Exosomal proteome as a source of biomarkers for human disease

Abstract

Exosomes are small lipid membrane bound vesicles formed as part of the endosomal pathway and released into the extracellular space following fusion of late endosomes with the plasma membrane. Exosomes have been shown to have a variety of biological roles and may represent a novel source of disease biomarkers. The objectives of this project were to develop a panel of techniques for identifying exosomes in human urine then establish an in vitro model to determine whether exosomes change with cellular activation. We then used the techniques developed with human urine to determine whether human cerebrospinal fluid (CSF) contains exosomes and applied a mass spectrometry based approach to characterise the exosomal proteome. We used western blot for three exosomal markers (tsg101, CD24 and flotillin- 1), isopycnic centrifugation on a sucrose density gradient and direct visualisation using transmission electron microscopy (TEM) to verify the presence of exosomes. Using GeLC-MS/MS, 88 proteins were identified in the urinary exosomes. Several of these proteins could be linked to diseases and specific sections of the nephron. A murine cortical collecting duct cell line was used to model exosome release into the urine. Firstly, exosome release was verified using the approach developed in the urine. Stimulation of the cells with desmopressin caused an increase in the presence of aquaporin 2 in the exosomes. This increase reflected a similar change in the cells and occurred over a similar time course. This supports the hypothesis that the exosomes reflect the state of the kidney cells. In contrast, stimulation with cisplatin did not alter the presence of Fetuin-A, a proposed biomarker of cisplatin-induced acute kidney injury, in exosomes and this was consistent with no change in Fetuin- A expression in the cells. The released exosomes may act as mediators of communication to other cells. Following incubation of mCCD cells with AQP2 containing exosomes AQP2 in the cell lysate was increased indicating interaction between the cells and exosomes and potentially internalisation. Exosomes have been shown to be released by neuronal cells in vitro. We identified exosomes in the CSF of humans using western blot for known exosomal markers, density determination and direct visualisation with TEM and Immuno-TEM using an antibody specific for the exosomal marker flotillin-1. Label-free quantitative mass spectrometry was used to compare multiple CSF samples. On a whole protein analysis 86% of the proteins identified varied by less than 2-fold in comparison to the average across samples. On a tryptic peptide analysis 75% of the peptides identified varied by less than 2-fold in comparison with the average across samples. We have demonstrated exosomes are present in urine, CSF and mCCD cell conditioned media. In the mCCD cell derived exosomes we have demonstrated that following stimulation the proteome of the exosomes changes and that this change reflects the change seen in the cells. For the urinary and CSF exosomes we have characterised their proteomes using GeLC-MS/MS. These findings are consistent with the hypothesis that exosomes are a rich source of information, including biomarkers, on their cells of origin.