners, dying cells still communicate with their environment. This communication was, for a long time, perceived as only driven by the release of soluble factors. However, it has now been reconsidered with the increasing interest in extracellular vesicles (EVs), which are discovered to be released during different regulated cell death programs, with the observation of specific effects. EVs are game changers in the paradigm of cell-cell communication with tremendous implications in fundamental research with regard to noncell autonomous functions, as well as in biomarkers research, all of which are geared toward diagnostic and therapeutic purposes. This review is composed of two main parts. The first is a comprehensive presentation of the state of the art of the EV field at large. In the second part, we focus on EVs discovered to be released during different regulated cell death programs, also known as cell death EVs (cdEVs), and EV-associated specific effects on recipient cells in the context of cell death and inflammation/inflammatory responses.
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Affiliation(s)
- Benjamin Cappe
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research (IRC), Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research (IRC), Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, VIB-UGent Center for Inflammation Research (IRC), Belgium
- Department of Biomedical Molecular Biology, Ghent University, Belgium
- University of Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, France
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4
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Kaurani L. Clinical Insights into MicroRNAs in Depression: Bridging Molecular Discoveries and Therapeutic Potential. Int J Mol Sci 2024; 25:2866. [PMID: 38474112 DOI: 10.3390/ijms25052866] [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: 01/31/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Depression is a major contributor to the overall global burden of disease. The discovery of biomarkers for diagnosis or prediction of treatment responses and as therapeutic agents is a current priority. Previous studies have demonstrated the importance of short RNA molecules in the etiology of depression. The most extensively researched of these are microRNAs, a major component of cellular gene regulation and function. MicroRNAs function in a temporal and tissue-specific manner to regulate and modify the post-transcriptional expression of target mRNAs. They can also be shuttled as cargo of extracellular vesicles between the brain and the blood, thus informing about relevant mechanisms in the CNS through the periphery. In fact, studies have already shown that microRNAs identified peripherally are dysregulated in the pathological phenotypes seen in depression. Our article aims to review the existing evidence on microRNA dysregulation in depression and to summarize and evaluate the growing body of evidence for the use of microRNAs as a target for diagnostics and RNA-based therapies.
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Affiliation(s)
- Lalit Kaurani
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
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5
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La Marca JE, Aubrey BJ, Yang B, Chang C, Wang Z, Kueh A, Tai L, Wilcox S, Milla L, Heinzel S, Vremec D, Whelan L, König C, Kaloni D, Voss AK, Strasser A, Diepstraten ST, Herold MJ, Kelly GL. Genome-wide CRISPR screening identifies a role for ARRDC3 in TRP53-mediated responses. Cell Death Differ 2024; 31:150-158. [PMID: 38097622 PMCID: PMC10850147 DOI: 10.1038/s41418-023-01249-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 02/09/2024] Open
Abstract
Whole-genome screens using CRISPR technologies are powerful tools to identify novel tumour suppressors as well as factors that impact responses of malignant cells to anti-cancer agents. Applying this methodology to lymphoma cells, we conducted a genome-wide screen to identify novel inhibitors of tumour expansion that are induced by the tumour suppressor TRP53. We discovered that the absence of Arrestin domain containing 3 (ARRDC3) increases the survival and long-term competitiveness of MYC-driven lymphoma cells when treated with anti-cancer agents that activate TRP53. Deleting Arrdc3 in mice caused perinatal lethality due to various developmental abnormalities, including cardiac defects. Notably, the absence of ARRDC3 markedly accelerated MYC-driven lymphoma development. Thus, ARRDC3 is a new mediator of TRP53-mediated suppression of tumour expansion, and this discovery may open new avenues to harness this process for cancer therapy.
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Affiliation(s)
- John E La Marca
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Brandon J Aubrey
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Bruce Yang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Catherine Chang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Zilu Wang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Kueh
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Liz Milla
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Environomics Future Science Platform, Centre for Australian National Biodiversity Research, CSIRO, Canberra, Australia
| | - Susanne Heinzel
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David Vremec
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Lauren Whelan
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Christina König
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Deeksha Kaloni
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Sarah T Diepstraten
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia.
| | - Gemma L Kelly
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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Badosa C, Roldán M, Fernández-Irigoyen J, Santamaria E, Jimenez-Mallebrera C. Proteomic and functional characterisation of extracellular vesicles from collagen VI deficient human fibroblasts reveals a role in cell motility. Sci Rep 2023; 13:14622. [PMID: 37670049 PMCID: PMC10480450 DOI: 10.1038/s41598-023-41632-1] [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: 04/17/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
Extracellular vesicles (EVs) are key mediators of cell-to-cell communication. Their content reflects the state of diseased cells representing a window into disease progression. Collagen-VI Related Muscular Dystrophy (COL6-RD) is a multi-systemic disease involving different cell types. The role of EVs in this disease has not been explored. We compared by quantitative proteomics the protein cargo of EVs released from fibroblasts from patients with COL6-RD and controls. Isolated EVs contained a significant proportion of the most frequently reported proteins in EVs according to Exocarta and Vesiclepedia. We identified 67 differentially abundant proteins associated with vesicle transport and exocytosis, actin remodelling and the cytoskeleton, hemostasis and oxidative stress. Treatment of control fibroblasts with EVs from either patient or healthy fibroblasts altered significantly the motility of cells on a cell migration assay highlighting the functional relevance of EVs. In parallel, we analysed the secretome from the same cells and found a distinctly different set of 48 differentially abundant proteins related to extracellular matrix organisation and remodelling, growth factor response, RNA metabolism and the proteasome. The EVs and secretome sets of proteins only shared two identifiers indicating that the sorting of proteins towards EVs or the secretory pathway is tightly regulated for different functions.
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Affiliation(s)
- Carmen Badosa
- Neuromuscular Unit, Neuropaediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, PCCB, 3rd Floor, Calle Santa Rosa 39-57, 08950, Barcelona, Spain
| | - Mónica Roldán
- Confocal Microscopy and Cellular Imaging Unit, IPER, Department of Genetic and Molecular Medicine, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Proteomics Platform, Proteored-ISCIII, Clinical Neuroproteomics Unit, Navarrabiomed (CHN-UPNA-idiSNA), Pamplona, Spain
| | - Enrique Santamaria
- Proteomics Platform, Proteored-ISCIII, Clinical Neuroproteomics Unit, Navarrabiomed (CHN-UPNA-idiSNA), Pamplona, Spain
| | - Cecilia Jimenez-Mallebrera
- Neuromuscular Unit, Neuropaediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, PCCB, 3rd Floor, Calle Santa Rosa 39-57, 08950, Barcelona, Spain.
- Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.
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7
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Whitley JA, Cai H. Engineering extracellular vesicles to deliver CRISPR ribonucleoprotein for gene editing. J Extracell Vesicles 2023; 12:e12343. [PMID: 37723839 PMCID: PMC10507228 DOI: 10.1002/jev2.12343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 09/20/2023] Open
Abstract
Clustered regularly interspaced palindromic repeats (CRISPR) is a gene editing tool with tremendous therapeutic potential. Recently, ribonucleoprotein (RNP) complex-based CRISPR systems have gained momentum due to their reduction of off-target editing. This has coincided with the emergence of extracellular vesicles (EVs) as a therapeutic delivery vehicle due to its low immunogenicity and high capacity for manipulation. EVs are cell-derived membranous nanoparticles which mediate the intercellular transfer of molecular components. Current technologies achieve CRISPR RNP encapsulation into EVs through EVs biogenesis, thereby avoiding unnecessary physical, chemical or biological manipulations to the vesicles directly. Herein, we identify sixteen EVs-based CRISPR RNP encapsulation strategies, each with distinct genetic features to encapsulate CRISPR RNP. According to the molecular mechanism facilitating the encapsulation process, there are six strategies of encapsulating Cas9 RNP into virus-like particles based on genetic fusion, seven into EVs based on protein tethering, and three based on sgRNA-coupled encapsulation. Additionally, the incorporation of a targeting moiety to the EVs membrane surface through EVs biogenesis confers tropism and increases delivery efficiency to specific cell types. The targeting moieties include viral envelope proteins, recombinant proteins containing a ligand peptide, single-chain fragment variable (scFv) antibodies, and integrins. However, current strategies still have a number of limitations which prevent their use in clinical trials. Among those, the incorporation of viral proteins for encapsulation of Cas9 RNP have raised issues of biocompatibility due to host immune response. Future studies should focus on genetically engineering the EVs without viral proteins, enhancing EVs delivery specificity, and promoting EVs-based homology directed repair. Nevertheless, the integration of CRISPR RNP encapsulation and tropism technologies will provide strategies for the EVs-based delivery of CRISPR RNP in gene therapy and disease treatment.
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Affiliation(s)
- Joseph Andrew Whitley
- Department of Pharmaceutical and Biomedical SciencesCollege of PharmacyUniversity of GeorgiaAthensGeorgiaUSA
| | - Houjian Cai
- Department of Pharmaceutical and Biomedical SciencesCollege of PharmacyUniversity of GeorgiaAthensGeorgiaUSA
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Wei J, Ou Z, Tong B, Liao Z, Yang C. Engineered extracellular vesicles as therapeutics of degenerative orthopedic diseases. Front Bioeng Biotechnol 2023; 11:1162263. [PMID: 37362216 PMCID: PMC10289007 DOI: 10.3389/fbioe.2023.1162263] [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: 02/09/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Degenerative orthopedic diseases, as a global public health problem, have made serious negative impact on patients' quality of life and socio-economic burden. Traditional treatments, including chemical drugs and surgical treatments, have obvious side effects and unsatisfactory efficacy. Therefore, biological therapy has become the focus of researches on degenerative orthopedic diseases. Extracellular vesicles (EVs), with superior properties of immunoregulatory, growth support, and drug delivery capabilities, have emerged as a new cell-free strategy for the treatment of many diseases, including degenerative orthopedic diseases. An increasing number of studies have shown that EVs can be engineered through cargo loading, surface modification, and chemical synthesis to improve efficiency, specificity, and safety. Herein, a comprehensive overview of recent advances in engineering strategies and applications of engineered EVs as well as related researches in degenerative orthopedic diseases, including osteoarthritis (OA), osteoporosis (OP), intervertebral disc degeneration (IDD) and osteonecrosis of the femoral head (ONFH), is provided. In addition, we analyze the potential and challenges of applying engineered EVs to clinical practice.
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Affiliation(s)
| | | | | | | | - Cao Yang
- *Correspondence: Zhiwei Liao, ; Cao Yang,
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9
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Obeng EM, Fianu I, Danquah MK. Multivalent ACE2 engineering-A promising pathway for advanced coronavirus nanomedicine development. NANO TODAY 2022; 46:101580. [PMID: 35942040 PMCID: PMC9350675 DOI: 10.1016/j.nantod.2022.101580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/26/2022] [Accepted: 07/30/2022] [Indexed: 05/06/2023]
Abstract
The spread of coronavirus diseases has resulted in a clarion call to develop potent drugs and vaccines even as different strains appear beyond human prediction. An initial step that is integral to the viral entry into host cells results from an active-targeted interaction of the viral spike (S) proteins and the cell surface receptor, called angiotensin-converting enzyme 2 (ACE2). Thus, engineered ACE2 has been an interesting decoy inhibitor against emerging coronavirus infestation. This article discusses promising innovative ACE2 engineering pathways for current and emerging coronavirus therapeutic development. First, we provide a brief discussion of some ACE2-associated human coronaviruses and their cell invasion mechanism. Then, we describe and contrast the individual spike proteins and ACE2 receptor interactions, highlighting crucial hotspots across the ACE2-associated coronaviruses. Lastly, we address the importance of multivalency in ACE2 nanomedicine engineering and discuss novel approaches to develop and achieve multivalent therapeutic outcomes. Beyond coronaviruses, these approaches will serve as a paradigm to develop new and improved treatment technologies against pathogens that use ACE2 receptor for invasion.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, 615 McCallie Ave, Chattanooga, TN 37403, United States
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10
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Protein content of the Oenococcus oeni extracellular vesicles-enriched fraction. Food Microbiol 2022; 106:104038. [DOI: 10.1016/j.fm.2022.104038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/04/2022] [Accepted: 04/10/2022] [Indexed: 11/23/2022]
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11
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Aguirre RS, Kulkarni A, Becker MW, Lei X, Sarkar S, Ramanadham S, Phelps EA, Nakayasu ES, Sims EK, Mirmira RG. Extracellular vesicles in β cell biology: Role of lipids in vesicle biogenesis, cargo, and intercellular signaling. Mol Metab 2022; 63:101545. [PMID: 35817393 PMCID: PMC9294332 DOI: 10.1016/j.molmet.2022.101545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/03/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is a complex autoimmune disorder whose pathogenesis involves an intricate interplay between β cells of the pancreatic islet, other islet cells, and cells of the immune system. Direct intercellular communication within the islet occurs via cell surface proteins and indirect intercellular communication has traditionally been seen as occurring via secreted proteins (e.g., endocrine hormones and cytokines). However, recent literature suggests that extracellular vesicles (EVs) secreted by β cells constitute an additional and biologically important mechanism for transmitting signals to within the islet. SCOPE OF REVIEW This review summarizes the general mechanisms of EV formation, with a particular focus on how lipids and lipid signaling pathways influence their formation and cargo. We review the implications of EV release from β cells for T1D pathogenesis, how EVs and their cargo might be leveraged as biomarkers of this process, and how EVs might be engineered as a therapeutic candidate to counter T1D outcomes. MAJOR CONCLUSIONS Islet β cells have been viewed as initiators and propagators of the cellular circuit giving rise to autoimmunity in T1D. In this context, emerging literature suggests that EVs may represent a conduit for communication that holds more comprehensive messaging about the β cells from which they arise. As the field of EV biology advances, it opens the possibility that intervening with EV formation and cargo loading could be a novel disease-modifying approach in T1D.
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Affiliation(s)
| | - Abhishek Kulkarni
- Department of Medicine and the Kovler Diabetes Center, The University of Chicago, Chicago, IL, USA
| | - Matthew W. Becker
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Xiaoyong Lei
- Department of Cell, Developmental, and Integrative Biology & The Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sasanka Ramanadham
- Department of Cell, Developmental, and Integrative Biology & The Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Edward A. Phelps
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Emily K. Sims
- Department of Pediatrics and the Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Raghavendra G. Mirmira
- Department of Medicine and the Kovler Diabetes Center, The University of Chicago, Chicago, IL, USA,Corresponding author. 900 E. 57th St., KCBD 8130, Chicago, IL, 60637, USA.
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Meldolesi J. Unconventional Protein Secretion Dependent on Two Extracellular Vesicles: Exosomes and Ectosomes. Front Cell Dev Biol 2022; 10:877344. [PMID: 35756998 PMCID: PMC9218857 DOI: 10.3389/fcell.2022.877344] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
In addition to conventional protein secretion, dependent on the specific cleavage of signal sequences, proteins are secreted by other processes, all together called unconventional. Among the mechanisms operative in unconventional secretion, some are based on two families of extracellular vesicle (EVs), expressed by all types of cells: the exosomes (before secretion called ILVs) and ectosomes (average diameters ∼70 and ∼250 nm). The two types of EVs have been largely characterized by extensive studies. ILVs are assembled within endocytic vacuoles by inward budding of small membrane microdomains associated to cytosolic cargos including unconventional secretory proteins. The vacuoles containing ILVs are called multivesicular bodies (MVBs). Upon their possible molecular exchange with autophagosomes, MVBs undergo two alternative forms of fusion: 1. with lysosomes, followed by large digestion of their cargo molecules; and 2. with plasma membrane (called exocytosis), followed by extracellular diffusion of exosomes. The vesicles of the other type, the ectosomes, are differently assembled. Distinct plasma membrane rafts undergo rapid outward budding accompanied by accumulation of cytosolic/secretory cargo molecules, up to their sewing and pinching off. Both types of EV, released to the extracellular fluid in their complete forms including both membrane and cargo, start navigation for various times and distances, until their fusion with target cells. Release/navigation/fusion of EVs establish continuous tridimensional networks exchanging molecules, signals and information among cells. The proteins unconventionally secreted via EVs are a few hundreds. Some of them are functionally relevant (examples FADD, TNF, TACE), governing physiological processes and important diseases. Such proteins, at present intensely investigated, predict future discoveries and innovative developments, relevant for basic research and clinical practice.
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Affiliation(s)
- Jacopo Meldolesi
- The San Raffaele Institute, Vita-Salute San Raffaele University, Milan, Italy.,The CNR Institute of Neuroscience at Milano-Bicocca University, Milan, Italy
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13
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Campos-Mora M, De Solminihac J, Rojas C, Padilla C, Kurte M, Pacheco R, Kaehne T, Wyneken Ú, Pino-Lagos K. Neuropilin-1 is present on Foxp3+ T regulatory cell-derived small extracellular vesicles and mediates immunity against skin transplantation. J Extracell Vesicles 2022; 11:e12237. [PMID: 35676234 PMCID: PMC9177693 DOI: 10.1002/jev2.12237] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/16/2022] [Accepted: 05/27/2022] [Indexed: 12/14/2022] Open
Abstract
Among the mechanisms of suppression that T regulatory (Treg) cells exert to control the immune responses, the secretion of small extracellular vesicles (sEV) has been recently proposed as a novel contact‐independent immunomodulatory mechanism. Previous studies have demonstrated that Treg cells produce sEV, including exosomes, able to modulate the effector function of CD4+ T cells, and antigen presenting cells (APCs) such as dendritic cells (DCs) through the transfer of microRNA, cytokines, the production of adenosine, among others. Previously, we have demonstrated that Neuropilin‐1 (Nrp1) is required for Tregs‐mediated immunosuppression mainly by impacting on the phenotype and function of effector CD4+ T cells. Here, we show that Foxp3+ Treg cells secrete sEV, which bear Nrp1 in their membrane. These sEV modulate effector CD4+ T cell phenotype and proliferation in vitro in a Nrp1‐dependent manner. Proteomic analysis indicated that sEV obtained from wild type (wt) and Nrp1KO Treg cells differed in proteins related to immune tolerance, finding less representation of CD73 and Granzyme B in sEV obtained from Nrp1KO Treg cells. Likewise, we show that Nrp1 is required in Treg cell‐derived sEV for inducing skin transplantation tolerance, since a reduction in graft survival and an increase on M1/M2 ratio were found in animals treated with Nrp1KO Treg cell‐derived sEV. Altogether, this study describes for the first time that Treg cells secrete sEV containing Nrp1 and that this protein, among others, is necessary to promote transplantation tolerance in vivo via sEV local administration.
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Affiliation(s)
- Mauricio Campos-Mora
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile
| | - Javiera De Solminihac
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile
| | - Carolina Rojas
- Periodontal Biology Laboratory, Faculty of Dentistry, Universidad de Chile, Santiago, Chile
| | - Cristina Padilla
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile
| | - Mónica Kurte
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile
| | - Rodrigo Pacheco
- Laboratorio de Neuroinmunología, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Thilo Kaehne
- Institute of Experimental Medicine, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Úrsula Wyneken
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile
| | - Karina Pino-Lagos
- Centro de Investigación e Innovación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile
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14
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An Updated View of the Importance of Vesicular Trafficking and Transport and Their Role in Immune-Mediated Diseases: Potential Therapeutic Interventions. MEMBRANES 2022; 12:membranes12060552. [PMID: 35736259 PMCID: PMC9230090 DOI: 10.3390/membranes12060552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022]
Abstract
Cellular trafficking is the set of processes of distributing different macromolecules by the cell. This process is highly regulated in cells, involving a system of organelles (endomembranous system), among which are a great variety of vesicles that can be secreted from the cell, giving rise to different types of extracellular vesicles (EVs) that can be captured by other cells to modulate their function. The cells of the immune system are especially sensitive to this cellular traffic, producing and releasing different classes of EVs, especially in disease states. There is growing interest in this field due to the therapeutic and translational possibilities it offers. Different ways of taking advantage of the understanding of cell trafficking and EVs are being investigated, and their use as biomarkers or therapeutic targets is being investigated. The objective of this review is to collect the latest results and knowledge in this area with a specific focus on immune-mediated diseases. Although some promising results have been obtained, further knowledge is still needed, at both the basic and translational levels, to understand and modulate cellular traffic and EVs for better clinical management of these patients.
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15
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Abstract
Significance: Thioredoxin-interacting protein (Txnip) is an α-arrestin protein that acts as a cancer suppressor. Txnip is simultaneously a critical regulator of energy metabolism. Other alpha-arrestin proteins also play key roles in cell biology and cancer. Recent Advances: Txnip expression is regulated by multilayered mechanisms, including transcriptional regulation, microRNA, messenger RNA (mRNA) stabilization, and protein degradation. The Txnip-based connection between cancer and metabolism has been widely recognized. Meanwhile, new aspects are proposed for the mechanism of action of Txnip, including the regulation of RNA expression and autophagy. Arrestin domain containing 3 (ARRDC3), another α-arrestin protein, regulates endocytosis and signaling, whereas ARRDC1 and ARRDC4 regulate extracellular vesicle formation. Critical Issues: The mechanism of action of Txnip is yet to be elucidated. The regulation of intracellular protein trafficking by arrestin family proteins has opened an emerging field of biology and medical research, which needs to be examined further. Future Directions: A fundamental understanding of the mechanism of action of Txnip and other arrestin family members needs to be explored in the future to combat diseases such as cancer and diabetes. Antioxid. Redox Signal. 36, 1001-1022.
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Affiliation(s)
- Hiroshi Masutani
- Department of Clinical Laboratory Sciences, Tenri Health Care University, Tenri, Japan.,Department of Infection and Prevention, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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16
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α-Arrestins and Their Functions: From Yeast to Human Health. Int J Mol Sci 2022; 23:ijms23094988. [PMID: 35563378 PMCID: PMC9105457 DOI: 10.3390/ijms23094988] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/10/2022] Open
Abstract
α-Arrestins, also called arrestin-related trafficking adaptors (ARTs), constitute a large family of proteins conserved from yeast to humans. Despite their evolutionary precedence over their extensively studied relatives of the β-arrestin family, α-arrestins have been discovered relatively recently, and thus their properties are mostly unexplored. The predominant function of α-arrestins is the selective identification of membrane proteins for ubiquitination and degradation, which is an important element in maintaining membrane protein homeostasis as well as global cellular metabolisms. Among members of the arrestin clan, only α-arrestins possess PY motifs that allow canonical binding to WW domains of Rsp5/NEDD4 ubiquitin ligases and the subsequent ubiquitination of membrane proteins leading to their vacuolar/lysosomal degradation. The molecular mechanisms of the selective substrate’s targeting, function, and regulation of α-arrestins in response to different stimuli remain incompletely understood. Several functions of α-arrestins in animal models have been recently characterized, including redox homeostasis regulation, innate immune response regulation, and tumor suppression. However, the molecular mechanisms of α-arrestin regulation and substrate interactions are mainly based on observations from the yeast Saccharomyces cerevisiae model. Nonetheless, α-arrestins have been implicated in health disorders such as diabetes, cardiovascular diseases, neurodegenerative disorders, and tumor progression, placing them in the group of potential therapeutic targets.
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17
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Petrov PB, Awoniyi LO, Šuštar V, Balci MÖ, Mattila PK. AutoCoEv—A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution. Int J Mol Sci 2022; 23:ijms23063351. [PMID: 35328772 PMCID: PMC8952222 DOI: 10.3390/ijms23063351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Protein–protein interactions govern cellular processes via complex regulatory networks, which are still far from being understood. Thus, identifying and understanding connections between proteins can significantly facilitate our comprehension of the mechanistic principles of protein functions. Coevolution between proteins is a sign of functional communication and, as such, provides a powerful approach to search for novel direct or indirect molecular partners. However, an evolutionary analysis of large arrays of proteins in silico is a highly time-consuming effort that has limited the usage of this method for protein pairs or small protein groups. Here, we developed AutoCoEv, a user-friendly, open source, computational pipeline for the search of coevolution between a large number of proteins. By driving 15 individual programs, culminating in CAPS2 as the software for detecting coevolution, AutoCoEv achieves a seamless automation and parallelization of the workflow. Importantly, we provide a patch to the CAPS2 source code to strengthen its statistical output, allowing for multiple comparison corrections and an enhanced analysis of the results. We apply the pipeline to inspect coevolution among 324 proteins identified to be located at the vicinity of the lipid rafts of B lymphocytes. We successfully detected multiple coevolutionary relations between the proteins, predicting many novel partners and previously unidentified clusters of functionally related molecules. We conclude that AutoCoEv, can be used to predict functional interactions from large datasets in a time- and cost-efficient manner.
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Affiliation(s)
- Petar B. Petrov
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- Correspondence: (P.B.P.); (P.K.M.)
| | - Luqman O. Awoniyi
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Vid Šuštar
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
| | - M. Özge Balci
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Pieta K. Mattila
- MediCity Research Laboratories, Institute of Biomedicine, University of Turku, 20014 Turku, Finland; (L.O.A.); (V.Š.); (M.Ö.B.)
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- Correspondence: (P.B.P.); (P.K.M.)
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18
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van Niel G, Carter DRF, Clayton A, Lambert DW, Raposo G, Vader P. Challenges and directions in studying cell-cell communication by extracellular vesicles. Nat Rev Mol Cell Biol 2022; 23:369-382. [PMID: 35260831 DOI: 10.1038/s41580-022-00460-3] [Citation(s) in RCA: 415] [Impact Index Per Article: 207.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) are increasingly recognized as important mediators of intercellular communication. They have important roles in numerous physiological and pathological processes, and show considerable promise as novel biomarkers of disease, as therapeutic agents and as drug delivery vehicles. Intriguingly, however, understanding of the cellular and molecular mechanisms that govern the many observed functions of EVs remains far from comprehensive, at least partly due to technical challenges in working with these small messengers. Here, we highlight areas of consensus as well as contentious issues in our understanding of the intracellular and intercellular journey of EVs: from biogenesis, release and dynamics in the extracellular space, to interaction with and uptake by recipient cells. We define knowledge gaps, identify key questions and challenges, and make recommendations on how to address these.
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Affiliation(s)
- Guillaume van Niel
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris, France. .,GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
| | - David R F Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK.,Evox Therapeutics Limited, Oxford Science Park, Oxford, UK
| | - Aled Clayton
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Daniel W Lambert
- School of Clinical Dentistry, The University of Sheffield, Sheffield, UK.,Neuroscience Institute, The University of Sheffield, Sheffield, UK.,Healthy Lifespan Institute, The University of Sheffield, Sheffield, UK
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Pieter Vader
- CDL Research, University Medical Center Utrecht, Utrecht, Netherlands. .,Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht, Netherlands.
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19
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Farooq AU, Gembus K, Sandow JJ, Webb A, Mathivanan S, Manning JA, Shah SS, Foot NJ, Kumar S. K-29 linked ubiquitination of Arrdc4 regulates its function in extracellular vesicle biogenesis. J Extracell Vesicles 2022; 11:e12188. [PMID: 35106941 PMCID: PMC8807422 DOI: 10.1002/jev2.12188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 12/14/2021] [Accepted: 01/02/2022] [Indexed: 12/04/2022] Open
Abstract
Extracellular vesicles (EVs) are important mediators of intercellular communication. However, EV biogenesis remains poorly understood. We previously defined a role for Arrdc4 (Arrestin domain containing protein 4), an adaptor for Nedd4 family ubiquitin ligases, in the biogenesis of EVs. Here we report that ubiquitination of Arrdc4 is critical for its role in EV secretion. We identified five potential ubiquitinated lysine residues in Arrdc4 using mass spectrometry. By analysing Arrdc4 lysine mutants we discovered that lysine 270 (K270) is critical for Arrdc4 function in EV biogenesis. Arrdc4K270R mutation caused a decrease in the number of EVs released by cells compared to Arrdc4WT , and a reduction in trafficking of divalent metal transporter (DMT1) into EVs. Furthermore, we also observed a decrease in DMT1 activity and an increase in its intracellular degradation in the presence of Arrdc4K270R . K270 was found to be ubiquitinated with K-29 polyubiquitin chains by the ubiquitin ligase Nedd4-2. Thus, our results uncover a novel role of K-29 polyubiquitin chains in Arrdc4-mediated EV biogenesis and protein trafficking.
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Affiliation(s)
- Ammara Usman Farooq
- Centre for Cancer BiologyUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Kelly Gembus
- Centre for Cancer BiologyUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | | | - Andrew Webb
- Walter and Eliza Hall InstituteParkvilleVictoriaAustralia
| | - Suresh Mathivanan
- La Trobe Institute for Molecular ScienceLa Trobe UniversityVictoriaAustralia
| | - Jantina A. Manning
- Centre for Cancer BiologyUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Sonia S. Shah
- Centre for Cancer BiologyUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Natalie J. Foot
- Centre for Cancer BiologyUniversity of South AustraliaAdelaideSouth AustraliaAustralia
| | - Sharad Kumar
- Centre for Cancer BiologyUniversity of South AustraliaAdelaideSouth AustraliaAustralia
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20
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Biogenesis and Function of Extracellular Vesicles in Pathophysiological Processes Skeletal Muscle Atrophy. Biochem Pharmacol 2022; 198:114954. [DOI: 10.1016/j.bcp.2022.114954] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/13/2022]
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21
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Chen Y, Zhao Y, Yin Y, Jia X, Mao L. Mechanism of cargo sorting into small extracellular vesicles. Bioengineered 2021; 12:8186-8201. [PMID: 34661500 PMCID: PMC8806638 DOI: 10.1080/21655979.2021.1977767] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) are special membranous structures released by almost every cell type that carry and protect some biomolecules from being degraded. They transport important signaling molecules involved in cell communication, migration, and numerous physiological processes. EVs can be categorized into two main types according to their size: i) small extracellular vesicles (sEVs), such as exosomes (30-150 nm), released from the fusion of multivesicular bodies (MVBs) with the plasma membrane, and ii) large EVs, such as microvesicles (100-1000 nm). These are no longer considered a waste product of cells, but regulators of intercellular communication, as they can transport specific repertoires of cargos, such as proteins, lipids, and nucleic acids to receptor cells to achieve cell-to-cell communication. This indicates the existence of different mechanisms, which controls the cargos sorting into EVs. This review mainly gives a description about the biological roles of the cargo and the sorting mechanisms of sEVs, especially exosomes.
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Affiliation(s)
- Yiwen Chen
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yuxue Zhao
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yiqian Yin
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaonan Jia
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, The Affiliated People’s Hospital, Jiangsu University, Zhenjiang, China
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22
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Chen HM, MacDonald JA. Network analysis identifies DAPK3 as a potential biomarker for lymphatic invasion and colon adenocarcinoma prognosis. iScience 2021; 24:102831. [PMID: 34368650 PMCID: PMC8326195 DOI: 10.1016/j.isci.2021.102831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/04/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Colon adenocarcinoma is a prevalent malignancy with significant mortality. Hence, the identification of molecular biomarkers with prognostic significance is important for improved treatment and patient outcomes. Clinical traits and RNA-Seq of 551 patient samples in the UCSC Toil Recompute Compendium of The Cancer Genome Atlas TARGET and Genotype Tissue Expression project datasets (primary_site = colon) were used for weighted gene co-expression network analysis to reveal the association between gene networks and cancer cell invasion. One module, containing 151 genes, was significantly correlated with lymphatic invasion, a histopathological feature of higher risk colon cancer. DAPK3 (death-associated protein kinase 3) was identified as the pseudohub of the module. Gene ontology identified gene enrichment related to cytoskeletal organization and apoptotic signaling processes, suggesting modular involvement in tumor cell survival, migration, and epithelial-mesenchymal transformation. Although DAPK3 expression was reduced in patients with colon cancer, high expression of DAPK3 was significantly correlated with greater lymphatic invasion and poor overall survival. WCGNA reveals a gene module linked to lymphatic invasion in colon adenocarcinoma DAPK3 is a pseudohub gene with differential expression in colon cancer Gene ontology identified relationships to cytoskeletal organization and apoptosis DAPK3 was correlated with lymphatic invasion and poor overall survival
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Affiliation(s)
- Huey-Miin Chen
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
| | - Justin A MacDonald
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
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23
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Foot NJ, Gonzalez MB, Gembus K, Fonseka P, Sandow JJ, Nguyen TT, Tran D, Webb AI, Mathivanan S, Robker RL, Kumar S. Arrdc4-dependent extracellular vesicle biogenesis is required for sperm maturation. J Extracell Vesicles 2021; 10:e12113. [PMID: 34188787 PMCID: PMC8217992 DOI: 10.1002/jev2.12113] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 01/04/2023] Open
Abstract
Extracellular vesicles (EVs) are important players in cell to cell communication in reproductive systems. Notably, EVs have been found and characterized in the male reproductive tract, however, direct functional evidence for their importance in mediating sperm function is lacking. We have previously demonstrated that Arrdc4, a member of the α-arrestin protein family, is involved in extracellular vesicle biogenesis and release. Here we show that Arrdc4-mediated extracellular vesicle biogenesis is required for proper sperm function. Sperm from Arrdc4-/- mice develop normally through the testis but fail to acquire adequate motility and fertilization capabilities through the epididymis, as observed by reduced motility, premature acrosome reaction, reduction in zona pellucida binding and two-cell embryo production. We found a significant reduction in extracellular vesicle production by Arrdc4-/- epididymal epithelial cells, and further, supplementation of Arrdc4-/- sperm with additional vesicles dampened the acrosome reaction defect and restored zona pellucida binding. These results indicate that Arrdc4 is important for proper sperm maturation through the control of extracellular vesicle biogenesis.
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Affiliation(s)
- Natalie J. Foot
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
- School of MedicineRobinson Research InstituteUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Macarena B. Gonzalez
- School of MedicineRobinson Research InstituteUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Kelly Gembus
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
| | - Pamali Fonseka
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneVictoriaAustralia
| | - Jarrod J. Sandow
- Advanced Technology and Biology DivisionWalter and Eliza Hall InstituteParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVICAustralia
| | - Thuy Tien Nguyen
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
- School of Biological SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Diana Tran
- School of Chemical Engineering & Advanced MaterialsUniversity of AdelaideAdelaideSouth AustraliaAustralia
| | - Andrew I. Webb
- Advanced Technology and Biology DivisionWalter and Eliza Hall InstituteParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVICAustralia
| | - Suresh Mathivanan
- Department of Biochemistry and GeneticsLa Trobe Institute for Molecular SciencesLa Trobe UniversityMelbourneVictoriaAustralia
| | - Rebecca L. Robker
- School of MedicineRobinson Research InstituteUniversity of AdelaideAdelaideSouth AustraliaAustralia
- Department of Anatomy and Developmental BiologyBiomedicine Discovery InstituteMonash UniversityMelbourneVictoriaAustralia
| | - Sharad Kumar
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth AustraliaAustralia
- Faculty of Health and Medical SciencesUniversity of AdelaideAdelaideSouth AustraliaAustralia
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24
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Martínez-Greene JA, Hernández-Ortega K, Quiroz-Baez R, Resendis-Antonio O, Pichardo-Casas I, Sinclair DA, Budnik B, Hidalgo-Miranda A, Uribe-Querol E, Ramos-Godínez MDP, Martínez-Martínez E. Quantitative proteomic analysis of extracellular vesicle subgroups isolated by an optimized method combining polymer-based precipitation and size exclusion chromatography. J Extracell Vesicles 2021; 10:e12087. [PMID: 33936570 PMCID: PMC8077108 DOI: 10.1002/jev2.12087] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
The molecular characterization of extracellular vesicles (EVs) has revealed a great heterogeneity in their composition at a cellular and tissue level. Current isolation methods fail to efficiently separate EV subtypes for proteomic and functional analysis. The aim of this study was to develop a reproducible and scalable isolation workflow to increase the yield and purity of EV preparations. Through a combination of polymer‐based precipitation and size exclusion chromatography (Pre‐SEC), we analyzed two subsets of EVs based on their CD9, CD63 and CD81 content and elution time. EVs were characterized using transmission electron microscopy, nanoparticle tracking analysis, and Western blot assays. To evaluate differences in protein composition between the early‐ and late‐eluting EV fractions, we performed a quantitative proteomic analysis of MDA‐MB‐468‐derived EVs. We identified 286 exclusive proteins in early‐eluting fractions and 148 proteins with a differential concentration between early‐ and late‐eluting fractions. A density gradient analysis further revealed EV heterogeneity within each analyzed subgroup. Through a systems biology approach, we found significant interactions among proteins contained in the EVs which suggest the existence of functional clusters related to specific biological processes. The workflow presented here allows the study of EV subtypes within a single cell type and contributes to standardizing the EV isolation for functional studies.
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Affiliation(s)
- Juan A Martínez-Greene
- Laboratory of Cell Communication & Extracellular Vesicles Instituto Nacional de Medicina Genómica Mexico City Mexico
| | - Karina Hernández-Ortega
- Departamento de Biología Facultad de Química Universidad Nacional Autónoma de México Ciudad de México México
| | - Ricardo Quiroz-Baez
- Departamento de Investigación Básica Instituto Nacional de Geriatría Mexico City Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory Instituto Nacional de Medicina Genómica Mexico City Mexico.,Coordinación de la Investigación Científica-Red de Apoyo a la Investigación Universidad Nacional Autónoma de México Mexico City Mexico
| | - Israel Pichardo-Casas
- Department of Genetics Paul F. Glenn Labs for the Biology of Aging Harvard Medical School Boston Massachusetts USA
| | - David A Sinclair
- Department of Genetics Paul F. Glenn Labs for the Biology of Aging Harvard Medical School Boston Massachusetts USA
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory Division of Science Harvard University Cambridge Massachusetts USA
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer Instituto Nacional de Medicina Genómica Mexico City Mexico
| | - Eileen Uribe-Querol
- Laboratorio de Biología del Desarrollo División de Estudios de Posgrado e Investigación Facultad de Odontología Universidad Nacional Autónoma de México Mexico City Mexico
| | | | - Eduardo Martínez-Martínez
- Laboratory of Cell Communication & Extracellular Vesicles Instituto Nacional de Medicina Genómica Mexico City Mexico
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Abstract
Extracellular vesicles (EVs) refer to vesicles that are released by cells into the extracellular space. EVs mediate cell-to-cell communication via delivery of functional biomolecules between host and recipient cells. EVs can be categorised based on their mode of biogenesis and secretion and include apoptotic bodies, ectosomes or shedding microvesicles and exosomes among others. EVs have gained immense interest in recent years owing to their implications in pathophysiological conditions. Indeed, EVs have been proven useful in clinical applications as potential drug delivery vehicles and as source of diagnostic biomarkers. Despite the growing body of evidence supporting the clinical benefits, the processes involved in the biogenesis of EVs are poorly understood. Hence, it is critical to gain a deeper understanding of the underlying molecular machineries that ultimately govern the biogenesis and secretion of EVs. This chapter discusses the current knowledge on molecular mechanisms involved in the biogenesis of various subtypes of EVs.
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Affiliation(s)
- Taeyoung Kang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ishara Atukorala
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
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26
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Kahlhofer J, Leon S, Teis D, Schmidt O. The α-arrestin family of ubiquitin ligase adaptors links metabolism with selective endocytosis. Biol Cell 2021; 113:183-219. [PMID: 33314196 DOI: 10.1111/boc.202000137] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022]
Abstract
The regulation of nutrient uptake into cells is important, as it allows to either increase biomass for cell growth or to preserve homoeostasis. A key strategy to adjust cellular nutrient uptake is the reconfiguration of the nutrient transporter repertoire at the plasma membrane by the addition of nutrient transporters through the secretory pathway and by their endocytic removal. In this review, we focus on the mechanisms that regulate selective nutrient transporter endocytosis, which is mediated by the α-arrestin protein family. In the budding yeast Saccharomyces cerevisiae, 14 different α-arrestins (also named arrestin-related trafficking adaptors, ARTs) function as adaptors for the ubiquitin ligase Rsp5. They instruct Rsp5 to ubiquitinate subsets of nutrient transporters to orchestrate their endocytosis. The ART proteins are under multilevel control of the major nutrient sensing systems, including amino acid sensing by the general amino acid control and target of rapamycin pathways, and energy sensing by 5'-adenosine-monophosphate-dependent kinase. The function of the six human α-arrestins is comparably under-characterised. Here, we summarise the current knowledge about the function, regulation and substrates of yeast ARTs and human α-arrestins, and highlight emerging communalities and general principles.
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Affiliation(s)
- Jennifer Kahlhofer
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Sebastien Leon
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - David Teis
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
| | - Oliver Schmidt
- Institute for Cell Biology, Biocenter, Medical University Innsbruck, Innsbruck, Austria
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27
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Abstract
Since the discovery that extracellular vesicles (EVs) mediate intercellular communication, there is an exponential increase in the interest on EVs, especially in pathological settings. EVs are membranous vesicles that are secreted by various cell types and the release of EVs is conserved in every prokaryotic and eukaryotic organism tested to date. These vesicles were initially thought to be garbage disposal vehicles and subsequent studies over the past 4 decades have attributed several functional roles to EVs, some of which are critical for homeostasis. The molecular cargo of nucleic acids, proteins, lipids and metabolites packaged in EVs often mirror the host cells phenotypic status. EVs can be taken up by recipient cells and upon uptake, EVs through its molecular cargo, can induce a cascade of signal transduction events in recipient cells. EVs are categorised into several subtypes depending on their biogenesis and secretion. Due to several subtypes, differing sizes within a subtype and varying cargo, EVs are heterogenous in nature and the biophysical and biochemical properties of EVs often overlap between EV subtypes. Hence, it is important to be cautious when selecting the method of EV isolation and characterisation. This chapter provides a brief introduction to EVs and their subtypes.
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Affiliation(s)
- Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Akbar L Marzan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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28
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Atukorala I, Mathivanan S. The Role of Post-Translational Modifications in Targeting Protein Cargo to Extracellular Vesicles. Subcell Biochem 2021; 97:45-60. [PMID: 33779913 DOI: 10.1007/978-3-030-67171-6_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Extracellular vesicles (EVs) are naturally occurring nanoparticles that contain proteins and nucleic acids. It is speculated that cells release EVs loaded with a selective cargo of proteins through highly regulated processes. Several proteomic and biochemical studies have highlighted phosphorylated, glycosylated, ubiquitinated, SUMOylated, oxidated and palmitoylated proteins within the EVs. Emerging evidences suggest that post-translational modifications (PTMs) can regulate the sorting of specific proteins into EVs and such proteins with specific PTMs have also been identified in clinical samples. Hence, it has been proposed that EV proteins with PTMs could be used as potential biomarkers of disease conditions. Among the other cellular mechanisms, the endosomal sorting complex required for transport (ESCRT) is also implicated in cargo sorting into EVs. In this chapter, various PTMs that are shown to regulate protein cargo sorting into EVs will be discussed.
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Affiliation(s)
- Ishara Atukorala
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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29
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Kalra H, Gangoda L, Fonseka P, Chitti SV, Liem M, Keerthikumar S, Samuel M, Boukouris S, Al Saffar H, Collins C, Adda CG, Ang CS, Mathivanan S. Extracellular vesicles containing oncogenic mutant β-catenin activate Wnt signalling pathway in the recipient cells. J Extracell Vesicles 2019; 8:1690217. [PMID: 31819794 PMCID: PMC6883417 DOI: 10.1080/20013078.2019.1690217] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/01/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Mutations in β-catenin, especially at the residues critical for its degradation, render it constitutively active. Here, we show that mutant β-catenin can be transported via extracellular vesicles (EVs) and activate Wnt signalling pathway in the recipient cells. An integrative proteogenomic analysis identified the presence of mutated β-catenin in EVs secreted by colorectal cancer (CRC) cells. Follow-up experiments established that EVs released from LIM1215 CRC cells stimulated Wnt signalling pathway in the recipient cells with wild-type β-catenin. SILAC-based quantitative proteomics analysis confirmed the transfer of mutant β-catenin to the nucleus of the recipient cells. In vivo tracking of DiR-labelled EVs in mouse implanted with RKO CRC cells revealed its bio-distribution, confirmed the activation of Wnt signalling pathway in tumour cells and increased the tumour burden. Overall, for the first time, this study reveals that EVs can transfer mutant β-catenin to the recipient cells and promote cancer progression.
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Affiliation(s)
- Hina Kalra
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Lahiru Gangoda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Sai V Chitti
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Michael Liem
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.,Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Monisha Samuel
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Stephanie Boukouris
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Haidar Al Saffar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Christine Collins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Christopher G Adda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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30
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Russell AE, Sneider A, Witwer KW, Bergese P, Bhattacharyya SN, Cocks A, Cocucci E, Erdbrügger U, Falcon-Perez JM, Freeman DW, Gallagher TM, Hu S, Huang Y, Jay SM, Kano SI, Lavieu G, Leszczynska A, Llorente AM, Lu Q, Mahairaki V, Muth DC, Noren Hooten N, Ostrowski M, Prada I, Sahoo S, Schøyen TH, Sheng L, Tesch D, Van Niel G, Vandenbroucke RE, Verweij FJ, Villar AV, Wauben M, Wehman AM, Yin H, Carter DRF, Vader P. Biological membranes in EV biogenesis, stability, uptake, and cargo transfer: an ISEV position paper arising from the ISEV membranes and EVs workshop. J Extracell Vesicles 2019; 8:1684862. [PMID: 31762963 PMCID: PMC6853251 DOI: 10.1080/20013078.2019.1684862] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Paracrine and endocrine roles have increasingly been ascribed to extracellular vesicles (EVs) generated by multicellular organisms. Central to the biogenesis, content, and function of EVs are their delimiting lipid bilayer membranes. To evaluate research progress on membranes and EVs, the International Society for Extracellular Vesicles (ISEV) conducted a workshop in March 2018 in Baltimore, Maryland, USA, bringing together key opinion leaders and hands-on researchers who were selected on the basis of submitted applications. The workshop was accompanied by two scientific surveys and covered four broad topics: EV biogenesis and release; EV uptake and fusion; technologies and strategies used to study EV membranes; and EV transfer and functional assays. In this ISEV position paper, we synthesize the results of the workshop and the related surveys to outline important outstanding questions about EV membranes and describe areas of consensus. The workshop discussions and survey responses reveal that while much progress has been made in the field, there are still several concepts that divide opinion. Good consensus exists in some areas, including particular aspects of EV biogenesis, uptake and downstream signalling. Areas with little to no consensus include EV storage and stability, as well as whether and how EVs fuse with target cells. Further research is needed in these key areas, as a better understanding of membrane biology will contribute substantially towards advancing the field of extracellular vesicles.
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Affiliation(s)
- Ashley E. Russell
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexandra Sneider
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kenneth W. Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Paolo Bergese
- Department of Molecular and Translational Medicine, Università degli Studi di Brescia, CSGI and INSTM, Brescia, Italy
| | | | | | - Emanuele Cocucci
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | | | - Juan M. Falcon-Perez
- Exosomes laboratory and Metabolomics Platform, CIC bioGUNE, CIBERehd, Bizkaia, Spain
- IKERBASQUE, Basque Foundation for Science, Bizkaia, Spain
| | - David W. Freeman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Thomas M. Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Chicago, IL, USA
| | - Shuaishuai Hu
- School of Biological and Healthy Sciences, Technological University Dublin, Dublin, Ireland
| | - Yiyao Huang
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Clinical Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Steven M. Jay
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Shin-ichi Kano
- Department of Psychiatry and Behavioral Neurobiology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Gregory Lavieu
- INSERM U932, Institut Curie, PSL Research University, France
| | | | - Alicia M. Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences Departments of Environmental Health, Genetics & Complex Diseases Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vasiliki Mahairaki
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Dillon C. Muth
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Matias Ostrowski
- INBIRS Institute, UBA-CONICET School of Medicine University of Buenos Aires, Buenos Aires, Argentina
| | | | - Susmita Sahoo
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tine Hiorth Schøyen
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- K. G. Jebsen - Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Lifu Sheng
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Deanna Tesch
- Department of Chemistry, Shaw University, Raleigh, NC, USA
| | - Guillaume Van Niel
- Institute for Psychiatry and Neuroscience of Paris, INSERM U1266, Hopital Saint-Anne, Université Descartes, Paris, France
| | - Roosmarijn E. Vandenbroucke
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Frederik J. Verweij
- Institute for Psychiatry and Neuroscience of Paris, INSERM U1266, Hopital Saint-Anne, Université Descartes, Paris, France
| | - Ana V. Villar
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-Universidad de Cantabria and Departamento de Fisiología y Farmacología, Universidad de Cantabria, Santander, Spain
| | - Marca Wauben
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ann M. Wehman
- Rudolf Virchow Center, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | | | - Pieter Vader
- Laboratory of Clinical Chemistry and Haematology & Department of Experimental Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
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31
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What if? Mouse proteomics after gene inactivation. J Proteomics 2019; 199:102-122. [DOI: 10.1016/j.jprot.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 12/17/2022]
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32
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Fonseka P, Liem M, Ozcitti C, Adda CG, Ang CS, Mathivanan S. Exosomes from N-Myc amplified neuroblastoma cells induce migration and confer chemoresistance to non-N-Myc amplified cells: implications of intra-tumour heterogeneity. J Extracell Vesicles 2019; 8:1597614. [PMID: 31007876 PMCID: PMC6461098 DOI: 10.1080/20013078.2019.1597614] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 02/18/2019] [Accepted: 03/18/2019] [Indexed: 12/17/2022] Open
Abstract
Neuroblastoma accounts for 15% of childhood cancer mortality. Amplification of the oncogene N-Myc is a well-established poor prognostic marker for neuroblastoma. Whilst N-Myc amplification status strongly correlates with higher tumour aggression and resistance to treatment, the role of N-Myc in the aggressiveness of the disease is poorly understood. Exosomes are released by many cell types including cancer cells and are implicated as key mediators in cell-cell communication via the transfer of molecular cargo. Hence, characterising the exosomal protein components from N-Myc amplified and non-amplified neuroblastoma cells will improve our understanding on their role in the progression of neuroblastoma. In this study, a comparative proteomic analysis of exosomes isolated from cells with varying N-Myc amplification status was performed. Label-free quantitative proteomic profiling revealed 968 proteins that are differentially abundant in exosomes released by the neuroblastoma cells. Gene ontology-based analysis highlighted the enrichment of proteins involved in cell communication and signal transduction in N-Myc amplified exosomes. Treatment of SH-SY5Y cells with N-Myc amplified SK-N-BE2 cell-derived exosomes increased the migratory potential, colony forming abilities and conferred resistance to doxorubicin induced apoptosis. Incubation of exosomes from N-Myc knocked down SK-N-BE2 cells abolished the transfer of resistance to doxorubicin induced apoptosis. These findings suggest that exosomes could play a pivotal role in N-Myc-driven aggressive neuroblastoma and transfer of chemoresistance between cells. Abbreviations: RNA = ribonucleic acid; DNA = deoxyribonucleic acid; FCS = foetal calf serum; NTA = nanoparticle tracking analysis; LC-MS = liquid chromatography–mass spectrometry; KD = knockdown; LTQ = linear trap quadropole; TEM = transmission electron microscopy
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Affiliation(s)
- Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Michael Liem
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Cemil Ozcitti
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Christopher G Adda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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33
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Ticket to a bubble ride: Cargo sorting into exosomes and extracellular vesicles. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140203. [PMID: 30822540 DOI: 10.1016/j.bbapap.2019.02.005] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) are released by cells into the extracellular milieu to facilitate intercellular communication in both physiological and pathological condition. EVs contain selective repertoires of proteins, RNAs, lipids and metabolites that moderate signalling pathways in the recipient cells. The enrichment of a particular set of proteins or RNAs within the EVs highlights the existence of specific sorting mechanisms that orchestrate the selective packaging of the cargo. The molecular machinery of cargo sorting has remained obscure over the years and functional studies are required to understand this complex mechanism. In this article, we offer a brief overview of the molecular mechanisms that are known to regulate sorting of various molecules into EVs. We also discuss how different pathways of biogenesis alter the exosomal cargo as well and the implications of the cellular state on the content of the EVs. Understanding the sorting of exosomal cargo could further be exploited in clinical settings for targeted drug delivery and to block disease progression.
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34
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Jimenez L, Yu H, McKenzie AJ, Franklin JL, Patton JG, Liu Q, Weaver AM. Quantitative Proteomic Analysis of Small and Large Extracellular Vesicles (EVs) Reveals Enrichment of Adhesion Proteins in Small EVs. J Proteome Res 2019; 18:947-959. [PMID: 30608700 DOI: 10.1021/acs.jproteome.8b00647] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Extracellular vesicles (EVs) are important mediators of cell-cell communication due to their cargo content of proteins, lipids, and RNAs. We previously reported that small EVs (SEVs) called exosomes promote directed and random cell motility, invasion, and serum-independent growth. In contrast, larger EVs (LEVs) were not active in those assays, but might have unique functional properties. In order to identify protein cargos that may contribute to different functions of SEVs and LEVs, we used isobaric tags for relative and absolute quantitation (iTRAQ)-liquid chromatography (LC) tandem mass spectrometry (MS) on EVs isolated from a colon cancer cell line. Bioinformatics analyses revealed that SEVs are enriched in proteins associated with cell-cell junctions, cell-matrix adhesion, exosome biogenesis machinery, and various signaling pathways. In contrast, LEVs are enriched in proteins associated with ribosome and RNA biogenesis, processing, and metabolism. Western blot analysis of EVs purified from two different cancer cell types confirmed the enrichment of cell-matrix and cell-cell adhesion proteins in SEVs. Consistent with those data, we found that cells exhibit enhanced adhesion to surfaces coated with SEVs compared to an equal protein concentration of LEVs. These data suggest that a major function of SEVs is to promote cellular adhesion.
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Affiliation(s)
- Lizandra Jimenez
- Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States
| | - Hui Yu
- Department of Internal Medicine , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Andrew J McKenzie
- Sarah Cannon Research Institute , Nashville , Tennessee 37203 , United States
| | - Jeffrey L Franklin
- Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Department of Medicine , Vanderbilt University Medical Center , Nashville , Tennessee 37212 , United States
| | - James G Patton
- Department of Biological Sciences , Vanderbilt University School of Medicine , Nashville , Tennessee 37212 , United States
| | - Qi Liu
- Department of Biostatistics , Vanderbilt University Medical Center , Nashville , Tennessee 37232 , United States
| | - Alissa M Weaver
- Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Department of Pathology, Microbiology and Immunology , Vanderbilt University Medical Center , Nashville , Tennessee 37212 , United States
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35
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Emerging role of extracellular vesicles in mediating cancer cachexia. Biochem Soc Trans 2018; 46:1129-1136. [PMID: 30242118 DOI: 10.1042/bst20180213] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 12/19/2022]
Abstract
Cancer cachexia is a multifactorial metabolic syndrome characterized by the rapid loss of skeletal muscle mass with or without the loss of fat mass. Nearly 50-80% of all cancer patients' experience rapid weight loss results in ∼20% of cancer-related deaths. The levels of pro-inflammatory and pro-cachectic factors were significantly up-regulated in cachexia patients when compared with the patients who were without cachexia. It is becoming evident that these factors work synergistically to induce cancer cachexia. Extracellular vesicles (EVs) including exosomes and microvesicles are implicated in cell-cell communication, immune response, tissue repair, epigenetic regulation, and in various diseases including cancer. It has been reported that these EVs regulate cancer progression, metastasis, organotropism and chemoresistance. In recent times, the role of EVs in regulating cancer cachexia is beginning to unravel. The aim of this mini article is to review the recent knowledge gained in the field of EVs and cancer cachexia. Specifically, the role of tumour cell-derived EVs in promoting catabolism in distally located skeletal muscles and adipose tissue will be discussed.
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