This work was supported, in whole or in part, by institutional funds from Dr. Jose&#769; A. Arruda and the Section of Nephrology, University of Illinois at Chicago (to J. S. L.); and funding from the Department of Medicine of McGill University and the Research Institute of the McGill University Health Centre (to J. R.)

1. Preparations
Note: In this protocol, two or more cell lines, or primary cell cultures, are independently prepared under specific conditions. These preparations include apoptotic cells (Protocol 1), necrotic cells (Protocol 2), and healthy responder cells (Protocol 3). After independent preparation, apoptotic or necrotic cells are added to responder cells and the resulting signal transduction is monitored (Protocols 4, 5, and 6).
<ol>
	<li>Prepare culture media and reagents
	<ol>
		<li>Prepare 500 mL of culture medium A (for use when growing cells under permissive conditions, see section 1.2) by combining the following: 1x Dulbecco&#39;s Modified Eagle&#39;s Medium (DMEM) containing 4.5 g/L glucose, 584 mg/L &#671;-glutamine, 110 mg/L sodium pyruvate, 100 units/mL penicillin-streptomycin, 10% (v/v) fetal bovine serum (FBS), and 10 units/mL of interferon-&#947; (IFN-&#947;).</li>
		<li>Prepare 500 mL of culture medium B (for use when serum-starving cells under non-permissive conditions, see section 1.2) by omitting FBS and IFN-&#947; from the recipe of culture medium A. To grow cells under non-permissive conditions (prior to serum-starvation), add 10% v/v FBS to culture medium B.</li>
		<li>Prepare 0.4% (v/v) paraformaldehyde, pH 7.2, in 1x Dulbecco&#39;s phosphate buffered saline (DPBS) from 4% stock paraformaldehyde for fixation of dead cells. 
		Note: Paraformaldehyde is toxic, and appropriate caution should be exercised in its use.</li>
	</ol>
	</li>
	<li>Culture BU.MPT cells
	<ol>
		<li>Thaw from liquid nitrogen one vial of BU.MPT cells. 
		Note: BU.MPT is a mouse kidney proximal tubular epithelial cell (PTEC) line derived from a transgenic mouse bearing a temperature-sensitive (ts) mutation (tsA58) of the SV40 large tumor antigen (TAg) under the control of the mouse major histocompatibility complex (MHC) H-2Kb class I promoter25,26.</li>
		<li>Plate cells on sterile polystyrene vacuum-gas plasma treated tissue culture dishes (~ 5 x 106 cells per 100 mm diameter dish).</li>
		<li>Grow cells under permissive conditions in a humidified 5% (v/v) CO2 atmosphere. 
		Note: Permissive conditions, which are defined as culture at 33 - 37 &#186;C in the presence of IFN-&#947;, enable stable expression of the tsA58-mutated TAg transgene. Unlike primary cultures of mouse kidney PTEC, which do not survive more than a single passage or two, BU.MPT cultured under permissive conditions can be passaged indefinitely.
		<ol>
			<li>Passage cells at least three times after thawing before using them in an experiment.
			<ol>
				<li>To passage cells, add 1 mL of 0.05% trypsin per 100 mm dish, and incubate in a humidified 5% (v/v) CO2&#160;atmosphere at 37 &#186;C for 5 min. Neutralize the trypsin by adding 10 mL of medium A. Aspirate the detached cells, and split 1:3 to 1:5 into new 100 mm sterile polystyrene vacuum-gas plasma treated tissue culture dishes. Add medium A to bring the volume up to a total of 10 mL per 100 mm dish.</li>
			</ol>
			</li>
		</ol>
		</li>
		<li>In preparation for experimental use as responding cells, grow cells to confluence in a humidified 5% (v/v) CO2 atmosphere under non-permissive conditions (i.e. at 39 &#186;C in the absence of IFN-&#947; [medium B containing 10% v/v FBS]). 
		Note: Under non-permissive conditions, expression of the tsA58-mutated TAg transgene is inhibited by &#62;95%, and BU.MPT cells behave like primary cultures of mouse kidney PTEC.</li>
	</ol>
	</li>
</ol>
2. Preparation of Apoptotic BU.MPT Cells (Protocol 1)
Note: This protocol is specific for BU.MPT cells as the source of apoptotic cells, and staurosporine as the method of apoptosis induction. Alternatively, another cell line, or primary cell culture, may be used as a source of apoptotic cells, with apoptosis induced by standardized protocols for that particular cell type and method of apoptosis induction.
<ol>
	<li>After passage onto 100 mm diameter sterile polystyrene vacuum-gas plasma treated tissue culture dishes, grow BU.MPT cells to confluence in a humidified 5% (v/v) CO2 atmosphere under permissive conditions (i.e. at 37 &#186;C in culture medium A at 10 mL per 100 mm dish), as described in section 1.2.3.</li>
	<li>Rinse the adherent cell monolayer three times with culture medium B, using 10 mL per rinse.</li>
	<li>Induce apoptosis by incubating the cells in culture medium B containing staurosporine, a nonselective protein kinase inhibitor, at 1 &#181;g/mL for 3 h in a humidified 5% (v/v) CO2 atmosphere at 37 &#186;C.</li>
	<li>Aspirate the staurosporine-containing medium containing &#34;floating&#34; apoptotic cells that have detached from the monolayer. Centrifuge this medium for 10 min at 500 x g, discard the supernatant, wash the pellet three times with culture medium B, and add the pellet back to cells collected in the next step, 2.5.</li>
	<li>Detach the remaining adherent cells from steps 2.3 and 2.4 by addition of 5 mM (ethylenediaminetetraacetic acid) EDTA in 1x Ca2+- and Mg2+-free DPBS at 1 mL per dish for 5 min. Aspirate the EDTA-containing medium containing detached apoptotic cells, and pool the detached cells with the &#34;floating&#34; apoptotic cells from step 2.4 in a sterile 15 mL polystyrene centrifuge tube.</li>
	<li>Wash the apoptotic cells three times by centrifugation for 10 min at 500 x g and resuspension in 10 mL of 1x Ca+2- and Mg+2-free DPBS per wash.</li>
	<li>After the last wash, suspend the apoptotic cells in fresh culture medium B at ~ 5 x 106&#160;cells per mL before use to stimulate responder cells. Alternatively, fix washed apoptotic cells in 0.4% (v/v) paraformaldehyde in 1x DPBS for 30 min, and then wash three times with culture medium B, before suspension in culture medium B.</li>
	<li>As appropriate, confirm induction of apoptosis by flow cytometry using a separate preparation of apoptotic cells (or by reserving some cells for this purpose), as previously described6,9,10,15. 
	Note: Early apoptotic cells have intact cell membranes, and appear as propidium iodide (PI)-negative and annexin V-positive cells of decreased cell size (relative to viable cells). Late apoptotic cells have non-intact cell membranes, and appear as PI-positive and annexin V-positive cells of decreased cell size. Using the current protocol, typical preparations contain ~ 85% early apoptotic and ~ 15% late apoptotic cells.</li>
	<li>Add apoptotic cells to BU.MPT responder cells (Protocol 3) at an apoptotic-to-responder cell ratio of 1:1, either directly or after fixation of apoptotic cells for 30 min with 0.4% (v/v) paraformaldehyde in 1x DPBS. 
	Note: Apoptotic cell fixation prior to stimulation of responders should not affect results, unless the observed signaling events are due to release of a soluble mediator (Table 1).</li>
</ol>
3. Preparation of Necrotic BU.MPT Cells (Protocol 2)
Note: This protocol is specific for BU.MPT cells as the source of necrotic cells, and heating as the method of necrosis induction. Alternatively, another cell line, or primary cell culture, may be used as a source of necrotic cells, with necrosis induced by standardized protocols for that particular cell type and method of necrosis induction.
<ol>
	<li>After passage onto 100 mm diameter sterile polystyrene vacuum-gas plasma treated tissue culture dishes, grow BU.MPT cells to confluence in a humidified 5% (v/v) CO2 atmosphere under permissive conditions (i.e. at 37 &#186;C in culture medium A at 10 mL per dish), as described in section 1.2.3.</li>
	<li>Rinse the adherent cell monolayer three times with culture medium B, using 10 mL per rinse.</li>
	<li>Detach the cells by addition of 5 mM EDTA in 1x Ca+2- and Mg+2-free DPBS at 1 mL per dish for 5 min. Aspirate the EDTA-containing medium containing detached cells, and add the cell suspension to a sterile 15 mL polystyrene centrifuge tube.</li>
	<li>Wash the cells three times by centrifugation for 10 min at 500 x g and resuspension in 10 mL of Ca+2- and Mg+2-free DPBS per wash.</li>
	<li>After the last wash, suspend the cells in fresh culture medium B at ~ 5 x 106 cells per mL.</li>
	<li>Induce necrosis by heating cells to 70 &#186;C for 45 min in a water bath, gently vortexing the cell suspension every 10 min.</li>
	<li>Incubate cells for 2 h in a humidified 5% (v/v) CO2 atmosphere at 37 &#176;C. Gently vortex the cell suspension every 15 min.</li>
	<li>As appropriate, confirm induction of necrosis by flow cytometry using a separate preparation of necrotic cells (or by reserving some cells for this purpose), as previously described6,9,10,15. 
	Note: Necrotic cells have ruptured cell membranes, and appear as PI-positive cells of increased cell size (relative to viable cells). Using the current protocol, typical preparations contain &#8805; 95% necrotic cells. Alternatively, induction of necrosis and loss of membrane integrity may be confirmed by Trypan blue staining.</li>
</ol>
4. Preparation of BU.MPT Responder Cells (Protocol 3)
Note: This protocol is specific for BU.MPT cells as the source of responder cells. Alternatively, another cell line, or primary cell culture, may be used as responder cells. Prior to experimental use, quiescence may be induced overnight by standardized protocols within the laboratory.
<ol>
	<li>Grow BU.MPT cells in sterile 100 mm tissue culture dishes under permissive conditions in culture medium A at 10 mL per dish until they achieve ~ 85% confluence.</li>
	<li>Aspirate culture medium A, and rinse the cells three times with culture medium B at 10 mL per rinse. Serum-starve the cells overnight for 18 to 24 h in a humidified 5% (v/v) CO2 atmosphere under non-permissive conditions (i.e. at 39 &#186;C in culture medium B at 10 mL per dish), as described in section 1.2.4, in order to induce quiescence. Alternatively, grow cells in culture medium B plus 10% (v/v) FBS at 39 &#186;C for one day before serum starving cells overnight in culture medium B without FBS.</li>
	<li>Label a separate tissue culture dish of confluent BU.MPT cells for each experimental condition.</li>
	<li>Include the following six conditions: stimulation of viable BU.MPT responders with either vehicle or epidermal growth factor (EGF) for 15 min, following their exposure for 30 min to either no cells, apoptotic cells, or necrotic cells. 
	Note: Exposure to dead cells may either stimulate or inhibit the level of activity of a given signaling molecule. Stimulation is best detected above a low baseline (e.g., absence of EGF), whereas inhibition is best detected from a high baseline (e.g., presence of EGF). Since the effect of stimulation with dead cells is a priori unknown, it is recommended to perform all studies in both the absence and the presence of EGF.</li>
</ol>
5. Stimulation of Responder Cells with Apoptotic and Necrotic Cells (Protocol 4)
<ol>
	<li>Aspirate culture medium B from pre-labeled dishes of quiescent (serum-starved) BU.MPT responder cells (Protocol 3). 
	Note: After overnight culture under non-permissive conditions, BU.MPT cells should behave like primary cultures of mouse kidney PTEC.</li>
	<li>Per 100 mm dish, add 2 mL of one of the following: culture medium B (no cells); apoptotic cell suspension at ~ 5 x 106 cells per mL in culture medium B (Protocol 1); or necrotic cell suspension at ~ 5 x 106 cells per mL in culture medium B (Protocol 2).
	<ol>
		<li>Distribute the 2 mL suspension of dead cells evenly over the 100 mm dish, and keep the time for them to settle to a minimum. To achieve this, distribute the dead cell suspension drop by drop with a wide tip pipette over the entire surface of the responder cell dishes. Use a volume of 2 mL as a compromise between minimizing the settling time and avoiding the clumping of dead cells. 
		Note: The use of a suspension of dead cells as a stimulus entails a number of special considerations, which are described below in greater detail (Table 2 and Discussion).</li>
		<li>Achieve a dead-to-responder cell ratio of ~ 1:1 by adding 2 mL of dead cells at ~ 5 x 106 cells per mL to a confluent 100 mm dish, which contains ~ 10 x 106 cells. Alternatively, in order to establish the dose-dependency of any observed signaling events, vary the ratio of dead to responder cells continuously by progressive dilution in culture medium B of the dead cell suspensions prepared in Protocols 1 and 2.</li>
	</ol>
	</li>
	<li>Gently swirl the dishes, then incubate at 37 &#186;C in a humidified 5% (v/v) CO2 atmosphere.</li>
	<li>After 30 min, stimulate the responder cells with either vehicle or 50 nM EGF, according to the pre-labeling of the culture dish.</li>
	<li>Incubate for 15 min at 37 &#176;C in a humidified 5% (v/v) CO2 atmosphere.</li>
	<li>Wash away the dead cells by adding 5 mL of ice-cold 1x DPBS, swirling the dish, and aspirating the wash fluid. Repeat three times.</li>
	<li>Immediately place the responder cell dishes on ice for further processing.</li>
	<li>Prepare cell lysates
	<ol>
		<li>Prepare cell lysis buffer containing the following: 1&#215; Tris buffered saline (TBS), 10 mM sodium pyrophosphate, 0.5% w/v deoxycholate, 0.1% w/v SDS, 10% glycerol, and 25 mM sodium fluoride.
		<ol>
			<li>Immediately prior to cell lysis, add the following in the exact order given at the indicated concentrations: mini EDTA-free protease inhibitor cocktail (1 tablet per 10 mL of lysis buffer), 10% (v/v) Triton X-100, 1 mM dithiothreitol (DTT), 1 mM phenylmethanesulfonyl fluoride (PMSF), and 10 mM sodium orthovanadate.</li>
		</ol>
		</li>
		<li>Add 700 &#181;L of ice-cold cell lysis buffer per 100 mm dish of freshly stimulated responder cells on ice from step 5.7. Scrape cells with a cell scraper, and transfer the lysate to pre-chilled 1.5 mL microtubes. Maintain the tubes on ice for 15 min.</li>
		<li>Sonicate lysates on ice with 10 pulses of 20 Hz, less than one second each in duration. Avoid the creation of foam at the gas/liquid interface, as this can overheat the samples. Fully immerse the sonicator probe into the microtubes containing lysates before switching the sonicator on, and switch the sonicator off before removing the probe from the lysates.</li>
		<li>Centrifuge at 20,000 x g for 10 min at 4 &#176;C, transfer the supernatants into fresh pre-chilled microtubes, and store at -70 &#186;C.</li>
		<li>Perform gel electrophoresis and immunoblotting on supernatants of lysates, as previously described6,9,10,15.</li>
	</ol>
	</li>
</ol>
6. Preventing Direct Physical Contact between Targets and Responders Using a Semipermeable Polycarbonate Membrane (Protocol 5)
<ol>
	<li>Prepare BU.MPT responder cells according to Protocol 3, with one exception; grow cells in sterile polystyrene tissue culture treated 12-well clusters.</li>
	<li>In selected wells, place a permeable support system containing a 0.4 &#181;m polycarbonate membrane to prevent physical interaction between dead and responder cells. Include control wells without a membrane in the same experiment.</li>
	<li>Aspirate culture medium B from experimental wells of serum-starved BU.MPT responder cells.</li>
	<li>Follow Protocol 4 for stimulation of responder cells with apoptotic or necrotic cells, with the following modifications:
	<ol>
		<li>Per well of the 12-well cluster, add 0.1 mL of one of the following: culture medium B (no cells); apoptotic cell suspension at ~5 x 106 cells per mL in culture medium B (Protocol 1); or necrotic cell suspension at ~5 x 106 cells per mL in culture medium B (Protocol 2). 
		Note: As a confluent well of a 12-well cluster contains ~ 0.5 x 106 cells, the addition of 0.1 mL of dead cells at ~ 5 x 106 cells per mL yields a dead-to-responder cell ratio of ~ 1:1.</li>
		<li>To wells containing the permeable support system, add the dead cells on top of the 0.4 &#181;m polycarbonate membrane within the permeable support system, so there is no direct physical interaction between dead and responder cells.</li>
	</ol>
	</li>
</ol>
7. Inhibition of Phagocytosis with Cytochalasin D (Protocol 6)
<ol>
	<li>Prepare BU.MPT responder cells according to Protocol 3.</li>
	<li>Prepare the cytoskeletal inhibitor cytochalasin D in dimethyl sulfoxide (DMSO) at 4 mg/mL (1,000&#215;). Add to pre-labeled dishes of BU.MPT responder cells either 10 &#956;L of vehicle (DMSO) or 10 &#956;L of cytochalasin D to achieve a final concentration of 4 &#956;g/mL in 10 mL of culture medium B. 
	Note: At this concentration of cytochalasin D, phagocytosis by BU.MPT cells and a macrophage cell line was inhibited by &#8805;90%9,10.</li>
	<li>Incubate for 2 h at 37 &#186;C in a humidified 5% (v/v) CO2 atmosphere.</li>
	<li>Follow Protocol 4 for stimulation of responder cells with apoptotic or necrotic cells.</li>
	<li>As appropriate, confirm inhibition of phagocytosis of dead cells by flow cytometry using a separate preparation of dead and responder cells (or cells reserved for this purpose), as previously described9,10.</li>
</ol>

<ol>
	<li>Galluzzi, 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=Essential+versus+accessory+aspects+of+cell+death:+recommendations+of+the+NCCD+2015.">Essential versus accessory aspects of cell death: recommendations of the NCCD 2015.</a> Cell Death Differ. 22, 58-73 (2015).</li><li>Wallach, D., Kang, T. -. B., Kovalenko, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Concepts+of+tissue+injury+and+cell+death+in+inflammation:+a+historical+perspective.">Concepts of tissue injury and cell death in inflammation: a historical perspective.</a> Nature Rev. Immunol. 14, 51-59 (2014).</li><li>Hochreiter-Hufford, A., Ravichandran, K. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clearing+the+dead:+Apoptotic+cell+sensing,+recognition,+engulfment,+and+digestion.">Clearing the dead: Apoptotic cell sensing, recognition, engulfment, and digestion.</a> Cold Spring Harb. Perspect. Biol. 5, a008748 (2013).</li><li>Reddy, S. 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=Phagocytosis+of+apoptotic+cells+by+macrophages+induces+novel+signaling+events+leading+to+cytokine-independent+survival+and+inhibition+of+proliferation:+activation+of+Akt+and+inhibition+of+extracellular+signal-regulated+kinases+1+and+2.">Phagocytosis of apoptotic cells by macrophages induces novel signaling events leading to cytokine-independent survival and inhibition of proliferation: activation of Akt and inhibition of extracellular signal-regulated kinases 1 and 2.</a> J. Immunol. 169, 702-713 (2002).</li><li>Cvetanovic, M., Ucker, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Innate+immune+discrimination+of+apoptotic+cells:+repression+of+proinflammatory+macrophage+transcription+is+coupled+directly+to+specific+recognition.">Innate immune discrimination of apoptotic cells: repression of proinflammatory macrophage transcription is coupled directly to specific recognition.</a> J. Immunol. 172, 880-889 (2004).</li><li>Patel, V. 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=Apoptotic+cells,+at+all+stages+of+the+death+process,+trigger+characteristic+signaling+events+that+are+divergent+from+and+dominant+over+those+triggered+by+necrotic+cells:+implications+for+the+delayed+clearance+model+of+autoimmunity.">Apoptotic cells, at all stages of the death process, trigger characteristic signaling events that are divergent from and dominant over those triggered by necrotic cells: implications for the delayed clearance model of autoimmunity.</a> J. Biol. Chem. 281, 4663-4670 (2006).</li><li>Cvetanovic, 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=Specific+recognition+of+apoptotic+cells+reveals+a+ubiquitous+and+unconventional+innate+immunity.">Specific recognition of apoptotic cells reveals a ubiquitous and unconventional innate immunity.</a> J. Biol. Chem. 281, 20055-20067 (2006).</li><li>Birge, R. B., Ucker, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Innate+apoptotic+immunity:+the+calming+touch+of+death.">Innate apoptotic immunity: the calming touch of death.</a> Cell Death Differ. 15, 1096-1102 (2008).</li><li>Patel, V. 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=Recognition+of+apoptotic+cells+by+epithelial+cells:+conserved+versus+tissue-specific+signaling+responses.">Recognition of apoptotic cells by epithelial cells: conserved versus tissue-specific signaling responses.</a> J. Biol. Chem. 285, 1829-1840 (2010).</li><li>Patel, V. 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=Recognition-dependent+signaling+events+in+response+to+apoptotic+targets+inhibit+epithelial+cell+viability+by+multiple+mechanisms:+implications+for+non-immune+tissue+homeostasis.">Recognition-dependent signaling events in response to apoptotic targets inhibit epithelial cell viability by multiple mechanisms: implications for non-immune tissue homeostasis.</a> J. Biol. Chem. 287, 13761-13777 (2012).</li><li>Voll, R. E., Herrmann, M., Roth, E. A., Stach, C., Kalden, J. R., Girkontaite, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immunosuppressive+effects+of+apoptotic+cells.">Immunosuppressive effects of apoptotic cells.</a> Nature. 390, 350-351 (1997).</li><li>Fadok, V. A., Bratton, D. L., Konowal, A., Freed, P. W., Westcott, J. Y., Henson, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Macrophages+that+have+ingested+apoptotic+cells+in+vitro+inhibit+proinflammatory+cytokine+production+through+autocrine/+paracrine+mechanisms+involving+TGF-&#946;,+PGE2,+and+PAF.">Macrophages that have ingested apoptotic cells in vitro inhibit proinflammatory cytokine production through autocrine/ paracrine mechanisms involving TGF-&#946;, PGE2, and PAF.</a> J. Clin. Investig. 101, 890-898 (1998).</li><li>Lucas, M., Stuart, L. M., Savill, J., Lacy-Hulbert, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Apoptotic+cells+and+innate+immune+stimuli+combine+to+regulate+macrophage+cytokine+secretion.">Apoptotic cells and innate immune stimuli combine to regulate macrophage cytokine secretion.</a> J. Immunol. 171, 2610-2615 (2003).</li><li>Ariel, 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=Apoptotic+neutrophils+and+T+cells+sequester+chemokines+during+immune+response+resolution+through+modulation+of+CCR5+expression.">Apoptotic neutrophils and T cells sequester chemokines during immune response resolution through modulation of CCR5 expression.</a> Nature Immunol. 7 (11), 1209-1216 (2006).</li><li>Schwab, J. M., Chiang, N., Arita, M., Serhan, C. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resolvin+E1+and+protectin+D1+activate+inflammation-resolution+programmes.">Resolvin E1 and protectin D1 activate inflammation-resolution programmes.</a> Nature. 447, 869-874 (2007).</li><li>Rothlin, C. V., Ghosh, S., Zuniga, E. I., Oldstone, M. B. A., Lemke, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TAM+receptors+are+pleiotropic+inhibitors+of+the+innate+immune+response.">TAM receptors are pleiotropic inhibitors of the innate immune response.</a> Cell. 131, 1124-1136 (2007).</li><li>Li, F., 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=Apoptotic+cells+can+activate+the+"phoenix+rising"+pathway+to+promote+wound+healing+and+tissue+regeneration.">Apoptotic cells can activate the "phoenix rising" pathway to promote wound healing and tissue regeneration.</a> Sci. Signal. 3, ra13 (2010).</li><li>Peter, C., Wesselborg, S., Hermann, M., Lauber, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dangerous+attraction:+phagocyte+recruitment+and+danger+signals+of+apoptotic+and+necrotic+cells.">Dangerous attraction: phagocyte recruitment and danger signals of apoptotic and necrotic cells.</a> Apoptosis. 15 (2010), 1007-1028 (2010).</li><li>Patel, V. 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=Apoptotic+cells+activate+AMPK+and+inhibit+epithelial+cell+growth+without+change+in+intracellular+energy+stores.">Apoptotic cells activate AMPK and inhibit epithelial cell growth without change in intracellular energy stores.</a> J. Biol. Chem. 290, 22352-22369 (2015).</li><li>Hess, K. L., Tudor, K. -. S. R. S., Johnson, J. D., Osati-Ashtiani, F., Askew, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cook-Mills+J.M.+Human+and+murine+high+endothelial+venule+cells+phagocytose+apoptotic+leukocytes.">Cook-Mills J.M. Human and murine high endothelial venule cells phagocytose apoptotic leukocytes.</a> Exp. Cell Res. 236, 404-411 (1997).</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> Sci. Signal. 2, ra51 (2009).</li><li>Esmann, 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=Phagocytosis+of+apoptotic+cells+by+neutrophil+granulocytes:+diminished+proinflammatory+neutrophil+functions+in+the+presence+of+apoptotic+cells.">Phagocytosis of apoptotic cells by neutrophil granulocytes: diminished proinflammatory neutrophil functions in the presence of apoptotic cells.</a> J. Immunol. 184, 391-400 (2010).</li><li>Obeid, 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=Calreticulin+exposure+dictates+the+immunogenicity+of+cancer+cell+death.">Calreticulin exposure dictates the immunogenicity of cancer cell death.</a> Nature Med. 13, 54-61 (2007).</li><li>Peter, C., Wesselborg, S., Hermann, M., Lauber, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dangerous+attraction:+phagocyte+recruitment+and+danger+signals+of+apoptotic+and+necrotic+cells.">Dangerous attraction: phagocyte recruitment and danger signals of apoptotic and necrotic cells.</a> Apoptosis. 15, 1007-1028 (2010).</li><li>Sinha, 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=Lithium+activates+the+Wnt+and+phosphatidylinositol+3-kinase+Akt+signaling+pathways+to+promote+cell+survival+in+the+absence+of+soluble+survival+factors.">Lithium activates the Wnt and phosphatidylinositol 3-kinase Akt signaling pathways to promote cell survival in the absence of soluble survival factors.</a> Am. J. Physiol. Renal Physiol. 288, F703-F713 (2005).</li><li>Jat, P. 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=Direct+derivation+of+conditionally+immortal+cell+lines+from+an+H-2Kb-tsA58+transgenic+mouse.">Direct derivation of conditionally immortal cell lines from an H-2Kb-tsA58 transgenic mouse.</a> Proc. Natl. Acad. Sci. U.S.A. 88, 5096-5100 (1991).</li><li>Wakasugi, K., Schimmel, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Two+distinct+cytokines+released+from+a+human+aminoacyl-tRNA-synthetase.">Two distinct cytokines released from a human aminoacyl-tRNA-synthetase.</a> Science. 284, 147-151 (1999).</li></ol>

The authors declare that they have no competing financial interests.

We provide here a protocol for characterizing the intracellular signaling events induced in viable cells following their exposure to cells undergoing apoptosis, or other forms of cell death. The protocol emphasizes the multiple mechanisms by which exposure to apoptotic cells can modulate intracellular signaling pathways within viable responder cells. These mechanisms include: the interaction (via bridging molecules or surface determinants on the dead cell or its shed vesicles and microvesicles, often termed apoptotic bodies) with specific receptors on the responder cell; the release of soluble mediators (or even their extracellular generation27); and the engagement of the phagocytic machinery. Under circumstances in which substantial phagocytosis occurs, an additional mechanism to be considered is delivery of mediators, such as microRNA, enriched within the apoptotic cell or its vesicles21. The significance of our protocol, as compared to other methodologies, lies in its careful dissection of the multiple mechanisms by which apoptotic cells can modulate signal transduction within responding cells. A major advantage is that most of the techniques required are straightforward and standard to cell culture.
While the protocol is specific for BU.MPT cells, an immortalized mouse kidney PTEC line, as the source of both dead and responding cells, adaptation of the protocol to other cell lines or primary cell cultures is straightforward and easily implemented. Moreover, as in our previous publications, the source of dead and responding cells need not necessarily be the same9,10,19. While we describe the use of staurosporine and heat as inducers of apoptosis and necrosis, respectively, the mode and triggers of cell death may also vary. While the signaling events induced in BU.MPT responders following exposure to apoptotic cells are largely independent of the mode of apoptosis induction, we have observed some differences9,10. For this reason, we recommend replicating key results with several different triggers of apoptotic cell death. For example, if highly phagocytic cells, such as macrophages, are used as responders4,6, or if the duration of interaction between responders and dead cells is long enough for substantial phagocytosis to occur, then one could consider a non-toxic inducer of apoptosis, such as ultraviolet- or gamma-irradiation4,9,10, to rule out potential phagocytic delivery of the toxin. Alternate methods of induction of necrosis may also be considered. While we have obtained identical results with heating and freeze-thawing of cells, the extensive cell clumping and debris occurring with freeze-thawing make its use problematic.
Several simple strategies can help to elucidate the particular mechanism responsible for any signaling events observed following exposure to apoptotic cells (Table 1). These strategies include: fixation of apoptotic cells prior to their addition to responding cells; physical separation of apoptotic and responding cells by a semipermeable membrane; the use of ultracentrifuged conditioned medium collected from cells undergoing apoptosis as a stimulus; and substitution of apoptotic cells with necrotic cells or latex beads. With certain caveats, as detailed in Table 1, the effect on the observed signaling event can pinpoint the responsible mechanism. For example, in the case of receptor-mediated recognition of the apoptotic cell, the signaling event should persist despite fixation of the apoptotic cell, and should be eliminated with replacement of apoptotic cells by conditioned medium or latex beads, as well as with physical separation of dead and responding cells. In response to necrotic cells, the signaling event should be eliminated or become oppositely directed (e.g., inhibition versus stimulation).
The use of a cellular suspension as a stimulus, rather than a soluble ligand, poses several inherent and largely unavoidable experimental obstacles. Awareness of these problems, as well as potential steps to limit their interference, is critical to the successful implementation of this protocol (Table 2). Most of these problems derive from the experimentally restricted number of apoptotic cells per responding cell. This is in contrast to soluble factors. Even when used at the extremely low femtomolar concentrations characteristic of cytokines, the number of soluble ligands far exceeds the number of responding cells. In the case of apoptotic cells, however, steric considerations preclude the addition of dead cells at a ratio much above one dead cell per viable responding cell. To a very real degree, therefore, every dead cell matters.
There are several consequences of this restricted dead-to-responder cell ratio that can lead to a reduction or obscuring of signaling events. To interact physically with a viable responder cell, an apoptotic cell must first settle through the column of suspending medium. Even with minimal volumes, the time for settling of cells can be appreciable, as long as 10 to 20 min. Intracellular signaling events will thus be uncoordinated among responding cells. Hence, the initial contact between responder and dead cells cannot be precisely timed, but rather falls within a somewhat broad range of times. For signaling events that occur on a timescale shorter than that required for settling, this lack of synchronization can lead to an obscuring of the signal such that it is no longer distinguishable from background. Even signals of extended duration, if not of sufficient magnitude, can be susceptible to this issue.
In addition to these temporal issues, spatial matters can also adversely impact results. Meniscal effects, especially in wells and dishes of small diameter (e.g., polystyrene tissue culture treated 96-well clusters), or fluid currents generated by too forceful pipetting can lead to a non-uniform distribution of dead cells, thereby creating a state of feast or famine among responder cells. Since the measured signal derives from that of all responder cells in a single well or plate, variation in the capture of dead cells may obscure weaker signals.
A final issue relates to the heterogeneity of the apoptotic cell population. Even with a strong trigger of apoptosis, such as staurosporine, any preparation of dead cells will contain cells at multiple stages of the death process. This becomes relevant, if the strength of the response to the apoptotic cell depends on its stage within the death process10,14. Since on average each responding cell encounters just one apoptotic cell, heterogeneity in this case can lead to weakening of the overall detected signaling event. Table 2 provides a summary of the major suspension-related issues, as well as strategies for their partial remedy.
There are several other experimental concerns uniquely associated with the use of dead cells as a stimulus. Importantly, culture conditions may affect not only the responding cells, but also the dead cells themselves. For example, serum proteins, if present, can attach to the surface of the dead cell, and enhance or inhibit its recognition by responding cells. In troubleshooting an inconsistent result, or a result differing from that reported in the literature, attention should be given to the following culture conditions (for both responder and dead cells): degree of confluence, passage number, presence of serum, heat inactivation of serum, and nature and duration of quiescence. Finally, one needs to be aware that cell death is an inexorable aspect of all cell culture, and responder cells are therefore continually exposed to a low level of dead cells. This exposure can potentially affect the experimental response to a bolus of dead cells, since the very signals under study are being continually induced. Signal modulation may ensue through normal feedback pathways, or even through selection of a subpopulation of responder cells, especially if the induced signaling events involve survival or proliferation.
In summary, we have described a protocol for the determination of intracellular signaling events induced in viable cells by their physical interaction with adjacent dead or dying cells. Although the focus is predominantly on signaling events induced by receptor-mediated recognition of dead cells, the protocol also permits the identification of signaling events induced by phagocytic uptake or the release of soluble mediators from the dead cells. The use of dead cells as a stimulus introduces several unique factors that can hinder the detection of intracellular signaling events. Awareness of these unique factors, as well as the multiple mechanisms by which dead cells modulate intracellular signaling, is critical to the design and interpretation of experiments within this growing field of study. The protocol described here should aid in understanding the mechanisms by which dead or dying cells affect their live neighbors in both health and disease.

Apoptosis, or regulated cell death1, contributes in an essential manner to the maintenance and development of tissues. Viewed most simply, apoptosis permits aged, damaged, or excess cells to be eliminated without harm to surrounding tissues2,3. The contribution of apoptosis to tissue homeostasis, however, is considerably more dynamic and varied. Cells dying by apoptosis acquire multiple new activities, both secreted and cell-associated, which enable them to influence the function of adjacent live cells4-10. Earlier studies focused on the ability of apoptotic cells to suppress inflammation11-16, but apoptotic cells also modulate a broad range of cellular functions, including such vital activities as survival4,9,10, proliferation4,9,10, differentiation17, migration18, and growth19. Moreover, these effects are not restricted to professional phagocytes, like macrophages, but extend to virtually all cell types and lineages, including traditionally non-phagocytic cells, such as epithelial and endothelial cells7,9,10,18-21.
The specific response of adjacent live cells following exposure to apoptotic cells depends on multiple factors that relate to both the viable responding cells and the apoptotic cells themselves. For example, although exposure to apoptotic cells inhibits the proliferation of both murine macrophages and kidney proximal tubular epithelial cells (PTECs), these two cell types differ dramatically in their survival response to apoptotic cells4,6,9,10. Apoptotic cells promote the survival of macrophages, but induce the apoptotic death of PTECs4,6,9,10. Notably, the response to apoptotic cells may differ even among responding cells of the same lineage, depending on the responding cell&#39;s organ of origin10 (e.g., kidney PTECs versus mammary epithelial cells) or state of activation22 (e.g., neutrophils). Conversely, apoptotic cells may evoke different responses in the very same cell depending on the nature of the apoptotic stimulus10,23 or the stage of apoptosis10,14.
Given the diverseness and complexity of the response to apoptotic cells, great care must be taken in dissecting the signaling events and pathways responsible for any particular outcome. First, responses requiring direct physical interaction between viable and apoptotic cells must be differentiated from those elicited by soluble mediators released or generated by the apoptotic cell3,6-10. If physical interaction is required, then a further differentiation should be performed. Signaling events may depend on receptor-mediated recognition of the apoptotic cell, independent of subsequent engulfment, or on phagocytic uptake, independent of the specific receptor that binds the apoptotic cell3-7,9,10,19. In the latter instance, the response is not specific to apoptotic cells, and can be triggered by any phagocytic material4,6.
The importance of these distinctions can again be appreciated by contrasting the responses of macrophages and kidney PTECs. For both cell types, exposure to apoptotic cells alters the activity of the pro-survival kinase Akt. Modulation is dependent on physical interaction, since separation of responding and apoptotic cells by a 0.4 &#956;m polycarbonate membrane abolishes the response4,9,10,19. However, the response of PTECs is receptor-mediated and independent of phagocytosis, whereas the response of macrophages is driven by phagocytosis4,9,10,19. This conclusion is reinforced by the fact that exposure to latex beads, a neutral phagocytic stimulus, has no effect on Akt activity in PTECs, but mimics the effect of apoptotic cells in macrophages4,9.
Although less well studied, cells dying by necrosis, or accidental cell death1, also modulate the function of nearby viable cells3-10,19. Like apoptotic cells, necrotic cells exert their effects through a variety of mechanisms, particularly the leakage of intracellular contents through their ruptured cell membrane3,5,6,9,24. Many cells, including PTECs and macrophages, possess distinct non-competing receptors for cells dying by necrosis5,9. Engagement of these receptors induces signaling events that are often opposite to those induced by engagement of the receptors for apoptotic cells4-10,19. For example, in PTECs, necrotic cells increase phosphorylation of Akt, whereas apoptotic cells decrease phosphorylation9,10,19.
Here, we describe a protocol for identifying intracellular signaling events induced in viable kidney PTECs through receptor-mediated recognition of adjacent apoptotic PTECs9,10,19. While the protocol is specific for a conditionally immortalized PTEC cell line known as BU.MPT cells9,10,19,25,26, it is easily adapted to cell lines that are non-epithelial in origin and/or derived from organs other than the kidney. Importantly, the use of apoptotic cells as a cell stimulus poses certain inherent experimental difficulties not present with soluble ligands. The most important of these is that apoptotic cells must be added as a suspension rather than as a solution. These difficulties, as well as strategies to minimize or circumvent them, are discussed within the protocol. Nearly all of the techniques described in the protocol are straightforward and standard to cell culture. The advantage of this protocol lies in its attention to the multiple mechanisms by which apoptotic cells modulate signal transduction within responding cells. These mechanisms include the binding via surface determinants or bridging molecules to specific receptors on the responding cell, the release of soluble mediators, and/or the engagement of the phagocytic machinery. Necrotic cells are included in all experiments to ensure that results are specific to the mode of cell death, and not a generalized response to dead cells. A careful approach, as recommended in this protocol, is critical to our understanding of the ever expanding influence that dying cells exert on their live neighbors, in both health and disease.

<table><tbody><tr><td>&lt;strong&gt;Cell culture materials&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>DMEM, 1x with [4.5 g/L] glucose, &amp;#671;-glutamine &amp;amp; sodium-pyruvate</td><td>Mediatech (Manassas, VA)</td><td>10-013-CV</td><td></td></tr><tr><td>HyClone Fetal Clone II, fetal bovine serum</td><td>GE Healthcare (Logan, UT)</td><td>SH30066.03</td><td>add 10% (v/v)&amp;nbsp; to the culture medium A</td></tr><tr><td>Penicillin-Streptomycin-Glutamine, 100x</td><td>Life Technologies (Grand Island, NY)</td><td>10378-016</td><td>add 100 units/mL to the culture media A and B</td></tr><tr><td>&amp;gamma;-Interferon, mouse recombinant, from &lt;em&gt;Escherichia coli&lt;/em&gt;</td><td>Calbiochem, Millipore (Billerica, MA)</td><td>407303</td><td>add 10 units/mL to the culture medium A</td></tr><tr><td>Falcon polystyrene tissue-culture treated dishes, non-pyrogenic</td><td>Corning (Durham, NC)</td><td>353003</td><td>sterile, 100 mm diameter</td></tr><tr><td>Falcon polystyrene centrifuge tubes, conical bottom</td><td>Corning (Durham, NC)</td><td>352095</td><td>sterile, 15 mL</td></tr><tr><td>Trypsin-EDTA, 0.05%, Gibco</td><td>Fisher (Waltham, MA)</td><td>25300062</td><td>sterile, 100 mL</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Chemicals and inhibitors&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Staurosporine, from &lt;em&gt;Streptomyces sp&lt;/em&gt;.</td><td>Sigma (St. Louis, MO)</td><td>S4400</td><td>use at [1 &amp;mu;g/mL] for 3 h to induce apoptosis</td></tr><tr><td>Epidermal growth factor (EGF), [1 mg/mL]</td><td>Millipore (Billerica, MA)</td><td>EA140</td><td>use at 50 nM to stimulate responder cells</td></tr><tr><td>UltraPure, 0.5 M EDTA, pH 8.0</td><td>Life Technologies (Grand Island, NY)</td><td>15575-038</td><td>use 5 mM to detach adherent cells</td></tr><tr><td>Trypan blue solution, 0.4%</td><td>MP Biomedicals (Santa Ana, CA)</td><td>91691049</td><td>for dead cells staining</td></tr><tr><td>Paraformaldehyde Solution, 4% in DPBS</td><td>Affymetrix (Santa Clara, CA)</td><td>19943</td><td>use 0.4% (v/v) in 1x DPBS for cell fixation</td></tr><tr><td>Dulbecco&#039;s phosphate-buffered saline (DPBS), 1x, Gibco</td><td>Life Technologies (Grand Island, NY)</td><td>14040133</td><td>stock solution</td></tr><tr><td>Dulbecco&#039;s phosphate-buffered saline (DPBS), Ca&lt;sup&gt;2+&lt;/sup&gt;- and Mg&lt;sup&gt;2+&lt;/sup&gt;-free, 1x, Gibco</td><td>Life Technologies (Grand Island, NY)</td><td>14190367</td><td>stock solution</td></tr><tr><td>Cytochalasin D, 4 mM in dimethyl sulfoxide (DMSO), from &lt;em&gt;Zygosporium mansonii&lt;/em&gt;</td><td>Sigma (St. Louis, MO)</td><td>C8273</td><td>use at [4 &amp;mu;g/mL] to inhibit phagocytosis</td></tr><tr><td>Dimethyl sulfoxide (DMSO)</td><td>Sigma (St. Louis, MO)</td><td>D2650</td><td>solvent for cytochalasin D</td></tr><tr><td colspan="4">[header]</td></tr><tr><td>&lt;strong&gt;Cell lysis buffer ingredients&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Tris-buffered saline (TBS), 10x, pH 7.4</td><td>BioRad (Hercules, CA)</td><td>1706435</td><td>for cell lysis buffer</td></tr><tr><td>Sodium pyrophosphate</td><td>Sigma-Aldrich (St. Louis, MO)</td><td>221368</td><td>10 mM for cell lysis buffer</td></tr><tr><td>Sodium deoxycholate</td><td>Sigma-Aldrich (St. Louis, MO)</td><td>D6750</td><td>0.5% w/v for cell lysis buffer</td></tr><tr><td>Sodium dodecyl sulfate (SDS)</td><td>Sigma-Aldrich (St. Louis, MO)</td><td>L3771&amp;nbsp;</td><td>0.1% w/v for cell lysis buffer</td></tr><tr><td>Glycerol</td><td>Sigma-Aldrich (St. Louis, MO)</td><td>G5516</td><td>10% for cell lysis buffer</td></tr><tr><td>Sodium fluoride</td><td>Sigma-Aldrich (St. Louis, MO)</td><td>450022</td><td>25 mM for cell lysis buffer</td></tr><tr><td>Complete mini EDTA-free protease inhibitor cocktail tablet</td><td>Roche Diagnostics (Indianapolis, IN)</td><td>4693159001</td><td>for cell lysis buffer, 1 tablet per 10 mL of buffer</td></tr><tr><td>Triton X-100</td><td>Sigma-Aldrich (St. Louis, MO)</td><td>T8787</td><td>10% for cell lysis buffer</td></tr><tr><td>Dithiothreitol (DTT)</td><td>MP Biomedicals (Santa Ana, CA)</td><td>11DTT00005</td><td>1 mM for cell lysis buffer</td></tr><tr><td>Phenylmethanesulfonyl fluoride (PMSF)</td><td>MP Biomedicals (Santa Ana, CA)</td><td>4800263</td><td>1 mM for cell lysis buffer</td></tr><tr><td>Sodium orthovandate</td><td>MP Biomedicals (Santa Ana, CA)</td><td>2159664</td><td>10 mM for cell lysis buffer</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Equipment&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Sorvall T6000B centrifuge</td><td>Du Pont (Wilmington, DE)</td><td>T6000B</td><td></td></tr><tr><td>Fisher Tissuemat, water bath</td><td>Fisher (Waltham, MA)</td><td></td><td></td></tr><tr><td>Sonic Dismembrator (sonicator), model 100</td><td>Fisher (Waltham, MA)</td><td></td><td></td></tr><tr><td>&lt;strong&gt;Miscellaneous&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Cell counting chamber, Neubauer</td><td>Hawksley (Lancing, Sussex, UK)</td><td>AC2000</td><td></td></tr><tr><td>Annexin V-FITC Apoptosis Detection Kit II</td><td>Millipore (Billerica, MA)</td><td>CBA059</td><td>for PI and Annexin V staining to determine the stage of apoptosis</td></tr><tr><td>Eppendorf microcntrifuge tubes, 1.5 mL</td><td>Sigma-Aldrich (St. Louis, MO)</td><td>T9661</td><td></td></tr><tr><td>Transwell permeable support, 0.4 &amp;mu;m polycarbonate membrane</td><td>Corning (Corning, NY)</td><td>3413</td><td>sterile, polystyrene, tissue culture treated</td></tr><tr><td>&lt;strong&gt;Name&lt;/strong&gt;</td><td>&lt;strong&gt;Company&lt;/strong&gt;</td><td>&lt;strong&gt;Catalog&lt;/strong&gt;</td><td>&lt;strong&gt;Comments&lt;/strong&gt;</td></tr><tr><td>&lt;strong&gt;Antibodies&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Phospho-glycogen synthase kinase-3&amp;alpha;/&amp;beta; (GSK-3&amp;alpha;/&amp;beta;) (Ser21/9), polyclonal antibody</td><td>Cell Signaling Technology</td><td>9331</td><td>rabbit polyclonal antibody</td></tr><tr><td>Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) monoclonal antobody ( (14C10) )</td><td>Cell Signaling Technology</td><td>2118</td><td>rabbit monoclonal antibody</td></tr></tbody></table>

identification of intracellular signaling events induced in viable cells by interaction with neighboring cells undergoing apoptotic cell death

Cells dying by apoptosis, also referred to as regulated cell death, acquire multiple new activities that enable them to influence the function of adjacent live cells. Vital activities, such as survival, proliferation, growth, and differentiation, are among the many cellular functions modulated by apoptotic cells. The ability to recognize and respond to apoptotic cells appears to be a universal feature of all cells, regardless of lineage or organ of origination. However, the diversity and complexity of the response to apoptotic cells mandates that great care be taken in dissecting the signaling events and pathways responsible for any particular outcome. In particular, one must distinguish among the multiple mechanisms by which apoptotic cells can influence intracellular signaling pathways within viable responder cells, including: receptor-mediated recognition of the apoptotic cell, release of soluble mediators by the apoptotic cell, and/or engagement of the phagocytic machinery. Here, we provide a protocol for identifying intracellular signaling events that are induced in viable responder cells following their exposure to apoptotic cells. A major advantage of the protocol lies in the attention it pays to dissection of the mechanism by which apoptotic cells modulate signaling events within responding cells. While the protocol is specific for a conditionally immortalized mouse kidney proximal tubular cell line (BU.MPT cells), it is easily adapted to cell lines that are non-epithelial in origin and/or derived from organs other than the kidney. The use of dead cells as a stimulus introduces several unique factors that can hinder the detection of intracellular signaling events. These problems, as well as strategies to minimize or circumvent them, are discussed within the protocol. Application of this protocol should aid our expanding knowledge of the broad influence that dead or dying cells exert on their live neighbors, both in health and in disease.

In Figure 1, we provide a schematic depicting the timing and critical steps involved in the preparation of apoptotic cells (Protocol 1) and necrotic cells (Protocol 2) and the stimulation of responder cells with suspensions of apoptotic and necrotic cells (Protocol 4).
In Figure 2, we provide representative results showing the effect of apoptotic cells on phosphorylation of the two isoforms of the serine-threonine kinase glycogen synthase kinase-3 (GSK-3), GSK-3&#945; and GSK-3&#946;. GSK-3&#945;/&#946; has a prominent role in the regulation of cellular proliferation and survival, as well as its important role in glucose metabolism. Phosphorylation of GSK-3&#945; at serine-21 and GSK-3&#946; at serine-9 inhibits kinase activity and, in turn, leads to decreased phosphorylation and increased stabilization of &#946;-catenin. &#946;-Catenin then translocates to the nucleus, where it promotes the transcription of genes known to stimulate cell proliferation and inhibit apoptosis. Therefore, increased phosphorylation of GSK-3&#945;/&#946; is associated with increased proliferation and survival, whereas decreased phosphorylation of GSK-3&#945;/&#946; correlates with decreased proliferation and survival.
Exposure of quiescent BU.MPT responders to apoptotic cells for 30 min strongly inhibited basal phosphorylation of GSK-3&#945;/&#946; (Figure 2A). Similarly, prior exposure to apoptotic targets for 30 min strongly inhibited subsequent epidermal growth factor (EGF)-induced phosphorylation of GSK-3&#945;/&#946; (Figure 2A). In contrast, exposure of BU.MPT responders to necrotic cells had no effect on either basal or EGF-induced phosphorylation of GSK-3&#945;/&#946;.
To prevent physical interaction between BU.MPT responders and apoptotic cells, BU.MPT responders were grown in a permeable support system and separated from apoptotic targets by a 0.4 &#181;m polycarbonate membrane. Prevention of physical interaction between BU.MPT responders and apoptotic cells abolished the ability of apoptotic targets to inhibit phosphorylation of GSK-3&#945;/&#946; (Figure 2B). To evaluate the role of phagocytosis, we used the cytoskeletal inhibitor cytochalasin D to prevent phagocytic uptake of dead cells. Inhibition of phosphorylation of GSK-3&#945;/&#946; in response to apoptotic cells occurred in the absence of phagocytosis (Figure 2C). We have previously shown that cytochalasin D, at the concentration used, inhibits PTEC and macrophage phagocytosis by &#8805;90%9,10. Taken together, our results show that apoptotic cell-mediated inhibition of phosphorylation of GSK3&#945;/&#946;&#160;requires direct physical interaction between targets and responder cells, but is independent of phagocytosis.
<img alt="Figure 1" src="/files/ftp_upload/54980/54980fig1.jpg" /> 
Figure 1. Schema for Induction of Intracellular Signaling Events in Viable Responder Cells by Physical Interaction with Neighboring Cells undergoing Cell Death. The line graphs depict the timing and critical events in the preparation of (A) apoptotic (Apo) cell and (B) necrotic (Necro) cell suspensions of BU.MPT cells, and in the (C) stimulation of viable BU.MPT responder cells with suspensions of apoptotic or necrotic cells. <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54980/54980fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 1" src="/files/ftp_upload/54980/54980fig2.jpg" /> 
Figure 2. Inhibition of Phosphorylation of GSK3&#945;/&#946; in BU.MPT Responder Cells Following Exposure to Apoptotic Cells Requires Direct Cell-Cell Interaction but Is Independent of Phagocytosis. Serum-starved BU.MPT responder cells were pretreated for 2 h with (A, B) vehicle or (C) cytochalasin D&#160;(4 &#956;g/mL), and then stimulated for 30 min with no cells (-), apoptotic cells (Apo), or necrotic cells (Nec) at a dead cell to responder cell ratio of 1:1. The responder cells were then washed, and incubated for a further 15 min in the absence or presence of EGF (50 nM), before harvesting. The source of apoptotic cells was staurosporine-treated BU.MPT cells. The source of necrotic cells was heat-treated BU.MPT cells. Interaction between dead cells and BU.MPT responders was either (A, C) unimpeded, enabling direct dead cell-responder physical interaction, or (B) with separation of dead cells and responders by a 0.4 &#181;m polycarbonate membrane in a permeable support system. Dead cells and non-adherent responder cells were removed by washing, and BU.MPT responder cell lysates were probed with anti-phosphorylated GSK3&#945;/&#946; antibodies as shown. Equal loading was confirmed by probing for total glyceraldehyde-3-phosphate dehydrogenase (GAPDH). <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54980/54980fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
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			<td></td>
			<td></td>
			<td>Effect on signaling event assuming this mechanism</td>
			<td></td>
		</tr>
		<tr>
			<td>Intervention</td>
			<td>Soluble mediator</td>
			<td>Receptor-mediated recognition</td>
			<td>Phagocytosis</td>
		</tr>
		<tr>
			<td>Fixation of apoptotic cells*</td>
			<td>Elimination</td>
			<td>Persistence</td>
			<td>Persistence</td>
		</tr>
		<tr>
			<td>Physical separation of apoptotic and responder cells&#8224;</td>
			<td>Persistence</td>
			<td>Elimination</td>
			<td>Elimination</td>
		</tr>
		<tr>
			<td>Ultracentrifuged conditioned medium from cells undergoing apoptosis as stimulus&#182;</td>
			<td>Persistence</td>
			<td>Elimination</td>
			<td>Elimination</td>
		</tr>
		<tr>
			<td>Necrotic cells as stimulus</td>
			<td>Elimination</td>
			<td>Elimination or oppositely directed response (e.g., inhibition versus stimulation)&#160;</td>
			<td>Persistence</td>
		</tr>
		<tr>
			<td>Latex beads as stimulus</td>
			<td>Elimination</td>
			<td>Elimination</td>
			<td>Persistence</td>
		</tr>
		<tr>
			<td>Pharmacologic inhibition of phagocytosis</td>
			<td>Persistence</td>
			<td>Persistence</td>
			<td>Elimination</td>
		</tr>
		<tr>
			<td colspan="4">* Predicted results assume that fixation does not alter critical surface determinants responsible for receptor-mediated recognition and/or phagocytosis.</td>
		</tr>
		<tr>
			<td colspan="4">&#8224; Predicted results entail two assumptions: first, that the soluble mediator is small enough to pass through the pores of the membrane separating the apoptotic and responding cells, and second, that any shed vesicles or microvesicles, often termed apoptotic bodies, are too large to pass through the membrane&#39;s pores.&#160; A role for vesicles or microvesicles would be suggested by a lack of concordance in the signaling events observed with physical separation of apoptotic and responder cells versus ultracentrifuged conditioned medium.</td>
		</tr>
		<tr>
			<td colspan="4">&#182; Ultracentrifugation (20,000 &#215; g for 30 min) is necessary to remove any apoptotic bodies or other shed insoluble material that may mimic the effects of the intact apoptotic cell.</td>
		</tr>
	</tbody>
</table>
Table 1. Identification of the Mechanism(s) Responsible for Signaling Events in Viable Cells Following Exposure to Apoptotic Cells. Several straightforward experimental strategies are provided to distinguish among the potential mechanism(s) responsible for signaling events observed following exposure to apoptotic cells. These mechanisms include: physical interaction of the apoptotic cell with specific receptors on the responder cell, release of soluble mediators from the apoptotic cell, and engagement of the responder cell&#39;s phagocytic machinery.
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Experimental issue</td>
			<td>Available strategies for minimization and/or circumvention</td>
		</tr>
		<tr>
			<td>Restricted number of apoptotic cells per responding cell (~1:1 ratio).&#160;</td>
			<td>1. Increase the number of apoptotic cells, but the apoptotic-to-responder cell ratio should be kept &#60;2:1.*</td>
		</tr>
		<tr>
			<td>Need for gravity-dependent settling of apoptotic cells.</td>
			<td>1. Minimize the volume of medium in which apoptotic cells are suspended.</td>
		</tr>
		<tr>
			<td></td>
			<td>2. Centrifuge the dish or plate to drive the apoptotic cells through the suspending medium more quickly.</td>
		</tr>
		<tr>
			<td>Uneven spatial distribution of apoptotic cells.</td>
			<td>1. Carefully distribute the apoptotic cell suspension drop by drop with a wide tip pipette over the entire surface of the responder cell dishes.</td>
		</tr>
		<tr>
			<td></td>
			<td>2. Avoid culture dishes or wells with a diameter &#60;35 mm, in which meniscal effects can lead to uneven distributions.</td>
		</tr>
		<tr>
			<td>Heterogeneity of the apoptotic cell population.</td>
			<td>1. Use a strong inducer of apoptosis.</td>
		</tr>
		<tr>
			<td></td>
			<td>2. After induction, fix the apoptotic cells with paraformaldehyde, and sort by flow cytometry to obtain a more uniform population.&#160;</td>
		</tr>
		<tr>
			<td colspan="2">* At apoptotic-to-responder cell ratios &#62;2:1, the apoptotic cells will form a confluent carpet and additional apoptotic cells will no longer make direct contact with responder cells</td>
		</tr>
	</tbody>
</table>
Table 2. Experimental Issues Associated with the Use of a Cellular Suspension as a Stimulus of Intracellular Signaling Events. Several experimental obstacles associated with the use of a cell suspension as a stimulus are listed, as well as strategies for their partial remedy.

Watch this Scientific Journal Video about Identification of Intracellular Signaling Events Induced in Viable Cells by Interaction with Neighboring Cells Undergoing Apoptotic Cell Death at JoVE.com

Identification of Intracellular Signaling Events Induced in Viable Cells by Interaction with Neighboring Cells Undergoing Apoptotic Cell Death | Biology | Video

Identification of Intracellular Signaling Events Induced in Viable Cells by Interaction with Neighboring Cells Undergoing Apoptotic Cell Death

Here, we present a protocol for the determination of intracellular signaling events induced in viable cells by physical interaction with adjacent dead or dying cells. The protocol focuses on signaling events induced by receptor-mediated recognition of the dead cells, as opposed to their phagocytic uptake or release of soluble mediators.

Cells dying by apoptosis, also referred to as regulated cell death, acquire multiple new activities that enable them to influence the function of adjacent ...

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8.6K Views.  University of Illinois at Chicago. Here, we present a protocol for the determination of intracellular signaling events induced in viable cells by physical interaction with adjacent dead or dying cells. The protocol focuses on signaling events induced by receptor-mediated recognition of the dead cells, as opposed to their phagocytic uptake or release of soluble mediators.

Video: Identification of Intracellular Signaling Events Induced in Viable Cells by Interaction with Neighboring Cells Undergoing Apoptotic Cell Death

Real Time Detection of In Vitro Tumor Cell Apoptosis Induced by CD8+ T Cells to Study Immune Suppressive Functions of Tumor-infiltrating Myeloid Cells

Potentiation of the tumor-killing ability of CD8+ T cells in tumors, along with their efficient tumor infiltration, is a key element of successful immunotherapies. Several studies have indicated that tumor infiltrating myeloid cells (e.g., myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs)) suppress cytotoxicity of CD8+ T cells in the tumor microenvironment, and that targeting these regulatory myeloid cells can improve immunotherapies. Here, we present an in vitro assay system to evaluate immune suppressive effects of monocytic-MDSCs and TAMs on the tumor-killing ability of CD8+ T cells. To this end, we first cultured na&#239;ve splenic CD8+ T cells with anti-CD3/CD28 activating antibodies in the presence or absence of suppressor cells, and then co-cultured the pre-activated T cells with target cancer cells in the presence of a fluorogenic caspase-3 substrate. Fluorescence from the substrate in cancer cells was detected by real-time fluorescence microscopy as an indicator of T-cell induced tumor cell apoptosis. In this assay, we can successfully detect the increase of tumor cell apoptosis by CD8+ T cells and its suppression by pre-culture with TAMs or MDSCs. This functional assay is useful for investigating CD8+ T cell suppression mechanisms by regulatory myeloid cells and identifying druggable targets to overcome it via high throughput screening.

Real Time Detection of In Vitro Tumor Cell Apoptosis Induced by CD8+ T Cells to Study Immune Suppressive Functions of Tumor-infiltrating Myeloid Cells

We describe here a protocol to investigate cytotoxicity of pre-activated CD8+ T cells against cancer cells by detecting apoptotic cancer cells via real-time microscopy. This protocol can investigate mechanisms behind myeloid cell-induced T cell suppression and evaluate compounds aimed at replenishing T cells via blockade of immune suppressive myeloid cells.

Potentiation of the tumor-killing ability of CD8+ T cells in tumors, along with their efficient tumor infiltration, is a key element of successful ...

Cancer Research

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%.

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. ...

Biochemistry

Flow Cytometric Analysis of Apoptotic Biomarkers in Actinomycin D-Treated SiHa Cervical Cancer Cells

Apoptosis biomarkers were investigated in actinomycin D-treated SiHa cervical cancer cells using a benchtop flow cytometer. Early biomarkers (Annexin V and mitochondrial membrane potential) and late biomarkers (caspases 3 and 7, and DNA damage) of apoptosis were measured in experimental and control cultures. Cultures were incubated for 24 hours in a humidified incubator at 37 &#176;C with 5% CO2. The cells were then detached using trypsin and enumerated using a flow cytometric cell count assay. Cells were further analyzed for apoptosis using an Annexin V assay, a mitochondrial electrochemical transmembrane potential assay, a caspase 3/7 assay, and a DNA damage assay. This article provides an overview of apoptosis and traditional flow cytometry, and elaborates flow cytometric protocols for processing and analyzing SiHa cells. The results describe positive, negative, and sub-optimal experimental data. Also discussed are interpretation and caveats in performing flow cytometric analysis of apoptosis using this analytical platform. Flow cytometric analysis provides an accurate measurement of early and late biomarkers for apoptosis.

Apoptosis can be characterized by flow cytometric analysis of early and late apoptotic biomarkers. The cervical cancer cell line, SiHa, was analyzed for apoptosis biomarkers after treatment with Actinomycin D using a benchtop flow cytometer.

Apoptosis biomarkers were investigated in actinomycin D-treated SiHa cervical cancer cells using a benchtop flow cytometer. Early biomarkers (Annexin V ...

Applying an Inducible Expression System to Study Interference of Bacterial Virulence Factors with Intracellular Signaling

The technique presented here allows one to analyze at which step a target protein, or alternatively a small molecule, interacts with the components of a signaling pathway. The method is based, on the one hand, on the inducible expression of a specific protein to initiate a signaling event at a defined and predetermined step in the selected signaling cascade. Concomitant expression, on the other hand, of the gene of interest then allows the investigator to evaluate if the activity of the expressed target protein is located upstream or downstream of the initiated signaling event, depending on the readout of the signaling pathway that is obtained. Here, the apoptotic cascade was selected as a defined signaling pathway to demonstrate protocol functionality. Pathogenic bacteria, such as Coxiella burnetii, translocate effector proteins that interfere with host cell death induction in the host cell to ensure bacterial survival in the cell and to promote their dissemination in the organism. The C. burnetii effector protein CaeB effectively inhibits host cell death after induction of apoptosis with UV-light or with staurosporine. To narrow down at which step CaeB interferes with the propagation of the apoptotic signal, selected proteins with well-characterized pro-apoptotic activity were expressed transiently in a doxycycline-inducible manner. If CaeB acts upstream of these proteins, apoptosis will proceed unhindered. If CaeB acts downstream, cell death will be inhibited. The test proteins selected were Bax, which acts at the level of the mitochondria, and caspase 3, which is the major executioner protease. CaeB interferes with cell death induced by Bax expression, but not by caspase 3 expression. CaeB, thus, interacts with the apoptotic cascade between these two proteins.

The method described here is used to induce the apoptotic signaling cascade at defined steps in order to dissect the activity of an anti-apoptotic bacterial effector protein. This method can also be used for inducible expression of pro-apoptotic or toxic proteins, or for dissecting interference with other signaling pathways.

The technique presented here allows one to analyze at which step a target protein, or alternatively a small molecule, interacts with the components of a ...

Immunology and Infection

Measuring Composition of CD95 Death-Inducing Signaling Complex and Processing of Procaspase-8 in this Complex

Extrinsic apoptosis is mediated by the activation of death receptors (DRs) such as CD95/Fas/APO-1 or tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-receptor 1/receptor 2 (TRAIL-R1/R2). Stimulation of these receptors with their cognate ligands leads to the assembly of the death-inducing signaling complex (DISC). DISC comprises DR, the adaptor protein Fas-associated protein with death domain (FADD), procaspases-8/-10, and cellular FADD-like interleukin (IL)-1&#946;-converting enzyme-inhibitory proteins (c-FLIPs). The DISC serves as a platform for procaspase-8 processing and activation. The latter occurs via its dimerization/oligomerization in the death effector domain (DED) filaments assembled at the DISC. 
Activation of procaspase-8 is followed by its processing, which occurs in several steps. In this work, an established experimental workflow is described that allows the measurement of DISC formation and the processing of procaspase-8 in this complex. The workflow is based on immunoprecipitation techniques supported by western blot analysis. This workflow allows careful monitoring of different steps of procaspase-8 recruitment to the DISC and its processing and is highly relevant for investigating molecular mechanisms of extrinsic apoptosis.

Here, an experimental workflow is presented that enables the detection of caspase-8 processing directly at the death-inducing signaling complex (DISC) and determines the composition of this complex. This methodology has broad applications, from unraveling the molecular mechanisms of cell death pathways to the dynamic modeling of apoptosis networks.

Extrinsic apoptosis is mediated by the activation of death receptors (DRs) such as CD95/Fas/APO-1 or tumor necrosis factor-related apoptosis-inducing ...

Quantification of Efferocytosis by Single-cell Fluorescence Microscopy

Studying the regulation of efferocytosis requires methods that are able to accurately quantify the uptake of apoptotic cells and to probe the signaling and cellular processes that control efferocytosis. This quantification can be difficult to perform as apoptotic cells are often efferocytosed piecemeal, thus necessitating methods which can accurately delineate between the efferocytosed portion of an apoptotic target versus residual unengulfed cellular fragments. The approach outlined herein utilizes dual-labeling approaches to accurately quantify the dynamics of efferocytosis and efferocytic capacity of efferocytes such as macrophages. The cytosol of the apoptotic cell is labeled with a cell-tracking dye to enable monitoring of all apoptotic cell-derived materials, while surface biotinylation of the apoptotic cell allows for differentiation between internalized and non-internalized apoptotic cell fractions. The efferocytic capacity of efferocytes is determined by taking fluorescent images of live or fixed cells and quantifying the amount of bound versus internalized targets, as differentiated by streptavidin staining. This approach offers several advantages over methods such as flow cytometry, namely the accurate delineation of non-efferocytosed versus efferocytosed apoptotic cell fractions, the ability to measure efferocytic dynamics by live-cell microscopy, and the capacity to perform studies of cellular signaling in cells expressing fluorescently-labeled transgenes. Combined, the methods outlined in this protocol serve as the basis for a flexible experimental approach that can be used to accurately quantify efferocytic activity and interrogate cellular signaling pathways active during efferocytosis.

Efferocytosis, the phagocytic removal of apoptotic cells, is required to maintain homeostasis and is facilitated by receptors and signaling pathways that allow for the recognition, engulfment, and internalization of apoptotic cells. Herein, we present a fluorescence microscopy protocol for the quantification of efferocytosis and the activity of efferocytic signaling pathways.

Studying the regulation of efferocytosis requires methods that are able to accurately quantify the uptake of apoptotic cells and to probe the signaling ...

Experimental Analysis of Apoptotic Thymocyte Engulfment by Macrophages

Cell apoptosis is a natural process and plays a critical role in embryonic development, homeostatic regulation, immune tolerance induction, and resolution of inflammation. Accumulation of apoptotic debris in the body may trigger chronic inflammatory responses that lead to systemic autoimmune diseases over time. Impaired apoptotic cell clearance has been implicated in a variety of autoimmune diseases. Apoptotic clearance is a complex process rarely detected under physiological conditions. It involves abundant surface receptors and signaling molecules. Studying the process of apoptotic cell clearance provides insightful molecular mechanisms and subsequent biological responses, which may lead to the development of new therapeutics. Here, we describe protocols for the induction of apoptotic thymocytes, the preparation of peritoneal macrophages, and the analysis of apoptotic cell clearance by flow cytometry and microscopy. All cells will undergo apoptosis at a certain stage, and many residential and circulating cells can uptake apoptotic debris. Therefore, the protocol described here can be used in many applications to characterize apoptotic cell binding and ingestion by many other cell types.

Here, we present a protocol to prepare apoptotic thymocytes and peritoneal macrophages and analyze the efficiency of efferocytosis and the specific inhibitor-mediated blocking of apoptotic thymocytes engulfment. This protocol has a broad application in cell-mediated clearance of other particles including artificial beads and bacteria.

Cell apoptosis is a natural process and plays a critical role in embryonic development, homeostatic regulation, immune tolerance induction, and resolution ...

Strategies for Tracking Anastasis, A Cell Survival Phenomenon that Reverses Apoptosis

Anastasis (Greek for &#8220;rising to life&#8221;) refers to the recovery of dying cells. Before these cells recover, they have passed through important checkpoints of apoptosis, including mitochondrial fragmentation, release of mitochondrial cytochrome c into the cytosol, activation of caspases, chromatin condensation, DNA damage, nuclear fragmentation, plasma membrane blebbing, cell shrinkage, cell surface exposure of phosphatidylserine, and formation of apoptotic bodies. Anastasis can occur when apoptotic stimuli are removed prior to death, thereby allowing dying cells to reverse apoptosis and potentially other death mechanisms. Therefore, anastasis appears to involve physiological healing processes that could also sustain damaged cells inappropriately. The functions and mechanisms of anastasis are still unclear, hampered in part by the limited tools for detecting past events after the recovery of apparently healthy cells. Strategies to detect anastasis will enable studies of the physiological mechanisms, the hazards of undead cells in disease pathology, and potential therapeutics to modulate anastasis. Here, we describe effective strategies using live cell microscopy and a mammalian caspase biosensor&#160;for identifying and tracking anastasis in mammalian cells.

The term anastasis refers to the phenomenon in which dying cells reverse a cell suicide process at a late stage, repair themselves, and ultimately survive. Here we demonstrate protocols for detecting and tracking cells that undergo anastasis.

Anastasis (Greek for &#8220;rising to life&#8221;) refers to the recovery of dying cells. Before these cells recover, they have passed through important ...

An Introduction to Cell Death

Necrosis, apoptosis, and autophagic cell death are all manners in which cells can die, and these mechanisms can be induced by different stimuli, such as cell injury, low nutrient levels, or signaling proteins. Whereas necrosis is considered to be an &#8220;accidental&#8221; or unexpected form of cell death, evidence exists that apoptosis and autophagy are both programmed and &#8220;planned&#8221; by cells.In this introductory video, JoVE highlights key discoveries pertaining to cell death, including recent work done in worms that helped identify genes involved in apoptosis. We then explore questions asked by scientists studying cell death, some of which look at different death pathways and their interactions. Finally, several methods to assess cell death are discussed, and we note how researchers are applying these techniques in their experiments today.

Cell Death: Apoptosis, Autophagy and Necrosis

Necrosis, apoptosis, and autophagic cell death are all manners in which cells can die, and these mechanisms can be induced by different stimuli, such as ...

JoVE Science Education

Advanced Biology

Cell Biology

The Extrinsic Apoptotic Pathway

The extrinsic apoptotic pathway is initiated when extracellular death-inducing signals, such as specific cytokines, activate the death receptors expressed on the cell surface. The immune cells involved in this pathway are natural killer cells (NK cells) and cytotoxic T-lymphocytes. NK cells are critical in innate immune response, while cytotoxic T-lymphocytes are associated with adaptive immune response. These cells recognize specific receptors expressed on the altered cells and activate their apoptotic pathway. The extrinsic apoptotic pathway is vital in removing cancerous cells or virus-infected cells.
Another example of external apoptotic signaling occurs during T-cell development in the thymus to eliminate self-reactive T-cells. T-cells are immune cells that bind foreign macromolecules and particles and target them for destruction by the immune system. In order to prevent the immune system from attacking the body&#39;s own cells, T-cells do not target &#8220;self&#8221; proteins (proteins of the same individual). Immature T-cells, or thymocytes, undergo a screening process to determine whether or not they bind self-proteins. If the T-cell binds to self-proteins, it is signaled for apoptosis, thus preventing an autoimmune response.
<h4>Inhibiting Apoptosis</h4>
Anti-apoptotic regulators are proteins that can inhibit the extrinsic apoptotic pathway in cells. The FLICE inhibitory protein, or c-FLIP is one of the master anti-apoptotic regulators that binds to FADD (Fas-associated death domain protein), and caspases such as caspase-8. This binding prevents the formation of the death-inducing signaling complex (DISC), thus preventing the apoptotic pathway.
Some portion of this text is adapted from <a href="https://openstax.org/books/biology-2e/pages/9-3-response-to-the-signal">Openstax, Biology 2e, Section: 9.3</a>

The extrinsic apoptotic pathway is initiated when extracellular death-inducing signals, such as specific cytokines, activate the death receptors expressed ...

Identification of Intracellular Signaling Events Induced in Viable Cells by Interaction with Neighboring Cells Undergoing Apoptotic Cell Death

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