Metabolic signature of extracellular vesicles depends on the cell culture conditions

ABSTRACT

One of the greatest bottlenecks in extracellular vesicle (EV) research is the production of sufficient material in a consistent and effective way using in vitro cell models. Although the production of EVs in bioreactors maximizes EV yield in comparison to conventional cell cultures, the impact of their cell growth conditions on EVs has not yet been established. In this study, we grew two prostate cancer cell lines, PC-3 and VCaP, in conventional cell culture dishes and in two-chamber bioreactors to elucidate how the growth environment affects the EV characteristics. Specifically, we wanted to investigate the growth condition-dependent differences by non-targeted metabolite profiling using liquid chromatography–mass spectrometry (LC–MS) analysis. EVs were also characterized by their morphology, size distribution, and EV protein marker expression, and the EV yields were quantified by NTA. The use of bioreactor increased the EV yield >100 times compared to the conventional cell culture system. Regarding morphology, size distribution and surface markers, only minor differences were observed between the bioreactor-derived EVs (BR-EVs) and the EVs obtained from cells grown in conventional cell cultures (C-EVs). In contrast, metabolomic analysis revealed statistically significant differences in both polar and non-polar metabolites when the BR-EVs were compared to the C-EVs. The results show that the growth conditions markedly affected the EV metabolite profiles and that metabolomics was a sensitive tool to study molecular differences of EVs. We conclude that the cell culture conditions of EV production should be standardized and carefully detailed in publications and care should be taken when EVs from different production platforms are compared with each other for systemic effects.

KEYWORDS:

• Conditioned medium
• cell culture
• bioreactor
• metabolomics
• extracellular vesicles (EVs)
• prostate cancer cell line

Acknowledgments

Biocenter Finland is acknowledged for support. Authors thank Professor Juan Falcòn-Pérez and Dr. Sebastiaan Martijn Van Liempd from CICbioGUNE for their valuable comments on statistical analysis. The authors would like to acknowledge networking support by the COST Action BM1202.

Disclosure of interest

The authors report no conflicts of interest.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This study has been funded by the Academy of Finland (grant 287089), Magnus Ehrnrooth Foundation and Medicinska Understödsföreningen Liv och Hälsa r.f.