A new transgene mouse model using an extravesicular EGFP tag enables affinity isolation of cell-specific extracellular vesicles

The in vivo function of cell-derived extracellular vesicles (EVs) is challenging to establish since cell-specific EVs are difficult to isolate and differentiate. We, therefore, created an EV reporter using truncated CD9 to display enhanced green fluorescent protein (EGFP) on the EV surface. CD9truc-EGFP expression in cells did not affect EV size and concentration but enabled co-precipitation of EV markers TSG101 and ALIX from the cell-conditioned medium by anti-GFP immunoprecipitation. We then created a transgenic mouse where CD9truc-EGFP was inserted in the inverse orientation and double-floxed, ensuring irreversible Cre recombinase-dependent EV reporter expression. We crossed the EV reporter mice with mice expressing Cre ubiquitously (CMV-Cre), in cardiomyocytes (αMHC-MerCreMer) and renal tubular epithelial cells (Pax8-Cre), respectively. The CD9truc-EGFP positive mice showed Cre-dependent EGFP expression, and plasma CD9truc-EGFP EVs were immunoprecipitated only from CD9truc-EGFP positive CD9truc-EGFPxCMV-Cre and CD9truc-EGFPxαMHC-Cre mice, but not in CD9truc-EGFPxPax8-Cre and CD9truc-EGFP negative mice. In urine samples, CD9truc-EGFP EVs were detected by immunoprecipitation only in CD9truc-EGFP positive CD9truc-EGFPxCMV-Cre and CD9truc-EGFPxPax8-Cre mice, but not CD9truc-EGFPxαMHC-Cre and CD9truc-EGFP negative mice. In conclusion, our EV reporter mouse model enables Cre-dependent EV labeling, providing a new approach to studying cell-specific EVs in vivo and gaining a unique insight into their physiological and pathophysiological function.

overcome major limitations of previous approaches using radioisotopes, fluorescent dyes, and magnetic conjugated nanoparticles conjugated to lipophilic reagents to label EVs [7][8][9] . The lipophilic reagents may be released from the EVs, resulting in the distribution of non-EV-associated fluorescent signal 12,13 . Furthermore, infusing labeled EVs generated in vitro into mice may not be at physiologically relevant concentrations. While N and C terminal fusion of reporter proteins to the tetraspanins enables tracking of cell-specific EVs, these reporter proteins do not allow for affinity isolation of the labeled EVs from biological fluids in that the tetraspanin terminals are located inside EVs 12,13 .
Tetraspanins, however, can be used to display fluorescent proteins on the EV surface 17 , and we, therefore, hypothesized that the fusion of EGFP to the C-terminal of a truncated form of the tetraspanin CD9, devoid of the large extracellular domain and the last transmembrane domain, would create fluorescence-labeled EVs with affinity tags. Furthermore, flanking the inverted EV reporter with loxP sites 20 would establish a genetic switch that enabled Cre recombinase-dependent EV reporter expression in vivo and allow easy and reliable tracking and isolation of cell-specific EVs. Using this novel transgenic mouse model enables the assimilation of new knowledge regarding EVs' physiological and pathophysiological functions.

Results
Fusion of EGFP to CD9 enable affinity isolation of EVs. We designed an EV reporter protein by fusion of mouse CD9 truncated after the first 117 amino acids (the third transmembrane domain) to EGFP (Fig. 1A). The predicted molecular weight of the fusion protein is 41.5 kDa. Stably transfected epithelial M1 cells-termed M1-CD9truc-EGFP cells-showed green fluorescent intracellular vesicles co-localized with CD9 ( Fig. 1B and C). Transfected fluorescent markers for the endoplasmic reticulum (mCherry-ER), early endosome marker Rab5 (mRFP-Rab5), and the tetraspanin CD81 (mTagBFP2-CD81) showed co-localization with EGFP in CD9truc-EGFP cells (Supplemental Figure S1A). Western blotting revealed EGFP expression restricted to transfected cells (Fig. 1D, the full-length blot is shown in Supplemental Figure S2A). While polyethylene glycol (PEG) precipitated cell-conditioned medium from M1 and M1-CD9truc-EGFP cells revealed enriched EV markers ALIX and flotillin, and not β-actin or nuclear Lamin A/C, EGFP was detected only in cell-conditioned medium from M1-CD9truc-EGFP cells (Fig. 1D, the full-length blots are shown in Supplemental Figure S2B-F). We noted that without the addition of protease inhibitors to the cell-conditioned medium, EGFP was present as two bands: one at ~ 37 kDa, slightly below the expected molecular weight of the fusion protein, and one at ~ 27 kDa, indicating partial proteolytic shedding of EGFP (Supplemental Figure S2B). Conditioned medium from M1 and M1-CD9truc-EGFP cells showed similar extracellular particle concentration and size distribution (Fig. 1E). Size-exclusion chromatography (SEC) of the cell-conditioned medium from M1-CD9truc-EGFP cells showed that full-length CD9truc-EGFP band was only present in the fractions 1-3 with a low protein content, while shedded EGFP was present in fractions 10-12 characterized by a higher protein content (Fig. 1F, the fulllength blot is shown in Supplemental Figure S2G). This indicates that full-length CD9truc-EGFP is associated with EVs. Consistent with this, EGFP immunoprecipitation from cell-conditioned medium isolated EGFP and EV markers TSG101 and ALIX only from M1-CD9truc-EGFP cells (Fig. 1G, the full-length blot is shown in Supplemental Figure S3A-C). Thus, EVs from CD9truc-EGFP expressing cells can be isolated using GFP immunoprecipitation.
Cre recombinase-dependent CD9truc-EGFP expression. To obtain cell-specific CD9truc-EGFP expression, we inverted the coding sequence of EV reporter protein CD9truc-EGFP and flanked it by double loxP sites, allowing for CD9truc-EGFP expression driven by a CAG promoter only in Cre recombinase expressing cells ( Fig. 2A). HEK293T cells were transiently transfected with CD9truc-EGFP, which only was expressed and yielded green fluorescent cells when co-transfected with Cre recombinase (Fig. 2B). CD9truc-EGFP expression was observed in Cre recombinase co-transfected cells and their corresponding condition medium (Fig. 2C, the full-length blot is shown in Supplemental Figure S3D and E). Next, we used our CD9truc-EGFP plasmid Figure 1. Expression of EGFP and associated EV markers M1-CD9truc-EGFP cells and their conditioned medium. (A) Illustration of our EV reporter gene and protein. The CD9truc-EGFP coding sequence is driven by the CMV promoter and encodes a fusion protein consisting of the first 3 transmembrane domains of CD9 and EGFP, enabling genetic labeling and EV surface display of EGFP. (B) M1 cells stable transfected with CD9truc-EGFP are green fluorescent in contrast to non-tansfected M1 cells. Nuclei (blue) and GFP (green). n = 3, ×200 magnification (C) Immunofluorescence labeling of CD9 in M1-CD9truc-EGFP cells using Anti-hCD9 AB shows colocalization between CD9 (red), EGFP (green) and nuclei (blue). ×200 magnification (n = 3) (D) M1 cells stable transfected with CD9truc-EGFP expressing a band reacting with an anti-GFP antibody in cells and PEG-precipitated conditioned medium. Actin and Lamin A/C were detected in cell lysates only, and EVs markers ALIX and Flotillin were detected in conditioned medium from transfected and non-transfected M1 cells (n = 3). Full-length blots are shown in Supplementary Figure   www.nature.com/scientificreports/ to generate transgenic mice through pro-nuclear injection of the linearized construct. We selected a founder mouse that showed specific and substantial expression of EGFP in Cre-expressing cardiomyocytes when crossed with the tamoxifen-treated αMHC-MerCreMer mouse (Supplemental Figure S1B). After backcrossing onto a C57Bl/6 background, we isolated genomic DNA from the liver of a transgene CD9truc-EGFP mouse. Nanopore sequencing revealed three reads (approximately 30 kb) containing mouse genomic sequence and CD9truc-EGFP insert sequence. The alignment of the sequenced reads was compatible with an integration of the insert in the mouse genome at approximately chromosomal location 4:99.620.973 (GRCm38.p6). The insert was present in two copies immediately adjacent to each other in opposite directions. The insert does not disrupt any known mouse genes at the location where it is embedded. The area of insertion is, however, an annotated constrained  www.nature.com/scientificreports/ conserved region between multiple eutherian mammals. We designed primers for genotyping ( Table 1) that produced PCR products of 449 bp in wild-type mice and 324 bp in homozygotes (Fig. 2D, the full-length gel is shown in Supplemental Figure S3F), enabling us to identify transgenic mice and distinguish heterozygotes from homozygotes.
Tissue-specific EGFP signal in different Cre-positive transgenic mice. We next used established transgenic Cre recombinase mice to enable tissue-specific activation of the EV reporter protein CD9truc-EGFP. Initially, we crossed the transgene CD9truc-EGFP mice with CMV-Cre mice 21 expressing Cre recombinase under the control of the ubiquitously active human cytomegalovirus (CMV) promoter. CD9truc-EGFP positive CD9truc-EGFPxCMV-Cre mice showed EGFP expression in kidney, liver, lung spleen, and heart by anti-GFP immunohistochemistry (IHC) (Fig. 3A). EGFP was undetectable in any of these tissues in CD9truc-EGFP negative littermates (Fig. 3A). To show cell-specific expression of our CD9truc-EGFP construct, we crossed our transgene CD9truc-EGFP mice with mice harboring tamoxifen-inducible cardiomyocyte-specific Cre activity  www.nature.com/scientificreports/ (αMHC-MerCreMer) 22 and Pax8-Cre mice expressing Cre recombinase kidney tubular epithelium 23 . In CD9truc-EGFP positive, tamoxifen-treated CD9truc-EGFPxαMHC-MerCreMer mice, EGFP was explicitly detected in the heart by western blotting and direct fluorescence microscopy ( Fig. 4A-B, the full-length blot is shown in Supplemental Figure S4A). EGFP was undetectable in kidneys, liver, lung, and spleen in tamoxifen-treated CD9truc-EGFP positive and negative CD9truc-EGFPxαMHC-Cre mice and the hearts of tamoxifen-treated CD9truc-EGFP negative CD9truc-EGFPxαMHC-Cre littermates (Fig. 4A). Likewise, we found EGFP expression specifically in the kidney of CD9truc-EGFP positive CD9truc-EGFPxPax8-Cre mice using western blotting (Fig. 5A, the fulllength blot is shown in Supplemental Figure S4B). By fluorescence microscopy, however, green fluorescence was not directly detectable in the kidney epithelium of kidney cryo-sections, and only low EGFP signals were associated with glomeruli (Fig. 5B). The preparation of cryo-sections involved exposure of the tissue to large osmotic gradients, and we tested whether epithelial EGFP expression was present in paraffin-embedded formalin-fixed kidneys. Using an anti-EGFP antibody, we detected kidney-specific EGFP expression in CD9truc-EGFP positive but not negative, CD9truc-EGFPxPax8-Cre mice (Fig. 5C). Thus, these data demonstrate that our transgene CD9truc-EGFP mouse, which we term EVRep, allows for cell-specific expression of CD9truc-EGFP.
Isolation of EGFP-positive extracellular vesicles from plasma and urine. Since EVs have been detected in most body fluids, we next used plasma and urine samples from CD9truc-EGFP positive and negative CD9truc-EGFPxCMV-Cre, tamoxifen-treated CD9truc-EGFPxαMHC-MerCreMer, and CD9truc-EGFPx-Pax8-Cre mice to determine the cell-specific contribution of EVs to plasma and urine fluid compartments. EVs were precipitated and isolated from plasma using anti-GFP nanobody conjugated beads. CD9truc-EGFP was www.nature.com/scientificreports/ detected in plasma from CD9truc-EGFP positive CD9truc-EGFPxCMV-Cre and tamoxifen-treated CD9truc-EGFPxαMHC-Cre mice, but not from CD9truc-EGFPxPax8-Cre and CD9truc-EGFP negative littermates (Fig. 6A, the full-length blot is shown in Supplemental Figure S5A). The EV marker ALIX co-precipitated with CD9truc-EGFP only in plasma from tamoxifen-treated CD9truc-EGFP positive CD9truc-EGFPxαMHC-Cre mice (Fig. 6A, the full-length blot is shown in Supplemental Figure S5B). In urine samples, CD9truc-EGFP was observed in CD9truc-EGFP positive CD9truc-EGFPxCMV-Cre, and CD9truc-EGFPxPax8-Cre mice, whereas tamoxifen-treated CD9truc-EGFPxαMHC-Cre urine samples were devoid of detectable CD9truc-EGFP (Fig. 6B, the full-length blot is shown in Supplemental Figure S5C). The EV marker CD81 co-precipitated with CD9truc-EGFP only in urine samples from CD9truc-EGFP positive CD9truc-EGFPxPax8-Cre (Fig. 6B, the full-length blot is shown in Supplemental Figure S5D). Together, these data suggest that the EVRep mouse allows for the isolation of cell-specific EVs from biological fluids.

Discussion
Using a genetically encoded CD9truc-EGFP fusion protein that displays EGFP on EVs combined with a Credependent switch, we have created a transgenic mouse enabling EV detection at the cellular level as well as rapid and selective isolation of cell-specific EVs from plasma and urine. This EVRep mouse model is thus the first genetic EV reporter model that allows easy tracking and isolation of EVs in vivo in mice. Therefore, we believe that this novel tool can be utilized to generate novel insights into EV biology.
Cell-to-cell EV communication has already been demonstrated in several settings. In vitro, the transport of miRNAs in EVs act as a neuron-to-astrocyte communication pathway in the central nervous system 24 , and stem cell-derived EVs appear to target bone marrow and peripheral sites 25 . In vivo, intravascular administration of mesenchymal stem cell-derived EVs (MSC-EV) labeled with PKH26 dye closely resembles the positive effect of MSCs on postischemic recovery after acute tubular injury 26 . Another example includes intravenous injection of endothelial progenitor cell-derived EVs labeled with PKH26 dye isolated from cell-conditioned medium that protects from complement-mediated mesangial injury after experimental anti-Thy1.1 glomerulonephritis 27 . Furthermore, similar positive effects have been obtained in the myocardium where intravenous administration www.nature.com/scientificreports/ of EVs isolated from plasma protected against Ischemia-Reperfusion Injury 28 . Altogether, this suggests that EVs retain regenerative abilities. However, for most EV studies, such injections cause a supra-physiological concentration of EVs from a single cell type, and the naturally occurring in vivo concentrations might not be sufficient to cause similar effects. Furthermore, important paracrine and autocrine effects might be altered or unobserved with this approach and affect the in vivo distribution and the biological function of the EVs. Importantly, injected EVs often accumulate in the liver, spleen, and lungs regardless of the origin 26,27,29 . We did not observe CD9truc-EGFP accumulation in these organs under normal physiological circumstances. These observations emphasize some of the hurdles with injections of labeled EVs 30,31 , which may be overcome using the EVRep mouse developed to enable a robust EV fate mapping. EVs isolated from biological fluid provide access to cell-derived lipids, RNAs, and proteins; however, the representation of EVs from different cell types in, for example, urine and plasma is not well described. Consistent with a previous study 32 , we found that EVs from cardiomyocytes were readily detectable in plasma samples. Intravascular injection of labeled EVs isolated from serum have been detected in urine 33 ; however, we did not detect cardiomyocyte-derived EVs in urine, indicating that EVs are not freely filtered across the glomerular filtration barrier in the kidney, probably as a result of their size and negative charge [34][35][36] . On the other hand, we detected kidney epithelial EVs in urine. This is consistent with our previous findings using proteomic database analysis showing that 99.96% of urinary EV-associated proteins are likely to originate from the kidney, the urinary tract epithelium, and the male reproductive tract in humans 37 . It should be noted that, for example, the CD9truc-EGFPxPax8-Cre mice only showed CD9truc-EGFP in some of the tubular epithelial cells; thus, methods with higher sensitivity than western blotting may be able to detect cardiomyocyte and renal tubular epithelial-derived EVs in plasma and urine. Nonetheless, the distribution of EVs appears to be fluid compartment restricted, and EVs isolated from different fluid compartments, e.g., plasma versus urine, may only represent a subset of cell types in the body.
We found that kidney epithelial-derived EV signal was significantly affected by preparation of frozen kidney cross-sections before fluorescence microscopy, while cardiomyocyte EV tissue abundance was less affected. Western blotting suggested that CD9truc-EGFP was abundantly expressed in CD9truc-EGFP positive CD9truc-EGFPxPax8-Cre mice, but in frozen kidney sections, the EGFP was only slightly visible in the glomerulus of kidneys by directed fluorescence microscopy. The reason for this discrepancy is not known, but renal epithelial cells are, however, highly water permeable 38 , and we speculate that rapid osmotic changes (e.g., 25% sucrose) imposed during tissue preparation are involved. Recently, it was shown that the handling and preparation of tissue samples significantly affect tissue EV abundance through release to, e.g., washing buffers 39 . Our observations agree with this and suggest that careful and specific tissue preparation is essential when analyzing tissue EV levels and intercellular communication.
Similar to our approach, three other studies have used genetic labeling of EVs 15,18,40 to track the faith of endogenous EVs. While their use of an intravesicular localization of the reporter proteins prevents affinity isolation, our approach shares the limitation that there is a risk that only a subpopulation of EVs is labeled. Notably, the number of identified EV subtypes is continuously growing, and there is no consensus on which protein markers represent the different populations. Thus, we cannot exclude that genetic labeling using CD9 may add a bias in the downstream analysis, as it may only represent EV fractions. Moreover, we used a truncated version of CD9 in which the large extracellular loop was deleted. The large extracellular loop mediates many lateral CD9 interactions, and its deletion might reduce potential adverse effects of its overexpression; however, the CD9truc-EGFP may not show the exact same behavior as wild-type CD9. Nonetheless, the ease at which cell-specific EVs can be isolated using the EVRep mouse will benefit a more comprehensive characterization and identification of EV subtypes and enable other cell-specific EV markers to be identified.
In summary, our novel transgenic EVRep mouse allows easy in vivo tracking and isolation of EVs and can be used to elucidate EV biology and their further use.

EV track data.
We have submitted all relevant data of our experiments to the EV-TRACK knowledgebase (EV-TRACK ID: EV210297) 41 .
Sample collection. 7-9 weeks old mice were transferred individually to metabolic cages (12:12 h lightdark cycle, 28 ± 1 °C) for three days with free access to water and regular rodent diet (LabDiet® 5001, Forth Worth, TX, USA). After 24 h acclimation, urine samples were collected on days 2 and 3. Subsequently, mice were used for perfusion fixation or direct organ harvest, as described below. Urine was stored at − 80 °C and a protease inhibitor (1:1000, P8340, Protease Inhibitor Cocktail, Sigma Aldrich, Denmark) were added when thawed. Mice used for immunohistochemistry and fluorescent microscopy were anesthetized by i.p. injection with 10 mg/kg Xylazine (Rompun, Bayer Healthcare, Shawnee Mission, KS) and 50 mg/kg Ketamine (Ketalar, Pfizer, Sandwich, Kent, UK). Blood samples were taken by cardiac puncture through the apex before mice were flushed with 1 × PBS and fixed with 4% paraformaldehyde by retrograde perfusion via the left ventricle. Subsequently, mice were fixed for an additional 6 h in paraformaldehyde and transferred to 1 × PBS. Mice used for western blotting were likewise anesthetized, blood samples were taken, and relevant organs were removed and snap-frozen in liquid nitrogen.
Immunohistochemistry and fluorescence microscopy. Staining was performed on 2 μm paraffinembedded tissue samples deparaffined in xylene and rehydrated in decreasing ethanol solutions (99-70%) followed by target retrieval in heated TEG buffer (1 mmol/L Tris, 0.5 mM EGTA, pH 9.0). After cooling, slides were exposed to a 50 mM NH 4 Cl and 0.3% H 2 O 2 solution for 10 min, washed in 1 × PBS, and incubated in 1 × PBS with 0.3% Triton for 30 min at room temperature. Next, the slides were incubated with primary antibody (Anti-GFP) diluted in 1 × PBS with 0.3% Triton × 100 at 4 °C overnight. Next, slides were incubated for 30 min at room temperature, washed in 1 × PBS + 0.05% tween five times, and incubated with secondary HRP antibody in PBS + 0.05% tween for 1 h at room temperature. Slides were then washed in PBS, and HRP was visualized by DAB-staining (3,3'-diaminobenzidine). Lastly, slides were stained in hematoxylin mounted with Aquatex (Merck KGaA, Darmstadt, Germany).
For fluorescence microscopy, snap-frozen organs were removed from mice and placed in 1 × PBS with 0.05% acid and 25% sucrose overnight. Next, organs were placed in 1 × PBS with 0.05% acid and 50% sucrose for 2 h, embedded in OCT tissue freezing medium and 5 μm cross-sectioned on a Cryostat (Leica CM3050 S, Leica Biosystems, USA). Cross-sections were placed in 1 × TBS for 10 min, dried, and one drop of Slowfade™ Gold antifade reagent with DAPI (Invitrogen, Thermo Fisher Scientific, Eugene, OR USA) was added before mounting. All tissue and cell samples were obtained using an Olympus BX51 Fluorescence microscope.

Isolation of extracellular vesicles from cells and medium.
48 h before, the cell medium was changed to PC1 serum-free medium (Lonza, No. 344018, Walkersville, MD, USA). Cells were lysed in RIPA Lysis buffer for 1 h at 4 °C on an orbital shaker. Next, 25 cm cell scrapers were used to release cells from the flask into the RIPA buffer. The solution was then centrifugated at 13,000g at 4 °C for 10 min, and the supernatant was stored in new tubes at − 80 °C. The medium was transferred to 15 mL tubes and centrifugated for 10 min at 5000 g. The supernatant was then transferred to new tubes and stored at − 80 °C. To isolate EVs, the thawed medium was centrifugated for 15 min at 5000 g at 4 °C. The supernatant was mixed with an equal amount of freshly made ExtraPEG 44 (16% PEG-6000, Sigma Aldrich, 1 M NaCl, Milli-Q water) and left in a Multi-Rotator at 4 °C overnight. Next, samples were centrifugated for 15 min at 5000 g at 4 °C, and the supernatant was discarded. The remaining pellet was resuspended in 100 μl × 1 RIPA buffer and stored at − 20 °C until further use.

Immunofluorescence of cells.
Cells were seeded on coverslips in multiple 12-wells plates (Biocoat Cell environments, Poly-D-Lysine Cellware) and given 24 h to attach to the coverslips. In the experiments with transfection of fluorescent organelle markers, the cells were transfected the day after seeding on coverslips using Metafectene Pro (Biontex, München, Germany) and grown for 24 h. Next, cells were fixed in 4% paraformaldehyde for 10 min and rinsed 2 times in 1 × PBS with 1 mM MgCl 2 and 0.1 mM CaCl 2 , followed by permeabilization with 0.3% Triton in 1 × PBS for 15 min and another wash in 1 × PBS with 1 mM MgCl 2 and 0.1 mM CaCl 2 . Cells where then incubated in 300 μl primary antibody (Table 2) at 4 °C overnight washed 3 times in 1xPBS and incubated with 300 μl secondary antibody for 1 h at room temperature. Afterward, cells were incubated with 4' ,6-diamidino-2-phenylindole (D9542-10MG DAPI, Sigma Aldrich, Denmark) to stain DNA followed by 5 washes in 1 × PBS. Lastly, coverslips containing cells were mounted with fluorescent mounting media (DAKO, Carpinteria, CA, USA) on coverslips. ImageJ, version 2.0.0-RC-43/1.10e) was used to analyze pictures. www.nature.com/scientificreports/ Immunoblotting. Samples were mixed with LDS sample buffer (NuPAGE, Invitrogen, Thermo Fischer Scientific, Van Allen Way, Carlsbad, USA) and sample reducing agent (NuPAGE, Invitrogen, Thermo Fischer Scientific, Van Allen Way, Carlsbad, USA) and heated for 10 min before they ran on a gel. For cell and tissue fractions, 10 μg was loaded per well. The protein was then transferred to a membrane activated in 99% Ethanol. Afterward, the membrane was blocked for 30 min in 5% skimmed milk and incubated overnight with primary antibodies at 4 °C (Table 2). Following, membranes were washed 3 times in Tris-Buffered saline with Tween-20 (TBST, 20 mM Tris-base, 137 nM NaCl, 0.05% Tween-20 (Merck), pH 7.6) and incubated with secondary antibody ( Table 2) for 1 h at room temperature. Next, membranes were washed 3 times in TBS-T, and proteins were visualized by ECL plus a Molecular Imager (ChemiDoc XRS + , BIO-RAD) with Image Lab software (BIO-RAD).
Immunoprecipitation of EGFP associated EVs. EVs containing EGFP were precipitated from 200 μl plasma and 750 μl urine with extraPEG as described above, except that the pellet was resuspended in 100 μl 1 × PBS to keep EVs intact. EVs immunoprecipitated using ChromoTek GFP-trap Magnetic Beads (Chromotek GmbH, Germany). 25 μl beads were added to a 1.5 ml tube and rinsed with 1000 μl ice-cold 1 × PBS. Next, plasma or urine was added to the equilibrated beads, and tubes were placed in a Multi-Rotator (Grant-bio, PTR-35) at 4 °C for 1 h. Samples were when placed back in the magnet and allowed to attach before the supernatant was discarded. Subsequently, beads were resuspended in 1 mL ice-cold 1 × PBS-T, and the samples were placed back in the magnet. The supernatant was discarded after 3 min when the beads were attached to the magnet, and this step was repeated 4 times.
Tunable resistive pulse sensing. A qNano platform with a Nanopore NP150 (Izon Science, Oxford, UK) and polystyrene calibration beads CPC200 (Izon Science), Oxford, UK) were used for calibration of relative particle size and speed. 35 μl cell media was loaded, and analyses were performed according to manufactory instructions.
Size exclusion chromatography. A qEVoriginal/35 nm SMART column (Izon Science, Oxford, UK) with optimal separation size between 35-350 nm was used to isolate EVs from 0.5 ml from M1-CD9-EGFP medium according to manufacturer's instructions. 0.5 mL fractions were collected, and western blotting was used to verify the presence of EGFP. To verify that proteins mainly were eluted in the last fractions, proteins concentrations were measured in each fraction with DC Protein Assay (Biorad, California, U. S.) according to the manufacturer's guidelines.
Nanopore sequencing. Mouse liver from a CD9truc-EGFP positive EVRep mouse was homogenized, and DNA was extracted using the Nanobind Tissue Big DNA Kit (Circulomics, Baltimore, MD, USA) according to the manufacturer's instructions. The DNA was prepared for Oxford Nanopore sequencing using the Ligation Sequencing Kit (Oxford Nanopore Technologies, Oxford, UK). The prepared library was then sequenced using one flow cell on the Oxford Nanopore PromethION sequencing platform. Base-calling was performed with MinKNOW software, and FASTQ files were aligned to a custom mouse genome (GRCm38.p6) containing