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Chitti SV, Gummadi S, Kang T, Shahi S, Marzan AL, Nedeva C, Sanwlani R, Bramich K, Stewart S, Petrovska M, Sen B, Ozkan A, Akinfenwa M, Fonseka P, Mathivanan S. Vesiclepedia 2024: an extracellular vesicles and extracellular particles repository. Nucleic Acids Res 2024; 52:D1694-D1698. [PMID: 37953359 PMCID: PMC10767981 DOI: 10.1093/nar/gkad1007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
Vesiclepedia (http://www.microvesicles.org) is a free web-based compendium of DNA, RNA, proteins, lipids and metabolites that are detected or associated with extracellular vesicles (EVs) and extracellular particles (EPs). EVs are membranous vesicles that are secreted ubiquitously by cells from all domains of life from archaea to eukaryotes. In addition to EVs, it was reported recently that EPs like exomeres and supermeres are secreted by some mammalian cells. Both EVs and EPs contain proteins, nucleic acids, lipids and metabolites and has been proposed to be implicated in several key biological functions. Vesiclepedia catalogues proteins, DNA, RNA, lipids and metabolites from both published and unpublished studies. Currently, Vesiclepedia contains data obtained from 3533 EV studies, 50 550 RNA entries, 566 911 protein entries, 3839 lipid entries, 192 metabolite and 167 DNA entries. Quantitative data for 62 822 entries from 47 EV studies is available in Vesiclepedia. The datasets available in Vesiclepedia can be downloaded as tab-delimited files or accessible through the FunRich-based Vesiclepedia plugin.
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Affiliation(s)
- Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Sanjay Shahi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Akbar L Marzan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Christina Nedeva
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Rahul Sanwlani
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Kyle Bramich
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Sarah Stewart
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Monika Petrovska
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Biswadeep Sen
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alper Ozkan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Maria Akinfenwa
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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Anand S, Nedeva C, Chitti SV, Fonseka P, Kang T, Gangoda L, Tabassum NI, Abdirahman S, Arumugam TV, Putoczki TL, Kumar S, Mathivanan S. The E3 ubiquitin ligase NEDD4 regulates chemoresistance to 5-fluorouracil in colorectal cancer cells by altering JNK signalling. Cell Death Dis 2023; 14:828. [PMID: 38097550 PMCID: PMC10721789 DOI: 10.1038/s41419-023-06349-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/12/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths. Though chemotherapy is the main treatment option for advanced CRC, patients invariably acquire resistance to chemotherapeutic drugs and fail to respond to the therapy. Although understanding the mechanisms regulating chemoresistance has been a focus of intense research to manage this challenge, the pathways governing resistance to drugs are poorly understood. In this study, we provide evidence for the role of ubiquitin ligase NEDD4 in resistance developed against the most commonly used CRC chemotherapeutic drug 5-fluorouracil (5-FU). A marked reduction in NEDD4 protein abundance was observed in a panel of CRC cell lines and patient-derived xenograft samples that were resistant to 5-FU. Knockout of NEDD4 in CRC cells protected them from 5-FU-mediated apoptosis but not oxaliplatin or irinotecan. Furthermore, NEDD4 depletion in CRC cells reduced proliferation, colony-forming abilities and tumour growth in mice. Follow-up biochemical analysis highlighted the inhibition of the JNK signalling pathway in NEDD4-deficient cells. Treatment with the JNK activator hesperidin in NEDD4 knockout cells sensitised the CRC cells against 5-FU. Overall, we show that NEDD4 regulates cell proliferation, colony formation, tumour growth and 5-FU chemoresistance in CRC cells.
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Affiliation(s)
- Sushma Anand
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Christina Nedeva
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Lahiru Gangoda
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Nishat I Tabassum
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Australia
| | - Suad Abdirahman
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3052, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3052, Australia
| | - Thiruma V Arumugam
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Australia
| | - Tracy L Putoczki
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5001, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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Marzan AL, Chitti SV, Gummadi S, Kang T, Ang CS, Mathivanan S. Proteomics analysis of C2C12 myotubes treated with atrophy inducing cancer cell-derived factors. Proteomics 2023:e2300020. [PMID: 37882347 DOI: 10.1002/pmic.202300020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
Cancer-associated cachexia is a wasting syndrome that results in dramatic loss of whole-body weight, predominantly due to loss of skeletal muscle mass. It has been established that cachexia inducing cancer cells secrete proteins and extracellular vesicles (EVs) that can induce muscle atrophy. Though several studies examined these cancer-cell derived factors, targeting some of these components have shown little or no clinical benefit. To develop new therapies, understanding of the dysregulated proteins and signaling pathways that regulate catabolic gene expression during muscle wasting is essential. Here, we sought to examine the effect of conditioned media (CM) that contain secreted factors and EVs from cachexia inducing C26 colon cancer cells on C2C12 myotubes using mass spectrometry-based label-free quantitative proteomics. We identified significant changes in the protein profile of C2C12 cells upon exposure to C26-derived CM. Functional enrichment analysis revealed enrichment of proteins associated with inflammation, mitochondrial dysfunction, muscle catabolism, ROS production, and ER stress in CM treated myotubes. Furthermore, strong downregulation in muscle structural integrity and development and/or regenerative pathways were observed. Together, these enriched proteins in atrophied muscle could be utilized as potential muscle wasting markers and the dysregulated biological processes could be employed for therapeutic benefit in cancer-induced muscle wasting.
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Affiliation(s)
- Akbar L Marzan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Institute of Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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Samuel M, Sanwlani R, Pathan M, Anand S, Johnston EL, Ang CS, Kaparakis-Liaskos M, Mathivanan S. Isolation and Characterization of Cow-, Buffalo-, Sheep- and Goat-Milk-Derived Extracellular Vesicles. Cells 2023; 12:2491. [PMID: 37887335 PMCID: PMC10605021 DOI: 10.3390/cells12202491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
Milk is a complex biological fluid that has high-quality proteins including growth factors and also contains extracellular vesicles (EVs). EVs are a lipid bilayer containing vesicles that contain proteins, metabolites and nucleic acids. Several studies have proposed that EVs in cow milk can survive the gut and can illicit cross-species communication in the consuming host organism. In this study, we isolated and characterized extracellular vesicles from the raw milk of the four species of the Bovidae family, namely cow, sheep, goat and buffalo, that contribute 99% of the total milk consumed globally. A comparative proteomic analysis of these vesicles was performed to pinpoint their potential functional role in health and disease. Vesicles sourced from buffalo and cow milk were particularly enriched with proteins implicated in modulating the immune system. Furthermore, functional studies were performed to determine the anti-cancer effects of these vesicles. The data obtained revealed that buffalo-milk-derived EVs induced significantly higher cell death in colon cancer cells. Overall, the results from this study highlight the potent immunoregulatory and anti-cancer nature of EVs derived from the milk of Bovidae family members.
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Affiliation(s)
- Monisha Samuel
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3083, Australia (R.S.); (S.A.)
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, VIC 3086, Australia
| | - Rahul Sanwlani
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3083, Australia (R.S.); (S.A.)
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mohashin Pathan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3083, Australia (R.S.); (S.A.)
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sushma Anand
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3083, Australia (R.S.); (S.A.)
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ella L. Johnston
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ching-Seng Ang
- Bio21 Institute, University of Melbourne, Victoria, VIC 2010, Australia
| | - Maria Kaparakis-Liaskos
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, VIC 3086, Australia
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3083, Australia (R.S.); (S.A.)
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, VIC 3086, Australia
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Sanwlani R, Kang T, Gummadi S, Nedeva C, Ang CS, Mathivanan S. Bovine milk-derived extracellular vesicles enhance doxorubicin sensitivity in triple negative breast cancer cells by targeting metabolism and STAT signalling. Proteomics 2023; 23:e2200482. [PMID: 37376799 DOI: 10.1002/pmic.202200482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Metastatic triple-negative breast cancer (TNBC) has a low 5-year survival rate of below 30% with systemic chemotherapy being the most widely used treatment. Bovine milk-derived extracellular vesicles (MEVs) have been previously demonstrated to have anti-cancer attributes. In this study, we isolated bovine MEVs from commercial milk and characterised them according to MISEV guidelines. Bovine MEVs sensitised TNBC cells to doxorubicin, resulting in reduced metabolic potential and cell-viability. Label-free quantitative proteomics of cells treated with MEVs and/or doxorubicin suggested that combinatorial treatment depleted various pro-tumorigenic interferon-inducible gene products and proteins with metabolic function, previously identified as therapeutic targets in TNBC. Combinatorial treatment also led to reduced abundance of various STAT proteins and their downstream oncogenic targets with roles in cell-cycle and apoptosis. Taken together, this study highlights the ability of bovine MEVs to sensitise TNBC cells to standard-of-care therapeutic drug doxorubicin, paving the way for novel treatment regimens.
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Affiliation(s)
- Rahul Sanwlani
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Christina Nedeva
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S. Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells. Proteomics 2023:e2100314. [PMID: 37309723 DOI: 10.1002/pmic.202100314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 05/07/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023]
Abstract
Cancer cachexia is a wasting syndrome characterised by the loss of fat and/or muscle mass in advanced cancer patients. It has been well-established that cancer cells themselves can induce cachexia via the release of several pro-cachectic and pro-inflammatory factors. However, it is unclear how this process is regulated and the key cachexins that are involved. In this study, we validated C26 and EL4 as cachexic and non-cachexic cell models, respectively. Treatment of adipocytes and myotubes with C26 conditioned medium induced lipolysis and atrophy, respectively. We profiled soluble secreted proteins (secretome) as well as small extracellular vesicles (sEVs) released from cachexia-inducing (C26) and non-inducing (EL4) cancer cells by label-free quantitative proteomics. A total of 1268 and 1022 proteins were identified in the secretome of C26 and EL4, respectively. Furthermore, proteomic analysis of sEVs derived from C26 and EL4 cancer cells revealed a distinct difference in the protein cargo. Functional enrichment analysis using FunRich highlighted the enrichment of proteins that are implicated in biological processes such as muscle atrophy, lipolysis, and inflammation in both the secretome and sEVs derived from C26 cancer cells. Overall, our characterisation of the proteomic profiles of the secretory factors and sEVs from cachexia-inducing and non-inducing cancer cells provides insights into tumour factors that promote weight loss by mediating protein and lipid loss in various organs and tissues. Further investigation of these proteins may assist in highlighting potential therapeutic targets and biomarkers of cancer cachexia.
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Affiliation(s)
- Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Akbar L Marzan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sarah Stewart
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sanjay Shahi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Kyle Bramich
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Institute of Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Mohashin Pathan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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Loo L, Waller MA, Moreno CL, Cole AJ, Stella AO, Pop OT, Jochum AK, Ali OH, Denes CE, Hamoudi Z, Chung F, Aggarwal A, Low JKK, Patel K, Siddiquee R, Kang T, Mathivanan S, Mackay JP, Jochum W, Flatz L, Hesselson D, Turville S, Neely GG. Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs. PLoS Biol 2023; 21:e3001967. [PMID: 36757924 PMCID: PMC9910744 DOI: 10.1371/journal.pbio.3001967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 02/10/2023] Open
Abstract
Although ACE2 is the primary receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, a systematic assessment of host factors that regulate binding to SARS-CoV-2 spike protein has not been described. Here, we use whole-genome CRISPR activation to identify host factors controlling cellular interactions with SARS-CoV-2. Our top hit was a TLR-related cell surface receptor called leucine-rich repeat-containing protein 15 (LRRC15). LRRC15 expression was sufficient to promote SARS-CoV-2 spike binding where they form a cell surface complex. LRRC15 mRNA is expressed in human collagen-producing lung myofibroblasts and LRRC15 protein is induced in severe Coronavirus Disease 2019 (COVID-19) infection where it can be found lining the airways. Mechanistically, LRRC15 does not itself support SARS-CoV-2 infection, but fibroblasts expressing LRRC15 can suppress both pseudotyped and authentic SARS-CoV-2 infection in trans. Moreover, LRRC15 expression in fibroblasts suppresses collagen production and promotes expression of IFIT, OAS, and MX-family antiviral factors. Overall, LRRC15 is a novel SARS-CoV-2 spike-binding receptor that can help control viral load and regulate antiviral and antifibrotic transcriptional programs in the context of COVID-19 infection.
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Affiliation(s)
- Lipin Loo
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Matthew A. Waller
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L. Moreno
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Alexander J. Cole
- Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Oltin-Tiberiu Pop
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Ann-Kristin Jochum
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Institute for Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Omar Hasan Ali
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Christopher E. Denes
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Zina Hamoudi
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Felicity Chung
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Karishma Patel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rezwan Siddiquee
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Taeyoung Kang
- 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
| | - Joel P. Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Wolfram Jochum
- Institute for Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Lukas Flatz
- Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
- Center for Dermatooncology, Department of Dermatology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Daniel Hesselson
- Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Stuart Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - G. Gregory Neely
- Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
- * E-mail:
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Gummadi S, Kang T, Fonseka P, Chitti SV, Ang CS, Mathivanan S. Pep2Graph: A standalone tool to analyse proteolytic cleavages by proteases from gel-based mass spectrometry data. Proteomics 2022; 22:e2200147. [PMID: 35924633 DOI: 10.1002/pmic.202200147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/14/2022] [Accepted: 07/28/2022] [Indexed: 12/29/2022]
Abstract
Proteases are enzymes that regulate substrates via proteolytic activation and coordinate essential cellular functions including DNA replication, DNA transcription, cell proliferation, differentiation, migration and apoptosis. However, techniques to identify proteolytic events in a high-throughput manner is limited. PROtein TOpography and Migration Analysis Platform (PROTOMAP) is a technique that relies on mass spectrometry-based proteomics to globally identify the shifts in the in-gel migration of proteins and their corresponding fragments that are obtained by proteolysis. However, user-friendly software tool to analyse the proteomic data to identify proteolytic events is needed. Here, we report Pep2Graph, a user-friendly standalone tool that integrates peptide sequence information from in-gel proteomics and presents the data as two-dimensional peptographs with in-gel migration, sequence coverage and MS/MS spectra counts. Pep2Graph (http://www.mathivananlab.org/Pep2Graph) allows users to utilize in-gel proteomics data to study proteolytic events that may play a significant role in normal physiology and pathology.
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Affiliation(s)
- Sriram Gummadi
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Taeyoung Kang
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Sai V Chitti
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Samuel M, Fonseka P, Sanwlani R, Gangoda L, Chee SH, Keerthikumar S, Spurling A, Chitti SV, Zanker D, Ang CS, Atukorala I, Kang T, Shahi S, Marzan AL, Nedeva C, Vennin C, Lucas MC, Cheng L, Herrmann D, Pathan M, Chisanga D, Warren SC, Zhao K, Abraham N, Anand S, Boukouris S, Adda CG, Jiang L, Shekhar TM, Baschuk N, Hawkins CJ, Johnston AJ, Orian JM, Hoogenraad NJ, Poon IK, Hill AF, Jois M, Timpson P, Parker BS, Mathivanan S. Oral administration of bovine milk-derived extracellular vesicles induces senescence in the primary tumor but accelerates cancer metastasis. Nat Commun 2021; 12:3950. [PMID: 34168137 PMCID: PMC8225634 DOI: 10.1038/s41467-021-24273-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 06/09/2021] [Indexed: 01/06/2023] Open
Abstract
The concept that extracellular vesicles (EVs) from the diet can be absorbed by the intestinal tract of the consuming organism, be bioavailable in various organs, and in-turn exert phenotypic changes is highly debatable. Here, we isolate EVs from both raw and commercial bovine milk and characterize them by electron microscopy, nanoparticle tracking analysis, western blotting, quantitative proteomics and small RNA sequencing analysis. Orally administered bovine milk-derived EVs survive the harsh degrading conditions of the gut, in mice, and is subsequently detected in multiple organs. Milk-derived EVs orally administered to mice implanted with colorectal and breast cancer cells reduce the primary tumor burden. Intriguingly, despite the reduction in primary tumor growth, milk-derived EVs accelerate metastasis in breast and pancreatic cancer mouse models. Proteomic and biochemical analysis reveal the induction of senescence and epithelial-to-mesenchymal transition in cancer cells upon treatment with milk-derived EVs. Timing of EV administration is critical as oral administration after resection of the primary tumor reverses the pro-metastatic effects of milk-derived EVs in breast cancer models. Taken together, our study provides context-based and opposing roles of milk-derived EVs as metastasis inducers and suppressors.
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Affiliation(s)
- Monisha Samuel
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Rahul Sanwlani
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Lahiru Gangoda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Sing Ho Chee
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Alex Spurling
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Sai V Chitti
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Damien Zanker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Ching-Seng Ang
- Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Ishara Atukorala
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Taeyoung Kang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Sanjay Shahi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Akbar L Marzan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Christina Nedeva
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Claire Vennin
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre & St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Morghan C Lucas
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre & St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Lesley Cheng
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - David Herrmann
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre & St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Mohashin Pathan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - David Chisanga
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Sean C Warren
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre & St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kening Zhao
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Nidhi Abraham
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Sushma Anand
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Stephanie Boukouris
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Christopher G Adda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Lanzhou Jiang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Tanmay M Shekhar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Nikola Baschuk
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Christine J Hawkins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Amelia J Johnston
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Jacqueline Monique Orian
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Nicholas J Hoogenraad
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Ivan K Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Markandeya Jois
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Paul Timpson
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre & St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Belinda S Parker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.
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11
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Lima LG, Ham S, Shin H, Chai EPZ, Lek ESH, Lobb RJ, Müller AF, Mathivanan S, Yeo B, Choi Y, Parker BS, Möller A. Tumor microenvironmental cytokines bound to cancer exosomes determine uptake by cytokine receptor-expressing cells and biodistribution. Nat Commun 2021; 12:3543. [PMID: 34112803 PMCID: PMC8192925 DOI: 10.1038/s41467-021-23946-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 05/26/2021] [Indexed: 01/17/2023] Open
Abstract
Metastatic spread of a cancer to secondary sites is a coordinated, non-random process. Cancer cell-secreted vesicles, especially exosomes, have recently been implicated in the guidance of metastatic dissemination, with specific surface composition determining some aspects of organ-specific localization. Nevertheless, whether the tumor microenvironment influences exosome biodistribution has yet to be investigated. Here, we show that microenvironmental cytokines, particularly CCL2, decorate cancer exosomes via binding to surface glycosaminoglycan side chains of proteoglycans, causing exosome accumulation in specific cell subsets and organs. Exosome retention results in changes in the immune landscape within these organs, coupled with a higher metastatic burden. Strikingly, CCL2-decorated exosomes are directed to a subset of cells that express the CCL2 receptor CCR2, demonstrating that exosome-bound cytokines are a crucial determinant of exosome-cell interactions. In addition to the finding that cytokine-conjugated exosomes are detected in the blood of cancer patients, we discovered that healthy subjects derived exosomes are also associated with cytokines. Although displaying a different profile from exosomes isolated from cancer patients, it further indicates that specific combinations of cytokines bound to exosomes could likewise affect other physiological and disease settings. Cancer derived exosomes are reported to promote metastatic dissemination. Here the authors show that cytokines in the tumor microenvironment bind to exosomes via glycosaminoglycan side chains of proteoglycans, and these exosomes are preferentially taken up by specific cell lineages and organs to promote metastasis.
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Affiliation(s)
- Luize G Lima
- Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Sunyoung Ham
- Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Hyunku Shin
- Department of Bio-convergence Engineering, Korea University, Seoul, South Korea
| | - Edna P Z Chai
- Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Erica S H Lek
- Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.,School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, Brisbane, QLD, Australia
| | - Richard J Lobb
- Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.,Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane, QLD, Australia
| | - Alexandra F Müller
- Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Belinda Yeo
- Olivia Newton-John Cancer Research Institute, Austin Hospital, Heidelberg, Melbourne, VIC, Australia
| | - Yeonho Choi
- Department of Bio-convergence Engineering, Korea University, Seoul, South Korea.,School of Biomedical Engineering, Korea University, Seoul, South Korea.,Department of Bioengineering, Korea University, Seoul, South Korea
| | - Belinda S Parker
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Andreas Möller
- Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia. .,School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia. .,Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
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12
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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: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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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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14
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Abstract
It has been well established that diet influences the health status of the consuming organism. Recently, extracellular vesicles (EVs) present in dietary sources are proposed to be involved in cross-species and kingdom communication. As EVs contain a lipid bilayer and carry bioactive cargo of proteins and nucleic acids, they are proposed to survive harsh degrading conditions of the gut and enter systemic circulation. Following the bioavailability, several studies have supported the functional role of dietary EVs in various tissues of the consuming organism. Simultaneously, multiple studies have refuted the possibility that dietary EVs mediate cross-species communication and hence the topic is controversial. The feasibility of the concept remains under scrutiny primarily owing to the lack of significant in vivo evidence to complement the in vitro speculations. Concerns surrounding EV stability in the harsh degrading gut environment, lack of mechanism explaining intestinal uptake and bioavailability in systemic circulation have impeded the acceptance of their functional role. This chapter discusses the current evidences that support dietary EV-based cross species communication and enlists several issues that need to be addressed in this field.
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Affiliation(s)
- Rahul Sanwlani
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- 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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15
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Phan TK, Fonseka P, Tixeira R, Pathan M, Ang CS, Ozkocak DC, Mathivanan S, Poon IKH. Pannexin-1 channel regulates nuclear content packaging into apoptotic bodies and their size. Proteomics 2021; 21:e2000097. [PMID: 33661579 DOI: 10.1002/pmic.202000097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/04/2021] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
Abstract
Apoptotic bodies (ApoBDs), which are large extracellular vesicles exclusively released by apoptotic cells, possess therapeutically exploitable properties including biomolecule loadability and transferability. However, current limited understanding of ApoBD biology has hindered its exploration for clinical use. Particularly, as ApoBD-accompanying cargoes (e.g., nucleic acids and proteins) have major influence on their functionality, further insights into the mechanism of biomolecule sorting into ApoBDs are critical to unleash their therapeutic potential. Previous studies suggested pannexin 1 (PANX1) channel, a negative regulator of ApoBD biogenesis, can modify synaptic vesicle contents. We also reported that trovafloxacin (a PANX1 inhibitor) increases proportion of ApoBDs containing DNA. Therefore, we sought to define the role of PANX1 in regulating the sorting of nuclear content into ApoBDs. Here, using flow cytometry and label-free quantitative proteomic analyses, we showed that targeting PANX1 activity during apoptosis, via either pharmacological inhibition or genetic disruption, resulted in enrichment of both DNA and nuclear proteins in ApoBDs that were unexpectedly smaller in size. Our data suggest that PANX1, besides being a key regulator of ApoBD formation, also functions as a negative regulator of nuclear content packaging and modulator of ApoBD size. Together, our findings provide further insights into ApoBD biology and form a novel conceptual framework for ApoBD-based therapies through pharmacologically manipulating ApoBD contents.
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Affiliation(s)
- Thanh Kha Phan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Rochelle Tixeira
- VIB-UGent Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mohashin Pathan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Dilara Ceyda Ozkocak
- 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
| | - Ivan Ka Ho Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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16
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Fonseka P, Chitti SV, Sanwlani R, Mathivanan S. Sulfisoxazole does not inhibit the secretion of small extracellular vesicles. Nat Commun 2021; 12:977. [PMID: 33579909 PMCID: PMC7881022 DOI: 10.1038/s41467-021-21074-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 01/07/2021] [Indexed: 01/14/2023] Open
Affiliation(s)
- Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Sai V Chitti
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Rahul Sanwlani
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia.
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17
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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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18
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Abstract
As living organisms constantly need energy to maintain and perform cellular functions, metabolism plays a vital role in producing the required energy to execute these processes. Hence, various metabolic pathways are highly regulated and disruption in critical pathways can result in the onset of multiple disorders such as hypertension, diabetes, obesity, and dyslipidaemia. Extracellular vesicles (EVs) are membrane-bound nanosized vesicles that are known to be secreted by various cell types into their respective extracellular environment. EVs have been implicated in cell-to-cell communication via mediating cellular signaling and can functionally impact recipient cells with the transport of bioactive proteins, nucleic acids, lipids and cellular metabolites. Recently, several studies have highlighted the role of EVs in metabolism. Alterations in the plasma derived EV concentration and their cargo in patients with metabolic disorders have been reported by multiple studies, further proposing EVs as a potential source of disease biomarkers. The following chapter will discuss the functional significance of EVs in metabolic diseases and the processes by which EVs act as cellular messengers to reprogram the metabolic machinery in recipient cells.
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Affiliation(s)
- Akbar L Marzan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Christina Nedeva
- 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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19
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Abstract
Extracellular vesicles (EVs) are lipid bilayer containing nanovesicles that have a predominant role in intercellular communication and cargo delivery. EVs have recently been used as a means for drug delivery and have been depicted to elicit no or minimal immune response in vivo. The stability, biocompatibility and manipulatable tumour homing capabilities of these biological vessels make them an attractive target for the packaging and delivery of drugs and molecules to treat various diseases including cancer. The following chapter will summarise current EV engineering techniques for the purpose of delivering putative drugs and therapeutic molecules for the treatment of cancer. The relevance of EV source will be discussed, as well as the specific modifications required to manufacture them into suitable vehicles for molecular drug delivery. Furthermore, methods of EV cargo encapsulation will be evaluated with emphasis on intercellular coordination to allow for the effective emptying of therapeutic contents into target cells. While EVs possess properties making them naturally suitable nanocarriers for drugs and molecules, many challenges with clinical translation of EV-based platforms remain. These issues need to be addressed in order to harness the true potential of the EV-based therapeutic avenue.
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Affiliation(s)
- Christina Nedeva
- 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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20
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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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21
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Abstract
Extracellular vesicles (EVs) are described as membranous vesicles that are secreted by various cell types. EVs can be categorised as exosomes, ectosomes, apoptotic bodies, large oncosomes and migrasomes. EVs are heterogeneous in nature according to their origin, mode of release, size, and biochemical contents. Herein, we discuss a recently discovered subpopulation of EVs called 'exomeres'. Unlike the other subtypes of EVs, exomeres are defined as non-membranous nanovesicles with a size ≤50 nm. They can be isolated using asymmetric-flow field-flow fractionation as well as ultracentrifugation. The cargo of exomeres are beginning to be unravelled and are highlighted to be enriched with proteins implicated in regulating metabolic pathways. Consistent with other types of EVs, exomeres also contain nucleic acids and lipids which can be delivered to recipient cells. These discoveries highlight the complex heterogeneity of EVs and thereby necessitates further attention to understand the nature of each subpopulation more exclusively. Overall, this chapter describes the current knowledge on exomeres.
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Affiliation(s)
- Sushma Anand
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Monisha Samuel
- Division of Immunology and Allergy, Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
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22
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Fonseka P, Pathan M, Chitti SV, Kang T, Mathivanan S. FunRich enables enrichment analysis of OMICs datasets. J Mol Biol 2020; 433:166747. [PMID: 33310018 DOI: 10.1016/j.jmb.2020.166747] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 01/17/2023]
Abstract
High-throughput methods to profile the genome, transcriptome, proteome and metabolome of various systems has become a routine in multiple research laboratories around the world. Hence, to analyse and interpret these heterogenous datasets user-friendly bioinformatics tools are needed. Here, we discuss FunRich tool that enables biologists to perform functional enrichment analysis on the generated datasets. Users can perform enrichment analysis with a variety of background databases and have complete control in updating or modifying the content in most of the databases. Specifically, users can download and update the background database from UniProt at any time thereby allowing a robust background database that can support annotations from >18 taxonomies. Users can create customizable Venn diagrams, pie charts, bar graphs and heatmaps of publication quality for their datasets using FunRich (http://www.funrich.org). Overall, FunRich tool is user-friendly and enables users to perform various analysis on their datasets with minimal or no aid from bioinformaticians.
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Affiliation(s)
- Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Mohashin Pathan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Sai V Chitti
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Taeyoung Kang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
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23
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Chellappan S, Mathivanan S, Thippeswamy R, Nagesh M, Savithri HS, Murthy MRN. Crystal Structure of Oxalate Decarboxylase from <i>Photorhabdus luminescens</i>, A Symbiotic Bacterium Associated with Entomopathogenic Nematodes. CURR SCI INDIA 2020. [DOI: 10.18520/cs/v119/i8/1349-1356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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24
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Gangoda L, Phan TK, Anand S, Hulett MD, Mathivanan S. Deubiquitinase enzyme STAMBP plays a broad role in both Toll-like and Nod-like receptor mediated inflammation. EUR J INFLAMM 2020. [DOI: 10.1177/2058739220960844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The innate immune system in mammals include pattern recognition receptors (PRRs), which initiate immune responses to microbial infection via several mechanisms. These PRRs include cell surface Toll-like receptors (TLRs) and cytosolic Nod-like receptors (NLRs) that recognizes extracellular and intracellular danger signals respectively. NLRs are poised to respond specifically to pathogens that access the host cell cytosol. The molecular mechanisms by which NLRs are activated to form inflammasomes and exert downstream inflammatory responses remain poorly understood. Additionally, very little is known about the regulation of cytosolic pathogen sensory NLR family members, except for NLRP3. Recently a deubiquitinase known as STAMBP has been implicated as a regulator of NLRP7 inflammasome assembly. We have investigated the role of STAMBP in regulation of other inflammasome components and its broader role in inflammation using genetic removal of STAMBP protein from cells using CRISPR/Cas9 gene editing and challenging these gene edited cells with an inflammatory stimuli. Our study demonstrated that STAMBP has a critical role in inflammation both in the context of NLR pathway, through NLRP stabilization and TLR pathway, through JNK signaling and downstream cytokine production. The findings indicate that STAMBP has a wider role in inflammation than previously thought to be the case.
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Affiliation(s)
- Lahiru Gangoda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Thanh Kha Phan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sushma Anand
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Mark D Hulett
- 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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25
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Fuller OK, Whitham M, Mathivanan S, Febbraio MA. The Protective Effect of Exercise in Neurodegenerative Diseases: The Potential Role of Extracellular Vesicles. Cells 2020; 9:cells9102182. [PMID: 32998245 PMCID: PMC7599526 DOI: 10.3390/cells9102182] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Physical activity has systemic effects on the body, affecting almost every organ. It is important not only for general health and wellbeing, but also in the prevention of diseases. The mechanisms behind the therapeutic effects of physical activity are not completely understood; however, studies indicate these benefits are not confined to simply managing energy balance and body weight. They also include systemic factors which are released into the circulation during exercise and which appear to underlie the myriad of benefits exercise can elicit. It was shown that along with a number of classical cytokines, active tissues also engage in inter-tissue communication via extracellular vesicles (EVs), specifically exosomes and other small EVs, which are able to deliver biomolecules to cells and alter their metabolism. Thus, EVs may play a role in the acute and systemic adaptations that take place during and after physical activity, and may be therapeutically useful in the treatment of a range of diseases, including metabolic disorders such as type 2 diabetes and obesity; and the focus of this review, neurological disorders such as Alzheimer's disease.
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Affiliation(s)
- Oliver K Fuller
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia;
| | - Martin Whitham
- College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK;
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3083, Australia;
| | - Mark A Febbraio
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia;
- Correspondence:
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26
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Atkin-Smith GK, Miles MA, Tixeira R, Lay FT, Duan M, Hawkins CJ, Phan TK, Paone S, Mathivanan S, Hulett MD, Chen W, Poon IKH. Plexin B2 Is a Regulator of Monocyte Apoptotic Cell Disassembly. Cell Rep 2020; 29:1821-1831.e3. [PMID: 31722200 DOI: 10.1016/j.celrep.2019.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/10/2019] [Accepted: 10/03/2019] [Indexed: 12/18/2022] Open
Abstract
Billions of cells undergo apoptosis daily and often fragment into small, membrane-bound extracellular vesicles termed apoptotic bodies (ApoBDs). We demonstrate that apoptotic monocytes undergo a highly coordinated disassembly process and form long, beaded protrusions (coined as beaded apoptopodia), which fragment to release ApoBDs. Here, we find that the protein plexin B2 (PlexB2), a transmembrane receptor that regulates axonal guidance in neurons, is enriched in the ApoBDs of THP1 monocytes and is a caspase 3/7 substrate. To determine whether PlexB2 is involved in the disassembly of apoptotic monocytes, we generate PlexB2-deficient THP1 monocytes and demonstrate that lack of PlexB2 impairs the formation of beaded apoptopodia and ApoBDs. Consequently, the loss of PlexB2 in apoptotic THP1 monocytes impairs their uptake by both professional and non-professional phagocytes. Altogether, these data identify PlexB2 as a positive regulator of apoptotic monocyte disassembly and demonstrate the importance of this process in apoptotic cell clearance.
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Affiliation(s)
- Georgia K Atkin-Smith
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mark A Miles
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Rochelle Tixeira
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Fung T Lay
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mubing Duan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Christine J Hawkins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Thanh Kha Phan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Stephanie Paone
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mark D Hulett
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Ivan K H Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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27
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Pathan M, Fonseka P, Chitti SV, Kang T, Sanwlani R, Van Deun J, Hendrix A, Mathivanan S. Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles. Nucleic Acids Res 2020; 47:D516-D519. [PMID: 30395310 PMCID: PMC6323905 DOI: 10.1093/nar/gky1029] [Citation(s) in RCA: 451] [Impact Index Per Article: 112.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/30/2018] [Indexed: 11/30/2022] Open
Abstract
Extracellular vesicles (EVs) are membranous vesicles that are released by both prokaryotic and eukaryotic cells into the extracellular microenvironment. EVs can be categorised as exosomes, ectosomes or shedding microvesicles and apoptotic bodies based on the mode of biogenesis. EVs contain biologically active cargo of nucleic acids, proteins, lipids and metabolites that can be altered based on the precise state of the cell. Vesiclepedia (http://www.microvesicles.org) is a web-based compendium of RNA, proteins, lipids and metabolites that are identified in EVs from both published and unpublished studies. Currently, Vesiclepedia contains data obtained from 1254 EV studies, 38 146 RNA entries, 349 988 protein entries and 639 lipid/metabolite entries. Vesiclepedia is publicly available and allows users to query and download EV cargo based on different search criteria. The mode of EV isolation and characterization, the biophysical and molecular properties and EV-METRIC are listed in the database aiding biomedical scientists in assessing the quality of the EV preparation and the corresponding data obtained. In addition, FunRich-based Vesiclepedia plugin is incorporated aiding users in data analysis.
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Affiliation(s)
- Mohashin Pathan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Sai V Chitti
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Taeyoung Kang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Rahul Sanwlani
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Jan Van Deun
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
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28
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Sanwlani R, Fonseka P, Chitti SV, Mathivanan S. Milk-Derived Extracellular Vesicles in Inter-Organism, Cross-Species Communication and Drug Delivery. Proteomes 2020; 8:11. [PMID: 32414045 PMCID: PMC7356197 DOI: 10.3390/proteomes8020011] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022] Open
Abstract
Milk is considered as more than a source of nutrition for infants and is a vector involved in the transfer of bioactive compounds and cells. Milk contains abundant quantities of extracellular vesicles (EVs) that may originate from multiple cellular sources. These nanosized vesicles have been well characterized and are known to carry a diverse cargo of proteins, nucleic acids, lipids and other biomolecules. Milk-derived EVs have been demonstrated to survive harsh and degrading conditions in gut, taken up by various cell types, cross biological barriers and reach peripheral tissues. The cargo carried by these dietary EVs has been suggested to have a role in cell growth, development, immune modulation and regulation. Hence, there is considerable interest in understanding the role of milk-derived EVs in mediating inter-organismal and cross-species communication. Furthermore, various attributes such as it being a natural source, as well as its abundance, scalability, economic viability and lack of unwarranted immunologic reactions, has generated significant interest in deploying milk-derived EVs for clinical applications such as drug delivery and disease therapy. In this review, the role of milk-derived EVs in inter-organismal, cross-species communication and in drug delivery is discussed.
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Affiliation(s)
| | | | | | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3083, Australia; (R.S.); (P.F.); (S.V.C.)
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29
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Shahi S, Ang CS, Mathivanan S. A High-Resolution Mass Spectrometry-Based Quantitative Metabolomic Workflow Highlights Defects in 5-Fluorouracil Metabolism in Cancer Cells with Acquired Chemoresistance. Biology (Basel) 2020; 9:biology9050096. [PMID: 32384705 PMCID: PMC7284906 DOI: 10.3390/biology9050096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022]
Abstract
Currently, 5-fluorouracil (5-FU)-based combination chemotherapy is the mainstay in the treatment of metastatic colorectal cancer (CRC), which benefits approximately 50% of the patients. However, these tumors inevitably acquire chemoresistance resulting in treatment failure. The molecular mechanisms driving acquired chemotherapeutic drug resistance in CRC is fundamental for the development of novel strategies for circumventing resistance. However, the specific phenomenon that drives the cancer cells to acquire resistance is poorly understood. Understanding the molecular mechanisms that regulate chemoresistance will uncover new avenues for the treatment of CRC. Among the various mechanisms of acquired chemoresistance, defects in the drug metabolism pathways could play a major role. In the case of 5-FU, it gets converted into various active metabolites, which, directly or indirectly, interferes with the replication and transcription of dividing cells causing DNA and RNA damage. In this project, we developed a high-resolution mass spectrometry-based method to effectively extract and quantify levels of the 5-FU metabolites in cell lysates and media of parental and 5-FU resistant LIM1215 CRC cells. The analysis highlighted that the levels of 5-FU metabolites are significantly reduced in 5-FU resistant cells. Specifically, the level of the nucleotide fluorodeoxyuridine monophosphate (FdUMP) is reduced with treatment of 5-FU clarifying the compromised 5-FU metabolism in resistant cells. Corroborating the metabolomic analysis, treatment of the resistant cells with FdUMP, an active metabolite of 5-FU, resulted in effective killing of the resistant cells. Overall, in this study, an effective protocol was developed for comparative quantitation of polar metabolites and nucleotide analogues from the adherent cells efficiently. Furthermore, the utility of FdUMP as an alternative for CRC therapy is highlighted.
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Affiliation(s)
- Sanjay Shahi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia;
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
- Correspondence: (C.-S.A.); (S.M.); Tel.: +61-03-8344-2540 (C.-S.A.); +61-03-9479-2565 (S.M.); Fax: +61-03-9479-1226 (S.M.)
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia;
- Correspondence: (C.-S.A.); (S.M.); Tel.: +61-03-8344-2540 (C.-S.A.); +61-03-9479-2565 (S.M.); Fax: +61-03-9479-1226 (S.M.)
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30
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Dávalos-Salas M, Montgomery MK, Reehorst CM, Nightingale R, Ng I, Anderton H, Al-Obaidi S, Lesmana A, Scott CM, Ioannidis P, Kalra H, Keerthikumar S, Tögel L, Rigopoulos A, Gong SJ, Williams DS, Yoganantharaja P, Bell-Anderson K, Mathivanan S, Gibert Y, Hiebert S, Scott AM, Watt MJ, Mariadason JM. Deletion of intestinal Hdac3 remodels the lipidome of enterocytes and protects mice from diet-induced obesity. Nat Commun 2019; 10:5291. [PMID: 31757939 PMCID: PMC6876593 DOI: 10.1038/s41467-019-13180-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Histone deacetylase 3 (Hdac3) regulates the expression of lipid metabolism genes in multiple tissues, however its role in regulating lipid metabolism in the intestinal epithelium is unknown. Here we demonstrate that intestine-specific deletion of Hdac3 (Hdac3IKO) protects mice from diet induced obesity. Intestinal epithelial cells (IECs) from Hdac3IKO mice display co-ordinate induction of genes and proteins involved in mitochondrial and peroxisomal β-oxidation, have an increased rate of fatty acid oxidation, and undergo marked remodelling of their lipidome, particularly a reduction in long chain triglycerides. Many HDAC3-regulated fatty oxidation genes are transcriptional targets of the PPAR family of nuclear receptors, Hdac3 deletion enhances their induction by PPAR-agonists, and pharmacological HDAC3 inhibition induces their expression in enterocytes. These findings establish a central role for HDAC3 in co-ordinating PPAR-regulated lipid oxidation in the intestinal epithelium, and identify intestinal HDAC3 as a potential therapeutic target for preventing obesity and related diseases. Histone deacetylase 3 (HDAC3) is a regulator of lipid homeostasis in several tissues, however, its role in intestinal lipid metabolism was not yet known. Here the authors study intestine specific HDAC3 knock out mice and report that these animals have increased fatty acid oxidation and undergo remodeling of the intestinal epithelial cell lipidome.
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Affiliation(s)
- Mercedes Dávalos-Salas
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Magdalene K Montgomery
- Department of Physiology, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Camilla M Reehorst
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Rebecca Nightingale
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Irvin Ng
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Holly Anderton
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Sheren Al-Obaidi
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Analia Lesmana
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Cameron M Scott
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Paul Ioannidis
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia
| | - Hina Kalra
- La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Shivakumar Keerthikumar
- La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Lars Tögel
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Angela Rigopoulos
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Sylvia J Gong
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia
| | - David S Williams
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia.,Department of Pathology, Austin Health, Melbourne, Victoria, Australia
| | | | - Kim Bell-Anderson
- Faculty of Science, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Suresh Mathivanan
- La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Yann Gibert
- Department of Medicine, Deakin University, Geelong, Victoria, Australia
| | | | - Andrew M Scott
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia.,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Matthew J Watt
- Department of Physiology, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.
| | - John M Mariadason
- Olivia Newton John Cancer Research Institute, Melbourne, Victoria, Australia. .,La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia. .,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia.
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31
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Vennin C, Mélénec P, Rouet R, Nobis M, Cazet AS, Murphy KJ, Herrmann D, Reed DA, Lucas MC, Warren SC, Elgundi Z, Pinese M, Kalna G, Roden D, Samuel M, Zaratzian A, Grey ST, Da Silva A, Leung W, Mathivanan S, Wang Y, Braithwaite AW, Christ D, Benda A, Parkin A, Phillips PA, Whitelock JM, Gill AJ, Sansom OJ, Croucher DR, Parker BL, Pajic M, Morton JP, Cox TR, Timpson P. CAF hierarchy driven by pancreatic cancer cell p53-status creates a pro-metastatic and chemoresistant environment via perlecan. Nat Commun 2019; 10:3637. [PMID: 31406163 PMCID: PMC6691013 DOI: 10.1038/s41467-019-10968-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
Heterogeneous subtypes of cancer-associated fibroblasts (CAFs) coexist within pancreatic cancer tissues and can both promote and restrain disease progression. Here, we interrogate how cancer cells harboring distinct alterations in p53 manipulate CAFs. We reveal the existence of a p53-driven hierarchy, where cancer cells with a gain-of-function (GOF) mutant p53 educate a dominant population of CAFs that establish a pro-metastatic environment for GOF and null p53 cancer cells alike. We also demonstrate that CAFs educated by null p53 cancer cells may be reprogrammed by either GOF mutant p53 cells or their CAFs. We identify perlecan as a key component of this pro-metastatic environment. Using intravital imaging, we observe that these dominant CAFs delay cancer cell response to chemotherapy. Lastly, we reveal that depleting perlecan in the stroma combined with chemotherapy prolongs mouse survival, supporting it as a potential target for anti-stromal therapies in pancreatic cancer.
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Affiliation(s)
- Claire Vennin
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
- Molecular Pathology department, the Netherlands Cancer Institute, Amsterdam, 1066CX, the Netherlands
| | - Pauline Mélénec
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Romain Rouet
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Max Nobis
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Aurélie S Cazet
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Kendelle J Murphy
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - David Herrmann
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Daniel A Reed
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Morghan C Lucas
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Sean C Warren
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Zehra Elgundi
- Graduate school of Biomedical Engineering, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
| | - Mark Pinese
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Gabriella Kalna
- Cancer Research UK Beatson Institute, Glasgow Scotland, G61 BD, UK
| | - Daniel Roden
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Monisha Samuel
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Anaiis Zaratzian
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
| | - Shane T Grey
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Andrew Da Silva
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
| | - Wilfred Leung
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Suresh Mathivanan
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Yingxiao Wang
- Department of Bioengineering, Institute of Engineering in Medicine, University of California, San Diego, CA, 92121, USA
| | - Anthony W Braithwaite
- Children's Medical Research Institute, University of Sydney, Sydney, NSW, 2006, Australia
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, 9054, New Zealand
- Maurice Wilkins Centre, University of Otago, Dunedin, 9054, New Zealand
| | - Daniel Christ
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Ales Benda
- Biomedical imaging facility, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ashleigh Parkin
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Phoebe A Phillips
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, School of Medical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for Nanomedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - John M Whitelock
- Graduate school of Biomedical Engineering, University of New South Wales Sydney, Sydney, NSW, 2052, Australia
| | - Anthony J Gill
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
- NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, Sydney, NSW, 2065, Australia
- Cancer Diagnosis and Pathology Research Group, Kolling Institute of Medical Research, St Leonards, NSW, 2065, Australia
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow Scotland, G61 BD, UK
| | - David R Croucher
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | - Benjamin L Parker
- Schools of Life and Environmental Sciences, the Charles Perkin Centre, the University of Sydney, Sydney, NSW, 2006, Australia
| | - Marina Pajic
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia
| | | | - Thomas R Cox
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia.
| | - Paul Timpson
- The Garvan Institute of Medical Research & The Kinghorn Cancer Centre, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Sydney, NSW, 2010, Australia.
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Zhao K, Bleackley M, Chisanga D, Gangoda L, Fonseka P, Liem M, Kalra H, Al Saffar H, Keerthikumar S, Ang CS, Adda CG, Jiang L, Yap K, Poon IK, Lock P, Bulone V, Anderson M, Mathivanan S. Extracellular vesicles secreted by Saccharomyces cerevisiae are involved in cell wall remodelling. Commun Biol 2019; 2:305. [PMID: 31428693 PMCID: PMC6688994 DOI: 10.1038/s42003-019-0538-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) are membranous vesicles that are released by cells. In this study, the role of the Endosomal Sorting Complex Required for Transport (ESCRT) machinery in the biogenesis of yeast EVs was examined. Knockout of components of the ESCRT machinery altered the morphology and size of EVs as well as decreased the abundance of EVs. In contrast, strains with deletions in cell wall biosynthesis genes, produced more EVs than wildtype. Proteomic analysis highlighted the depletion of ESCRT components and enrichment of cell wall remodelling enzymes, glucan synthase subunit Fks1 and chitin synthase Chs3, in yeast EVs. Interestingly, EVs containing Fks1 and Chs3 rescued the yeast cells from antifungal molecules. However, EVs from fks1∆ or chs3∆ or the vps23∆chs3∆ double knockout strain were unable to rescue the yeast cells as compared to vps23∆ EVs. Overall, we have identified a potential role for yeast EVs in cell wall remodelling.
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Affiliation(s)
- Kening Zhao
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Mark Bleackley
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - David Chisanga
- 2Department of Computer Science and Information Technology, La Trobe University, Melbourne, VIC 3086 Australia
| | - Lahiru Gangoda
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Pamali Fonseka
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Michael Liem
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Hina Kalra
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Haidar Al Saffar
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Shivakumar Keerthikumar
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
- 3Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia
- 4Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ching-Seng Ang
- 5Bio21 Institute, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Christopher G Adda
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Lanzhou Jiang
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Kuok Yap
- 6ARC Centre of Excellence in Plant Cell Walls and Adelaide Glycomics, The University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Ivan K Poon
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Peter Lock
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Vincent Bulone
- 6ARC Centre of Excellence in Plant Cell Walls and Adelaide Glycomics, The University of Adelaide, Waite Campus, Urrbrae, SA 5064 Australia
| | - Marilyn Anderson
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Suresh Mathivanan
- 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
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Young AR, Duarte JDG, Coulson R, O'Brien M, Deb S, Lopata A, Behren A, Mathivanan S, Lim E, Meeusen E. Immunoprofiling of Breast Cancer Antigens Using Antibodies Derived from Local Lymph Nodes. Cancers (Basel) 2019; 11:cancers11050682. [PMID: 31100936 PMCID: PMC6562983 DOI: 10.3390/cancers11050682] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 01/09/2023] Open
Abstract
Tumor antigens are responsible for initiating an immune response in cancer patients, and their identification may provide new biomarkers for cancer diagnosis and targets for immunotherapy. The general use of serum antibodies to identify tumor antigens has several drawbacks, including dilution, complex formation, and background reactivity. In this study, antibodies were generated from antibody-secreting cells (ASC) present in tumor-draining lymph nodes of 20 breast cancer patients (ASC-probes) and were used to screen breast cancer cell lines and protein microarrays. Half of the ASC-probes reacted strongly against extracts of the MCF-7 breast cancer cell line, but each with a distinct antigen recognition profile. Three of the positive ASC-probes reacted differentially with recombinant antigens on a microarray containing cancer-related proteins. The results of this study show that lymph node-derived ASC-probes provide a highly specific source of tumor-specific antibodies. Each breast cancer patient reacts with a different antibody profile which indicates that targeted immunotherapies may need to be personalized for individual patients. Focused microarrays in combination with ASC-probes may be useful in providing immune profiles and identifying tumor antigens of individual cancer patients.
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Affiliation(s)
- Anna Rachel Young
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia.
| | - Jessica Da Gama Duarte
- Olivia Newton-John Cancer Research Institute, Level 5, ONJ Centre, Heidelberg Vic 3084, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne 3086, Australia.
| | - Rhiannon Coulson
- Garvan Institute of Medical Research, St Vincent's Clinical School, Darlinghurst, NSW 2010, Australia.
| | - Megan O'Brien
- Olivia Newton-John Cancer Research Institute, Level 5, ONJ Centre, Heidelberg Vic 3084, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne 3086, Australia.
| | - Siddhartha Deb
- Consultant Pathologist, Anatpath. 120 Gardenvale Rd, Gardenvale Melbourne 3185, Australia.
| | - Alex Lopata
- CancerProbe Pty Ltd, PO Box 2237, Prahran 3181, Australia.
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, Level 5, ONJ Centre, Heidelberg Vic 3084, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne 3086, Australia.
| | - Suresh Mathivanan
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia.
| | - Elgene Lim
- Garvan Institute of Medical Research, St Vincent's Clinical School, Darlinghurst, NSW 2010, Australia.
| | - Els Meeusen
- La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne 3086, Australia.
- CancerProbe Pty Ltd, PO Box 2237, Prahran 3181, Australia.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bleackley MR, Samuel M, Garcia-Ceron D, McKenna JA, Lowe RGT, Pathan M, Zhao K, Ang CS, Mathivanan S, Anderson MA. Extracellular Vesicles From the Cotton Pathogen Fusarium oxysporum f. sp. vasinfectum Induce a Phytotoxic Response in Plants. Front Plant Sci 2019; 10:1610. [PMID: 31998330 PMCID: PMC6965325 DOI: 10.3389/fpls.2019.01610] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/15/2019] [Indexed: 05/17/2023]
Abstract
Extracellular vesicles (EVs) represent a system for the coordinated secretion of a variety of molecular cargo including proteins, lipids, nucleic acids, and metabolites. They have an essential role in intercellular communication in multicellular organisms and have more recently been implicated in host-pathogen interactions. Study of the role for EVs in fungal biology has focused on pathogenic yeasts that are major pathogens in humans. In this study we have expanded the investigation of fungal EVs to plant pathogens, specifically the major cotton pathogen Fusarium oxysporum f. sp. vasinfectum. EVs isolated from F. oxysporum f. sp. vasinfectum culture medium have a morphology and size distribution similar to EVs from yeasts such as Candida albicans and Cryptococcus neoformans. A unique feature of the EVs from F. oxysporum f. sp. vasinfectum is their purple color, which is predicted to arise from a napthoquinone pigment being packaged into the EVs. Proteomic analysis of F. oxysporum f. sp. vasinfectum EVs revealed that they are enriched in proteins that function in synthesis of polyketides as well as proteases and proteins that function in basic cellular processes. Infiltration of F. oxysporum f. sp. vasinfectum EVs into the leaves of cotton or N. benthamiana plants led to a phytotoxic response. These observations lead to the hypothesis that F. oxysporum f. sp. vasinfectum EVs are likely to play a crucial role in the infection process.
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Affiliation(s)
- Mark R. Bleackley
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Monisha Samuel
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Donovan Garcia-Ceron
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - James A. McKenna
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Rohan G. T. Lowe
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Mohashin Pathan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Kening Zhao
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Ching-Seng Ang
- Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Marilyn A. Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
- *Correspondence: Marilyn A. Anderson,
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Affiliation(s)
- Suresh Mathivanan
- Editor and Chair of Communications, Australian Society for Biochemistry and Molecular Biology, Laboratory head, Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences (LIMS), La Trobe University, Melbourne, Australia
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Théry C, Witwer KW, Aikawa E, Alcaraz MJ, Anderson JD, Andriantsitohaina R, Antoniou A, Arab T, Archer F, Atkin-Smith GK, Ayre DC, Bach JM, Bachurski D, Baharvand H, Balaj L, Baldacchino S, Bauer NN, Baxter AA, Bebawy M, Beckham C, Bedina Zavec A, Benmoussa A, Berardi AC, Bergese P, Bielska E, Blenkiron C, Bobis-Wozowicz S, Boilard E, Boireau W, Bongiovanni A, Borràs FE, Bosch S, Boulanger CM, Breakefield X, Breglio AM, Brennan MÁ, Brigstock DR, Brisson A, Broekman MLD, Bromberg JF, Bryl-Górecka P, Buch S, Buck AH, Burger D, Busatto S, Buschmann D, Bussolati B, Buzás EI, Byrd JB, Camussi G, Carter DRF, Caruso S, Chamley LW, Chang YT, Chen C, Chen S, Cheng L, Chin AR, Clayton A, Clerici SP, Cocks A, Cocucci E, Coffey RJ, Cordeiro-da-Silva A, Couch Y, Coumans FAW, Coyle B, Crescitelli R, Criado MF, D’Souza-Schorey C, Das S, Datta Chaudhuri A, de Candia P, De Santana EF, De Wever O, del Portillo HA, Demaret T, Deville S, Devitt A, Dhondt B, Di Vizio D, Dieterich LC, Dolo V, Dominguez Rubio AP, Dominici M, Dourado MR, Driedonks TAP, Duarte FV, Duncan HM, Eichenberger RM, Ekström K, EL Andaloussi S, Elie-Caille C, Erdbrügger U, Falcón-Pérez JM, Fatima F, Fish JE, Flores-Bellver M, Försönits A, Frelet-Barrand A, Fricke F, Fuhrmann G, Gabrielsson S, Gámez-Valero A, Gardiner C, Gärtner K, Gaudin R, Gho YS, Giebel B, Gilbert C, Gimona M, Giusti I, Goberdhan DCI, Görgens A, Gorski SM, Greening DW, Gross JC, Gualerzi A, Gupta GN, Gustafson D, Handberg A, Haraszti RA, Harrison P, Hegyesi H, Hendrix A, Hill AF, Hochberg FH, Hoffmann KF, Holder B, Holthofer H, Hosseinkhani B, Hu G, Huang Y, Huber V, Hunt S, Ibrahim AGE, Ikezu T, Inal JM, Isin M, Ivanova A, Jackson HK, Jacobsen S, Jay SM, Jayachandran M, Jenster G, Jiang L, Johnson SM, Jones JC, Jong A, Jovanovic-Talisman T, Jung S, Kalluri R, Kano SI, Kaur S, Kawamura Y, Keller ET, Khamari D, Khomyakova E, Khvorova A, Kierulf P, Kim KP, Kislinger T, Klingeborn M, Klinke DJ, Kornek M, Kosanović MM, Kovács ÁF, Krämer-Albers EM, Krasemann S, Krause M, Kurochkin IV, Kusuma GD, Kuypers S, Laitinen S, Langevin SM, Languino LR, Lannigan J, Lässer C, Laurent LC, Lavieu G, Lázaro-Ibáñez E, Le Lay S, Lee MS, Lee YXF, Lemos DS, Lenassi M, Leszczynska A, Li ITS, Liao K, Libregts SF, Ligeti E, Lim R, Lim SK, Linē A, Linnemannstöns K, Llorente A, Lombard CA, Lorenowicz MJ, Lörincz ÁM, Lötvall J, Lovett J, Lowry MC, Loyer X, Lu Q, Lukomska B, Lunavat TR, Maas SLN, Malhi H, Marcilla A, Mariani J, Mariscal J, Martens-Uzunova ES, Martin-Jaular L, Martinez MC, Martins VR, Mathieu M, Mathivanan S, Maugeri M, McGinnis LK, McVey MJ, Meckes DG, Meehan KL, Mertens I, Minciacchi VR, Möller A, Møller Jørgensen M, Morales-Kastresana A, Morhayim J, Mullier F, Muraca M, Musante L, Mussack V, Muth DC, Myburgh KH, Najrana T, Nawaz M, Nazarenko I, Nejsum P, Neri C, Neri T, Nieuwland R, Nimrichter L, Nolan JP, Nolte-’t Hoen ENM, Noren Hooten N, O’Driscoll L, O’Grady T, O’Loghlen A, Ochiya T, Olivier M, Ortiz A, Ortiz LA, Osteikoetxea X, Østergaard O, Ostrowski M, Park J, Pegtel DM, Peinado H, Perut F, Pfaffl MW, Phinney DG, Pieters BCH, Pink RC, Pisetsky DS, Pogge von Strandmann E, Polakovicova I, Poon IKH, Powell BH, Prada I, Pulliam L, Quesenberry P, Radeghieri A, Raffai RL, Raimondo S, Rak J, Ramirez MI, Raposo G, Rayyan MS, Regev-Rudzki N, Ricklefs FL, Robbins PD, Roberts DD, Rodrigues SC, Rohde E, Rome S, Rouschop KMA, Rughetti A, Russell AE, Saá P, Sahoo S, Salas-Huenuleo E, Sánchez C, Saugstad JA, Saul MJ, Schiffelers RM, Schneider R, Schøyen TH, Scott A, Shahaj E, Sharma S, Shatnyeva O, Shekari F, Shelke GV, Shetty AK, Shiba K, Siljander PRM, Silva AM, Skowronek A, Snyder OL, Soares RP, Sódar BW, Soekmadji C, Sotillo J, Stahl PD, Stoorvogel W, Stott SL, Strasser EF, Swift S, Tahara H, Tewari M, Timms K, Tiwari S, Tixeira R, Tkach M, Toh WS, Tomasini R, Torrecilhas AC, Tosar JP, Toxavidis V, Urbanelli L, Vader P, van Balkom BWM, van der Grein SG, Van Deun J, van Herwijnen MJC, Van Keuren-Jensen K, van Niel G, van Royen ME, van Wijnen AJ, Vasconcelos MH, Vechetti IJ, Veit TD, Vella LJ, Velot É, Verweij FJ, Vestad B, Viñas JL, Visnovitz T, Vukman KV, Wahlgren J, Watson DC, Wauben MHM, Weaver A, Webber JP, Weber V, Wehman AM, Weiss DJ, Welsh JA, Wendt S, Wheelock AM, Wiener Z, Witte L, Wolfram J, Xagorari A, Xander P, Xu J, Yan X, Yáñez-Mó M, Yin H, Yuana Y, Zappulli V, Zarubova J, Žėkas V, Zhang JY, Zhao Z, Zheng L, Zheutlin AR, Zickler AM, Zimmermann P, Zivkovic AM, Zocco D, Zuba-Surma EK. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines. J Extracell Vesicles 2018; 7:1535750. [PMID: 30637094 PMCID: PMC6322352 DOI: 10.1080/20013078.2018.1535750] [Citation(s) in RCA: 6219] [Impact Index Per Article: 1036.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 11/04/2022] Open
Abstract
The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.
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Affiliation(s)
- Clotilde Théry
- Institut Curie, INSERM U932, PSL Research University, Paris, France
| | - Kenneth W Witwer
- The Johns Hopkins University School of Medicine, Department of Molecular and Comparative Pathobiology, Baltimore, MD, USA
- The Johns Hopkins University School of Medicine, Department of Neurology, Baltimore, MD, USA
| | - Elena Aikawa
- Brigham and Women’s Hospital, Center for Interdisciplinary Cardiovascular Sciences, Boston, MA, USA
- Harvard Medical School, Cardiovascular Medicine, Boston, MA, USA
| | - Maria Jose Alcaraz
- Interuniversity Research Institute for Molecular Recognition and Technological Development (IDM), University of Valencia, Polytechnic University of Valencia, Valencia, Spain
| | | | | | - Anna Antoniou
- German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany
- University Hospital Bonn (UKB), Bonn, Germany
| | - Tanina Arab
- Université de Lille, INSERM, U-1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse - PRISM, Lille, France
| | - Fabienne Archer
- University of Lyon, INRA, EPHE, UMR754 Viral Infections and Comparative Pathology, Lyon, France
| | - Georgia K Atkin-Smith
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - D Craig Ayre
- Atlantic Cancer Research Institute, Moncton, Canada
- Mount Allison University, Department of Chemistry and Biochemistry, Sackville, Canada
| | - Jean-Marie Bach
- Université Bretagne Loire, Oniris, INRA, IECM, Nantes, France
| | - Daniel Bachurski
- University of Cologne, Department of Internal Medicine I, Cologne, Germany
| | - Hossein Baharvand
- Royan Institute for Stem Cell Biology and Technology, ACECR, Cell Science Research Center, Department of Stem Cells and Developmental Biology, Tehran, Iran
- University of Science and Culture, ACECR, Department of Developmental Biology, Tehran, Iran
| | - Leonora Balaj
- Massachusetts General Hospital, Department of Neurosurgery, Boston, MA, USA
| | | | - Natalie N Bauer
- University of South Alabama, Department of Pharmacology, Center for Lung Biology, Mobile, AL, USA
| | - Amy A Baxter
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Mary Bebawy
- University of Technology Sydney, Discipline of Pharmacy, Graduate School of Health, Sydney, Australia
| | | | - Apolonija Bedina Zavec
- National Institute of Chemistry, Department of Molecular Biology and Nanobiotechnology, Ljubljana, Slovenia
| | - Abderrahim Benmoussa
- Université Laval, Centre de Recherche du CHU de Québec, Department of Infectious Diseases and Immunity, Quebec City, Canada
| | | | - Paolo Bergese
- CSGI - Research Center for Colloids and Nanoscience, Florence, Italy
- INSTM - National Interuniversity Consortium of Materials Science and Technology, Florence, Italy
- University of Brescia, Department of Molecular and Translational Medicine, Brescia, Italy
| | - Ewa Bielska
- University of Birmingham, Institute of Microbiology and Infection, Birmingham, UK
| | | | - Sylwia Bobis-Wozowicz
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Kraków, Poland
| | - Eric Boilard
- Université Laval, Centre de Recherche du CHU de Québec, Department of Infectious Diseases and Immunity, Quebec City, Canada
| | - Wilfrid Boireau
- FEMTO-ST Institute, UBFC, CNRS, ENSMM, UTBM, Besançon, France
| | - Antonella Bongiovanni
- Institute of Biomedicine and Molecular Immunology (IBIM), National Research Council (CNR) of Italy, Palermo, Italy
| | - Francesc E Borràs
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, REMAR-IVECAT Group, Badalona, Spain
- Germans Trias i Pujol University Hospital, Nephrology Service, Badalona, Spain
- Universitat Autònoma de Barcelona, Department of Cell Biology, Physiology & Immunology, Barcelona, Spain
| | - Steffi Bosch
- Université Bretagne Loire, Oniris, INRA, IECM, Nantes, France
| | - Chantal M Boulanger
- INSERM UMR-S 970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Xandra Breakefield
- Massachusetts General Hospital and Neuroscience Program, Harvard Medical School, Department of Neurology and Radiology, Boston, MA, USA
| | - Andrew M Breglio
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- National Institutes of Health, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, USA
| | - Meadhbh Á Brennan
- Harvard University, School of Engineering and Applied Sciences, Cambridge, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Department of Neurology, Boston, MA, USA
- Université de Nantes, INSERM UMR 1238, Bone Sarcoma and Remodeling of Calcified Tissues, PhyOS, Nantes, France
| | - David R Brigstock
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Alain Brisson
- UMR-CBMN, CNRS-Université de Bordeaux, Bordeaux, France
| | - Marike LD Broekman
- Haaglanden Medical Center, Department of Neurosurgery, The Hague, The Netherlands
- Leiden University Medical Center, Department of Neurosurgery, Leiden, The Netherlands
- Massachusetts General Hospital, Department of Neurology, Boston, MA, USA
| | - Jacqueline F Bromberg
- Memorial Sloan Kettering Cancer Center, Department of Medicine, New York City, NY, USA
- Weill Cornell Medicine, Department of Medicine, New York City, NY, USA
| | | | - Shilpa Buch
- University of Nebraska Medical Center, Department of Pharmacology and Experimental Neuroscience, Omaha, NE, USA
| | - Amy H Buck
- University of Edinburgh, Institute of Immunology & Infection Research, Edinburgh, UK
| | - Dylan Burger
- Kidney Research Centre, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Sara Busatto
- Mayo Clinic, Department of Transplantation, Jacksonville, FL, USA
- University of Brescia, Department of Molecular and Translational Medicine, Brescia, Italy
| | - Dominik Buschmann
- Technical University of Munich, TUM School of Life Sciences Weihenstephan, Division of Animal Physiology and Immunology, Freising, Germany
| | - Benedetta Bussolati
- University of Torino, Department of Molecular Biotechnology and Health Sciences, Torino, Italy
| | - Edit I Buzás
- MTA-SE Immuno-Proteogenomics Research Groups, Budapest, Hungary
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | - James Bryan Byrd
- University of Michigan, Department of Medicine, Ann Arbor, MI, USA
| | - Giovanni Camussi
- University of Torino, Department of Medical Sciences, Torino, Italy
| | - David RF Carter
- Oxford Brookes University, Department of Biological and Medical Sciences, Oxford, UK
| | - Sarah Caruso
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Lawrence W Chamley
- University of Auckland, Department of Obstetrics and Gynaecology, Auckland, New Zealand
| | - Yu-Ting Chang
- National Taiwan University Hospital, Department of Internal Medicine, Taipei, Taiwan
| | - Chihchen Chen
- National Tsing Hua University, Department of Power Mechanical Engineering, Hsinchu, Taiwan
- National Tsing Hua University, Institute of Nanoengineering and Microsystems, Hsinchu, Taiwan
| | - Shuai Chen
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Reproductive Biology, Dummerstorf, Germany
| | - Lesley Cheng
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | | | - Aled Clayton
- Cardiff University, School of Medicine, Cardiff, UK
| | | | - Alex Cocks
- Cardiff University, School of Medicine, Cardiff, UK
| | - Emanuele Cocucci
- The Ohio State University, College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, Columbus, OH, USA
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, USA
| | - Robert J Coffey
- Vanderbilt University Medical Center, Epithelial Biology Center, Department of Medicine, Nashville, TN, USA
| | | | - Yvonne Couch
- University of Oxford, Radcliffe Department of Medicine, Acute Stroke Programme - Investigative Medicine, Oxford, UK
| | - Frank AW Coumans
- Academic Medical Centre of the University of Amsterdam, Department of Clinical Chemistry and Vesicle Observation Centre, Amsterdam, The Netherlands
| | - Beth Coyle
- The University of Nottingham, School of Medicine, Children’s Brain Tumour Research Centre, Nottingham, UK
| | - Rossella Crescitelli
- University of Gothenburg, Institute of Medicine at Sahlgrenska Academy, Krefting Research Centre, Gothenburg, Sweden
| | | | | | - Saumya Das
- Massachusetts General Hospital, Boston, MA, USA
| | - Amrita Datta Chaudhuri
- The Johns Hopkins University School of Medicine, Department of Neurology, Baltimore, MD, USA
| | | | - Eliezer F De Santana
- The Sociedade Beneficente Israelita Brasileira Albert Einstein, São Paulo, Brazil
| | - Olivier De Wever
- Cancer Research Institute Ghent, Ghent, Belgium
- Ghent University, Department of Radiation Oncology and Experimental Cancer Research, Laboratory of Experimental Cancer Research, Ghent, Belgium
| | - Hernando A del Portillo
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Institut d’Investigació Germans Trias i Pujol (IGTP), PVREX group, Badalona, Spain
- ISGlobal, Hospital Clínic - Universitat de Barcelona, PVREX Group, Barcelona, Spain
| | - Tanguy Demaret
- Université Catholique de Louvain, Institut de Recherche Expérimentale et Clinique (IREC), Laboratory of Pediatric Hepatology and Cell Therapy, Brussels, Belgium
| | - Sarah Deville
- Universiteit Hasselt, Diepenbeek, Belgium
- Vlaamse Instelling voor Technologisch Onderzoek (VITO), Mol, Belgium
| | - Andrew Devitt
- Aston University, School of Life & Health Sciences, Birmingham, UK
| | - Bert Dhondt
- Cancer Research Institute Ghent, Ghent, Belgium
- Ghent University Hospital, Department of Urology, Ghent, Belgium
- Ghent University, Department of Radiation Oncology and Experimental Cancer Research, Laboratory of Experimental Cancer Research, Ghent, Belgium
| | | | | | - Vincenza Dolo
- University of L’Aquila, Department of Life, Health and Environmental Sciences, L’Aquila, Italy
| | - Ana Paula Dominguez Rubio
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Buenos Aires, Argentina
| | - Massimo Dominici
- TPM of Mirandola, Mirandola, Italy
- University of Modena and Reggio Emilia, Division of Oncology, Modena, Italy
| | - Mauricio R Dourado
- University of Campinas, Piracicaba Dental School, Department of Oral Diagnosis, Piracicaba, Brazil
- University of Oulu, Faculty of Medicine, Cancer and Translational Medicine Research Unit, Oulu, Finland
| | - Tom AP Driedonks
- Utrecht University, Faculty of Veterinary Medicine, Department of Biochemistry and Cell Biology, Utrecht, The Netherlands
| | | | - Heather M Duncan
- McGill University, Division of Experimental Medicine, Montreal, Canada
- McGill University, The Research Institute of the McGill University Health Centre, Child Health and Human Development Program, Montreal, Canada
| | - Ramon M Eichenberger
- James Cook University, Australian Institute of Tropical Health and Medicine, Centre for Biodiscovery and Molecular Development of Therapeutics, Cairns, Australia
| | - Karin Ekström
- University of Gothenburg, Institute of Clinical Sciences at Sahlgrenska Academy, Department of Biomaterials, Gothenburg, Sweden
| | - Samir EL Andaloussi
- Evox Therapeutics Limited, Oxford, UK
- Karolinska Institute, Stockholm, Sweden
| | | | - Uta Erdbrügger
- University of Virginia Health System, Department of Medicine, Division of Nephrology, Charlottesville, VA, USA
| | - Juan M Falcón-Pérez
- CIC bioGUNE, CIBERehd, Exosomes Laboratory & Metabolomics Platform, Derio, Spain
- IKERBASQUE Research Science Foundation, Bilbao, Spain
| | - Farah Fatima
- University of São Paulo, Ribeirão Preto Medical School, Department of Pathology and Forensic Medicine, Ribeirão Preto, Brazil
| | - Jason E Fish
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- University of Toronto, Department of Laboratory Medicine and Pathobiology, Toronto, Canada
| | - Miguel Flores-Bellver
- University of Colorado, School of Medicine, Department of Ophthalmology, Cell Sight-Ocular Stem Cell and Regeneration Program, Aurora, CO, USA
| | - András Försönits
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | | | - Fabia Fricke
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Applied Tumor Biology, Heidelberg, Germany
- University Hospital Heidelberg, Institute of Pathology, Applied Tumor Biology, Heidelberg, Germany
| | - Gregor Fuhrmann
- Helmholtz-Centre for Infection Research, Braunschweig, Germany
- Helmholtz-Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
- Saarland University, Saarbrücken, Germany
| | - Susanne Gabrielsson
- Karolinska Institute, Department of Medicine Solna, Division for Immunology and Allergy, Stockholm, Sweden
| | - Ana Gámez-Valero
- Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, REMAR-IVECAT Group, Badalona, Spain
- Universitat Autònoma de Barcelona, Hospital Universitari and Health Sciences Research Institute Germans Trias i Pujol, Department of Pathology, Barcelona, Spain
| | | | - Kathrin Gärtner
- Helmholtz Center Munich German Research Center for Environmental Health, Research Unit Gene Vectors, Munich, Germany
| | - Raphael Gaudin
- INSERM U1110, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Yong Song Gho
- POSTECH (Pohang University of Science and Technology), Department of Life Sciences, Pohang, South Korea
| | - Bernd Giebel
- University Hospital Essen, University Duisburg-Essen, Institute for Transfusion Medicine, Essen, Germany
| | - Caroline Gilbert
- Université Laval, Centre de Recherche du CHU de Québec, Department of Infectious Diseases and Immunity, Quebec City, Canada
| | - Mario Gimona
- Paracelsus Medical University, GMP Unit, Salzburg, Austria
| | - Ilaria Giusti
- University of L’Aquila, Department of Life, Health and Environmental Sciences, L’Aquila, Italy
| | - Deborah CI Goberdhan
- University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, UK
| | - André Görgens
- Evox Therapeutics Limited, Oxford, UK
- Karolinska Institute, Clinical Research Center, Department of Laboratory Medicine, Stockholm, Sweden
- University Hospital Essen, University Duisburg-Essen, Institute for Transfusion Medicine, Essen, Germany
| | - Sharon M Gorski
- BC Cancer, Canada’s Michael Smith Genome Sciences Centre, Vancouver, Canada
- Simon Fraser University, Department of Molecular Biology and Biochemistry, Burnaby, Canada
| | - David W Greening
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Julia Christina Gross
- University Medical Center Göttingen, Developmental Biochemistry, Göttingen, Germany
- University Medical Center Göttingen, Hematology and Oncology, Göttingen, Germany
| | - Alice Gualerzi
- IRCCS Fondazione Don Carlo Gnocchi, Laboratory of Nanomedicine and Clinical Biophotonics (LABION), Milan, Italy
| | - Gopal N Gupta
- Loyola University Chicago, Department of Urology, Maywood, IL, USA
| | - Dakota Gustafson
- University of Toronto, Department of Laboratory Medicine and Pathobiology, Toronto, Canada
| | - Aase Handberg
- Aalborg University Hospital, Department of Clinical Biochemistry, Aalborg, Denmark
- Aalborg University, Clinical Institute, Aalborg, Denmark
| | - Reka A Haraszti
- University of Massachusetts Medical School, RNA Therapeutics Institute, Worcester, MA, USA
| | | | - Hargita Hegyesi
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | - An Hendrix
- Cancer Research Institute Ghent, Ghent, Belgium
- Ghent University, Department of Radiation Oncology and Experimental Cancer Research, Laboratory of Experimental Cancer Research, Ghent, Belgium
| | - Andrew F Hill
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Fred H Hochberg
- Scintillon Institute, La Jolla, CA, USA
- University of California, San Diego, Department of Neurosurgery, La Jolla, CA, USA
| | - Karl F Hoffmann
- Aberystwyth University, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth, United Kingdom
| | - Beth Holder
- Imperial College London, London, UK
- MRC The Gambia, Fajara, The Gambia
| | | | - Baharak Hosseinkhani
- Hasselt University, Biomedical Research Institute (BIOMED), Department of Medicine and Life Sciences, Hasselt, Belgium
| | - Guoku Hu
- University of Nebraska Medical Center, Department of Pharmacology and Experimental Neuroscience, Omaha, NE, USA
| | - Yiyao Huang
- Nanfang Hospital, Southern Medical University, Department of Clinical Laboratory Medicine, Guangzhou, China
- The Johns Hopkins University School of Medicine, Department of Molecular and Comparative Pathobiology, Baltimore, MD, USA
| | - Veronica Huber
- Fondazione IRCCS Istituto Nazionale dei Tumori, Unit of Immunotherapy of Human Tumors, Milan, Italy
| | | | | | - Tsuneya Ikezu
- Boston University School of Medicine, Boston, MA, USA
| | - Jameel M Inal
- University of Hertfordshire, School of Life and Medical Sciences, Biosciences Research Group, Hatfield, UK
| | - Mustafa Isin
- Istanbul University Oncology Institute, Basic Oncology Department, Istanbul, Turkey
| | - Alena Ivanova
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, Heidelberg, Germany
| | - Hannah K Jackson
- The University of Nottingham, School of Medicine, Children’s Brain Tumour Research Centre, Nottingham, UK
| | - Soren Jacobsen
- Copenhagen Lupus and Vasculitis Clinic, Section 4242 - Rigshospitalet, Copenhagen, Denmark
- University of Copenhagen, Institute of Clinical Medicine, Copenhagen, Denmark
| | - Steven M Jay
- University of Maryland, Fischell Department of Bioengineering, College Park, MD, USA
| | - Muthuvel Jayachandran
- Mayo Clinic, College of Medicine, Department of Physiology and Biomedical Engineering, Rochester, MN, USA
| | | | - Lanzhou Jiang
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Suzanne M Johnson
- University of Manchester, Division of Cancer Sciences, Manchester Cancer Research Centre, Manchester, UK
| | - Jennifer C Jones
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Bethesda, MD, USA
| | - Ambrose Jong
- Children’s Hospital of Los Angeles, Los Angeles, CA, USA
- University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Tijana Jovanovic-Talisman
- City of Hope Comprehensive Cancer Center, Beckman Research Institute, Department of Molecular Medicine, Duarte, CA, USA
| | - Stephanie Jung
- German Research Center for Environmental Health, Institute for Virology, Munich, Germany
| | - Raghu Kalluri
- University of Texas MD Anderson Cancer Center, Department of Cancer Biology, Metastasis Research Center, Houston, TX, USA
| | - Shin-ichi Kano
- The Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - Sukhbir Kaur
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Pathology, Bethesda, MD, USA
| | - Yumi Kawamura
- National Cancer Center Research Institute, Tokyo, Japan
- University of Tsukuba, Tsukuba, Japan
| | - Evan T Keller
- University of Michigan, Biointerfaces Institute, Ann Arbor, MI, USA
- University of Michigan, Department of Urology, Ann Arbor, MI, USA
| | - Delaram Khamari
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | - Elena Khomyakova
- École normale supérieure, Paris, France
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Anastasia Khvorova
- University of Massachusetts Medical School, RNA Therapeutics Institute, Worcester, MA, USA
| | - Peter Kierulf
- Oslo University Hospital, Department of Medical Biochemistry, Blood Cell Research Group, Oslo, Norway
| | - Kwang Pyo Kim
- Kyung Hee University, Department of Applied Chemistry, Yongin, Korea
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- University of Toronto, Department of Medical Biophysics, Toronto, Canada
| | | | - David J Klinke
- West Virginia University, Department of Chemical and Biomedical Engineering and WVU Cancer Institute, Morgantown, WV, USA
- West Virginia University, Department of Microbiology Immunology and Cell Biology, Morgantown, WV, USA
| | - Miroslaw Kornek
- German Armed Forces Central Hospital, Department of General, Visceral and Thoracic Surgery, Koblenz, Germany
- Saarland University Medical Center, Department of Medicine II, Homburg, Germany
| | - Maja M Kosanović
- University of Belgrade, Institute for the Application of Nuclear Energy, INEP, Belgrade, Serbia
| | - Árpád Ferenc Kovács
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | | | - Susanne Krasemann
- University Medical Center Hamburg-Eppendorf, Institute of Neuropathology, Hamburg, Germany
| | - Mirja Krause
- Hudson Institute of Medical Research, Melbourne, Australia
| | | | - Gina D Kusuma
- Hudson Institute of Medical Research, Melbourne, Australia
- Monash University, Melbourne, Australia
| | - Sören Kuypers
- Hasselt University, Biomedical Research Institute (BIOMED), Hasselt, Belgium
| | - Saara Laitinen
- Finnish Red Cross Blood Service, Research and Development, Helsinki, Finland
| | - Scott M Langevin
- Cincinnati Cancer Center, Cincinnati, OH, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lucia R Languino
- Thomas Jefferson University, Sidney Kimmel Medical School, Department of Cancer Biology, Philadelphia, PA, USA
| | - Joanne Lannigan
- University of Virginia, Flow Cytometry Core, School of Medicine, Charlottesville, VA, USA
| | - Cecilia Lässer
- University of Gothenburg, Institute of Medicine at Sahlgrenska Academy, Krefting Research Centre, Gothenburg, Sweden
| | - Louise C Laurent
- University of California, San Diego, Department of Obstetrics, Gynecology, and Reproductive Sciences, La Jolla, CA, USA
| | - Gregory Lavieu
- Institut Curie, INSERM U932, PSL Research University, Paris, France
| | | | - Soazig Le Lay
- INSERM U1063, Université d’Angers, CHU d’Angers, Angers, France
| | - Myung-Shin Lee
- Eulji University, School of Medicine, Daejeon, South Korea
| | | | - Debora S Lemos
- Federal University of Paraná, Department of Genetics, Human Molecular Genetics Laboratory, Curitiba, Brazil
| | - Metka Lenassi
- University of Ljubljana, Faculty of Medicine, Institute of Biochemistry, Ljubljana, Slovenia
| | | | - Isaac TS Li
- University of British Columbia Okanagan, Kelowna, Canada
| | - Ke Liao
- University of Nebraska Medical Center, Department of Pharmacology and Experimental Neuroscience, Omaha, NE, USA
| | - Sten F Libregts
- University of Cambridge School of Clinical Medicine, Addenbrooke’s Hospital, Department of Medicine, Cambridge NIHR BRC Cell Phenotyping Hub, Cambridge, UK
| | - Erzsebet Ligeti
- Semmelweis University, Department of Physiology, Budapest, Hungary
| | - Rebecca Lim
- Hudson Institute of Medical Research, Melbourne, Australia
- Monash University, Melbourne, Australia
| | - Sai Kiang Lim
- Institute of Medical Biology (IMB), Agency for Science and Technology (A*STAR), Singapore
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Karen Linnemannstöns
- University Medical Center Göttingen, Developmental Biochemistry, Göttingen, Germany
- University Medical Center Göttingen, Hematology and Oncology, Göttingen, Germany
| | - Alicia Llorente
- Oslo University Hospital-The Norwegian Radium Hospital, Institute for Cancer Research, Department of Molecular Cell Biology, Oslo, Norway
| | - Catherine A Lombard
- Université Catholique de Louvain, Institut de Recherche Expérimentale et Clinique (IREC), Laboratory of Pediatric Hepatology and Cell Therapy, Brussels, Belgium
| | - Magdalena J Lorenowicz
- Utrecht University, University Medical Center Utrecht, Center for Molecular Medicine & Regenerative Medicine Center, Utrecht, The Netherlands
| | - Ákos M Lörincz
- Semmelweis University, Department of Physiology, Budapest, Hungary
| | - Jan Lötvall
- University of Gothenburg, Institute of Medicine at Sahlgrenska Academy, Krefting Research Centre, Gothenburg, Sweden
| | - Jason Lovett
- Stellenbosch University, Department of Physiological Sciences, Stellenbosch, South Africa
| | - Michelle C Lowry
- Trinity College Dublin, School of Pharmacy and Pharmaceutical Sciences, Panoz Institute & Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Xavier Loyer
- INSERM UMR-S 970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Quan Lu
- Harvard University, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Barbara Lukomska
- Mossakowski Medical Research Centre, NeuroRepair Department, Warsaw, Poland
| | - Taral R Lunavat
- K.G. Jebsen Brain Tumor Research Centre, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sybren LN Maas
- Utrecht University, University Medical Center Utrecht, Department of Neurosurgery, Brain Center Rudolf Magnus, Institute of Neurosciences, Utrecht, The Netherlands
- Utrecht University, University Medical Center Utrecht, Department of Pathology, Utrecht, The Netherlands
| | | | - Antonio Marcilla
- Universitat de València, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Àrea de Parasitologia, Valencia, Spain
- Universitat de València, Health Research Institute La Fe, Joint Research Unit on Endocrinology, Nutrition and Clinical Dietetics, Valencia, Spain
| | - Jacopo Mariani
- Università degli Studi di Milano, Department of Clinical Sciences and Community Health, EPIGET LAB, Milan, Italy
| | | | | | | | | | | | - Mathilde Mathieu
- Institut Curie, INSERM U932, PSL Research University, Paris, France
| | - Suresh Mathivanan
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Marco Maugeri
- University of Gothenburg, Sahlgrenska Academy, Department of Rheumatology and Inflammation Research, Gothenburg, Sweden
| | | | - Mark J McVey
- SickKids Hospital, Department of Anesthesia and Pain Medicine, Toronto, Canada
- University of Toronto, Department of Anesthesia, Toronto, Canada
| | - David G Meckes
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, FL, USA
| | - Katie L Meehan
- The School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Inge Mertens
- University of Antwerp, Centre for Proteomics, Antwerp, Belgium
- Vlaamse Instelling voor Technologisch Onderzoek (VITO), Mol, Belgium
| | - Valentina R Minciacchi
- Georg-Speyer-Haus Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany
| | - Andreas Möller
- QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Malene Møller Jørgensen
- Aalborg University Hospital, Department of Clinical Immunology, Aalborg, Denmark
- EVSEARCH.DK, Denmark
| | - Aizea Morales-Kastresana
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Bethesda, MD, USA
| | | | - François Mullier
- Namur Thrombosis and Hemostasis Center (NTHC), NARILIS, Namur, Belgium
- Université Catholique de Louvain, CHU UCL Namur, Hematology-Hemostasis Laboratory, Yvoir, Belgium
| | - Maurizio Muraca
- University of Padova, Department of Women’s and Children’s Health, Padova, Italy
| | - Luca Musante
- University of Virginia Health System, Department of Medicine, Division of Nephrology, Charlottesville, VA, USA
| | - Veronika Mussack
- Technical University of Munich, TUM School of Life Sciences Weihenstephan, Division of Animal Physiology and Immunology, Freising, Germany
| | - Dillon C Muth
- The Johns Hopkins University School of Medicine, Department of Molecular and Comparative Pathobiology, Baltimore, MD, USA
| | - Kathryn H Myburgh
- Stellenbosch University, Department of Physiological Sciences, Stellenbosch, South Africa
| | - Tanbir Najrana
- Brown University, Women and Infants Hospital, Providence, RI, USA
| | - Muhammad Nawaz
- University of Gothenburg, Sahlgrenska Academy, Department of Rheumatology and Inflammation Research, Gothenburg, Sweden
| | - Irina Nazarenko
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Freiburg, Germany
| | - Peter Nejsum
- Aarhus University, Department of Clinical Medicine, Aarhus, Denmark
| | - Christian Neri
- Sorbonne Université, Centre National de la Recherche Scientifique, Research Unit Biology of Adaptation and Aging (B2A), Team Compensation in Neurodegenerative and Aging (Brain-C), Paris, France
| | - Tommaso Neri
- University of Pisa, Centro Dipartimentale di Biologia Cellulare Cardio-Respiratoria, Pisa, Italy
| | - Rienk Nieuwland
- Academic Medical Centre of the University of Amsterdam, Department of Clinical Chemistry and Vesicle Observation Centre, Amsterdam, The Netherlands
| | - Leonardo Nimrichter
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia, Rio de Janeiro, Brazil
| | | | - Esther NM Nolte-’t Hoen
- Utrecht University, Faculty of Veterinary Medicine, Department of Biochemistry and Cell Biology, Utrecht, The Netherlands
| | - Nicole Noren Hooten
- National Institutes of Health, National Institute on Aging, Baltimore, MD, USA
| | - Lorraine O’Driscoll
- Trinity College Dublin, School of Pharmacy and Pharmaceutical Sciences, Panoz Institute & Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Tina O’Grady
- University of Liège, GIGA-R(MBD), PSI Laboratory, Liège, Belgium
| | - Ana O’Loghlen
- Queen Mary University of London, Blizard Institute, Epigenetics & Cellular Senescence Group, London, UK
| | - Takahiro Ochiya
- National Cancer Center Research Institute, Division of Molecular and Cellular Medicine, Tokyo, Japan
| | - Martin Olivier
- McGill University, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Alberto Ortiz
- IIS-Fundacion Jimenez Diaz-UAM, Department of Nephrology and Hypertension, Madrid, Spain
- Spanish Kidney Research Network, REDINREN, Madrid, Spain
- Universidad Autónoma de Madrid, School of Medicine, Department of Medicine, Madrid, Spain
| | - Luis A Ortiz
- Graduate School of Public Health at the University of Pittsburgh, Division of Occupational and Environmental Medicine, Pittsburgh, PA, USA
| | | | - Ole Østergaard
- Statens Serum Institut, Department of Autoimmunology and Biomarkers, Copenhagen, Denmark
- University of Copenhagen, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Matias Ostrowski
- University of Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Buenos Aires, Argentina
| | - Jaesung Park
- POSTECH (Pohang University of Science and Technology), Department of Life Sciences, Pohang, South Korea
| | - D. Michiel Pegtel
- Amsterdam University Medical Centers, Department of Pathology, Amsterdam, The Netherlands
| | - Hector Peinado
- Spanish National Cancer Research Center (CNIO), Molecular Oncology Programme, Microenvironment and Metastasis Laboratory, Madrid, Spain
| | - Francesca Perut
- IRCCS - Istituto Ortopedico Rizzoli, Laboratory for Orthopaedic Pathophysiology and Regenerative Medicine, Bologna, Italy
| | - Michael W Pfaffl
- Technical University of Munich, TUM School of Life Sciences Weihenstephan, Division of Animal Physiology and Immunology, Freising, Germany
| | - Donald G Phinney
- The Scripps Research Institute-Scripps Florida, Department of Molecular Medicine, Jupiter, FL, USA
| | - Bartijn CH Pieters
- Radboud University Medical Center, Department of Rheumatology, Nijmegen, The Netherlands
| | - Ryan C Pink
- Oxford Brookes University, Department of Biological and Medical Sciences, Oxford, UK
| | - David S Pisetsky
- Duke University Medical Center, Departments of Medicine and Immunology, Durham, NC, USA
- Durham VAMC, Medical Research Service, Durham, NC, USA
| | | | - Iva Polakovicova
- Pontificia Universidad Católica de Chile, Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
- Pontificia Universidad Católica de Chile, Faculty of Medicine, Department of Hematology-Oncology, Santiago, Chile
| | - Ivan KH Poon
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Bonita H Powell
- The Johns Hopkins University School of Medicine, Department of Molecular and Comparative Pathobiology, Baltimore, MD, USA
| | | | - Lynn Pulliam
- University of California, San Francisco, CA, USA
- Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Peter Quesenberry
- The Warren Alpert Medical School of Brown University, Department of Medicine, Providence, RI, USA
| | - Annalisa Radeghieri
- CSGI - Research Center for Colloids and Nanoscience, Florence, Italy
- University of Brescia, Department of Molecular and Translational Medicine, Brescia, Italy
| | - Robert L Raffai
- Department of Veterans Affairs, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Stefania Raimondo
- University of Palermo, Department of Biopathology and Medical Biotechnologies, Palermo, Italy
| | - Janusz Rak
- McGill University, Montreal, Canada
- McGill University, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Marcel I Ramirez
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
- Universidade Federal de Paraná, Paraná, Brazil
| | - Graça Raposo
- Institut Curie, CNRS UMR144, PSL Research University, Paris, France
| | - Morsi S Rayyan
- University of Michigan Medical School, Ann Arbor, MI, USA
| | - Neta Regev-Rudzki
- Weizmann Institute of Science, Department of Biomolecular Sciences, Rehovot, Israel
| | - Franz L Ricklefs
- University Medical Center Hamburg-Eppendorf, Department of Neurosurgery, Hamburg, Germany
| | - Paul D Robbins
- University of Minnesota Medical School, Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, MN, USA
| | - David D Roberts
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Laboratory of Pathology, Bethesda, MD, USA
| | | | - Eva Rohde
- Paracelsus Medical University, Department of Transfusion Medicine, Salzburg, Austria
- Paracelsus Medical University, GMP Unit, Salzburg, Austria
- Spinal Cord Injury & Tissue Regeneration Center Salzburg (SCI-TReCS), Salzburg, Austria
| | - Sophie Rome
- University of Lyon, Lyon-Sud Faculty of Medicine, CarMeN Laboratory (UMR INSERM 1060-INRA 1397), Pierre-Bénite, France
| | - Kasper MA Rouschop
- Maastricht University, GROW, School for Oncology and Developmental Biology, Maastricht Radiation Oncology (MaastRO) Lab, Maastricht, The Netherlands
| | - Aurelia Rughetti
- Sapienza University of Rome, Department of Experimental Medicine, Rome, Italy
| | | | - Paula Saá
- American Red Cross, Scientific Affairs, Gaithersburg, MD, USA
| | - Susmita Sahoo
- Icahn School of Medicine at Mount Sinai, Department of Medicine, Cardiology, New York City, NY, USA
| | - Edison Salas-Huenuleo
- Advanced Center for Chronic Diseases, Santiago, Chile
- University of Chile, Faculty of Chemical and Pharmaceutical Science, Laboratory of Nanobiotechnology and Nanotoxicology, Santiago, Chile
| | - Catherine Sánchez
- Clínica las Condes, Extracellular Vesicles in Personalized Medicine Group, Santiago, Chile
| | - Julie A Saugstad
- Oregon Health & Science University, Department of Anesthesiology & Perioperative Medicine, Portland, OR, USA
| | - Meike J Saul
- Technische Universität Darmstadt, Department of Biology, Darmstadt, Germany
| | - Raymond M Schiffelers
- University Medical Center Utrecht, Laboratory for Clinical Chemistry & Hematology, Utrecht, The Netherlands
| | - Raphael Schneider
- University of Toronto, Department of Laboratory Medicine and Pathobiology, Toronto, Canada
- University of Toronto, Department of Medicine, Division of Neurology, Toronto, Canada
| | - Tine Hiorth Schøyen
- The Johns Hopkins University School of Medicine, Department of Molecular and Comparative Pathobiology, Baltimore, MD, USA
| | | | - Eriomina Shahaj
- Fondazione IRCCS Istituto Nazionale dei Tumori, Unit of Immunotherapy of Human Tumors, Milan, Italy
| | - Shivani Sharma
- University of California, Los Angeles, California NanoSystems Institute, Los Angeles, CA, USA
- University of California, Los Angeles, Department of Pathology and Laboratory Medicine, Los Angeles, CA, USA
- University of California, Los Angeles, Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Olga Shatnyeva
- AstraZeneca, Discovery Sciences, IMED Biotech Unit, Gothenburg, Sweden
| | - Faezeh Shekari
- Royan Institute for Stem Cell Biology and Technology, ACECR, Cell Science Research Center, Department of Stem Cells and Developmental Biology, Tehran, Iran
| | - Ganesh Vilas Shelke
- University of Gothenburg, Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Cancer Center, Gothenburg, Sweden
- University of Gothenburg, Institute of Medicine at Sahlgrenska Academy, Krefting Research Centre, Gothenburg, Sweden
| | - Ashok K Shetty
- Research Service, Olin E. Teague Veterans’ Medical Center, Temple, TX, USA
- Texas A&M University College of Medicine, Institute for Regenerative Medicine and Department of Molecular and Cellular Medicine, College Station, TX, USA
| | | | - Pia R-M Siljander
- University of Helsinki, EV Core Facility, Helsinki, Finland
- University of Helsinki, Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme, EV group, Helsinki, Finland
| | - Andreia M Silva
- INEB - Instituto de Engenharia Biomédica, Porto, Portugal
- University of Porto, i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- University of Porto, ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Porto, Portugal
| | - Agata Skowronek
- Maria Sklodowska-Curie Institute - Oncology Center, Gliwice Branch, Gliwice, Poland
| | - Orman L Snyder
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, USA
| | | | - Barbara W Sódar
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | - Carolina Soekmadji
- QIMR Berghofer Medical Research Institute, Herston, Australia
- The University of Queensland, Brisbane, Australia
| | - Javier Sotillo
- James Cook University, Australian Institute of Tropical Health and Medicine, Centre for Biodiscovery and Molecular Development of Therapeutics, Cairns, Australia
| | | | - Willem Stoorvogel
- Utrecht University, Faculty of Veterinary Medicine, Department of Biochemistry and Cell Biology, Utrecht, The Netherlands
| | - Shannon L Stott
- Harvard Medical School, Department of Medicine, Boston, MA, USA
- Massachusetts General Cancer Center, Boston, MA, USA
| | - Erwin F Strasser
- FAU Erlangen-Nuremberg, Transfusion and Haemostaseology Department, Erlangen, Germany
| | - Simon Swift
- University of Auckland, Department of Molecular Medicine and Pathology, Auckland, New Zealand
| | - Hidetoshi Tahara
- Hiroshima University, Institute of Biomedical & Health Sciences, Department of Cellular and Molecular Biology, Hiroshima, Japan
| | - Muneesh Tewari
- University of Michigan, Biointerfaces Institute, Ann Arbor, MI, USA
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI, USA
- University of Michigan, Department of Internal Medicine - Hematology/Oncology Division, Ann Arbor, MI, USA
| | - Kate Timms
- University of Manchester, Manchester, UK
| | - Swasti Tiwari
- Georgetown University, Department of Medicine, Washington, DC, USA
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Department of Molecular Medicine & Biotechnology, Lucknow, India
| | - Rochelle Tixeira
- La Trobe University, La Trobe Institute for Molecular Science, Department of Biochemistry and Genetics, Bundoora, Australia
| | - Mercedes Tkach
- Institut Curie, INSERM U932, PSL Research University, Paris, France
| | - Wei Seong Toh
- National University of Singapore, Faculty of Dentistry, Singapore
| | - Richard Tomasini
- INSERM U1068, Aix Marseille University, CNRS UMR7258, Marseille, France
| | | | - Juan Pablo Tosar
- Institut Pasteur de Montevideo, Functional Genomics Unit, Montevideo, Uruguay
- Universidad de la República, Faculty of Science, Nuclear Research Center, Analytical Biochemistry Unit, Montevideo, Uruguay
| | | | - Lorena Urbanelli
- University of Perugia, Department of Chemistry, Biology and Biotechnology, Perugia, Italy
| | - Pieter Vader
- University Medical Center Utrecht, Laboratory for Clinical Chemistry & Hematology, Utrecht, The Netherlands
| | - Bas WM van Balkom
- University Medical Center Utrecht, Department of Nephrology and Hypertension, Utrecht, The Netherlands
| | - Susanne G van der Grein
- Utrecht University, Faculty of Veterinary Medicine, Department of Biochemistry and Cell Biology, Utrecht, The Netherlands
| | - Jan Van Deun
- Cancer Research Institute Ghent, Ghent, Belgium
- Ghent University, Department of Radiation Oncology and Experimental Cancer Research, Laboratory of Experimental Cancer Research, Ghent, Belgium
| | - Martijn JC van Herwijnen
- Utrecht University, Faculty of Veterinary Medicine, Department of Biochemistry and Cell Biology, Utrecht, The Netherlands
| | | | | | - Martin E van Royen
- Department of Pathology, Erasmus MC, Erasmus Optical Imaging Centre, Rotterdam, The Netherlands
| | | | - M Helena Vasconcelos
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- University of Porto, Faculty of Pharmacy (FFUP), Porto, Portugal
- University of Porto, i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Ivan J Vechetti
- University of Kentucky, College of Medicine, Department of Physiology, Lexington, KY, USA
| | - Tiago D Veit
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Microbiologia, Imunologia e Parasitologia, Porto Alegre, Brazil
| | - Laura J Vella
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia
- The University of Melbourne, The Department of Medicine, Melbourne, Australia
| | - Émilie Velot
- UMR 7365 CNRS-Université de Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Beate Vestad
- Oslo University Hospital Rikshospitalet, Research Institute of Internal Medicine, Oslo, Norway
- Regional Research Network on Extracellular Vesicles, RRNEV, Oslo, Norway
- University of Oslo, Institute of Clinical Medicine, Oslo, Norway
| | - Jose L Viñas
- Kidney Research Centre, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Tamás Visnovitz
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | - Krisztina V Vukman
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | - Jessica Wahlgren
- University of Gothenburg, The Sahlgrenska Academy, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, Mölndal, Sweden
| | - Dionysios C Watson
- Case Western Reserve University, Department of Medicine, Cleveland, OH, USA
- University Hospitals Cleveland Medical Center, Department of Medicine, Cleveland, OH, USA
| | - Marca HM Wauben
- Utrecht University, Faculty of Veterinary Medicine, Department of Biochemistry and Cell Biology, Utrecht, The Netherlands
| | - Alissa Weaver
- Vanderbilt University School of Medicine, Department of Cell and Developmental Biology, Nashville, TN, USA
| | | | - Viktoria Weber
- Danube University Krems, Department for Biomedical Research and Christian Doppler Laboratory for Innovative Therapy Approaches in Sepsis, Krems an der Donau, Austria
| | - Ann M Wehman
- University of Würzburg, Rudolf Virchow Center, Würzburg, Germany
| | - Daniel J Weiss
- The University of Vermont Medical Center, Department of Medicine, Burlington, VT, USA
| | - Joshua A Welsh
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Bethesda, MD, USA
| | - Sebastian Wendt
- University Hospital RWTH Aachen, Department of Thoracic and Cardiovascular Surgery, Aachen, Germany
| | - Asa M Wheelock
- Karolinska Institute, Department of Medicine and Center for Molecular Medicine, Respiratory Medicine Unit, Stockholm, Sweden
| | - Zoltán Wiener
- Semmelweis University, Department of Genetics, Cell- and Immunobiology, Budapest, Hungary
| | - Leonie Witte
- University Medical Center Göttingen, Developmental Biochemistry, Göttingen, Germany
- University Medical Center Göttingen, Hematology and Oncology, Göttingen, Germany
| | - Joy Wolfram
- Chinese Academy of Sciences, Wenzhou Institute of Biomaterials and Engineering, Wenzhou, China
- Houston Methodist Research Institute, Department of Nanomedicine, Houston, TX, USA
- Mayo Clinic, Department of Transplantation Medicine/Department of Physiology and Biomedical Engineering, Jacksonville, FL, USA
| | - Angeliki Xagorari
- George Papanicolaou Hospital, Public Cord Blood Bank, Department of Haematology - BMT Unit, Thessaloniki, Greece
| | - Patricia Xander
- Universidade Federal de São Paulo Campus Diadema, Departamento de Ciências Farmacêuticas, Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários, São Paulo, Brazil
| | - Jing Xu
- BC Cancer, Canada’s Michael Smith Genome Sciences Centre, Vancouver, Canada
- Simon Fraser University, Department of Molecular Biology and Biochemistry, Burnaby, Canada
| | - Xiaomei Yan
- Xiamen University, Department of Chemical Biology, Xiamen, China
| | - María Yáñez-Mó
- Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
- Universidad Autónoma de Madrid, Departamento de Biología Molecular, Madrid, Spain
| | - Hang Yin
- Tsinghua University, School of Pharmaceutical Sciences, Beijing, China
| | - Yuana Yuana
- Technical University Eindhoven, Faculty Biomedical Technology, Eindhoven, The Netherlands
| | - Valentina Zappulli
- University of Padova, Department of Comparative Biomedicine and Food Science, Padova, Italy
| | - Jana Zarubova
- Institute of Physiology CAS, Department of Biomaterials and Tissue Engineering, BIOCEV, Vestec, Czech Republic
- Institute of Physiology CAS, Department of Biomaterials and Tissue Engineering, Prague, Czech Republic
- University of California, Los Angeles, Department of Bioengineering, Los Angeles, CA, USA
| | - Vytautas Žėkas
- Vilnius University, Institute of Biomedical Sciences, Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Vilnius, Lithuania
| | - Jian-ye Zhang
- Guangzhou Medical University, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, Guangzhou, China
| | - Zezhou Zhao
- The Johns Hopkins University School of Medicine, Department of Molecular and Comparative Pathobiology, Baltimore, MD, USA
| | - Lei Zheng
- Nanfang Hospital, Southern Medical University, Department of Clinical Laboratory Medicine, Guangzhou, China
| | | | - Antje M Zickler
- Karolinska Institute, Clinical Research Center, Unit for Molecular Cell and Gene Therapy Science, Stockholm, Sweden
| | - Pascale Zimmermann
- Aix-Marseille Université, Institut Paoli-Calmettes, INSERM U1068, CNRS UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- KU Leuven (Leuven University), Department of Human Genetics, Leuven, Belgium
| | - Angela M Zivkovic
- University of California, Davis, Department of Nutrition, Davis, CA, USA
| | | | - Ewa K Zuba-Surma
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Kraków, Poland
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Anand S, Foot N, Ang CS, Gembus KM, Keerthikumar S, Adda CG, Mathivanan S, Kumar S. Front Cover: Arrestin-Domain Containing Protein 1 (Arrdc1) Regulates the Protein Cargo and Release of Extracellular Vesicles. Proteomics 2018. [DOI: 10.1002/pmic.201870151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Anand S, Foot N, Ang C, Gembus KM, Keerthikumar S, Adda CG, Mathivanan S, Kumar S. Arrestin‐Domain Containing Protein 1 (Arrdc1) Regulates the Protein Cargo and Release of Extracellular Vesicles. Proteomics 2018; 18:e1800266. [DOI: 10.1002/pmic.201800266] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/10/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Sushma Anand
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Natalie Foot
- Center for Cancer Biology University of South Australia and SA Pathology Adelaide South Australia 5000 Australia
| | - Ching‐Seng Ang
- Bio21 Institute University of Melbourne Victoria Melbourne 3010 Australia
| | - Kelly M. Gembus
- Center for Cancer Biology University of South Australia and SA Pathology Adelaide South Australia 5000 Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Christopher G. Adda
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora Victoria 3086 Australia
| | - Sharad Kumar
- Center for Cancer Biology University of South Australia and SA Pathology Adelaide South Australia 5000 Australia
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41
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Gangoda L, Liem M, Ang CS, Keerthikumar S, Adda CG, Parker BS, Mathivanan S. Proteomic Profiling of Exosomes Secreted by Breast Cancer Cells with Varying Metastatic Potential. Proteomics 2018; 17. [PMID: 29115712 DOI: 10.1002/pmic.201600370] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 11/02/2017] [Indexed: 12/17/2022]
Abstract
Cancer cells actively release extracellular vesicles, including exosomes, into the surrounding microenvironment. Exosomes play pleiotropic roles in cancer progression and metastasis, including invasion, angiogenesis, and immune modulation. However, the proteome profile of exosomes isolated from cells with different metastatic potential and the role of these exosomes in driving metastasis remains unclear. Here, we conduct a comparative proteomic analysis of exosomes isolated from several genetically related mouse breast tumor lines with different metastatic propensity. The amount of exosomes produced and the extent of cancer-associated protein cargo vary significantly between nonmetastatic and metastatic cell-derived exosomes. Metastatic cell-derived exosomes contain proteins that promote migration, proliferation, invasion, and angiogenesis while the nonmetastatic cell-derived exosomes contain proteins involved in cell-cell/cell-matrix adhesion and polarity maintenance. The metastatic exosomes contain a distinct set of membrane proteins including Ceruloplasmin and Metadherin which could presumably aid in targeting the primary cancer cells to specific metastatic sites. Hence, it can be concluded that the exosomes contain different protein cargo based on the host cells metastatic properties and can facilitate in the dissemination of the primary tumors to distant sites.
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Affiliation(s)
- Lahiru Gangoda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Michael Liem
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Christopher G Adda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Belinda S Parker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
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42
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Atukorala I, Mathivanan S. PO-066 Knockdown of cadherin 17 inactivates WNT signalling pathway and induces apoptosis in colorectal cancer cells. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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43
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Dona MSI, Prendergast LA, Mathivanan S, Keerthikumar S, Salim A. Powerful differential expression analysis incorporating network topology for next-generation sequencing data. Bioinformatics 2018; 33:1505-1513. [PMID: 28172447 DOI: 10.1093/bioinformatics/btw833] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/28/2016] [Indexed: 12/15/2022] Open
Abstract
Motivation RNA-seq has become the technology of choice for interrogating the transcriptome. However, most methods for RNA-seq differential expression (DE) analysis do not utilize prior knowledge of biological networks to detect DE genes. With the increased availability and quality of biological network databases, methods that can utilize this prior knowledge are needed and will offer biologists with a viable, more powerful alternative when analyzing RNA-seq data. Results We propose a three-state Markov Random Field (MRF) method that utilizes known biological pathways and interaction to improve sensitivity and specificity and therefore reducing false discovery rates (FDRs) when detecting differentially expressed genes from RNA-seq data. The method requires normalized count data (e.g. in Fragments or Reads Per Kilobase of transcript per Million mapped reads (FPKM/RPKM) format) as its input and it is implemented in an R package pathDESeq available from Github. Simulation studies demonstrate that our method outperforms the two-state MRF model for various sample sizes. Furthermore, for a comparable FDR, it has better sensitivity than DESeq, EBSeq, edgeR and NOISeq. The proposed method also picks more top Gene Ontology terms and KEGG pathways terms when applied to real dataset from colorectal cancer and hepatocellular carcinoma studies, respectively. Overall, these findings clearly highlight the power of our method relative to the existing methods that do not utilize prior knowledge of biological network. Availability and Implementation As an R package at https://github.com/MalathiSIDona/pathDESeq. To install the package type install_github("MalathiSIDona/pathDESeq",build_vignettes = TRUE). After installation, type vignette("pathDESeq") to access the vignette. Contact a.salim@latrobe.edu.au. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Malathi S I Dona
- Department of Mathematics and Statistics, La Trobe University, Melbourne, VIC, Australia
| | - Luke A Prendergast
- Department of Mathematics and Statistics, La Trobe University, Melbourne, VIC, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute of Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Agus Salim
- Department of Mathematics and Statistics, La Trobe University, Melbourne, VIC, Australia
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Abstract
Extracellular vesicles (EVs) are a class of membranous vesicles that are released by multiple cell types into the extracellular environment. This unique class of extracellular organelles which play pivotal role in intercellular communication are conserved across prokaryotes and eukaryotes. Depending upon the cell origin and the functional state, the molecular cargo including proteins, lipids, and RNA within the EVs are modulated. Owing to this, EVs are considered as a subrepertoire of the host cell and are rich reservoirs of disease biomarkers. In addition, the availability of EVs in multiple bodily fluids including blood has created significant interest in biomarker and signaling research. With the advancement in high-throughput techniques, multiple EV studies have embarked on profiling the molecular cargo. To benefit the scientific community, existing free Web-based resources including ExoCarta, EVpedia, and Vesiclepedia catalog multiple datasets. These resources aid in elucidating molecular mechanism and pathophysiology underlying different disease conditions from which EVs are isolated. Here, the existing bioinformatics tools to perform integrated analysis to identify key functional components in the EV datasets are discussed.
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Affiliation(s)
- Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, LIMS1, Bundoora, Melbourne, VIC, 3086, Australia
| | - Lahiru Gangoda
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, LIMS1, Bundoora, Melbourne, VIC, 3086, Australia
| | - Yong Song Gho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, LIMS1, Bundoora, Melbourne, VIC, 3086, Australia.
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45
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Vo JL, Martínez Ortiz GC, Subedi P, Keerthikumar S, Mathivanan S, Paxman JJ, Heras B. Front Cover: Autotransporter Adhesins in Escherichia coli Pathogenesis. Proteomics 2017. [DOI: 10.1002/pmic.2017700181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Liem M, Ang CS, Mathivanan S. Inside Front Cover: Insulin Mediated Activation of PI3K/Akt Signalling Pathway Modifies the Proteomic Cargo of Extracellular Vesicles. Proteomics 2017. [DOI: 10.1002/pmic.2017700182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Witwer KW, Soekmadji C, Hill AF, Wauben MH, Buzás EI, Di Vizio D, Falcon-Perez JM, Gardiner C, Hochberg F, Kurochkin IV, Lötvall J, Mathivanan S, Nieuwland R, Sahoo S, Tahara H, Torrecilhas AC, Weaver AM, Yin H, Zheng L, Gho YS, Quesenberry P, Théry C. Updating the MISEV minimal requirements for extracellular vesicle studies: building bridges to reproducibility. J Extracell Vesicles 2017; 6:1396823. [PMID: 29184626 PMCID: PMC5698937 DOI: 10.1080/20013078.2017.1396823] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/20/2017] [Indexed: 01/10/2023] Open
Affiliation(s)
- Kenneth W Witwer
- Departments of Molecular and Comparative Pathobiology and Neurology, The Johns Hopkins University School of Medicine, Baltimore,
| | - Carolina Soekmadji
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Andrew F Hill
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Marca H Wauben
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Edit I Buzás
- Department of Genetics, Cell- and Immunobiology, Semmelweis University and MTA-SE Immunoproteogenomics Extracellular Vesicle Research Group, Budapest, Hungary
| | - Dolores Di Vizio
- Division of Cancer Biology and Therapeutics, Departments of Surgery, Biomedical Sciences, and Pathology and Laboratory Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Juan M Falcon-Perez
- Exosomes Laboratory & Metabolomics Platform, CIC bioGUNE, CIBERehd, Derio, Spain.,IKERBASQUE Research Science Foundation, Bilbao, Spain
| | - Chris Gardiner
- Research Department of Haematology, University College London, London, UK
| | - Fred Hochberg
- Neurosurgery, University of California at San Diego, San Diego, CA, USA.,The Scintillon Institute, La Jolla, CA, USA
| | | | - Jan Lötvall
- Codiak BioSciences, Cambridge, MA, USA.,Krefting Research Centre, University of Gothenburg, Gothenburg, Sweden
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia
| | - Rienk Nieuwland
- Department of Clinical Chemistry and Vesicle Observation Centre, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Susmita Sahoo
- Department of Medicine, Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | | | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hang Yin
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China.,Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yong Song Gho
- Department of Life Sciences, POSTECH (Pohang University of Science and Technology), Pohang, South Korea
| | | | - Clotilde Théry
- Institut Curie, INSERM U932, PSL Research University, Paris,
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48
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Meeusen E, Lim E, Mathivanan S. Secreted Tumor Antigens - Immune Biomarkers for Diagnosis and Therapy. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600442] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/29/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Els Meeusen
- Department of Biochemistry and Genetics; La Trobe Institute for Molecular Science; La Trobe University; Bundoora Victoria Australia
| | - Elgene Lim
- Garvan Institute of Medical Research; St. Vincent's Health; University of New South Wales; Darlinghurst NSW Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics; La Trobe Institute for Molecular Science; La Trobe University; Bundoora Victoria Australia
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49
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Liem M, Ang CS, Mathivanan S. Insulin Mediated Activation of PI3K/Akt Signalling Pathway Modifies the Proteomic Cargo of Extracellular Vesicles. Proteomics 2017; 17. [PMID: 28842968 DOI: 10.1002/pmic.201600371] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/26/2017] [Indexed: 12/16/2022]
Abstract
Epidemiological studies suggest that diabetes and obesity increases the risk of colorectal cancer (CRC) and lowers the patient survival rate. An important attribute in diabetes and obesity is the presence of high levels of growth factors including insulin in blood which can activate the PI3K/Akt signalling pathway. Dysregulation of PI3K/Akt signalling pathway leads to sustained proliferative signals thereby allowing the cells susceptible to cancer. Extracellular vesicles (EVs), secreted nanovesicles of endocytic origin, are implicated in mediating the transfer of oncogenic cargo in the tumour microenvironment. In this study, CRC cells were treated with insulin to activate PI3K/Akt signaling pathway. Insulin treatment significantly increased the number of EVs secreted by CRC cells. Furthermore, pAkt was exclusively packaged in EVs secreted by PI3K/Akt activated cells. Quantitative proteomics analysis confirmed that the protein cargo of EVs are modified upon activation of PI3K/Akt signaling pathway. Bioinformatics analysis highlighted the enrichment of proteins implicated in cell proliferation in EVs secreted by PI3K/Akt activated cells. Furthermore, incubation of EVs secreted by PI3K/Akt activated cells induced proliferation in recipient CRC cells. These findings suggest that EVs can amplify the signal provided by the growth factors in the tumor microenvironment and hence aid in cancer progression.
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Affiliation(s)
- Michael Liem
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
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50
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Vo JL, Martínez Ortiz GC, Subedi P, Keerthikumar S, Mathivanan S, Paxman JJ, Heras B. Autotransporter Adhesins in Escherichia coli Pathogenesis. Proteomics 2017; 17. [PMID: 28665015 DOI: 10.1002/pmic.201600431] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 06/21/2017] [Indexed: 12/14/2022]
Abstract
Most bacteria produce adhesion molecules to facilitate the interaction with host cells and establish successful infections. An important group of bacterial adhesins belong to the autotransporter (AT) superfamily, the largest group of secreted and outer membrane proteins in Gram-negative bacteria. AT adhesins possess diverse functions that facilitate bacterial colonisation, survival and persistence, and as such are often associated with increased bacterial fitness and pathogenic potential. In this review, we will describe AIDA-I type AT adhesins, which comprise the biggest and most diverse group in the AT family. We will focus on Escherichia coli proteins and define general aspects of their biogenesis, distribution, structural properties and key roles in infection.
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Affiliation(s)
- Julieanne L Vo
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Gabriela Constanza Martínez Ortiz
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Shivakumar Keerthikumar
- 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
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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