Extracellular small non-coding RNA contaminants in fetal bovine serum and serum-free media

Abstract

In the research field of extracellular vesicles (EVs), the use of fetal bovine serum (FBS) depleted of EVs for in vitro studies is advocated to eliminate the confounding effects of media derived EVs. EVdepleted FBS may either be prepared by ultracentrifugation or purchased commercially. Nevertheless, these preparations do not guarantee an RNA-free FBS for in vitro use. In this study we address the RNA contamination issue, of small non-coding (nc)RNA in vesicular or non-vesicular fractions of FBS, ultracentrifugation EV-depleted FBS, commercial EV-depleted FBS, and in our recently developed filtration based EV-depleted FBS. Commercially available serum-and xeno-free defined media were also screened for small ncRNA contamination. Our small ncRNA sequencing data showed that all EVdepleted media and commercially available defined media contained small ncRNA contaminants. Out of the different FBS preparations studied, our ultrafiltration-based method for EV depletion performed the best in depleting miRNAs. Certain miRNAs such miR-122 and miR-203a proved difficult to remove completely and were found in all media. Compared to miRNAs, other small ncRNA (snRNA, Y RNA, snoRNA, and piRNA) were difficult to eliminate from all the studied media. Additionally, our tested defined media contained miRNAs and other small ncRNAs, albeit at a much lower level than in serum preparations. our study showed that no media is free of small ncRNA contaminants. therefore, in order to screen for baseline RNA contamination in culturing media, RNA sequencing data should be carefully controlled by adding a media sample as a control. this should be a mandatory step before performing cell culture experiments in order to eliminate the confounding effects of media. Fetal bovine serum (FBS) contains essential factors required for cell growth, metabolism, attachment, and stimulation of proliferation 1. Thus, it is the most widely used supplement for culturing human and animal cells. One of the major concerns that has become evident recently is the presence of large amounts of extracellular vesicles (EVs) in FBS 2-4. Secreted by most cell types, EVs are mediators of cell-to-cell communication and immune regulation 5,6. They carry the genetic material (DNA and RNA) as well as proteins, lipids and other molecules, the transfer of which can alter the functions of the recipient cells. EVs present in FBS are co-isolated with cell-derived EVs and therefore act as contaminants that, affect the reliability of the read-out from cell culture experiments, as FBS-derived EVs are structurally and functionally similar to cell-derived EVs 7. In addition, FBS-EVs taken up by cultured cells cause substantial physiological effects 2. To overcome this problem, different methods are used to deplete EVs from FBS. Ultracentrifugation (UC) is commonly used, but this method removes EVs only partially 3,4,8. Commercially available depleted FBS are produced using proprietary protocols to reach higher purity levels. Also, commercially available defined, serum-free and animal pr...

Profiling of extracellular small RNAs highlights a strong bias towards non-vesicular secretion

“…Further complexity in studying EV-RNA arises from the low overall abundance of specific miRNA molecules in EVs [12][13][14][15] and the knowledge that sRNAs cover only the minority of reads, even when concentrating on studying short reads 23,24 . Another aspect in such global analysis is the presence of bovine serum-derived miRNAs, which can contaminate both EV and non-EV samples when EV-depleted serum is used 19,20 .…”

Foetal bovine serum influence on in vitro extracellular vesicle analyses

“…Although serum‐free media will not contain FBS‐derived EVs, there may still exist EV‐like particles detected via nanoparticle tracking analysis (e.g., protein aggregates), particularly in serum‐replacement supplements compared to non‐supplemented medium, that may interfere with downstream EV analyses (Lee et al., 2019). The UC pellet from serum‐free media has been shown to contain protein aggregates and vesicular structures when visualized under transmission electron microscopy, along with displaying the presence of transferrin receptor/CD71 on western blot (Mannerström et al., 2019). Moreover, these defined serum‐free media conditions contained detectable RNA species, which may be derived from other source materials (e.g., amino acids, vitamins) (Mannerström et al., 2019).…”

“…The UC pellet from serum‐free media has been shown to contain protein aggregates and vesicular structures when visualized under transmission electron microscopy, along with displaying the presence of transferrin receptor/CD71 on western blot (Mannerström et al., 2019). Moreover, these defined serum‐free media conditions contained detectable RNA species, which may be derived from other source materials (e.g., amino acids, vitamins) (Mannerström et al., 2019). Altogether, these results suggest that while FBS‐derived EVs are absent in serum‐free media, preventing RNA/protein contamination from other sources remain a potential concern.…”

Use of Stem Cell Extracellular Vesicles as a “Holistic” Approach to CNS Repair

“…With respect to EV-associated cargo, it is important to acknowledge the recent work of others who have reported that media components often contain contaminating RNAs that co-precipitate with EVs. For instance, Mannerström et al (2019) screened multiple samples of EV-depleted FBS as well as commercially manufactured serum-and xeno-free media. RNA sequencing data confirmed the presence of small ncRNA (e.g., miRNA, tRNA, yRNA, and snRNA) contaminants in each of these samples (Mannerström et al, 2019).…”

“…For instance, Mannerström et al (2019) screened multiple samples of EV-depleted FBS as well as commercially manufactured serum-and xeno-free media. RNA sequencing data confirmed the presence of small ncRNA (e.g., miRNA, tRNA, yRNA, and snRNA) contaminants in each of these samples (Mannerström et al, 2019). In a similar study, Auber et al (2019) also analyzed the RNA content of chemically defined, serum free media and found that exogenous miRNAs co-isolated with EVs.…”