This work was supported by the National Science Centre, Poland, grant number 2019/33/B/NZ5/00647. We would like to thank Professor Tomasz Gosiewski and Agnieszka Krawczyk from the Department of Molecular Medical Microbiology, Jagiellonian University Medical College for their invaluable help in the detection of bacterial DNA in EVs.

1. Preparation of ultracentrifuge tubes
<ol>
	<li>Use sterile, single-use tubes. If this is not possible, reuse the ultracentrifuge tubes after washing them with a detergent using a sterile Pasteur pipette or other single-use applicators. Remember that ultracentrifuge tubes should be dedicated to one type of centrifuged material (cell culture supernatant/serum/plasma) and species (human/mouse/etc.).</li>
	<li>After a detergent wash, rinse the ultracentrifuge tubes with deionized, LPS-free water 3x.<br ...

<ol>
	<li>Th&#233;ry, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Minimal+information+for+studies+of+extracellular+vesicles+2018+(MISEV2018):+a+position+statement+of+the+International+Society+for+Extracellular+Vesicles+and+update+of+the+MISEV2014+guidelines.">Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines.</a> Journal of Extracellular Vesicles. 7 (1), 1535750 (2018).</li><li>Y&#225;&#241;ez-M&#243;, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biological+properties+of+extracellular+vesicles+and+their+physiological+functions.">Biological properties of extracellular vesicles and their physiological functions.</a> Journal of Extracellular Vesicles. 4, 27066 (2015).</li><li>van Niel, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Challenges+and+directions+in+studying+cell-cell+communication+by+extracellular+vesicles.">Challenges and directions in studying cell-cell communication by extracellular vesicles.</a> Nature Reviews Molecular Cell Biology. 23 (5), 369-382 (2022).</li><li>Ngkelo, A., Meja, K., Yeadon, M., Adcock, I., Kirkham, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=LPS+induced+inflammatory+responses+in+human+peripheral+blood+mononuclear+cells+is+mediated+through+NOX4+and+Gi&#945;+dependent+PI-3+kinase+signalling.">LPS induced inflammatory responses in human peripheral blood mononuclear cells is mediated through NOX4 and Gi&#945; dependent PI-3 kinase signalling.</a> Journal of Inflammation. 9 (1), (2012).</li><li>Schwarz, H., Schmittner, M., Duschl, A., Horejs-Hoeck, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Residual+endotoxin+contaminations+in+recombinant+proteins+are+sufficient+to+activate+human+CD1c++dendritic+cells.">Residual endotoxin contaminations in recombinant proteins are sufficient to activate human CD1c+ dendritic cells.</a> PLOS ONE. 9 (12), 113840 (2014).</li><li>Zanoni, I., Granucci, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+CD14+in+host+protection+against+infections+and+in+metabolism+regulation.">Role of CD14 in host protection against infections and in metabolism regulation.</a> Frontiers in Cellular and Infection Microbiology. 3, 32 (2013).</li><li>Takashiba, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differentiation+of+monocytes+to+macrophages+primes+cells+for+lipopolysaccharide+stimulation+via+accumulation+of+cytoplasmic+nuclear+factor+kB.">Differentiation of monocytes to macrophages primes cells for lipopolysaccharide stimulation via accumulation of cytoplasmic nuclear factor kB.</a> Infection and Immunity. 67 (11), 5573-5578 (1999).</li><li>Schwarz, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biological+activity+of+masked+endotoxin.">Biological activity of masked endotoxin.</a> Scientific Reports. 7, 44750 (2017).</li><li>Danesh, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Granulocyte-derived+extracellular+vesicles+activate+monocytes+and+are+associated+with+mortality+in+intensive+care+unit+patients.">Granulocyte-derived extracellular vesicles activate monocytes and are associated with mortality in intensive care unit patients.</a> Frontiers in Immunology. 9, 956 (2018).</li><li>Barry, O. P., Pratico, D., Savani, R. C., FitzGerald, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modulation+of+monocyte-endothelial+cell+interactions+by+platelet+microparticles.">Modulation of monocyte-endothelial cell interactions by platelet microparticles.</a> The Journal of Clinical Investigation. 102 (1), 136-144 (1998).</li><li>Sadallah, S., Eken, C., Martin, P. J., Schifferli, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microparticles+(ectosomes)+shed+by+stored+human+platelets+downregulate+macrophages+and+modify+the+development+of+dendritic+cells.">Microparticles (ectosomes) shed by stored human platelets downregulate macrophages and modify the development of dendritic cells.</a> Journal of Immunology. 186 (11), 6543-6552 (2011).</li><li>Soekmadji, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+future+of+Extracellular+Vesicles+as+Theranostics+-+an+ISEV+meeting+report.">The future of Extracellular Vesicles as Theranostics - an ISEV meeting report.</a> Journal of Extracellular Vesicles. 9 (1), 1809766 (2020).</li><li>Gioannini, T. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+an+endotoxin-MD-2+complex+that+produces+Toll-like+receptor+4-dependent+cell+activation+at+picomolar+concentrations.">Isolation of an endotoxin-MD-2 complex that produces Toll-like receptor 4-dependent cell activation at picomolar concentrations.</a> Proceedings of the National Academy of Sciences. 101 (12), 4186-4191 (2004).</li><li>Roslansky, P. F., Dawson, M. E., Novitsky, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Plastics,+endotoxins,+and+the+Limulus+amebocyte+lysate+test.">Plastics, endotoxins, and the Limulus amebocyte lysate test.</a> Journal of Parenteral Science and Technology. 45 (2), 83-87 (1991).</li><li>Fishel, S., Jackson, P., Webster, J., Faratian, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endotoxins+in+culture+medium+for+human+in+vitro+fertilization.">Endotoxins in culture medium for human in vitro fertilization.</a> Fertility and Sterility. 49 (1), 108-111 (1988).</li><li>Schulz, E., Karagianni, A., Koch, M., Fuhrmann, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hot+EVs+-+How+temperature+affects+extracellular+vesicles.">Hot EVs - How temperature affects extracellular vesicles.</a> European Journal of Pharmaceutics and Biopharmaceutics. 5 (146), 55-63 (2020).</li><li>Osteikoetxea, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+detergent+sensitivity+of+extracellular+vesicle+subpopulations.">Differential detergent sensitivity of extracellular vesicle subpopulations.</a> Organic &amp; Biomolecular Chemistry. 13 (38), 9775-9782 (2015).</li><li>Sakudo, A., Yagyu, Y., Onodera, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Disinfection+and+sterilization+using+plasma+technology:+fundamentals+and+future+perspectives+for+biological+applications.">Disinfection and sterilization using plasma technology: fundamentals and future perspectives for biological applications.</a> International Journal of Molecular Sciences. 20 (20), 5216 (2019).</li><li>Shintani, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ethylene+oxide+gas+sterilization+of+medical+devices.">Ethylene oxide gas sterilization of medical devices.</a> Biocontrol Science. 22 (1), 1-16 (2017).</li><li>Cvjetkovic, A., L&#246;tvall, J., L&#228;sser, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+influence+of+rotor+type+and+centrifugation+time+on+the+yield+and+purity+of+extracellular+vesicles.">The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles.</a> Journal of Extracellular Vesicles. 3, (2014).</li><li>Salamon, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+iSeq+and+MiSeq+as+the+two+platforms+for+16S+rRNA+sequencing+in+the+study+of+the+gut+of+rat+microbiome.">Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome.</a> Applied Microbiology and Biotechnology. 106 (22), 7671-7681 (2022).</li><li>Baj-Krzyworzeka, M., Szatanek, R., Weglarczyk, K., Baran, J., Zembala, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tumour-derived+microvesicles+modulate+biological+activity+of+human+monocytes.">Tumour-derived microvesicles modulate biological activity of human monocytes.</a> Immunology Letters. 113 (2), 76-82 (2007).</li><li>Chaiwut, R., Kasinrerk, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Very+low+concentration+of+lipopolysaccharide+can+induce+the+production+of+various+cytokines+and+chemokines+in+human+primary+monocytes.">Very low concentration of lipopolysaccharide can induce the production of various cytokines and chemokines in human primary monocytes.</a> BMC Research Notes. 15 (1), 42 (2022).</li><li>Van Deun, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+impact+of+disparate+isolation+methods+for+extracellular+vesicles+on+downstream+RNA+profiling.">The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling.</a> Journal of Extracellular Vesicles. 3, 24858 (2014).</li><li>Lehrich, B. M., Liang, Y., Fiandaca, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Foetal+bovine+serum+influence+on+in+vitro+extracellular+vesicle+analyses.">Foetal bovine serum influence on in vitro extracellular vesicle analyses.</a> Journal of Extracellular Vesicles. 10 (3), 12061 (2021).</li><li>Pham, C. V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bovine+extracellular+vesicles+contaminate+human+extracellular+vesicles+produced+in+cell+culture+conditioned+medium+when+'exosome-depleted+serum'+is+utilised.">Bovine extracellular vesicles contaminate human extracellular vesicles produced in cell culture conditioned medium when 'exosome-depleted serum' is utilised.</a> Archives of Biochemistry and Biophysics. 708, 108963 (2021).</li><li>Li, Y., Boraschi, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endotoxin+contamination:+a+key+element+in+the+interpretation+of+nanosafety+studies.">Endotoxin contamination: a key element in the interpretation of nanosafety studies.</a> Nanomedicine. 11 (3), 269-287 (2016).</li><li>&#193;lvarez, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+system+dynamics+model+to+predict+the+human+monocyte+response+to+endotoxins.">A system dynamics model to predict the human monocyte response to endotoxins.</a> Frontiers in Immunology. 8, 915 (2017).</li><li>Busatto, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tangential+flow+filtration+for+highly+efficient+concentration+of+extracellular+vesicles+from+large+volumes+of+fluid.">Tangential flow filtration for highly efficient concentration of extracellular vesicles from large volumes of fluid.</a> Cells. 7 (12), 273 (2018).</li><li>Ga&#322;uszka, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transition+metal+containing+particulate+matter+promotes+Th1+and+Th17+inflammatory+response+by+monocyte+activation+in+organic+and+inorganic+compounds+dependent+manner.">Transition metal containing particulate matter promotes Th1 and Th17 inflammatory response by monocyte activation in organic and inorganic compounds dependent manner.</a> International Journal of Environmental Research and Public Health. 17 (4), 1227 (2020).</li><li>Falagas, M. E., Kasiakou, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Toxicity+of+polymyxins:+a+systematic+review+of+the+evidence+from+old+and+recent+studies.">Toxicity of polymyxins: a systematic review of the evidence from old and recent studies.</a> Critical Care. 10 (1), 27 (2006).</li><li>Petsch, D., Anspach, F. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endotoxin+removal+from+protein+solutions.">Endotoxin removal from protein solutions.</a> Journal of Biotechnology. 76 (2-3), 97-119 (2000).</li></ol>

In the last few years, methods for proper EVs isolation have become increasingly important, enabling their further reliable analyses, for example, in the context of obtaining reliable omics and functional data24. Based on previous research experience, it seems that not only the type of isolation method, but also other conditions during this procedure may be important. The use of EV-depleted FBS is widely recognized as a necessity25,26; how...

Extracellular vesicles (EVs), according to the MISEV 2018 nomenclature, are a collective term describing various subtypes of cell-secreted membranous vesicles that play crucial roles in numerous physiological and pathological processes1,2. Moreover, EVs show promise as novel biomarkers for various diseases, as well as therapeutic agents and drug delivery vehicles. However, realizing their full potential is difficult as there are still many technical obstacles related to their acquisition3. One such challenge is the isolation of endotoxin-free EVs, which has been neglected in many cases. One of the most common endotoxins is lipopolysaccharide (LPS), which is a major component of gram-negative bacterial cell walls and can cause an acute inflammatory response, owing to the release of a large number of inflammatory cytokines by various cells4,5. LPS induces a response by binding to LPS binding protein, followed by interaction with the CD14/TLR4/MD2 complex on myeloid cells. This interaction leads to the activation of MyD88- and TRIF-dependent signaling pathways, which in turn triggers the nuclear factor kappa B (NFkB). Translocation of NFkB to the nucleus initiates the production of cytokines6. Monocytes and macrophages are highly sensitive to LPS, and their exposure to LPS results in a release of inflammatory cytokines and chemokines (e.g., IL-6, IL-12, CXCL8, and TNF-&#945;)7,8. The CD14 structure enables the binding of different LPS species with similar affinity and serves as a co-receptor for other toll-like receptors (TLRs) (TLR1, 2, 3, 4, 6, 7, and 9)6. The number of studies being conducted on the effects of EVs on monocytes/macrophages is still increasing9,10,11. Especially from the perspective of studying the functions of monocytes, their subpopulations, and other immune cells, the presence of endotoxin and even their masked presence in EVs is of great importance12. The overlooked contamination of EVs with endotoxins may lead to misleading conclusions and hide their true biological activity. In other words, working with monocytic cells requires confidence in the absence of endotoxin contamination13. Potential sources of endotoxins can be water, commercially obtained media and sera, media components and additives, laboratory glassware, and plasticware5,14,15.
Therefore, this study aimed to develop a protocol for the isolation of low endotoxin-containing EVs. The protocol provides simple hints on how to avoid endotoxin contamination during EVs isolation instead of removing endotoxins from EVs. Previously, many protocols have been presented on how to remove endotoxins from, for example, engineered nanoparticles used in nanomedicine; however, none of them are useful for biological structures such as EVs. The effective depyrogenation of nanoparticles can be carried out by ethanol or acetic acid rinsing, heating at 175 &#176;C for 3 h, &#947; irradiation, or triton X-100 treatment; however, these procedures lead to the destruction of EVs16,17.
The presented protocol is a pioneering study focused on avoiding endotoxin impurities in EVs, unlike previous studies on the effect of EVs on monocytes9. Applying proposed principles to laboratory practice may help to obtain reliable research results, which can be crucial when considering the potential use of EVs as therapeutic agents in the clinic12.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>&#160;Alix (3A9) Mouse mAb&#160;</td>
			<td>Cell Signaling Technology</td>
			<td>2171</td>
			<td></td>
		</tr>
		<tr>
			<td>1250ul Filter Universal Pipette Tips, Clear, Polypropylene, Non-Pyrogenic</td>
			<td>GoogLab Scientific</td>
			<td>GBFT1250-R-NS</td>
			<td></td>
		</tr>
		<tr>
			<td>BD FACSCanto II Flow Cytometr</td>
			<td>BD Biosciences</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>CBA Human Th1/Th2 Cytokine Kit II</td>
			<td>BD Biosciences</td>
			<td>551809</td>
			<td></td>
		</tr>
		<tr>
			<td>CD9 (D8O1A) Rabbit mAb</td>
			<td>Cell Signaling Technology</td>
			<td>13174</td>
			<td></td>
		</tr>
		<tr>
			<td>ChemiDoc Imaging System</td>
			<td>Bio-Rad Laboratories, Inc.&#160;</td>
			<td>17001401</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM (Dulbecco&#8217;s Modified Eagle&#8217;s Medium)&#160;</td>
			<td>Corning</td>
			<td>10-013-CV</td>
			<td></td>
		</tr>
		<tr>
			<td>ELX800NB, Universal Microplate Reader</td>
			<td>BIO-TEK INSTRUMENTS, INC</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Gibco</td>
			<td>16000044</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum South America Ultra Low Endotoxin</td>
			<td>&#160;Biowest</td>
			<td>&#160;S1860-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Gentamicin, 50 mg/mL</td>
			<td>&#160;PAN &#8211; Biotech</td>
			<td>P06-13100</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-Mouse IgG- HRP</td>
			<td>Santa Cruz Biotechnology</td>
			<td>sc-2004</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-Rabbit IgG- HRP</td>
			<td>Santa Cruz Biotechnology</td>
			<td>sc-2005</td>
			<td></td>
		</tr>
		<tr>
			<td>Immun-Blot PVDF Membrane</td>
			<td>Bio-Rad Laboratories, Inc.&#160;</td>
			<td>1620177</td>
			<td></td>
		</tr>
		<tr>
			<td>LPS from Salmonella abortus equi S-form (TLRGRADE)</td>
			<td>&#160;Enzo Life Sciences, Inc.</td>
			<td>ALX-581-009-L002</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini Trans-Blot Electrophoretic Transfer Cell</td>
			<td>Bio-Rad Laboratories, Inc.&#160;</td>
			<td>1703930</td>
			<td></td>
		</tr>
		<tr>
			<td>Nanoparticle Tracking Analysis&#160;</td>
			<td>Malvern Instruments Ltd</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>NuPAGE LDS Sample Buffer (4X)</td>
			<td>&#160;Invitrogen</td>
			<td>&#160;NP0007</td>
			<td></td>
		</tr>
		<tr>
			<td>NuPAGE Sample Reducing Agent (10x)</td>
			<td>&#160;Invitrogen</td>
			<td>NP0004</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Sigma Aldrich</td>
			<td>P7793</td>
			<td>transparent film</td>
		</tr>
		<tr>
			<td>Perfect 100-1000 bp DNA Ladder</td>
			<td>EURx</td>
			<td>E3141-01&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>PierceTM Chromogenic Endotoxin Quant Kit</td>
			<td>Thermo Scientific</td>
			<td>A39552</td>
			<td></td>
		</tr>
		<tr>
			<td>PP Oak Ridge Tube with sealing caps</td>
			<td>Thermo Scientific</td>
			<td>3929, 03613</td>
			<td></td>
		</tr>
		<tr>
			<td>RPMI 1640</td>
			<td>RPMI-1640 (Gibco)</td>
			<td>11875093</td>
			<td></td>
		</tr>
		<tr>
			<td>SimpliAmp Thermal Cycler</td>
			<td>Applied Biosystem</td>
			<td>A24811</td>
			<td></td>
		</tr>
		<tr>
			<td>Sorvall wX+ ULTRA SERIES Centrifuge with T-1270 rotor</td>
			<td>Thermo Scientific</td>
			<td>75000100</td>
			<td></td>
		</tr>
		<tr>
			<td>Sub-Cell GT Horizontal Electrophoresis System</td>
			<td>Bio-Rad Laboratories, Inc.&#160;</td>
			<td>1704401</td>
			<td></td>
		</tr>
		<tr>
			<td>SuperSignal West Pico PLUS Chemiluminescent Substrate</td>
			<td>Thermo Scientific</td>
			<td>34577</td>
			<td></td>
		</tr>
		<tr>
			<td>SW480 cell line</td>
			<td>American Type Culture Collection(ATCC)</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SW480 cell line</td>
			<td>American Type Culture Collection (ATCC)</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe filter 0.22 um</td>
			<td>TPP</td>
			<td>99722</td>
			<td></td>
		</tr>
		<tr>
			<td>Trans-Blot SD Semi-Dry Transfer Cell</td>
			<td>Bio-Rad Laboratories, Inc.&#160;</td>
			<td>1703940</td>
			<td>Transfer machine</td>
		</tr>
		<tr>
			<td>Transfer pipette, 3.5 mL</td>
			<td>SARSTEDT</td>
			<td>86.1171.001</td>
			<td></td>
		</tr>
	</tbody>
</table>

isolation of low endotoxin content extracellular vesicles derived from cancer cell lines

Extracellular vesicles (EVs) are a heterogeneous population of membrane vesicles released by cells in vitro and in vivo. Their omnipresence and significant role as carriers of biological information make them intriguing study objects, requiring reliable and repetitive protocols for their isolation. However, realizing their full potential is difficult as there are still many technical obstacles related to their research (like proper acquisition). This study presents a protocol for the isolation of small EVs (according to the MISEV 2018 nomenclature) from the culture supernatant of tumor cell lines based on differential centrifugation. The protocol includes guidelines on how to avoid contamination with endotoxins during the isolation of EVs and how to properly evaluate them. Endotoxin contamination of EVs can significantly hinder subsequent experiments or even mask their true biological effects. On the other hand, the overlooked presence of endotoxins may lead to incorrect conclusions. This is of particular importance when referring to cells of the immune system, including monocytes, because monocytes constitute a population that is especially sensitive to endotoxin residues. Therefore, it is highly recommended to screen EVs for endotoxin contamination, especially when working with endotoxin-sensitive cells such as monocytes, macrophages, myeloid-derived suppressor cells, or dendritic cells.

A prerequisite or obligatory step for this protocol is the exclusion of possible endotoxin contamination from reagents. All the reagents being used, such as FBS, DMEM, RPMI, PBS, and even ultracentrifuge tubes, must be endotoxin-free (&#60;0.005 EU/mL). Maintaining the regime of no endotoxin contamination is not easy as, for example, the regular/standard serum for cell culture can be its rich source (0.364 EU/mL; see Table 1).
Although this protocol was developed to isolate EV...

Watch this Scientific Journal Video about Isolation of Low Endotoxin Content Extracellular Vesicles Derived from Cancer Cell Lines at JoVE.com

Isolation of Low Endotoxin Content Extracellular Vesicles Derived from Cancer Cell Lines

The proposed protocol includes guidelines on how to avoid contamination with endotoxin during the isolation of extracellular vesicles from cell culture supernatants, and how to properly evaluate them.

Extracellular vesicles (EVs) are a heterogeneous population of membrane vesicles released by cells in vitro and in vivo. Their omnipresence and ...

This protocol provide guidelines on how to avoid contamination with endotoxin during the isolation of extracellular vesicles from cell culture supernatants, and how to properly evaluate them. The main advantage of this protocol is that every lab concerned with EVs may limit endotoxin contamination by keeping an aseptic procedure and using simple and widely available equipment. Everyone who is trying this technique for the first time should start with new media, reagents, and plasticware which are low-endotoxin, non-pyrogenic labeled.For this protocol, use endotoxin-free reagents, water, culture media, filtered PBS, ultra low-endotoxin FBS, and ultracentrifuge tubes. To begin, collect the supernatant from previously cultured SW480 and SW620 cell lines into appropriately labeled 15-milliliter tubes. Remove cell debris by centrifuging the supernatant at 500 x g for five minutes at room temperature.Without disturbing the debris, collect the supernatant into a new labeled tube, and centrifuge at 3, 200 x g for 12 minutes at four degrees Celsius. Carefully transfer 45 milliliters of the supernatant into a vertically-placed sterile 50-milliliter tube, without wetting the edges of the tube. Wrap the tube's cap with a sterile, transparent film, and store it vertically at minus 80 degrees Celsius for subsequent isolation of extracellular vesicles.Begin isolation by preparing 0.22-micrometer syringe filters, syringes, and tubes containing approximately 90 milliliters of supernatant. Fill a syringe with the supernatant, and fix the filter to the needle adapter. Filter the supernatant through the filter into a 50-milliliter tube.Pipette seven milliliters of the filtrate into a prepared ultracentrifuge tube, and centrifuge at 100, 000 x g for two hours at four degrees Celsius. Use a sterile Pasteur pipette to discard the supernatant. Pull the pellets into an ultracentrifuge tube using a long filtered pipette tip.Rinse the extracellular vesicles by adding seven milliliters of filtered endotoxin-free PBS. After ultracentrifugation, discard the supernatant using a sterile Pasteur pipette and resuspend the pellet in 200 microliters of endotoxin-free PBS. Transfer the suspension to a sterile 1.5-milliliter low protein binding test tube.Then transfer 10 microliters of suspension to a new 1.5-milliliter tube for further analysis. Wrap the cap of the tube, and store it at minus 80 degrees Celsius. Now, into a new tube, dilute one microliter of suspension using filtered PBS at a ratio of 1 to 1000 for nanoparticle tracking analysis.To perform blotting analysis, first mix 20 micrograms of the samples with a loading buffer. Incubate the samples at 70 degrees Celsius for 10 minutes. Then load 20 micrograms of the sample into each well of a 10 to 14%polyacrylamide gel with SDS, and perform electrophoresis for 45 minutes at 150 volts, with running buffer.Next, place the gel in a transfer machine with Towbin buffer, and perform a semi-dry transfer of proteins onto a polyvinylidene difluoride membrane at 25 volts for one hour. Block the membrane with 1%BSA by incubating it for one hour on a rocker. Add BSA diluted antibodies, anti-CD9 or anti-Alix, to the membrane, and incubate overnight at four degrees Celsius on a rocker.After removing the antibodies, wash the membrane thrice with 10 milliliters of TBST for 10 minutes. Now add goat anti-rabbit or anti-mouse secondary antibody, and incubate again on a rocker for one hour at room temperature. Discard the antibody, and wash the membrane as demonstrated previously.Pour one milliliter of the solution containing substrate and luminol at an equal ratio on the membrane. Immediately place the membrane in an imaging system, and visualize the protein bands on the screen. In the present study, western blot analysis confirmed the presence of two extracellular vesicle markers, CD9 and Alix.The mean size and concentrations of the vesicles isolated from both SW480 and SW620 were similar. Stimulation of monocyte with different doses of lipopolysaccharide, or LPS, showed the lowest dose of LPS enabling the secretion of interleukin 10 and tumor necrosis factor in monocytes was 50 picogram per milliliter. The chromogenic LAL test indicated that LPS contamination of the extracellular vesicles was around 50 picograms per milliliter for both cell lines.The most important thing to remember is the use of LPS-free or depleted reagents, and routine LPS measurement at each step of the procedure. Preventing endotoxin contamination is easier than eliminating it. The proposed protocol limits the possibility of false results due to the contamination of EVs with endotoxin, and allows for assessing the EVs activity per cell.The proposed protocol is useful for researchers working with endotoxin-sensitive cells, like monocytes, dendritic cells, and macrophages.

isolation-low-endotoxin-content-extracellular-vesicles-derived-from

Research

JoVE Journal

Immunology and Infection

893 ビュー.  Jagiellonian University Medical College. このプロトコルは、細胞培養上清から細胞外小胞を単離する際にエンドトキシンによる汚染を回避する方法と、それらを適切に評価する方法に関するガイドラインを提供します。このプロトコルの主な利点は、EVに関係するすべてのラボが、無菌手順を維持し、シンプルで広く利用可能な機器を使用することにより、エンドトキシン汚染を制限できることです。この技術...