1
|
van Eijndhoven MAJ, Scheepbouwer C, Aparicio-Puerta E, Hackenberg M, Pegtel DM. IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution. STAR Protoc 2023; 4:102645. [PMID: 37858475 PMCID: PMC10594637 DOI: 10.1016/j.xpro.2023.102645] [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: 06/26/2023] [Revised: 08/09/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
Besides canonical microRNAs (miRNAs), sequence-based variations called isomiRs have biological relevance and diagnostic potential; however, accurate calling of these post-transcriptional modifications is challenging, especially for low input samples. Here, we present IsoSeek, a sequencing protocol that reduces ligation and PCR amplification bias and improves the accuracy of miRNA detection in low input samples. We describe steps for using randomized adapters combined with unique molecular identifiers (UMI), library quantification, and sequencing, followed by detailed procedures for data processing and analysis. For complete details on the use and execution of this protocol, please refer to C. Gómez-Martín et al. (2023)1 and Van Eijndhoven et al. (2021).2.
Collapse
Affiliation(s)
- Monique A J van Eijndhoven
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, 1081 HV Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, 1081 HV Amsterdam, the Netherlands.
| | - Chantal Scheepbouwer
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, 1081 HV Amsterdam, the Netherlands; Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, 1081 HV Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology, 1081 HV Amsterdam, the Netherlands
| | - Ernesto Aparicio-Puerta
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain; Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigacion Biomedica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigacion Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain; Excellence Research Unit ''Modelling Nature'' (MNat), University of Granada, 18071 Granada, Spain
| | - Michael Hackenberg
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain; Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigacion Biomedica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigacion Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain; Excellence Research Unit ''Modelling Nature'' (MNat), University of Granada, 18071 Granada, Spain
| | - D Michiel Pegtel
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Pathology, 1081 HV Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, 1081 HV Amsterdam, the Netherlands.
| |
Collapse
|
2
|
Scheepbouwer C, Hackenberg M, van Eijndhoven MAJ, Gerber A, Pegtel M, Gómez-Martín C. NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods. Nucleic Acids Res 2023:7175338. [PMID: 37216599 DOI: 10.1093/nar/gkad429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/24/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
RNA-sequencing has become one of the most used high-throughput approaches to gain knowledge about the expression of all different RNA subpopulations. However, technical artifacts, either introduced during library preparation and/or data analysis, can influence the detected RNA expression levels. A critical step, especially in large and low input datasets or studies, is data normalization, which aims at eliminating the variability in data that is not related to biology. Many normalization methods have been developed, each of them relying on different assumptions, making the selection of the appropriate normalization strategy key to preserve biological information. To address this, we developed NormSeq, a free web-server tool to systematically assess the performance of normalization methods in a given dataset. A key feature of NormSeq is the implementation of information gain to guide the selection of the best normalization method, which is crucial to eliminate or at least reduce non-biological variability. Altogether, NormSeq provides an easy-to-use platform to explore different aspects of gene expression data with a special focus on data normalization to help researchers, even without bioinformatics expertise, to obtain reliable biological inference from their data. NormSeq is freely available at: https://arn.ugr.es/normSeq.
Collapse
Affiliation(s)
- Chantal Scheepbouwer
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, The Netherlands
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
| | - Michael Hackenberg
- Genetics Genetics Department, Faculty of Science, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain
- Bioinformatics Laboratory, Biomedical Research Centre (CIBM), Biotechnology Institute, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
- Excellence Research Unit "Modeling Nature" (MNat), University of Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospitals of Granada-University of Granada, Spain, Conocimiento s/n, 18100, Granada, Spain
| | - Monique A J van Eijndhoven
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, The Netherlands
| | - Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Cristina Gómez-Martín
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| |
Collapse
|
3
|
Bracht JWP, Los M, van Eijndhoven MAJ, Bettin B, van der Pol E, Pegtel DM, Nieuwland R. Platelet removal from human blood plasma improves detection of extracellular vesicle-associated miRNA. J Extracell Vesicles 2023; 12:e12302. [PMID: 36788785 PMCID: PMC9929339 DOI: 10.1002/jev2.12302] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/12/2022] [Accepted: 01/04/2023] [Indexed: 02/16/2023] Open
Abstract
Human blood plasma prepared by centrifugation contains not only extracellular vesicles (EVs) but also platelets and erythrocyte ghosts (ery-ghosts). Here we studied whether analysis of miRNA associated with plasma EVs (EV-miRNA) is affected by the presence of platelets and ery-ghosts. EDTA blood was collected from healthy donors (n = 3), and plasma was prepared by the centrifugation protocol recommended by the International Society on Thrombosis and Haemostasis (ISTH), and by a centrifugation protocol from an EV-miRNA expert lab (non-ISTH protocol). EVs were isolated from plasma by size-exclusion chromatography CL-2B (SEC2B), and concentrations of platelets, activated platelets, ery-ghosts and EVs (150-1000 nm) were measured by calibrated flow cytometry. Two EV-associated miRNAs (let7a-5p and miR-21-5p), and one platelet-associated miRNA (miR-223-3p), were measured by qRT-PCR. Measurements were performed with and without filtration using 0.8 μm track-etched filters to remove platelets and ery-ghosts from plasma and EV-enriched SEC fractions. Plasma prepared by both centrifugation protocols contained platelets and ery-ghosts, which co-migrated with EVs into the EV-enriched SEC2B fractions. Filtration removed platelets and ery-ghosts (>97%; p ≤ 0.05) and did not affect the EV concentrations (p > 0.17). The miRNA concentrations were 2-4-fold overestimated due to the presence of platelets but not ery-ghosts. Thus, filtration of human plasma is expected to improve comparability and reproducibility of quantitative EV-miRNA studies. Therefore, we recommend to measure and report the plasma concentration of platelets for EV-miRNA studies, and to filter plasma before downstream analyses or storage in biobanks.
Collapse
Affiliation(s)
- Jillian W. P. Bracht
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam Cardiovascular Sciences, Atherosclerosis and Ischemic SyndromesAmsterdamThe Netherlands
| | - Mandy Los
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
| | - Monique A. J. van Eijndhoven
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Boelelaan 1117AmsterdamThe Netherlands
| | - Britta Bettin
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Biomedical Engineering and Physics, Meibergdreef 9AmsterdamThe Netherlands
| | - Edwin van der Pol
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam Cardiovascular Sciences, Atherosclerosis and Ischemic SyndromesAmsterdamThe Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Biomedical Engineering and Physics, Meibergdreef 9AmsterdamThe Netherlands
| | - D. Michiel Pegtel
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, Boelelaan 1117AmsterdamThe Netherlands
| | - Rienk Nieuwland
- Amsterdam UMC location University of Amsterdam, Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Meibergdreef 9AmsterdamThe Netherlands
- Cancer Centre Amsterdam, Imaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam Cardiovascular Sciences, Atherosclerosis and Ischemic SyndromesAmsterdamThe Netherlands
| |
Collapse
|
4
|
Drees EEE, Driessen J, Zwezerijnen GJC, Verkuijlen SAWM, Eertink JJ, van Eijndhoven MAJ, Groenewegen NJ, Vallés‐Martí A, de Jong D, Boellaard R, de Vet HCW, Pegtel DM, Zijlstra JM. Blood-circulating EV-miRNAs, serum TARC, and quantitative FDG-PET features in classical Hodgkin lymphoma. EJHaem 2022; 3:908-912. [PMID: 36051072 PMCID: PMC9422001 DOI: 10.1002/jha2.432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 05/27/2023]
Abstract
Blood-based biomarkers are gaining interest for response evaluation in classical Hodgkin lymphoma (cHL). However, it is unknown how blood-based biomarkers relate to quantitative 18F-FDG-PET features. We correlated extracellular vesicle-associated miRNAs (EV-miRNA), serum TARC, and complete blood count (CBC) with PET features (e.g., metabolic tumor volume [MTV], dissemination and intensity features) in 30 cHL patients at baseline. EV-miR127-3p, EV-miR24-3p, sTARC, and several CBC parameters showed weak to strong correlations with MTV and dissemination features, but not with intensity features. Two other EV-miRNAs only showed weak correlations with PET features. Therefore, blood-based biomarkers may be complementary to PET features, which warrants further exploration of combining these biomarkers in prognostic models.
Collapse
Affiliation(s)
- Esther E. E. Drees
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
| | - Julia Driessen
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMClocation University of AmsterdamDepartment of HematologyLYMMCARE (Lymphoma and Myeloma Center)MeibergdreefAmsterdamThe Netherlands
| | - Gerben J. C. Zwezerijnen
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of Radiology and Nuclear MedicineBoelelaanAmsterdamThe Netherlands
| | - Sandra A. W. M. Verkuijlen
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
| | - Jakoba J. Eertink
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of HematologyBoelelaanAmsterdamThe Netherlands
| | - Monique A. J. van Eijndhoven
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
| | - Nils J. Groenewegen
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
- Exbiome B.V.AmsterdamThe Netherlands
| | - Andrea Vallés‐Martí
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
| | - Daphne de Jong
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
| | - Ronald Boellaard
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of Radiology and Nuclear MedicineBoelelaanAmsterdamThe Netherlands
| | - Henrica C. W. de Vet
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of Epidemiology and Data ScienceAmsterdam Public Health research instituteBoelelaanAmsterdamThe Netherlands
| | - Dirk M. Pegtel
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Cancer Center AmsterdamImaging and BiomarkersAmsterdamThe Netherlands
- Exbiome B.V.AmsterdamThe Netherlands
| | - Josée M. Zijlstra
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of PathologyBoelelaanAmsterdamThe Netherlands
- Amsterdam UMCLocation Vrije Universiteit AmsterdamDepartment of HematologyBoelelaanAmsterdamThe Netherlands
| |
Collapse
|
5
|
Drees EEE, Roemer MGM, Groenewegen NJ, Perez‐Boza J, van Eijndhoven MAJ, Prins LI, Verkuijlen SAWM, Tran X, Driessen J, Zwezerijnen GJC, Stathi P, Mol K, Karregat JJJP, Kalantidou A, Vallés‐Martí A, Molenaar TJ, Aparicio‐Puerta E, van Dijk E, Ylstra B, Groothuis‐Oudshoorn CGM, Hackenberg M, de Jong D, Zijlstra JM, Pegtel DM. Extracellular vesicle miRNA predict FDG-PET status in patients with classical Hodgkin Lymphoma. J Extracell Vesicles 2021; 10:e12121. [PMID: 34295456 PMCID: PMC8282992 DOI: 10.1002/jev2.12121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 01/21/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022] Open
Abstract
Minimally-invasive tools to assess tumour presence and burden may improve clinical management. FDG-PET (metabolic) imaging is the current gold standard for interim response assessment in patients with classical Hodgkin Lymphoma (cHL), but this technique cannot be repeated frequently. Here we show that microRNAs (miRNA) associated with tumour-secreted extracellular vesicles (EVs) in the circulation of cHL patients may improve response assessment. Small RNA sequencing and qRT-PCR reveal that the relative abundance of cHL-expressed miRNAs, miR-127-3p, miR-155-5p, miR-21-5p, miR-24-3p and let-7a-5p is up to hundred-fold increased in plasma EVs of cHL patients pre-treatment when compared to complete metabolic responders (CMR). Notably, in partial responders (PR) or treatment-refractory cases (n = 10) the EV-miRNA levels remain elevated. In comparison, tumour specific copy number variations (CNV) were detected in cell-free DNA of 8 out of 10 newly diagnosed cHL patients but not in patients with PR. Combining EV-miR-127-3p and/or EV-let-7a-5p levels, with serum TARC (a validated protein cHL biomarker), increases the accuracy for predicting PET-status (n = 129) to an area under the curve of 0.93 (CI: 0.87-0.99), 93.5% sensitivity, 83.8/85.0% specificity and a negative predictive value of 96%. Thus the level of tumour-associated miRNAs in plasma EVs is predictive of metabolic tumour activity in cHL patients. Our findings suggest that plasma EV-miRNA are useful for detection of small residual lesions and may be applied as serial response prediction tool.
Collapse
Affiliation(s)
- Esther E. E. Drees
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Margaretha G. M. Roemer
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Nils J. Groenewegen
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
- ExBiome B.V.AmsterdamThe Netherlands
| | - Jennifer Perez‐Boza
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | | | - Leah I. Prins
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Sandra A. W. M. Verkuijlen
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Xuan‐Mai Tran
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Julia Driessen
- Department of HematologyAmsterdam UMCCancer Center Amsterdam, University of AmsterdamAmsterdamThe Netherlands
| | - G. J. C. Zwezerijnen
- Department of Radiology and Nuclear MedicineCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Phylicia Stathi
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Kevin Mol
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Joey J. J. P. Karregat
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Aikaterini Kalantidou
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Andrea Vallés‐Martí
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - T. J. Molenaar
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Ernesto Aparicio‐Puerta
- Department of GeneticsComputational Epigenomics and BioinformaticsUniversity of GranadaGranadaSpain
| | - Erik van Dijk
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Bauke Ylstra
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | | | - Michael Hackenberg
- ExBiome B.V.AmsterdamThe Netherlands
- Department of GeneticsComputational Epigenomics and BioinformaticsUniversity of GranadaGranadaSpain
| | - Daphne de Jong
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Josée M. Zijlstra
- Department of HematologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - D. Michiel Pegtel
- Department of PathologyCancer Center AmsterdamAmsterdam UMCVrije Universiteit AmsterdamAmsterdamThe Netherlands
| |
Collapse
|
6
|
Affiliation(s)
- Monique A J van Eijndhoven
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - S Rubina Baglio
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
7
|
Baglio SR, Lagerweij T, Pérez-Lanzón M, Ho XD, Léveillé N, Melo SA, Cleton-Jansen AM, Jordanova ES, Roncuzzi L, Greco M, van Eijndhoven MAJ, Grisendi G, Dominici M, Bonafede R, Lougheed SM, de Gruijl TD, Zini N, Cervo S, Steffan A, Canzonieri V, Martson A, Maasalu K, Köks S, Wurdinger T, Baldini N, Pegtel DM. Blocking Tumor-Educated MSC Paracrine Activity Halts Osteosarcoma Progression. Clin Cancer Res 2017; 23:3721-3733. [PMID: 28053020 DOI: 10.1158/1078-0432.ccr-16-2726] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 11/16/2022]
Abstract
Purpose: Human osteosarcoma is a genetically heterogeneous bone malignancy with poor prognosis despite the employment of aggressive chemotherapy regimens. Because druggable driver mutations have not been established, dissecting the interactions between osteosarcoma cells and supporting stroma may provide insights into novel therapeutic targets.Experimental Design: By using a bioluminescent orthotopic xenograft mouse model of osteosarcoma, we evaluated the effect of tumor extracellular vesicle (EV)-educated mesenchymal stem cells (TEMSC) on osteosarcoma progression. Characterization and functional studies were designed to assess the mechanisms underlying MSC education. Independent series of tissue specimens were analyzed to corroborate the preclinical findings, and the composition of patient serum EVs was analyzed after isolation with size-exclusion chromatography.Results: We show that EVs secreted by highly malignant osteosarcoma cells selectively incorporate a membrane-associated form of TGFβ, which induces proinflammatory IL6 production by MSCs. TEMSCs promote tumor growth, accompanied with intratumor STAT3 activation and lung metastasis formation, which was not observed with control MSCs. Importantly, intravenous administration of the anti-IL6 receptor antibody tocilizumab abrogated the tumor-promoting effects of TEMSCs. RNA-seq analysis of human osteosarcoma tissues revealed a distinct TGFβ-induced prometastatic gene signature. Tissue microarray immunostaining indicated active STAT3 signaling in human osteosarcoma, consistent with the observations in TEMSC-treated mice. Finally, we isolated pure populations of EVs from serum and demonstrated that circulating levels of EV-associated TGFβ are increased in osteosarcoma patients.Conclusions: Collectively, our findings suggest that TEMSCs promote osteosarcoma progression and provide the basis for testing IL6- and TGFβ-blocking agents as new therapeutic options for osteosarcoma patients. Clin Cancer Res; 23(14); 3721-33. ©2017 AACR.
Collapse
Affiliation(s)
- S Rubina Baglio
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands.
| | - Tonny Lagerweij
- Department of Neurosurgery, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Maria Pérez-Lanzón
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Xuan Dung Ho
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.,Department of Oncology, Hue College of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Nicolas Léveillé
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), Amsterdam, the Netherlands
| | - Sonia A Melo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S) and Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200 Porto, Portugal
| | | | - Ekaterina S Jordanova
- Department of Obstetrics and Gynecology, Center for Gynecological Oncology Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Laura Roncuzzi
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Michelina Greco
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Monique A J van Eijndhoven
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Giulia Grisendi
- Division of Oncology, Department of Medical and Surgical Sciences for Children and Adults, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Massimo Dominici
- Division of Oncology, Department of Medical and Surgical Sciences for Children and Adults, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Roberta Bonafede
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurosciences, Biomedicine and Movement Sciences. University of Verona, Verona, Italy
| | - Sinead M Lougheed
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Tanja D de Gruijl
- Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
| | - Nicoletta Zini
- CNR-National Research Council of Italy, Institute of Molecular Genetics, Bologna, Italy.,Laboratory of Musculoskeletal Cell Biology, Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Silvia Cervo
- CRO-Biobank, CRO Aviano National Cancer Institute, Aviano, Italy.,Clinical Cancer Pathology, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Agostino Steffan
- CRO-Biobank, CRO Aviano National Cancer Institute, Aviano, Italy.,Clinical Cancer Pathology, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Vincenzo Canzonieri
- CRO-Biobank, CRO Aviano National Cancer Institute, Aviano, Italy.,Division of Pathology, CRO Aviano National Cancer Institute, Aviano, Italy
| | - Aare Martson
- Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.,Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia
| | - Katre Maasalu
- Department of Traumatology and Orthopedics, University of Tartu, Tartu, Estonia.,Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia
| | - Sulev Köks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Tom Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nicola Baldini
- Orthopaedic Pathophysiology and Regenerative Medicine Unit, Istituto Ortopedico Rizzoli, Bologna, Italy. .,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - D Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands.
| |
Collapse
|
8
|
Koppers-Lalic D, Hackenberg M, Bijnsdorp IV, van Eijndhoven MAJ, Sadek P, Sie D, Zini N, Middeldorp JM, Ylstra B, de Menezes RX, Würdinger T, Meijer GA, Pegtel DM. Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes. Cell Rep 2014; 8:1649-1658. [PMID: 25242326 DOI: 10.1016/j.celrep.2014.08.027] [Citation(s) in RCA: 420] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 03/25/2014] [Accepted: 08/13/2014] [Indexed: 01/11/2023] Open
Abstract
Functional biomolecules, including small noncoding RNAs (ncRNAs), are released and transmitted between mammalian cells via extracellular vesicles (EVs), including endosome-derived exosomes. The small RNA composition in cells differs from exosomes, but underlying mechanisms have not been established. We generated small RNA profiles by RNA sequencing (RNA-seq) from a panel of human B cells and their secreted exosomes. A comprehensive bioinformatics and statistical analysis revealed nonrandomly distributed subsets of microRNA (miRNA) species between B cells and exosomes. Unexpectedly, 3' end adenylated miRNAs are relatively enriched in cells, whereas 3' end uridylated isoforms appear overrepresented in exosomes, as validated in naturally occurring EVs isolated from human urine samples. Collectively, our findings suggest that posttranscriptional modifications, notably 3' end adenylation and uridylation, exert opposing effects that may contribute, at least in part, to direct ncRNA sorting into EVs.
Collapse
Affiliation(s)
- Danijela Koppers-Lalic
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands; Exosomes Research Group, VU University Medical Center, 1007MB Amsterdam, the Netherlands.
| | - Michael Hackenberg
- Department of Genetics, Computational Genomics and Bioinformatics Group, University of Granada, Granada 18071, Spain
| | - Irene V Bijnsdorp
- Department of Urology, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - Monique A J van Eijndhoven
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands; Exosomes Research Group, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - Payman Sadek
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands; Exosomes Research Group, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - Daud Sie
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - Nicoletta Zini
- CNR-National Research Council of Italy, IGM, and SC Laboratory of Musculoskeletal Cell Biology, IOR, 40136 Bologna, Italy
| | - Jaap M Middeldorp
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - Renee X de Menezes
- Department of Epidemiology and Biostatistics, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - Thomas Würdinger
- Department of Neurosurgery, Neuro-Oncology Research Group, VU University Medical Center, 1007MB Amsterdam, the Netherlands; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands
| | - D Michiel Pegtel
- Department of Pathology, VU University Medical Center, 1007MB Amsterdam, the Netherlands; Exosomes Research Group, VU University Medical Center, 1007MB Amsterdam, the Netherlands.
| |
Collapse
|
9
|
Verweij FJ, van Eijndhoven MAJ, Hopmans ES, Vendrig T, Wurdinger T, Cahir-McFarland E, Kieff E, Geerts D, van der Kant R, Neefjes J, Middeldorp JM, Pegtel DM. LMP1 association with CD63 in endosomes and secretion via exosomes limits constitutive NF-κB activation. EMBO J 2011; 30:2115-29. [PMID: 21527913 DOI: 10.1038/emboj.2011.123] [Citation(s) in RCA: 177] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 03/25/2011] [Indexed: 02/01/2023] Open
Abstract
The ubiquitous Epstein Barr virus (EBV) exploits human B-cell development to establish a persistent infection in ∼90% of the world population. Constitutive activation of NF-κB by the viral oncogene latent membrane protein 1 (LMP1) has an important role in persistence, but is a risk factor for EBV-associated lymphomas. Here, we demonstrate that endogenous LMP1 escapes degradation upon accumulation within intraluminal vesicles of multivesicular endosomes and secretion via exosomes. LMP1 associates and traffics with the intracellular tetraspanin CD63 into vesicles that lack MHC II and sustain low cholesterol levels, even in 'cholesterol-trapping' conditions. The lipid-raft anchoring sequence FWLY, nor ubiquitylation of the N-terminus, controls LMP1 sorting into exosomes. Rather, C-terminal modifications that retain LMP1 in Golgi compartments preclude assembly within CD63-enriched domains and/or exosomal discharge leading to NF-κB overstimulation. Interference through shRNAs further proved the antagonizing role of CD63 in LMP1-mediated signalling. Thus, LMP1 exploits CD63-enriched microdomains to restrain downstream NF-κB activation by promoting trafficking in the endosomal-exosomal pathway. CD63 is thus a critical mediator of LMP1 function in- and outside-infected (tumour) cells.
Collapse
Affiliation(s)
- Frederik J Verweij
- Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|