Exosomes Research Group

I) Tumor Exosome Biology

Tumor-derived extracellular vesicles, including exosomes, are increasingly recognized as key players in cell-cell communication and have been implicated in cancer initiation, invasive behavior, metastatic outgrowth and immunescape. However, insight into the regulatory control of EV biogensis and in particular exosome dynamics hampers direct demonstration on their actions in vitro and in vivo. We pioneered a method based on live internal fluorescence (TIRF)-microscopy to directly visualize exosome release dynamics from a single living cell.

Michiel Pegtel

With this tool that has now been widely adapted we aim to unravel which external signals and intracellular compartments are involved. With this fundamental knowledge we aim translate this knowledge into finding novel drug targets.

II) Development of novel Next Generation equencing methods, bioinformatics and deconvolution to determine tissue origin of secreted EVs

Secreted microRNAs (miRNAs) are proposed as powerful disease indicators and when associated with extracellular vesicles (EVs), have an active role in organ crosstalk. Because the majority of miRNAs are broadly expressed across cell-types and tissues, a single miRNA is rarely informative for a disease condition. Recent advances show that non-templated nucleotide additions (isomiRs) change miRNA gene-regulatory functions and incorporating this additional layer of complexity increases diagnostic accuracy of miRNAs. Standard sequencing techniques lack single-nucleotide resolution. We developed a method we called ‘IsoSeek’ that makes use of 5N-randomized 3’ and 5’ adapters and unique molecular identifier (UMI) dramatically reducing bias in detection. Next to microRNAs, EVs contain tRNAs, in fact in much large numbers and with ALL-tRNAseq developed by and with our collaborators we can profile EV-associated tRNAs and their post-transcriptional modifications.

III) Extracellular Vesicle RNA biology and personalized cancer diagnostics

The genetic profiling of patient material has yielded reliable prognostic biomarkers that are paramount for early detection, diagnosis and assessment of effective therapy. One drawback is that patient tissue is not always available or accessible without conducting timely and painful procedures. The presence of small genetic molecules called ‘microRNAs’ in cell-secreted extracellular vesicles (EV) opens unique possibilities for using such circulating RNA as easily accessible biomarkers. Our laboratory uses multi-modal ‘liquid biopsy’ strategies to accurately diagnose cancer by a simple blood and/or urine tests. Our latest studies suggest that our tool can not only diagnose disease but can measure response to therapy and even forecast whether an individual patient is likely to respond to a given treatment.

Group members

Group members:

  • Michiel Pegtel (PI)
  • Monique van Eijndhoven
  • Steven Wang
  • Nils Groenewegen
  • Cristina Gómez-Martín
  • Diogo Lazaro Fortunato
  • Leontien Bosch
  • ​Maaike Dekker
  • Amber Linders
  • Parisa Mapar
  • Saba Ghasemi
  • Shweta Godbole

                Key publications

                Towards IVDR-compliance by implementing quality control steps in a quantitative extracellular vesicle-miRNA liquid biopsy assay for response monitoring in patients with classic Hodgkin lymphoma
                Drees EEE, Groenewegen NJ, Verkuijlen SAWM, van Eijndhoven MAJ, Ramaker J, Veenstra P, Hussain M, Groothuis-Oudshoorn CGM, de Jong D, Zijlstra JM, de Rooij J, Pegtel DM. J Extracell Biol. 2024 Jun 28;3(7):e164. doi: 10.1002/jex2.164. eCollection 2024 Jul. PMID: 38947877

                Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing
                Gómez-Martín C, Aparicio-Puerta E, van Eijndhoven MAJ, Medina JM, Hackenberg M, Pegtel DM. Cell Reports Methods.2023 May

                Real-time imaging of multivesicular body-plasma membrane fusion to quantify exosome release from single cells.
                Bebelman MP, Bun P, Huveneers S, van Niel G, Verweij FJ, Pegtel DM. Nat Protoc. 2020 Jan;15(1):102-121. doi: 10.1038/s41596-019-0245-4. Epub 2019 Dec 13. PMID: 31836866

                Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling
                Verweij FJ, Bebelman MP, Jimenez CR, Garcia-Vallejo JJ, Janssen H, Neefjes J, Knol JC, de Goeij-de Haas R, Piersma SR, Baglio SR, Verhage M, Middeldorp JM, Zomer A, van Rheenen J, Coppolino MG, Hurbain I, Raposo G, Smit MJ, Toonen RFG, van Niel G, Pegtel DM. J Cell Biol. 2018 Jan 16.

                Sensing of latent EBV infection through exosomal transfer of 5'pppRNA.
                Baglio SR, van Eijndhoven MA, Koppers-Lalic D, Berenguer J, Lougheed SM, Gibbs S, Léveillé N, Rinkel RN, Hopmans ES, Swaminathan S, Verkuijlen SA, Scheffer GL, van Kuppeveld FJ, de Gruijl TD, Bultink IE, Jordanova ES, Hackenberg M, Piersma SR, Knol JC, Voskuyl AE, Wurdinger T, Jiménez CR, Middeldorp JM, Pegtel DM. Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):E587-96. doi: 10.1073/pnas.1518130113. Epub 2016 Jan 14. PMID: 26768848

                Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes
                Koppers-Lalic D, Hackenberg M, Bijnsdorp IV, van Eijndhoven MAJ, Sadek P, Sie D, Zini N, Middeldorp JM, Ylstra B, de Menezes RX, Wurdinger T, Meijer GA, and Pegtel DM. Cell Rep. 2014;8(6):1649–58.

                LMP1 association with CD63 in endosomes and secretion via exosomes limits constitutive NF-κB activation
                Verweij FJ, van Eijndhoven MA, Hopmans ES, Vendrig T, Wurdinger T, Cahir-McFarland E, Kieff E, Geerts D, van der Kant R, Neefjes J, Middeldorp JM, Pegtel DM. EMBO Journal 2011; 30: 2115-2129

                Functional delivery of viral miRNAs via exosomes
                Pegtel DM, Cosmopoulos K, Thorley-Lawson DA, van Eijndhoven MA, Hopmans ES, et al. Proc Natl Acad Sci USA. 2010;107:6328-6333.

                  Contact

                  d.pegtel@amsterdamumc.nl
                  +31 (0)20 4444052

                  Keywords

                  Biomarkers | Exosome biology | miRNA biology | mRNA deconvolution | cfDNA | machine learning