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>Pre...

<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. 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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 bod...

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 border="0" cellpadding="0" cellspacing="0" width="1278">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Cell culture materials</td>
			<td style="width:263px;"></td>
			<td style="width:127px;"></td>
			<td style="width:427px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMEM, 1X with [4.5 g/L] glucose, L-glutamine &#38; sodium-pyruvate</td>
			<td>Mediatech (Manassas, VA)</td>
			<td style="width:127px;">10-013-CV</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HyClone Fetal Clone II, fetal bovine serum</td>
			<td style="width:263px;">GE Healthcare (Logan, UT)</td>
			<td style="width:127px;">SH30066.03</td>
			<td>add 10% (v/v)&#160; to the culture medium A</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Penicillin-Streptomycin-Glutamine, 100X</td>
			<td style="width:263px;">Life Technologies (Grand Island, NY)</td>
			<td style="width:127px;">10378-016</td>
			<td>add 100 units/mL to the culture media A and B</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#947;-Interferon, mouse recombinant, from Escherichia coli</td>
			<td style="width:263px;">Calbiochem, Millipore (Billerica, MA)</td>
			<td style="width:127px;">407303</td>
			<td>add 10 units/mL to the culture medium A</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Falcon polystyrene tissue-culture treated dishes, non-pyrogenic</td>
			<td style="width:263px;">Corning (Durham, NC)</td>
			<td style="width:127px;">353003</td>
			<td>sterile, 100 mm diameter</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Falcon polystyrene centrifuge tubes, conical bottom</td>
			<td style="width:263px;">Corning (Durham, NC)</td>
			<td style="width:127px;">352095</td>
			<td>sterile, 15 mL</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Trypsin-EDTA, 0.05%, Gibco</td>
			<td style="width:263px;">Fisher (Waltham, MA)</td>
			<td style="width:127px;">25300062</td>
			<td>sterile, 100 mL</td>
		</tr>
		<tr height="21">
			<td>Name</td>
			<td>Company</td>
			<td>Catalog</td>
			<td>Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Chemicals and inhibitors</td>
			<td style="width:263px;"></td>
			<td style="width:127px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Staurosporine, from Streptomyces sp.</td>
			<td style="width:263px;">Sigma (St. Louis, MO)</td>
			<td style="width:127px;">S4400</td>
			<td>use at [1 &#956;g/mL] for 3 h to induce apoptosis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Epidermal growth factor (EGF), [1 mg/ml]</td>
			<td style="width:263px;">Millipore (Billerica, MA)</td>
			<td style="width:127px;">EA140</td>
			<td>use at 50 nM to stimulate responder cells</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">UltraPure, 0.5 M EDTA, pH 8.0</td>
			<td style="width:263px;">Life Technologies (Grand Island, NY)</td>
			<td style="width:127px;">15575-038</td>
			<td>use 5 mM to detach adherent cells</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Trypan blue solution, 0.4%</td>
			<td style="width:263px;">MP Biomedicals (Santa Ana, CA)</td>
			<td style="width:127px;">91691049</td>
			<td>for dead cells staining</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Paraformaldehyde Solution, 4% in DPBS</td>
			<td style="width:263px;">Affymetrix (Santa Clara, CA)</td>
			<td>19943</td>
			<td>use 0.4% (v/v) in 1&#215; DPBS for cell fixation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Dulbecco&#39;s phosphate-buffered saline (DPBS), 1&#215;, Gibco</td>
			<td style="width:263px;">Life Technologies (Grand Island, NY)</td>
			<td>14040133</td>
			<td>stock solution</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:461px;">Dulbecco&#39;s phosphate-buffered saline (DPBS), Ca+2- and Mg+2-free, 1&#215;, Gibco</td>
			<td style="width:263px;">Life Technologies (Grand Island, NY)</td>
			<td style="width:127px;">14190367</td>
			<td>stock solution</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:461px;">Cytochalasin D, 4 mM in dimethyl sulfoxide (DMSO), from Zygosporium mansonii</td>
			<td style="width:263px;">Sigma (St. Louis, MO)</td>
			<td style="width:127px;">C8273</td>
			<td>use at [4 &#956;g/mL] to inhibit phagocytosis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Dimethyl sulfoxide (DMSO)</td>
			<td style="width:263px;">Sigma (St. Louis, MO)</td>
			<td style="width:127px;">D2650</td>
			<td>solvent for cytochalasin D</td>
		</tr>
		<tr height="21">
			<td>Name</td>
			<td>Company</td>
			<td>Catalog</td>
			<td>Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cell lysis buffer ingredients</td>
			<td style="width:263px;"></td>
			<td style="width:127px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Tris-buffered saline (TBS), 10&#215;, pH 7.4</td>
			<td style="width:263px;">BioRad (Hercules, CA)</td>
			<td style="width:127px;">1706435</td>
			<td>for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Sodium pyrophosphate</td>
			<td style="width:263px;">Sigma-Aldrich (St. Louis, MO)</td>
			<td style="width:127px;">221368</td>
			<td>10 mM for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Sodium deoxycholate</td>
			<td style="width:263px;">Sigma-Aldrich (St. Louis, MO)</td>
			<td style="width:127px;">D6750</td>
			<td>0.5% w/v for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Sodium dodecyl sulfate (SDS)</td>
			<td style="width:263px;">Sigma-Aldrich (St. Louis, MO)</td>
			<td style="width:127px;">L3771&#160;</td>
			<td>0.1% w/v for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Glycerol</td>
			<td style="width:263px;">Sigma-Aldrich (St. Louis, MO)</td>
			<td style="width:127px;">G5516</td>
			<td>10% for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Sodium fluoride</td>
			<td style="width:263px;">Sigma-Aldrich (St. Louis, MO)</td>
			<td style="width:127px;">450022</td>
			<td>25 mM for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Complete mini EDTA-free protease inhibitor cocktail tablet</td>
			<td style="width:263px;">Roche Diagnostics (Indianapolis, IN)</td>
			<td style="width:127px;">4693159001</td>
			<td>for cell lysis buffer, 1 tablet per 10 mL of buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Triton X-100</td>
			<td style="width:263px;">Sigma-Aldrich (St. Louis, MO)</td>
			<td style="width:127px;">T8787</td>
			<td>10% for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Dithiothreitol (DTT)</td>
			<td style="width:263px;">MP Biomedicals (Santa Ana, CA)</td>
			<td style="width:127px;">11DTT00005</td>
			<td>1 mM for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Phenylmethanesulfonyl fluoride (PMSF)</td>
			<td style="width:263px;">MP Biomedicals (Santa Ana, CA)</td>
			<td style="width:127px;">4800263</td>
			<td>1 mM for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Sodium orthovandate</td>
			<td style="width:263px;">MP Biomedicals (Santa Ana, CA)</td>
			<td>2159664</td>
			<td>10 mM for cell lysis buffer</td>
		</tr>
		<tr height="21">
			<td>Name</td>
			<td>Company</td>
			<td>Catalog</td>
			<td>Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Equipment</td>
			<td style="width:263px;"></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Sorvall T6000B centrifuge</td>
			<td style="width:263px;">Du Pont (Wilmington, DE)</td>
			<td style="width:127px;">T6000B</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Fisher Tissuemat, water bath</td>
			<td style="width:263px;">Fisher (Waltham, MA)</td>
			<td style="width:127px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Sonic Dismembrator (sonicator), model 100</td>
			<td style="width:263px;">Fisher (Waltham, MA)</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Miscellaneous</td>
			<td style="width:263px;"></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Cell counting chamber, Neubauer</td>
			<td style="width:263px;">Hawksley (Lancing, Sussex, UK)</td>
			<td style="width:127px;">AC2000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Annexin V-FITC Apoptosis Detection Kit II</td>
			<td style="width:263px;">Millipore (Billerica, MA)</td>
			<td style="width:127px;">CBA059</td>
			<td>for PI and Annexin V staining to determine the stage of apoptosis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Eppendorf microcntrifuge tubes, 1.5 ml</td>
			<td style="width:263px;">Sigma-Aldrich (St. Louis, MO)</td>
			<td style="width:127px;">T9661</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:461px;">Transwell permeable support, 0.4 &#956;m polycarbonate membrane</td>
			<td style="width:263px;">Corning (Corning, NY)</td>
			<td style="width:127px;">3413</td>
			<td>sterile, polystyrene, tissue culture treated</td>
		</tr>
		<tr height="21">
			<td>Name</td>
			<td>Company</td>
			<td>Catalog</td>
			<td>Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Antibodies</td>
			<td style="width:263px;"></td>
			<td style="width:127px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:461px;">Phospho-glycogen synthase kinase-3&#945;/&#946; (GSK-3&#945;/&#946;) (Ser21/9), polyclonal antibody</td>
			<td style="width:263px;">Cell Signaling Technology</td>
			<td style="width:127px;">9331</td>
			<td>rabbit polyclonal antibody</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:461px;">Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) monoclonal antobody ( (14C10) )</td>
			<td style="width:263px;">Cell Signaling Technology</td>
			<td style="width:127px;">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 t...

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

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 ...

The overall goal of this procedure is to identify signaling events induced and viable responder cells following their physical interaction with nearby dead cells. This method can help answer key questions in the fields of cell biology, pathology and physiology such as the influence that dead or dying cells exert on their live neighbors. The main advantages of this technique are that it is straightforward and inexpensive, and that it can be applied to study biologic effects induced in live cells following their interaction with neighboring cells undergoing apoptosis.Demonstrating the technique will be Lanfei Feng, a technician in my laboratory. To begin this procedure after passing the BUNPT cells on to 100 millimeter vacuum gas plasma treated tissue culture dishes, grow them in culture medium A to confluence and humidified 5%carbon-dioxide atmosphere at 37 degrees Celsius. After that, rinse the adherent cell monolayer three times with culture medium B.Then, induce apoptosis by incubating the cells in culture medium B, containing staurosporine, a nonselective protein kinase inhibitor, for 3 hours at 37 degrees Celsius.After 3 hours, collect the medium containing floating apoptotic cells that have detached from the monolayer. Subsequently, centrifuge this medium for ten minutes at 500 times G.Afterward, discard the supernatant, wash the pellet three times with culture medium B, before adding it back to the adherent cells. Following this washing step, detach the remaining adherent cells by adding 5 millimolar EDTA in 1X calcium and magnesium free DPBS.Collect the medium containing detached apoptotic cells and put the detached cells with the floating apoptotic cells in a sterile 15 milliliter polystyrene centrifuge tube. Then wash the apoptotic cells three times by centrifugation for ten minutes at 500 x G.Followed by resuspension in ten milliliters of 1X calcium and magnesium-free DPBS per wash. After the last wash, suspend the apoptotic cells in fresh culture medium B at 5x10^6 cells per milliliter, before using them to stimulate the responder cells.Alternatively, fix the washed apoptotic cells in 0.4 paraformaldehyde in 1X DPBS for 30 minutes, then wash them three times with culture medium B, and suspend them in it at 5x10^6 cells per milliliter before using them to stimulate the responder cells. After passaging the BUNPT cells on to 100 millimeter diameter sterile polystyrene vacuum gas plasma treated tissue culture dishes, grow them to confluence and humidified 5%carbon-dioxide atmosphere under permissive conditions. Then rinse the adherent cell monolayer three times with 10 mLs of culture medium B per rinse.Subsequently, detach the cells by adding 5 mM EDTA in 1X calcium and magnesium-free DPBS. Collect the detached cells from the EDTA containing medium and add the cell suspension to a sterile 15 mL polystyrene centrifuge tube. Next, wash the cells three times by centrifugation for ten minutes at 500 times G and resuspension in 10 mLs of calcium and magnesium-free DPBS per wash.After the last wash, suspend the cells in fresh culture medium B at 5x10^6 cells per milliliter. Following this, induce necrosis by heating the cells to 70 degrees Celsius for 45 minutes in a water bath, gently vortexing this cell suspension every ten minutes. After the induction of necrosis, incubate the cells for two hours in a humidified 5%carbon-dioxide atmosphere at 37 degrees Celsius, and gently vortex the cell suspension every 15 minutes.In this procedure, grow the BUNPT cells in sterile 100 millimeter tissue culture dishes under permissive conditions, until they achieve about 85%confluence. Afterward, aspirate culture medium A and rinse the cells three times with 10 mL of culture medium B per rinse. Then, serum starve the cells in culture medium B for 18 to 24 hours in a humidified 5%carbon-dioxide atmosphere under non-permissive conditions, in order to induce quiescence.Label a separate tissue culture dish of confluent BUNPT cells for the six experimental conditions for the next procedure. Now, aspirate culture medium B from the pre-labeled dishes of quiescent BUNPT responder cells. To prepare the 100 millimeter dishes in different conditions, add two mL of either culture medium B with no cells, the apoptotic cell suspension at 5X10^6 cells per milliliter in culture medium B, or the necrotic cell suspension at 5X10^6 cells per mL in culture medium B.Achieve a dead to responder cell ratio of one to one by adding to mL of dead cells at 5X10^6 cells per milliliter to a confluent 100 millimeter dish, which contains 10X10^6 cells.Gently swirl the dishes. Then incubate them at 37 degrees Celsius in the humidified 5%carbon-dioxide atmosphere. After 30 minutes, stimulate the responder cells with either vehicle or 15 nMOL EGF, according to the pre-labeling of the culture dish.Incubate the cells for 15 minutes at 37 degrees Celsius in a humidified 5%carbon-dioxide atmosphere. Afterward, wash away the dead cells by adding five millimeters of ice-cold DPBS. Swirl the dish and aspirate the wash fluid.Repeat the wash three times. Then immediately place the responder cell dishes on ice for further processing. This figure shows that exposure of quiescent BUNPT responders to apoptotic cells for 30 minutes strongly inhibited basal phosphorylation of GSK3 alpha beta.To prevent physical interaction between BUNPT responders and apoptotic cells, BUNPT responders were grown in a permeable support system, and separated from apoptotic targets by of 0.4 micron polycarbonate membrane. Prevention of physical interaction between BUNPT responders and apoptotic cells abolished the ability of apoptotic targets to inhibit phosphorylation of GSK3 alpha beta. To evaluate the role of phagocytosis, the cytoskeletal inhibitor Cytochalasin D was used to prevent phagocytic uptake of dead cells.Inhibition of phosphorylation of GSK3 alpha beta in response to apoptotic cells occurred in the absence of phagocytosis. Once mastered, this technique can be done in 4-6 hours if it is performed properly, excluding the time required for gel electrophoresis and immunoblotting. While attempting this procedure, it's important to remember that using a cellular suspension as opposed to a soluble ligand as a stimulus poses several inherent and largely unavoidable experimental obstacles.Using the same procedure, one can study other cell functions, such as survival or proliferation or cell growth in order to determine the functional consequences of the signaling events that are induced in live responding cells following their interaction with nearby dead cells. After watching this video, you should have a good understanding of how to identify specific signaling events that are induced in viable responder cells following their physical interaction with nearby dead cells.

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8.5K vistas.  University of Illinois at Chicago. The overall goal of this procedure is to identify signaling events induced and viable responder cells following their physical interaction with nearby dead cells. This method can help answer key questions in the fields of cell biology, pathology and physiology such as the influence that dead or dying cells exert on their live neighbors. The main advantages of this technique are that it is straightforward and inexpensive, and that it can be applied to study biologic effects induced in live cel...