Name: detection and isolation of apoptotic bodies to high purity
Uploaded: 2018-08-12T15:00:00
Description: Watch this Scientific Journal Video about Detection and Isolation of Apoptotic Bodies to High Purity at JoVE.com

This worked was supported by grants from National Health and Medical Research Council (GNT1125033 and GNT1140187) and Australian Research Council (DP170103790) to I.K.H.P.

1. Induction of Apoptosis
<ol>
	<li>Centrifuge cell sample at 300 x g for 5 min and discard supernatant to remove any pre-existing cell debris. 
	NOTE: When using adherent cells, seed cells in advance and wash with 1x phosphate-buffered solution (PBS) prior to apoptosis induction.</li>
	<li>Determine cell number and collect cells. 
	NOTE: Depending on the assay post-isolation, we recommend a starting cell number of at least 1 x 107 cells.</li>
	<li>Resuspend in complete media (respective medium con...

<ol>
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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=Membrane+blebbing+during+apoptosis+results+from+caspase-mediated+activation+of+ROCK+I.">Membrane blebbing during apoptosis results from caspase-mediated activation of ROCK I.</a> Nature Cell Biology. 3, 339-345 (2001).</li><li>Atkin-Smith, G. K., 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+novel+mechanism+of+generating+extracellular+vesicles+during+apoptosis+via+a+beads-on-a-string+membrane+structure.">A novel mechanism of generating extracellular vesicles during apoptosis via a beads-on-a-string membrane structure.</a> Nature Communications. 6, 7439 (2015).</li><li>Poon, I. K., 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=Unexpected+link+between+an+antibiotic,+pannexin+channels+and+apoptosis.">Unexpected link between an antibiotic, pannexin channels and apoptosis.</a> Nature. 507, 329-334 (2014).</li><li>Moss, D. K., Betin, V. M., Malesinski, S. D., Lane, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+role+for+microtubules+in+apoptotic+chromatin+dynamics+and+cellular+fragmentation.">A novel role for microtubules in apoptotic chromatin dynamics and cellular fragmentation.</a> Journal of Cell Science. 119, 2362-2374 (2006).</li><li>Kerr, J. F., Wyllie, A. H., Currie, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Apoptosis:+a+basic+biological+phenomenon+with+wide-ranging+implications+in+tissue+kinetics.">Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics.</a> British journal of cancer. 26, 239-257 (1972).</li><li>Witasp, 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=Bridge+over+troubled+water:+milk+fat+globule+epidermal+growth+factor+8+promotes+human+monocyte-derived+macrophage+clearance+of+non-blebbing+phosphatidylserine-positive+target+cells.">Bridge over troubled water: milk fat globule epidermal growth factor 8 promotes human monocyte-derived macrophage clearance of non-blebbing phosphatidylserine-positive target cells.</a> Cell Death and Differentiation. 14, 1063-1065 (2007).</li><li>Orlando, K. A., Stone, N. L., Pittman, R. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rho+kinase+regulates+fragmentation+and+phagocytosis+of+apoptotic+cells.">Rho kinase regulates fragmentation and phagocytosis of apoptotic cells.</a> Experimental Cell Research. 312, 5-15 (2006).</li><li>Holmgren, 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=Horizontal+transfer+of+DNA+by+the+uptake+of+apoptotic+bodies.">Horizontal transfer of DNA by the uptake of apoptotic bodies.</a> Blood. 93, 3956-3963 (1999).</li><li>Zernecke, 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=Delivery+of+microRNA-126+by+apoptotic+bodies+induces+CXCL12-dependent+vascular+protection.">Delivery of microRNA-126 by apoptotic bodies induces CXCL12-dependent vascular protection.</a> Science Signaling. 2, ra81 (2009).</li><li>Schiller, 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=Autoantigens+are+translocated+into+small+apoptotic+bodies+during+early+stages+of+apoptosis.">Autoantigens are translocated into small apoptotic bodies during early stages of apoptosis.</a> Cell Death and Differentiation. 15, 183-191 (2008).</li><li>Elamin, M. 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=Curcumin+inhibits+the+Sonic+Hedgehog+signaling+pathway+and+triggers+apoptosis+in+medulloblastoma+cells.">Curcumin inhibits the Sonic Hedgehog signaling pathway and triggers apoptosis in medulloblastoma cells.</a> Molecular Carcinogenesis. 49, 302-314 (2010).</li><li>Sagulenko, 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=AIM2+and+NLRP3+inflammasomes+activate+both+apoptotic+and+pyroptotic+death+pathways+via+ASC.">AIM2 and NLRP3 inflammasomes activate both apoptotic and pyroptotic death pathways via ASC.</a> Cell Death and Differentiation. 20, 1149-1160 (2013).</li><li>Crescitelli, R., 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=Distinct+RNA+profiles+in+subpopulations+of+extracellular+vesicles:+apoptotic+bodies,+microvesicles+and+exosomes.">Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes.</a> Journal of Extracellular Vesicles. 2, (2013).</li><li>Turiak, 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=Proteomic+characterization+of+thymocyte-derived+microvesicles+and+apoptotic+bodies+in+BALB/c+mice.">Proteomic characterization of thymocyte-derived microvesicles and apoptotic bodies in BALB/c mice.</a> Journal of Proteomics. 74, 2025-2033 (2011).</li><li>Vermes, I., Haanen, C., Steffens-Nakken, H., Reutelingsperger, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+assay+for+apoptosis.+Flow+cytometric+detection+of+phosphatidylserine+expression+on+early+apoptotic+cells+using+fluorescein+labelled+Annexin+V.">A novel assay for apoptosis. Flow cytometric detection of phosphatidylserine expression on early apoptotic cells using fluorescein labelled Annexin V.</a> Journal of Immunological Methods. 184, 39-51 (1995).</li><li>Jiang, 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=Monitoring+the+progression+of+cell+death+and+the+disassembly+of+dying+cells+by+flow+cytometry.">Monitoring the progression of cell death and the disassembly of dying cells by flow cytometry.</a> Nature Protocols. 11, 655-663 (2016).</li><li>Berda-Haddad, Y., 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=Sterile+inflammation+of+endothelial+cell-derived+apoptotic+bodies+is+mediated+by+interleukin-1alpha.">Sterile inflammation of endothelial cell-derived apoptotic bodies is mediated by interleukin-1alpha.</a> Proceedings of the National Academy of Sciences of the United States of America. 108, 20684-20689 (2011).</li><li>Lleo, 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=Shotgun+proteomics:+identification+of+unique+protein+profiles+of+apoptotic+bodies+from+biliary+epithelial+cells.">Shotgun proteomics: identification of unique protein profiles of apoptotic bodies from biliary epithelial cells.</a> Hepatology. 60, 1314-1323 (2014).</li><li>Atkin-Smith, G. K., 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+cell+type-specific+apoptotic+bodies+by+fluorescence-activated+cell+sorting.">Isolation of cell type-specific apoptotic bodies by fluorescence-activated cell sorting.</a> Scientific Reports. 7, 39846 (2017).</li><li>Jiang, 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=Determining+the+contents+and+cell+origins+of+apoptotic+bodies+by+flow+cytometry.">Determining the contents and cell origins of apoptotic bodies by flow cytometry.</a> Scientific Reports. 7, 14444 (2017).</li></ol>

Since its early description in the 1950s, the field of apoptosis has advanced markedly, becoming a prominent research area. Despite the broad interest and extensive efforts, certain aspects of apoptosis, in particular the formation of ApoBDs, have not been well studied due to the lack of appropriate methodologies. These notably include the limitation in tracking apoptosis progression and ApoBD formation simultaneously using the traditional flow cytometry A5/PI analysis and the impurities of ApoBD isolation. We have recen...

Apoptosis, a well-studied form of programmed cell death, is required to maintain physiological homeostasis and remove potentially harmful cells within the human body1. After the induction of apoptosis, apoptotic cells (ApoCells) can undergo a series of morphological changes and disassemble into small membrane-bound vesicles termed ApoBDs. Overall, this process is known as apoptotic cell disassembly and can be divided into 3 distinct steps based on morphology2,3. Step 1 (plasma membrane blebbing) is characterized by the formation of balloon-like structures on the cell surface known as blebs4,5. Step 2 (apoptotic protrusion formation) includes the formation of long membrane protrusions such as apoptopodia, beaded-apoptopodia and microtubule spikes6,7,8. Lastly, Step 3 (ApoBD formation) includes the fragmentation of the apoptotic protrusions and/or ApoCells to generate ApoBDs6,9. Previous findings have suggested a role of ApoBDs in aiding apoptotic cell clearance and mediating intercellular communication. For example, it is proposed that the fragmentation of an ApoCell into ApoBDs may generate small &#39;bite-sized&#39; pieces that could be easily removed by surrounding phagocytes2,10,11. Furthermore, ApoBDs may harbor a series of biomolecules such as DNA, RNA and proteins, which may be trafficked to surrounding cells to facilitate cell-cell communication12,13,14. To functionally investigate these processes, it is vital to confirm three key parameters including (i) validation of apoptosis induction and ApoBD formation, (ii) isolation of ApoBDs, and (iii) confirmation of ApoBD purity.
Previously, a number of methods including flow cytometry and electron microscopy have been used to study apoptosis and ApoBDs15,16,17,18. However, ApoBD detection and quantification are often difficult or overlooked. For instance, the most routinely-used flow cytometry-based apoptosis assay employs annexin V (A5, a protein that binds the externalized &#39;eat-me&#39; signal phosphatidylserine (PtdSer)) and nucleic acid stain propidium iodide (PI)19. However, by using this universal stain combination, analysis assumes that there are only three types of cell subsets (viable cells, ApoCells and necrotic cells) in the sample. Furthermore, though considered as &#34;a gold standard&#34; by many researchers for apoptosis, flow cytometry assays and subsequent data analysis often excludes ApoBDs through an initial gating step selecting FSC/SSCintermediate-high events. Therefore, we have recently developed a novel flow cytometry assay using A5 and TO-PRO-3, another nucleic stain that can be selectively taken up by caspase 3/7-activated pannexin 1 (PANX1) channels7,20. As caspase 3-induced PANX1 activation precedes PtdSer exposure at the early stage of apoptosis, TO-PRO-3 differentially stains apoptotic and necrotic cells. In addition, this approach combined with our novel gating strategy includes all acquired events during data analysis and as a result, six cell/particle subsets are identified, including: (i) viable cells (FSC/SSCintermediate/high, A5low, TO-PRO-3low), (ii) A5- early ApoCells (FSC/SSCintermediate/high, A5low, TO-PRO-3intermediate), (iii) A5+ ApoCells (FSC/SSCintermediate/high, A5high, TO-PRO-3intermediate), (iv) necrotic cells or late ApoCells (FSC/SSCintermediate/high, A5high, TO-PRO-3high), (v) ApoBDs (FSC/SSClow, A5intermediate, TO-PRO-3low/intermediate), and (vi) debris (FSC/SSClow, A5low, TO-PRO-3low)20. Our approach emphasizes the importance of analyzing all cells/particle subsets and, more importantly, the separation of ApoBDs from cells and debris20. Thus, this approach demonstrates an efficient technique to validate the induction of apoptosis and ApoBD formation simultaneously.
Traditionally, ApoBDs have been isolated through a variety of differential centrifugation approaches whereby ApoBDs can be separated from cells or other extracellular vesicles based on density. However, such centrifugation methods are often limited by low ApoBD purity, lack of a quantification step to confirm sample purity, and/or inability to separate cell type-specific ApoBDs17,21,22. Therefore, we recently developed two approaches, a FACS-based and a new differential centrifugation-based approach which can be coupled with our previously established flow cytometry method to validate the induction of apoptosis and sample purity23. ApoBD isolation via our FACS-based approach can enrich ApoBDs to up to 99% purity, and can be coupled with a variety of cell type-specific antibodies to isolate ApoBDs from mixed cell populations, tissue samples and bodily fluids23. Furthermore, our revised differential centrifugation approach demonstrates an efficient method to isolate ApoBDs to &#62;90% purity23.
In this paper, we describe in detail our experimental procedure to validate apoptosis induction, and to detect and quantify ApoBD formation. The ApoBD isolation workflows using FACS-based and differential centrifugation-based methods are also elaborated and compared. The representative data demonstrate that the described methodology provides an effective cutting-edge tool for future ApoBD studies.

<table border="0" cellpadding="0" cellspacing="0" style="width:1309px;" width="1309">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">Cells e.g. cultured human THP-1 monocytes (clone number: TIB-202)</td>
			<td style="width:149px;">ATCC</td>
			<td style="width:119px;">-</td>
			<td style="width:513px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">RPMI 1640 medium</td>
			<td style="width:149px;">Life Technologies</td>
			<td style="width:119px;">22400-089</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">Penicillin-streptomycin mixture</td>
			<td style="width:149px;">Life Technologies</td>
			<td style="width:119px;">15140122</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">FSC</td>
			<td style="width:149px;">Gibco</td>
			<td style="width:119px;">10099-141</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1x PBS</td>
			<td style="width:149px;">-</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Annexin V FITC</td>
			<td style="width:149px;">BD Bioscience</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TO-PRO-3 iodide</td>
			<td style="width:149px;">Life Technologies</td>
			<td style="width:119px;">T3605</td>
			<td>TO-PRO-3 may cause skin, eye and respiratory irration. Avoid direct contact.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">10x Annexin V binding buffer</td>
			<td style="width:149px;">BD Bioscience</td>
			<td style="width:119px;">556454</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">EDTA</td>
			<td style="width:149px;">Sigma-Aldrich</td>
			<td style="width:119px;">1001710526</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">Centrifuge tube (15 mL)</td>
			<td style="width:149px;">Cellstar</td>
			<td style="width:119px;">188271</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">Microcentrifuge tube (1.5 mL)</td>
			<td style="width:149px;">Sarstedt</td>
			<td style="width:119px;">72.690.001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">Tissue culture incubator (37 &#176;C, 5% CO2)</td>
			<td style="width:149px;">-</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">Centrifuge</td>
			<td style="width:149px;">Beckman Coulter</td>
			<td style="width:119px;">392932</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">FACS ARIA III Flow cytometer, configured with two lasers for FITC and APC detection</td>
			<td style="width:149px;">BD Bioscience</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">FACS Canto II Flow cytometer, configured with two lasers for FITC and APC detection</td>
			<td style="width:149px;">BD Bioscience</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">FACS Diva 6.1.1 software</td>
			<td style="width:149px;">BD Bioscience</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:528px;">FlowJo 8.8.6 software</td>
			<td style="width:149px;">-</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#160;UV Stratalinker 1800</td>
			<td style="width:149px;">Stratagene</td>
			<td style="width:119px;">-</td>
			<td></td>
		</tr>
	</tbody>
</table>

detection and isolation of apoptotic bodies to high purity

Apoptotic bodies (ApoBDs), microvesicles and exosomes are the key members of the extracellular vesicle family, with ApoBDs being one of the largest type. It has been proposed that ApoBDs can aid cell clearance as well as intercellular communication through trafficking biomolecules. Conventional approaches used for the identification and isolation of ApoBDs are often limited by the lack of accurate quantification and low sample purity. Here, we describe a workflow to confirm the induction of apoptosis, validate ApoBD formation, and isolate ApoBDs to high purity. We will also outline and compare fluorescence-activated cell sorting (FACS) and differential centrifugation based approaches to isolate ApoBDs. Furthermore, the purity of isolated ApoBDs will be confirmed using a previously establish flow cytometry-based staining and analytical method. Taken together, using the described approach, THP-1 monocyte apoptosis and apoptotic cell disassembly was induced and validated, and ApoBD generated from THP-1 monocytes were isolated to a purity of 97-99%.

Using the procedure outlined here, THP-1 monocyte apoptosis was induced and ApoBDs were detected and isolated via either a FACS-based or a differential centrifugation approach (Figure 1). Firstly, apoptosis was induced by UV irradiation and samples were collected after 2-3 h of incubation when cells exhibited apoptotic morphologies, including blebbing, apoptotic membrane protrusion formation and the generation of ApoBDs6. A TO-PRO-3 an...

Watch this Scientific Journal Video about Detection and Isolation of Apoptotic Bodies to High Purity at JoVE.com

Detection and Isolation of Apoptotic Bodies to High Purity

A workflow using flow cytometry or differential centrifugation is developed to detect, quantify and isolate apoptotic bodies from an apoptotic sample to high purity.

Apoptotic bodies (ApoBDs), microvesicles and exosomes are the key members of the extracellular vesicle family, with ApoBDs being one of the largest type. ...

The overall goal of this protocol is to both detect and isolate apoptotic bodies to high purity. Apoptotic bodies are a type of extracellular vesicles generated to help the induction of hematosis. They are the largest type of extracellular physical family typically ranging from one to five micrometer diameter.It is now becoming apparent that apoptotic bodies can aid cellular processes, such as apoptotic cell clearance and intracellular communication. Therefore, the development of an accurate methodology to detect, quantify, and isolate apoptotic bodies is critical for the personalization of their functions and mechanisms. In this series of perparedments we're gonna show you how to detect and quantify and isolate apoptotic bodies from apoptotic samples.Part A, the induction of apoptosis. To induce apoptosis in cell lines, such as THB1 monocytes, first start by collecting the cells. Count cells and collect approximately 10 million cells or as required.We recommend 10 million for analysis of apoptotic bodies. Alloquate two million cells per well of a six well plate. Remove the lid from the six well plate and UV cells using the UV Stratalinker 1800.Irradiate cells at 150 millijules per centimeter squared. This irradiation should take approximately 30 to 60 seconds. After the irradiation is complete, incubate cells for two to eight hours, depending on the cell line.At this point, cells should exhibit apoptotic morphologies, such as apoptotic blemming and apoptotic body formation. Collect apoptotic cells with a P1000 pipette. Collect approximately 1/10th of the apoptotic sample for the whole apoptotic sample control.Also collect an untreated or viable sample. Centrifuge both the whole apoptotic sample and untreated sample at 3, 000g for six minutes. Re suspend in PBS and set aside on ice.For apoptotic body isolation, continue to either step B or C.B, Apoptotic body isolation using FACS. Centrifuge the remaining apoptotic sample at 3, 000g for six minutes. Remove the supernatant from the remaining apoptotic sample.Re suspend the remaining apoptotic sample in staining solution containing the nexum 550 and topo three staining for 10 minutes, at room temperature, in the dark. After centrifugation, re suspend in FACS buffer and then filter through a 70 micron cell strainer to ensure cells are efficiently separated. Perform a standard setup of the FACS machine.Acquire the whole apoptotic sample and change the voltage settings to ensure that all events are within the FACS bots and populations can be easily separated. Setup the gating strategy as described in the flow cytometry gating strategy section later. Select gated apoptotic body population and the desired number of apoptotic bodies for collection.Perform an initial sort to confirm the sort settings and apoptotic body purity. After a sort has been performed, perform a system black flush and reanalyze the sorted sample. If high purity is achieved, continue to sort the desired number of apoptotic bodies.Once sorting is complete, take a small portion of the pro sort apoptotic body sample and reanalyze to confirm purity. Part C, apoptotic body isolation via differential centrifugation. Centrifuge the remaining apoptotic sample at 300g for 10 minutes.This centrifugation step will separate cells, including apoptotic cells, viable cells, and necrotic cells from small extracellular vesicles, which will remain in the supernatant. In a new falcon tube, collect the supernatant containing the extracellular vesicles. Re suspend the apoptotic enriched faction in PBS and set aside on ice with the untreated and whole apoptotic samples.Centrifuge the collected supernatant containing the apoptotic bodies at 3, 000g for 20 minutes. Remove the supernatant containing the smaller, extracellular vesicles, being careful to not disrupt the pellet which will contain the apoptotic bodies. Re suspend the apoptotic bodies in PBS and collect 100 microliters of each the untreated, whole apoptotic sample, the apoptotic cells enriched, and the apoptotic bodies enriched sample and stain with the nexum five and topo three staining solution.Stand in the dark for 10 minutes at room temperature before performing flow cytometry analysis. Analyze as described in the laid out gating strategy. Part D, flow cytometry gating strategy.To begin flow cytometry analysis, separate topo three high necrotic cells from all other events by comparing topo three and four together. From the non-permeabilization events, perform the next gate. Select the non-permeabilization events and compare a side scatter verse a nexum five.Select two populations, including a side scatter intermediate in high, a nexum five low to intermediate cells. This population is P1.Also create a second population including all other events. This population is P2.P1 will contain viable cells and early apoptotic cells.P2 will contain all apoptotic events and debris. Select P2 for further gating. From P2, remove all debris by comparing topo three verse a nexum five.Select all of nexum five intermediate and high events. This population will now include all apoptotic bodies and apoptotic cells. Select this population.To separate apoptotic bodies from apoptotic cells, compare full scatter to the nexum five. To select apoptotic bodies, select full scatter low. To select apoptotic cells, select full scatter intermediate to high events.When performing apoptotic body isolation by FACS we recommend performing one final gating strategy by selecting the apoptotic body fraction and viewing it by topo three verse a nexum five. Select all events. This is used to select the gating strategy based on florescence rather than full scatter and side scatter properties to increase accuracy for sorting.To identify viable cells, go back to P1 population. For general viable cell analysis, select P1 and compare full scatter to the nexum five. Select all full scatter intermediate to high cells.This will include all viable cells, removing any remaining debris. Alternatively, for more in depth apoptosis analysis, viable and early apoptotic cells can be separated. For this, compare topo three verse full scatter.Viable cells will be topo three low, full scatter intermediate to high. Early apoptotic cells contain intermediate topo three staining. This entire gating strategy can then be applied to all samples being analyzed.For example, for the apoptotic bodies isolated after FACS. Apply the gating strategy to all samples. Apoptotic body purity can then be prepared.For example, by selecting only the nexum five positive populations, comparing full scatter and a nexum five. This therefore demonstrates the apoptotic bodies post-isolation. Representative results.Flow cytometry analysis was performed to confirm the induction of apoptosis. This gating strategy allows the identification of viable cells, early apoptotic cells, late apoptotic cells, and necrotic cells in the UV irradiated sample. This methodology demonstrated the isolation of apoptotic bodies by two approaches.Firstly, a FACS-based approach, where apoptotic bodies were enriched to 99%purity and a differential centrifugation approach where apoptotic bodies were isolated to 97%purity. This was confirmed by flow cytometry where apoptotic bodies were separated by cells, including viable cells, apoptotic cells, and necrotic.Conclusion. Our approach may provide a new tool for apoptosis and apoptotic body research.Therefore contributing to their advances in personalization of these mechanisms and to help produce new developments in targeting these processes.

Research

JoVE Journal

Biochemistry

Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification

The diversity of small non-coding RNAs (sRNA) is rapidly expanding and their roles in biological processes, including gene regulation, are emerging. Most ...

A Tailored HPLC Purification Protocol That Yields High-purity Amyloid Beta 42 and Amyloid Beta 40 Peptides, Capable of Oligomer Formation

Amyloidogenic peptides such as the Alzheimer's disease-implicated Amyloid beta (A&#946;), can present a significant challenge when trying to obtain high ...

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) ...

A High-Throughput Luciferase Assay to Evaluate Proteolysis of the Single-Turnover Protease PCSK9

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a single-turnover protease which regulates serum low-density lipoprotein (LDL) levels and, ...

Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions

Secreted factors, membrane-tethered receptors, and their interacting partners are main regulators of cellular communication and initiation of signaling ...

Preparation of Fungal and Plant Materials for Structural Elucidation Using Dynamic Nuclear Polarization Solid-State NMR

This protocol shows how uniformly 13C, 15N-labeled fungal materials can be produced and how these soft materials should be proceeded for solid-state NMR ...

Study on the Metabolism of Six Systemic Insecticides in a Newly Established Cell Suspension Culture Derived from Tea (Camellia Sinensis L.) Leaves

Study on the Metabolism of Six Systemic Insecticides in a Newly Established Cell Suspension Culture Derived from Tea Camellia Sinensis L. Leaves

A platform for studying insecticide metabolism using in vitro tissues of tea plant was developed. Leaves from sterile tea plantlets were induced to form ...

Examining the Dynamics of Cellular Adhesion and Spreading of Epithelial Cells on Fibronectin During Oxidative Stress

The adhesion and spreading of cells onto the extracellular matrix (ECM) are essential cellular processes during organismal development and for the ...

High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Neutron scattering offers the possibility to probe the dynamics within samples for a wide range of energies in a nondestructive manner and without ...

Optimization of Flow Cytometric Sorting Parameters for High-Throughput Isolation and Purification of Small Extracellular Vesicles

Small extracellular vesicles (sEV) can be released from all cell types and carry protein, DNA, and RNA. Signaling molecules serve as indicators of the ...