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Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine

Bert Dhondt (UGent) , Edward Geeurickx (UGent) , Joeri Tulkens (UGent) , Jan Van Deun (UGent) , Glenn Vergauwen (UGent) , Lien Lippens (UGent) , Ilkka Miinalainen, Pekka Rappu, Jyrki Heino, Piet Ost (UGent) , et al.
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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.
Keywords
Extracellular vesicles, exosomes, separation, isolation, urine, cancer, biomarkers, proteomics, EXOSOMES, PROTEIN, IDENTIFICATION, BIOMARKERS, DIFFERENTIATION, MICROVESICLES, EXPRESSION, GROWTH

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Citation

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MLA
Dhondt, Bert, et al. “Unravelling the Proteomic Landscape of Extracellular Vesicles in Prostate Cancer by Density-Based Fractionation of Urine.” JOURNAL OF EXTRACELLULAR VESICLES, vol. 9, no. 1, 2020, doi:10.1080/20013078.2020.1736935.
APA
Dhondt, B., Geeurickx, E., Tulkens, J., Van Deun, J., Vergauwen, G., Lippens, L., … Hendrix, A. (2020). Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine. JOURNAL OF EXTRACELLULAR VESICLES, 9(1). https://doi.org/10.1080/20013078.2020.1736935
Chicago author-date
Dhondt, Bert, Edward Geeurickx, Joeri Tulkens, Jan Van Deun, Glenn Vergauwen, Lien Lippens, Ilkka Miinalainen, et al. 2020. “Unravelling the Proteomic Landscape of Extracellular Vesicles in Prostate Cancer by Density-Based Fractionation of Urine.” JOURNAL OF EXTRACELLULAR VESICLES 9 (1). https://doi.org/10.1080/20013078.2020.1736935.
Chicago author-date (all authors)
Dhondt, Bert, Edward Geeurickx, Joeri Tulkens, Jan Van Deun, Glenn Vergauwen, Lien Lippens, Ilkka Miinalainen, Pekka Rappu, Jyrki Heino, Piet Ost, Nicolaas Lumen, Olivier De Wever, and An Hendrix. 2020. “Unravelling the Proteomic Landscape of Extracellular Vesicles in Prostate Cancer by Density-Based Fractionation of Urine.” JOURNAL OF EXTRACELLULAR VESICLES 9 (1). doi:10.1080/20013078.2020.1736935.
Vancouver
1.
Dhondt B, Geeurickx E, Tulkens J, Van Deun J, Vergauwen G, Lippens L, et al. Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine. JOURNAL OF EXTRACELLULAR VESICLES. 2020;9(1).
IEEE
[1]
B. Dhondt et al., “Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine,” JOURNAL OF EXTRACELLULAR VESICLES, vol. 9, no. 1, 2020.
@article{8653373,
  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.},
  articleno    = {1736935},
  author       = {Dhondt, Bert and Geeurickx, Edward and Tulkens, Joeri and Van Deun, Jan and Vergauwen, Glenn and Lippens, Lien and Miinalainen, Ilkka and Rappu, Pekka and Heino, Jyrki and Ost, Piet and Lumen, Nicolaas and De Wever, Olivier and Hendrix, An},
  issn         = {2001-3078},
  journal      = {JOURNAL OF EXTRACELLULAR VESICLES},
  keywords     = {Extracellular vesicles,exosomes,separation,isolation,urine,cancer,biomarkers,proteomics,EXOSOMES,PROTEIN,IDENTIFICATION,BIOMARKERS,DIFFERENTIATION,MICROVESICLES,EXPRESSION,GROWTH},
  language     = {eng},
  number       = {1},
  pages        = {24},
  title        = {Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density-based fractionation of urine},
  url          = {http://dx.doi.org/10.1080/20013078.2020.1736935},
  volume       = {9},
  year         = {2020},
}

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