1
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Dhondt B, Pinheiro C, Geeurickx E, Tulkens J, Vergauwen G, Van Der Pol E, Nieuwland R, Decock A, Miinalainen I, Rappu P, Schroth G, Kuersten S, Vandesompele J, Mestdagh P, Lumen N, De Wever O, Hendrix A. Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics. J Extracell Vesicles 2023; 12:e12315. [PMID: 37202906 DOI: 10.1002/jev2.12315] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 05/20/2023] Open
Abstract
The analysis of extracellular vesicles (EV) in blood samples is under intense investigation and holds the potential to deliver clinically meaningful biomarkers for health and disease. Technical variation must be minimized to confidently assess EV-associated biomarkers, but the impact of pre-analytics on EV characteristics in blood samples remains minimally explored. We present the results from the first large-scale EV Blood Benchmarking (EVBB) study in which we systematically compared 11 blood collection tubes (BCT; six preservation and five non-preservation) and three blood processing intervals (BPI; 1, 8 and 72 h) on defined performance metrics (n = 9). The EVBB study identifies a significant impact of multiple BCT and BPI on a diverse set of metrics reflecting blood sample quality, ex-vivo generation of blood-cell derived EV, EV recovery and EV-associated molecular signatures. The results assist the informed selection of the optimal BCT and BPI for EV analysis. The proposed metrics serve as a framework to guide future research on pre-analytics and further support methodological standardization of EV studies.
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Affiliation(s)
- Bert Dhondt
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Cláudio Pinheiro
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Edward Geeurickx
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Joeri Tulkens
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Glenn Vergauwen
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Edwin Van Der Pol
- Laboratory of Experimental Clinical Chemistry, Amsterdam UCM, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Vesicle Observation Centre, Amsterdam UCM, location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Biomedical Engineering and Physics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Rienk Nieuwland
- Laboratory of Experimental Clinical Chemistry, Amsterdam UCM, location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anneleen Decock
- Cancer Research Institute Ghent, Ghent, Belgium
- OncoRNALab, Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ilkka Miinalainen
- Biocenter Oulu, Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Pekka Rappu
- Department of Biochemistry, University of Turku, Turku, Finland
| | | | | | - Jo Vandesompele
- Cancer Research Institute Ghent, Ghent, Belgium
- OncoRNALab, Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Pieter Mestdagh
- Cancer Research Institute Ghent, Ghent, Belgium
- OncoRNALab, Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Nicolaas Lumen
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
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2
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Bhome R, Emaduddin M, James V, House LM, Thirdborough SM, Mellone M, Tulkens J, Primrose JN, Thomas GJ, De Wever O, Mirnezami AH, Sayan AE. Epithelial to mesenchymal transition influences fibroblast phenotype in colorectal cancer by altering miR-200 levels in extracellular vesicles. J Extracell Vesicles 2022; 11:e12226. [PMID: 35595718 PMCID: PMC9122835 DOI: 10.1002/jev2.12226] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 02/24/2021] [Revised: 02/14/2022] [Accepted: 04/26/2022] [Indexed: 12/28/2022] Open
Abstract
Colorectal cancer (CRC) with a mesenchymal gene expression signature has the greatest propensity for distant metastasis and is characterised by the accumulation of cancer‐associated fibroblasts in the stroma. We investigated whether the epithelial to mesenchymal transition status of CRC cells influences fibroblast phenotype, with a focus on the transfer of extracellular vesicles (EVs), as a controlled means of cell–cell communication. Epithelial CRC EVs suppressed TGF‐β‐driven myofibroblast differentiation, whereas mesenchymal CRC EVs did not. This was driven by miR‐200 (miR‐200a/b/c, ‐141), which was enriched in epithelial CRC EVs and transferred to recipient fibroblasts. Ectopic miR‐200 expression or ZEB1 knockdown, in fibroblasts, similarly suppressed myofibroblast differentiation. Supporting these findings, there was a strong negative correlation between miR‐200 and myofibroblastic markers in a cohort of CRC patients in the TCGA dataset. This was replicated in mice, by co‐injecting epithelial or mesenchymal CRC cells with fibroblasts and analysing stromal markers of myofibroblastic phenotype. Fibroblasts from epithelial tumours contained more miR‐200 and expressed less ACTA2 and FN1 than those from mesenchymal tumours. As such, these data provide a new mechanism for the development of fibroblast heterogeneity in CRC, through EV‐mediated transfer of miRNAs, and provide an explanation as to why CRC tumours with greater metastatic potential are CAF rich.
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Affiliation(s)
- Rahul Bhome
- Cancer Sciences Unit, University of Southampton, Southampton, UK.,University Surgery, University of Southampton, Southampton, UK
| | | | - Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Louise M House
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | | | | | - Joeri Tulkens
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - John N Primrose
- University Surgery, University of Southampton, Southampton, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Alex H Mirnezami
- Cancer Sciences Unit, University of Southampton, Southampton, UK.,University Surgery, University of Southampton, Southampton, UK
| | - A Emre Sayan
- Cancer Sciences Unit, University of Southampton, Southampton, UK
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3
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Peirsman A, Blondeel E, Ahmed T, Anckaert J, Audenaert D, Boterberg T, Buzas K, Carragher N, Castellani G, Castro F, Dangles-Marie V, Dawson J, De Tullio P, De Vlieghere E, Dedeyne S, Depypere H, Diosdi A, Dmitriev RI, Dolznig H, Fischer S, Gespach C, Goossens V, Heino J, Hendrix A, Horvath P, Kunz-Schughart LA, Maes S, Mangodt C, Mestdagh P, Michlíková S, Oliveira MJ, Pampaloni F, Piccinini F, Pinheiro C, Rahn J, Robbins SM, Siljamäki E, Steigemann P, Sys G, Takayama S, Tesei A, Tulkens J, Van Waeyenberge M, Vandesompele J, Wagemans G, Weindorfer C, Yigit N, Zablowsky N, Zanoni M, Blondeel P, De Wever O. MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity. Nat Methods 2021; 18:1294-1303. [PMID: 34725485 PMCID: PMC8566242 DOI: 10.1038/s41592-021-01291-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 06/07/2020] [Accepted: 09/09/2021] [Indexed: 01/21/2023]
Abstract
Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility.
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Affiliation(s)
- Arne Peirsman
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
| | - Eva Blondeel
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Tasdiq Ahmed
- Wallace H Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Jasper Anckaert
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Dominique Audenaert
- VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium
| | - Tom Boterberg
- Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Krisztina Buzas
- Department of Immunology, University of Szeged, Faculty of Medicine-Faculty of Science and Informatics, Szeged, Hungary
| | - Neil Carragher
- Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Flávia Castro
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Virginie Dangles-Marie
- Translational Research Department, Institut Curie, PSL Research University, and Faculty of Pharmacy, Paris, France
- Faculty of Pharmacy, Université Paris Descartes, Paris, France
| | - John Dawson
- Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Pascal De Tullio
- Center for Interdisciplinary Research on Medicines (CIRM), Metabolomics Group, Université de Liège, Liège, Belgium
| | - Elly De Vlieghere
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Sándor Dedeyne
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Herman Depypere
- Menopause and Breast Clinic, Ghent University Hospital, Ghent, Belgium
| | - Akos Diosdi
- Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Helmut Dolznig
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Suzanne Fischer
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Christian Gespach
- INSERM U938 Hospital Saint-Antoine Research Center CRSA, Team Céline Prunier, TGFbeta Signaling in Cellular Plasticity and Cancer, Sorbonne University, Paris, France
| | - Vera Goossens
- VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium
| | - Jyrki Heino
- Department of Life Technologies, University of Turku, Turku, Finland
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary
| | - Leoni A Kunz-Schughart
- OncoRay - National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Sebastiaan Maes
- Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
| | - Christophe Mangodt
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Soňa Michlíková
- OncoRay - National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Maria José Oliveira
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Francesco Pampaloni
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Filippo Piccinini
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Cláudio Pinheiro
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Jennifer Rahn
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Stephen M Robbins
- Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Elina Siljamäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Gwen Sys
- Department of Orthopedics and Traumatology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Shuichi Takayama
- Wallace H Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA
| | - Anna Tesei
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Joeri Tulkens
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | | | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Glenn Wagemans
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Claudia Weindorfer
- Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Nurten Yigit
- OncoRNALab, Cancer Research Institute, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Michele Zanoni
- IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy
| | - Phillip Blondeel
- Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
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4
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Vergauwen G, Tulkens J, Pinheiro C, Avila Cobos F, Dedeyne S, De Scheerder M, Vandekerckhove L, Impens F, Miinalainen I, Braems G, Gevaert K, Mestdagh P, Vandesompele J, Denys H, De Wever O, Hendrix A. Robust sequential biophysical fractionation of blood plasma to study variations in the biomolecular landscape of systemically circulating extracellular vesicles across clinical conditions. J Extracell Vesicles 2021; 10:e12122. [PMID: 34429857 PMCID: PMC8363909 DOI: 10.1002/jev2.12122] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 07/27/2020] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/25/2022] Open
Abstract
Separating extracellular vesicles (EV) from blood plasma is challenging and complicates their biological understanding and biomarker development. In this study, we fractionate blood plasma by combining size-exclusion chromatography (SEC) and OptiPrep density gradient centrifugation to study clinical context-dependent and time-dependent variations in the biomolecular landscape of systemically circulating EV. Using pooled blood plasma samples from breast cancer patients, we first demonstrate the technical repeatability of blood plasma fractionation. Using serial blood plasma samples from HIV and ovarian cancer patients (n = 10) we next show that EV carry a clinical context-dependent and/or time-dependent protein and small RNA composition, including miRNA and tRNA. In addition, differential analysis of blood plasma fractions provides a catalogue of putative proteins not associated with systemically circulating EV. In conclusion, the implementation of blood plasma fractionation allows to advance the biological understanding and biomarker development of systemically circulating EV.
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Affiliation(s)
- Glenn Vergauwen
- Department of Human Structure and RepairLaboratory of Experimental Cancer ResearchGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
- Department of GynecologyGhent University HospitalGhentBelgium
| | - Joeri Tulkens
- Department of Human Structure and RepairLaboratory of Experimental Cancer ResearchGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Cláudio Pinheiro
- Department of Human Structure and RepairLaboratory of Experimental Cancer ResearchGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Francisco Avila Cobos
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular MedicineOncoRNALabGhent UniversityGhentBelgium
| | - Sándor Dedeyne
- Department of Human Structure and RepairLaboratory of Experimental Cancer ResearchGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | | | - Linos Vandekerckhove
- Department of Internal Medicine and PediatricsHIV Cure Research CenterGhent University HospitalGhentBelgium
| | - Francis Impens
- VIB Center for Medical BiotechnologyGhentBelgium
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
- VIB Proteomics CoreGhentBelgium
| | | | - Geert Braems
- Cancer Research Institute GhentGhentBelgium
- Department of GynecologyGhent University HospitalGhentBelgium
| | - Kris Gevaert
- VIB Center for Medical BiotechnologyGhentBelgium
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Pieter Mestdagh
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular MedicineOncoRNALabGhent UniversityGhentBelgium
| | - Jo Vandesompele
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular MedicineOncoRNALabGhent UniversityGhentBelgium
| | - Hannelore Denys
- Cancer Research Institute GhentGhentBelgium
- Department of Medical OncologyGhent University HospitalGhentBelgium
| | - Olivier De Wever
- Department of Human Structure and RepairLaboratory of Experimental Cancer ResearchGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - An Hendrix
- Department of Human Structure and RepairLaboratory of Experimental Cancer ResearchGhent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
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5
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Everaert C, Helsmoortel H, Decock A, Hulstaert E, Van Paemel R, Verniers K, Nuytens J, Anckaert J, Nijs N, Tulkens J, Dhondt B, Hendrix A, Mestdagh P, Vandesompele J. Abstract B51: Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-b51] [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]
Abstract
Abstract
RNA profiling has emerged as a powerful tool to investigate the biomarker potential of human biofluids. Despite the interest in extracellular nucleic acids, RNA sequencing methods to quantify the total RNA content outside cells are rare. Therefore, we evaluated the performance of the SMARTer Stranded Total RNA-Seq method in human platelet-rich plasma, platelet-free plasma, urine, conditioned medium, and extracellular vesicles (EVs) from these biofluids. We found the method to be accurate, precise, compatible with low-input volumes, and able to quantify a few thousand genes. We picked up distinct classes of RNA molecules, including mRNA, lncRNA, circRNA, miscRNA, and pseudogenes. Notably, the read distribution and gene content drastically differed among biofluids. We also observed differences between EDTA and citrate platelet-free plasma, which are identical biofluids collected in different blood tubes and prepared with a slightly different centrifugation protocol. In conclusion, we are the first to show that the SMARTer method can be used for unbiased charting of the complete transcriptome of a wide range of biofluids and their extracellular vesicles. The advantage of the SMARTer Stranded Total RNA-Seq method is its potential to process low amounts of input material. Indeed, collecting samples is often the bottleneck in fundamental, (pre)clinical, or translational research projects, and being able to disseminate large amounts of information from only 200 μL (or less) can substantially impact research progress.
Citation Format: Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele. Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B51.
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6
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Dhondt B, Geeurickx E, Tulkens J, Van Deun J, Vergauwen G, Lippens L, Miinalainen I, Rappu P, Heino J, Ost P, Lumen N, De Wever O, Hendrix A. Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine. J Extracell Vesicles 2020; 9:1736935. [PMID: 32284825 PMCID: PMC7144211 DOI: 10.1080/20013078.2020.1736935] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [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: 09/04/2019] [Revised: 01/29/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EV) are increasingly being recognized as important vehicles of intercellular communication and promising diagnostic and prognostic biomarkers in cancer. Despite this enormous clinical potential, the plethora of methods to separate EV from biofluids, providing material of highly variable purity, and lacking knowledge regarding methodological repeatability pose a barrier to clinical translation. Urine is considered an ideal proximal fluid for the study of EV in urological cancers due to its direct contact with the urogenital system. We demonstrate that density-based fractionation of urine by bottom-up Optiprep density gradient centrifugation separates EV and soluble proteins with high specificity and repeatability. Mass spectrometry-based proteomic analysis of urinary EV (uEV) in men with benign and malignant prostate disease allowed us to significantly expand the known human uEV proteome with high specificity and identifies a unique biological profile in prostate cancer not uncovered by the analysis of soluble proteins. In addition, profiling the proteome of EV separated from prostate tumour conditioned medium and matched uEV confirms the specificity of the identified uEV proteome for prostate cancer. Finally, a comparative proteomic analysis with uEV from patients with bladder and renal cancer provided additional evidence of the selective enrichment of protein signatures in uEV reflecting their respective cancer tissues of origin. In conclusion, this study identifies hundreds of previously undetected proteins in uEV of prostate cancer patients and provides a powerful toolbox to map uEV content and contaminants ultimately allowing biomarker discovery in urological cancers.
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Affiliation(s)
- Bert Dhondt
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium.,Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Edward Geeurickx
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Joeri Tulkens
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Jan Van Deun
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Glenn Vergauwen
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium.,Department of Gynaecology, Ghent University Hospital, Ghent, Belgium
| | - Lien Lippens
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Ilkka Miinalainen
- Biocenter Oulu, Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Pekka Rappu
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Jyrki Heino
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Piet Ost
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Nicolaas Lumen
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
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Tulkens J, Vergauwen G, Van Deun J, Geeurickx E, Dhondt B, Lippens L, De Scheerder MA, Miinalainen I, Rappu P, De Geest BG, Vandecasteele K, Laukens D, Vandekerckhove L, Denys H, Vandesompele J, De Wever O, Hendrix A. Increased levels of systemic LPS-positive bacterial extracellular vesicles in patients with intestinal barrier dysfunction. Gut 2020; 69:191-193. [PMID: 30518529 PMCID: PMC6943244 DOI: 10.1136/gutjnl-2018-317726] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/05/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Joeri Tulkens
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Glenn Vergauwen
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium,Department of Gynaecology, Ghent University Hospital, Ghent, Belgium
| | - Jan Van Deun
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Edward Geeurickx
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Bert Dhondt
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium,Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Lien Lippens
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium,Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | | | | | - Pekka Rappu
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Bruno G De Geest
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium,Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Katrien Vandecasteele
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium,Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
| | - Debby Laukens
- Department of Gastroenterology, Ghent University, Ghent, Belgium,Ghent Gut Inflammation Group, Ghent University, Ghent, Belgium
| | | | - Hannelore Denys
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium,Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | - Jo Vandesompele
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
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Tulkens J, De Wever O, Hendrix A. Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization. Nat Protoc 2019; 15:40-67. [PMID: 31776460 DOI: 10.1038/s41596-019-0236-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/27/2019] [Indexed: 01/08/2023]
Abstract
Gram-negative and Gram-positive bacteria release a variety of membrane vesicles through different formation routes. Knowledge of the structure, molecular cargo and function of bacterial extracellular vesicles (BEVs) is primarily obtained from bacteria cultured in laboratory conditions. BEVs in human body fluids have been less thoroughly investigated most probably due to the methodological challenges in separating BEVs from their matrix and host-derived eukaryotic extracellular vesicles (EEVs) such as exosomes and microvesicles. Here, we present a step-by-step procedure to separate and characterize BEVs from human body fluids. BEVs are separated through the orthogonal implementation of ultrafiltration, size-exclusion chromatography (SEC) and density-gradient centrifugation. Size separates BEVs from bacteria, flagella and cell debris in stool; and blood cells, high density lipoproteins (HDLs) and soluble proteins in blood. Density separates BEVs from fibers, protein aggregates and EEVs in stool; and low-density lipoproteins (LDLs), very-low-density lipoproteins (VLDLs), chylomicrons, protein aggregates and EEVs in blood. The procedure is label free, maintains the integrity of BEVs and ensures reproducibility through the use of automated liquid handlers. Post-separation BEVs are characterized using orthogonal biochemical endotoxin and Toll-like receptor-based reporter assays in combination with proteomics, electron microscopy and nanoparticle tracking analysis (NTA) to evaluate BEV quality, abundance, structure and molecular cargo. Separation and characterization of BEVs from body fluids can be done within 72 h, is compatible with EEV analysis and can be readily adopted by researchers experienced in basic molecular biology and extracellular vesicle analysis. We anticipate that this protocol will expand our knowledge on the biological heterogeneity, molecular cargo and function of BEVs in human body fluids and steer the development of laboratory research tools and clinical diagnostic kits.
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Affiliation(s)
- Joeri Tulkens
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent, Ghent, Belgium.
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Tulkens J, Wever OD, Hendrix A. Abstract 1489: Increased levels of systemic LPS-positive bacterial extracellular vesicles in cancer patients with chemotherapy-induced intestinal barrier dysfunction. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1489] [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]
Abstract
Abstract
Bacterial extracellular vesicles (EV) are nanometer-sized membrane particles transporting nucleic acids, metabolites, proteins and endotoxins (lipopolysaccharide (LPS)). As such, bacterial EV that enter the systemic circulation may deliver and elicit a variety of immunological and metabolic responses in different organs including the brain. To date, the systemic presence and activity of bacterial EV in patients with intestinal barrier dysfunction have not been investigated. We combined size exclusion chromatography and density gradient (DG) centrifugation to fractionate plasma LPS in two dimensions to separate bacterial EV-associated LPS from other LPS products. We evaluated plasma from healthy donors asymptomatic of intestinal barrier dysfunction versus cancer patients with radiation- or chemotherapy (with or without gastrointestinal mucositis). We quantitatively measured bacterial EV-associated LPS and other LPS products by performing Limulus Amebocyte Lysate (LAL) and Toll-like receptor 4 (TLR4) reporter assays and qualitatively confirmed the results by immunoelectron microscopy. LAL analysis of DG fractions corresponding to the density of bacterial EV, demonstrated significantly increased LPS activity in patients diagnosed with therapy-induced gastrointestinal mucositis compared to respective controls. In accordance, we detected elevated amounts of microbial pattern recognition receptor (PRR) ligands by determining TLR4 agonistic activity. Immunoelectron microscopy confirmed bacterial EV-associated LPS. In conclusion, LPS-positive bacterial EV are present in plasma, and correlate with impaired barrier integrity in cancer therapy-induced intestinal mucositis. Further studies are needed to understand systemic functions of circulating bacterial EV in cancer patients and cancer therapy-induced conditions.
Citation Format: Joeri Tulkens, Olivier De Wever, An Hendrix. Increased levels of systemic LPS-positive bacterial extracellular vesicles in cancer patients with chemotherapy-induced intestinal barrier dysfunction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1489.
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