Research in the Shao Lab is supported by Research Innovative Award from the College of Medicine and the Junior Faculty Pilot Award from the Department of Internal Medicine, University of Cincinnati and grant DK K01_095067 from NIDDK/NIH.

Experimental mice were bred and maintained in our mice colony. All animal work was conducted according to the guidelines of the Institutional Animal Care and Use Committee (IACUC) of the University of Cincinnati.
1. Preparation of CFSE labeled apoptotic thymocytes
<ol>
	<li>Euthanize two na&#239;ve C57/B6 mice by CO2 inhalation for 10 min and dissect to open the chest cavity, remove (pull out) the thymus with curved fine-tip forceps into tissue culture petri dish containing 10 mL of RPMI1640 medium.</li>
	<li>Obtain single cell suspension by grinding the whole thymus against two frosted ends of the microscope slides and then filter the suspension through 100 &#956;m cell strainer.</li>
	<li>Collect the 10 mL thymus suspension into a 50 mL tube and centrifuge at 300 x g for 5 min.</li>
	<li>Remove the supernatant, resuspend in 40 mL of 1x PBS, and count cell numbers with a hemocytometer.</li>
	<li>Centrifuge at 300 x g for 5 min and remove the supernatant.</li>
	<li>Resuspend in 20 mL of 1x PBS in a 50 mL tube as a single cell suspension with up to 2 x&#160;108 cells (if more than 2 x&#160;108 cells, resuspend the rest of the cells in another 20 mL of 1 x&#160;PBS in a different 50 mL tube).</li>
	<li>Make 5 &#956;M of CFSE in equal volume (20 mL) of 1x PBS in a separate 50 mL tube by pipetting 40 &#956;L of CFSE stock solution (2.5 mM) into 20 mL of 1x PBS and mix well by inverting the tube 2 - 3 times.</li>
	<li>Add the 20 mL of CFSE from step 1.7 into the 20 mL of cell suspension from step 1.6 (the final concentration of CFSE is now 2.5 &#956;M). 
	NOTE: For every 20 mL cell suspension, a 20 mL of CFSE tube is needed.</li>
	<li>Invert the cell and CFSE mixture tube 2 - 3 times and incubate the mixture in the dark at room temperature for a maximum of 2 min, then stop the reaction by adding 10 mL of heat-inactivated horse serum.</li>
	<li>Centrifuge the 50 mL tube mixture at 300 x g for 5 min at room temperature. 
	NOTE: If the CFSE labeling is successful, cell pellet will become light yellow in color.</li>
	<li>Remove the supernatant and resuspend the cell pellet in 40 mL of 1x PBS and count cell numbers with a hemocytometer.</li>
	<li>Centrifuge the cell suspension at 300 x g for 5 min and discard the supernatant.</li>
	<li>Wash the cell pellet again with 40 mL of RPMI1640 medium.</li>
	<li>Remove the supernatant and resuspend cells with RPMI1640 tissue culture medium (RPMI1640, 20 mM HEPES, 10% FBS (heat inactivated), 20 mM glutamine, and 1x Pen/Strep) at a concentration of 7 x&#160;106 cells/mL in a 100 mm tissue culture dish. 
	NOTE: If more cells are obtained, a separate 100 mm tissue culture dish will be needed.</li>
	<li>Add staurosporine into the cell suspension culture at a final concentration of 1 &#956;M and culture for 4 h at 37 &#176;C in a tissue culture incubator supplied with 5% CO2.</li>
</ol>
2. Preparation of peritoneal macrophages
<ol>
	<li>Inject two C57B6 mice (or any gene-manipulated mice in the lab) intraperitoneally with 1 mL of 3% aged thioglycollate at day 0.</li>
	<li>Euthanize the mice at day 5 as in step 1.1, cut and peel open the abdominal skin but leave the peritoneum intact. Flush the peritoneal cavity by quickly pushing 10 mL of wash buffer (RPMI1640, 2% FBS, 0.04% EDTA) into the peritoneal cavity using a 10 mL syringe attached with a 18&#160;G needle.</li>
	<li>Retrieve the wash buffer slowly with the same needle/syringe, and collect the wash buffer into a 50 mL tube (details refer to Janssen lab article15).</li>
	<li>Wash the peritoneal gavage twice with 1x PBS, resuspend the peritoneal macrophages in RPMI1640 tissue culture medium at a density of 2 x&#160;106 cells/mL and aliquot 500 &#956;L into each well of the 24-well plate. Leave the plate in a tissue culture incubator for 2 h.</li>
	<li>Remove the floating cells by aspirating and replacing with 500 &#956;L of fresh culture medium, twice.</li>
	<li>Optionally, add TAM receptor tyrosine inhibitor, RXDX-106, at concentrations indicated in the figure legends into each well of the macrophage culture and incubate for another 2 h.</li>
</ol>
3. Co-culture of peritoneal macrophages with apoptotic thymocytes
<ol>
	<li>Collect apoptotic thymocytes from step 1 and wash three times with RPMI1640 medium. The efficiency of apoptotic induction can be measured at this stage with the Annexin V/7-AAD kit.</li>
	<li>Distribute 0 - 12 x&#160;106 cells (in 500 &#956;L medium) into each well of the macrophage cultures from protocol #2, according to the experimental arrangement (e.g., see Figure 1). This makes the whole culture volume of 1 mL in each well of the 24-well plate. Add the blocking antibody into the culture immediately before the addition of apoptotic thymocytes.</li>
	<li>Culture the cell mixture at 37 &#176;C for 4 h in a tissue culture incubator supplied with 5% CO2.</li>
	<li>Wash each well of the culture with 1x PBS (containing 500 &#956;M EDTA) twice to remove the free-floating apoptotic cells.</li>
	<li>Stain the plate-bound macrophages with CD11b-PE at this stage.
	<ol>
		<li>Wash the plate-bound macrophages with staining buffer (1x PBS, 1% BSA) once.</li>
		<li>Add 200 &#956;L of staining buffer containing 2 &#956;L CD11b-PE into each well.</li>
		<li>Incubate the plate at 4 &#176;C for 20 min.</li>
		<li>Wash each well of plate three times with the staining buffer.</li>
		<li>Add 200 &#956;L of staining buffer and proceed the plate for image analysis under the fluorescent microscope.</li>
	</ol>
	</li>
	<li>Alternatively, detach the plate-bound macrophages by adding 1 mL of 1% lidocaine in PBS and incubating for 10 min at 37 &#176;C.</li>
	<li>Detach plate-bound macrophages with repeat pipetting.</li>
	<li>Transfer macrophage suspension into an individual 5 mL round-bottom FACS tube from each well of the 24-well plate.</li>
	<li>Centrifuge at 300 x g for 5 min.</li>
	<li>Remove the supernatant and add 200 &#956;L of staining buffer containing 2 &#956;L of CD11b-PE (1:200 dilution in staining buffer).</li>
	<li>Incubate the cell suspension in staining buffer at 4 &#176;C for 20 min.</li>
	<li>Wash the cell suspension twice with staining buffer.</li>
	<li>Add 200 &#956;L of staining buffer and proceed for FACS analysis with a flow cytometer and analyze for the percentage of CFSE positivity macrophages.</li>
</ol>

<ol>
	<li>Shao, W. H., Cohen, P. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Disturbances+of+apoptotic+cell+clearance+in+systemic+lupus+erythematosus.">Disturbances of apoptotic cell clearance in systemic lupus erythematosus.</a> Arthritis Research and Therapy. 13 (1), 202 (2011).</li><li>Cohen, P. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Apoptotic+cell+death+and+lupus.">Apoptotic cell death and lupus.</a> Springer Seminars in Immunopathology. 28 (2), 145-152 (2006).</li><li>Wong, R. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Apoptosis+in+cancer:+from+pathogenesis+to+treatment.">Apoptosis in cancer: from pathogenesis to treatment.</a> Journal of Experimental and Clinical Cancer Research. 30, 87 (2011).</li><li>Baig, 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=Potential+of+apoptotic+pathway-targeted+cancer+therapeutic+research:+Where+do+we+stand.">Potential of apoptotic pathway-targeted cancer therapeutic research: Where do we stand.</a> Cell Death and Disease. 7, 2058 (2016).</li><li>Poon, I. K., Lucas, C. D., Rossi, A. G., 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=Apoptotic+cell+clearance:+basic+biology+and+therapeutic+potential.">Apoptotic cell clearance: basic biology and therapeutic potential.</a> Nature Reviews Immunology. 14 (3), 166-180 (2014).</li><li>Qian, Y., Wang, H., Clarke, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impaired+clearance+of+apoptotic+cells+induces+the+activation+of+autoreactive+anti-Sm+marginal+zone+and+B-1+B+cells.">Impaired clearance of apoptotic cells induces the activation of autoreactive anti-Sm marginal zone and B-1 B cells.</a> Journal of Immunology. 172 (1), 625-635 (2004).</li><li>Hawkins, L. A., Devitt, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Current+understanding+of+the+mechanisms+for+clearance+of+apoptotic+cells-a+fine+balance.">Current understanding of the mechanisms for clearance of apoptotic cells-a fine balance.</a> Journal of Cell Death. 6, 57-68 (2013).</li><li>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=Biology+of+the+TAM+receptors.">Biology of the TAM receptors.</a> Cold Spring Harbor Perspective in Biology. 5 (11), 009076 (2013).</li><li>Stitt, T. N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+anticoagulation+factor+protein+S+and+its+relative,+Gas6,+are+ligands+for+the+Tyro+3/Axl+family+of+receptor+tyrosine+kinases.">The anticoagulation factor protein S and its relative, Gas6, are ligands for the Tyro 3/Axl family of receptor tyrosine kinases.</a> Cell. 80 (4), 661-670 (1995).</li><li>Linger, R. M., Keating, A. K., Earp, H. S., Graham, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TAM+receptor+tyrosine+kinases:+biologic+functions,+signaling,+and+potential+therapeutic+targeting+in+human+cancer.">TAM receptor tyrosine kinases: biologic functions, signaling, and potential therapeutic targeting in human cancer.</a> Advances in Cancer Research. 100, 35-83 (2008).</li><li>van der Meer, J. H., van der Poll, T., van 'T Veer, C. <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,+Gas6,+and+protein+S:+roles+in+inflammation+and+hemostasis.">TAM receptors, Gas6, and protein S: roles in inflammation and hemostasis.</a> Blood. 123 (16), 2460-2469 (2014).</li><li>Lemke, G., Burstyn-Cohen, T. <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+and+the+clearance+of+apoptotic+cells.">TAM receptors and the clearance of apoptotic cells.</a> Annal of the New York Academy of Sciences. 1209, 23-29 (2010).</li><li>Shao, W. H., Zhen, Y., Eisenberg, R. A., Cohen, P. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Mer+receptor+tyrosine+kinase+is+expressed+on+discrete+macrophage+subpopulations+and+mainly+uses+Gas6+as+its+ligand+for+uptake+of+apoptotic+cells.">The Mer receptor tyrosine kinase is expressed on discrete macrophage subpopulations and mainly uses Gas6 as its ligand for uptake of apoptotic cells.</a> Clinical Immunology. 133 (1), 138-144 (2009).</li><li>Scott, R. 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=Phagocytosis+and+clearance+of+apoptotic+cells+is+mediated+by+MER.">Phagocytosis and clearance of apoptotic cells is mediated by MER.</a> Nature. 411 (6834), 207-211 (2001).</li><li>Klarquist, J., Janssen, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+bm12+Inducible+Model+of+Systemic+Lupus+Erythematosus+(SLE)+in+C57BL/6+Mice.">The bm12 Inducible Model of Systemic Lupus Erythematosus (SLE) in C57BL/6 Mice.</a> Journal of Visualized Experiment. (105), e53319 (2015).</li><li>Malawista, A., Wang, X., Trentalange, M., Allore, H. G., Montgomery, R. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coordinated+expression+of+tyro3,+axl,+and+mer+receptors+in+macrophage+ontogeny.">Coordinated expression of tyro3, axl, and mer receptors in macrophage ontogeny.</a> Macrophage (Houst). 3, (2016).</li><li>Elmore, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Apoptosis:+a+review+of+programmed+cell+death.">Apoptosis: a review of programmed cell death.</a> Toxicologic Pathology. 35 (4), 495-516 (2007).</li><li>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=Find-me+and+eat-me+signals+in+apoptotic+cell+clearance:+progress+and+conundrums.">Find-me and eat-me signals in apoptotic cell clearance: progress and conundrums.</a> Journal of Experimental Medicine. 207 (9), 1807-1817 (2010).</li><li>Rock, K. L., Kono, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+inflammatory+response+to+cell+death.">The inflammatory response to cell death.</a> Annual Review in Pathology. 3, 99-126 (2008).</li><li>Roberts, K. M., Rosen, A., Casciola-Rosen, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+for+inducing+apoptosis.">Methods for inducing apoptosis.</a> Methods in Molecular Medicine. 102, 115-128 (2004).</li><li>Progatzky, F., Dallman, M. J., Lo Celso, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=From+seeing+to+believing:+labelling+strategies+for+in+vivo+cell-tracking+experiments.">From seeing to believing: labelling strategies for in vivo cell-tracking experiments.</a> Interface Focus. 3 (3), 20130001 (2013).</li><li>Stijlemans, B., 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=Development+of+a+pHrodo-based+assay+for+the+assessment+of+in+vitro+and+in+vivo+erythrophagocytosis+during+experimental+trypanosomosis.">Development of a pHrodo-based assay for the assessment of in vitro and in vivo erythrophagocytosis during experimental trypanosomosis.</a> PLoS Neglected Tropical Diseases. 9 (3), 0003561 (2015).</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 Harbor Perspective in Biology. 5 (1), 008748 (2013).</li><li>Chen, S., So, E. C., Strome, S. E., Zhang, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+Detachment+Methods+on+M2+Macrophage+Phenotype+and+Function.">Impact of Detachment Methods on M2 Macrophage Phenotype and Function.</a> Journal of Immunology Methods. 426, 56-61 (2015).</li><li>Fleit, S. A., Fleit, H. B., Zolla-Pazner, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Culture+and+recovery+of+macrophages+and+cell+lines+from+tissue+culture-treated+and+-untreated+plastic+dishes.">Culture and recovery of macrophages and cell lines from tissue culture-treated and -untreated plastic dishes.</a> Journal of Immunology Methods. 68 (1-2), 119-129 (1984).</li><li>Fine, N., Barzilay, O., Glogauer, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+Human+and+Mouse+Neutrophil+Phagocytosis+by+Flow+Cytometry.">Analysis of Human and Mouse Neutrophil Phagocytosis by Flow Cytometry.</a> Methods Molecular Biology. 1519, 17-24 (2017).</li><li>Summers, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neutrophil+kinetics+in+health+and+disease.">Neutrophil kinetics in health and disease.</a> Trends in Immunology. 31 (8), 318-324 (2010).</li><li>Dale, D. C., Boxer, L., Liles, W. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+phagocytes:+neutrophils+and+monocytes.">The phagocytes: neutrophils and monocytes.</a> Blood. 112 (4), 935-945 (2008).</li></ol>

The authors have nothing to disclose.

Apoptosis is a highly conserved cell death process that involves many signal cascades and induces protein expression, secretion, and transportation. Apoptosis is often associated with cellular morphology changes17. Apoptotic cells actively release cytokines and chemokines that attract phagocytes to migrate to the site and initiate the process of engulfment, an extremely complex pathway under tight control18. On the other hand, necrotic cell death releases danger signals tha...

Our body generates 1-10 billion apoptotic cells on a daily basis. Such a large number of apoptotic cells must be cleared in a way that the immune responses remain quiescent. To ensure the clearance of apoptotic cells in a timely manner, numerous types of tissue resident cells and circulating cells develop mechanisms to engulf apoptotic cells1. Dysfunctional regulation of apoptosis has been implicated in the onset and progression of various inflammatory disease and autoimmunity2. Apoptosis also plays a critical role in the pathogenesis of cancer development and its subsequent resistance to conventional treatments3,4. Removal of apoptotic cells generally promotes an anti-inflammatory response, which may be linked to immunological tolerance5. Disturbance of apoptotic cell clearance drives self-immunization and contributes to the development of systemic autoimmune diseases in both humans and mice6.
When cells undergo apoptosis, they expose the phosphatidylserine (PtdSer) from the inner leaflet to the outer leaflet of the membrane. PtdSer will then be recognized by phagocytes through surface receptors. Over a dozen receptors have been identified to recognize and/or facilitate the engulfment of apoptotic cells. In general, there are at least three types of surface receptors involved in the apoptotic cell clearance: tethering receptors, recognize apoptotic cells; tickling receptors, initiate engulfment; chaperoning receptors, facilitate the whole process7. TAM receptor tyrosine kinases (TAM RTKs) consist of Tyro-3, Axl, and Mer and are primarily expressed by myeloid cells of the immune system8. The primary function of TAM RTKs is to serve as tethering receptors, facilitating the phagocytic removal of apoptotic cells and debris. Our group has studied TAM mediated apoptotic cell clearance in the setting of autoimmunity for many years. The vitamin K-dependent protein growth arrest specific protein 6 (Gas6) and protein S (ProS) binds to and activates TAM receptors9,10. Gas6 is produced in the heart, kidneys, and lungs. ProS is mainly produced in the liver11. TAM recognizes of apoptotic cells in such a way that the N-terminal of Gas6/ProS binds to the PtdSer on an apoptotic cell and the C-terminal of Gas6/ProS binds to TAM receptors that anchored on the surface of phagocytes. Together with the other receptors, engulfment of apoptotic cells occurs12. Though Mer can bind to both the ligands ProS and Gas6, we found that Gas6 appears to be the sole ligand for Mer-mediated macrophage phagocytosis of apoptotic cells, which can be blocked by anti-Mer antibody13. Macrophages are professional phagocytes. Rapid clearance of apoptotic cells by macrophages is important for the inhibition of inflammation and autoimmune responses against intracellular antigens. Mer receptor tyrosine kinase is critical for the macrophage engulfment and efficient clearance of apoptotic cells14. In mouse spleen, Mer mainly expresses on the marginal zone and tangible body macrophages13.
The protocol presented here describes a basic method to induce cell apoptosis and demonstrate ways to measure the process and the efficiency of efferocytosis. These protocols can be readily adapted to study efferocytosis by other cell types in engulfment of apoptotic cells of different origins.

<table><tbody><tr><td>Ack lysing buffer</td><td>GIBCO</td><td>A10492</td><td></td></tr><tr><td>Annexin V/7-AAD</td><td>BD Pharmingen</td><td>559763</td><td></td></tr><tr><td>Anti-Mer antibody</td><td>R&amp;amp;D Systems</td><td>BAF591</td><td></td></tr><tr><td>CD11b-PE (clone M1/70)</td><td>BD Pharmingen</td><td>553311</td><td></td></tr><tr><td>CFSE</td><td>Invitrogen</td><td>C1157</td><td></td></tr><tr><td>DMSO</td><td>Sigma-Aldrich</td><td>D-2650</td><td></td></tr><tr><td>EDTA (0.5 mM)</td><td>GIBCO</td><td>15575-020</td><td></td></tr><tr><td>FACS tubes</td><td>BD Biosciences</td><td>352017</td><td></td></tr><tr><td>Frosted slides</td><td>Fisher Scientific</td><td>12-552-343</td><td></td></tr><tr><td>Horse Serum (Heat-inactivated)</td><td>Invitrogen</td><td>26050088</td><td></td></tr><tr><td>Lidocaine</td><td>Sigma-Aldrich</td><td>L-5647</td><td>Prepare 1% buffer in 1x PBS</td></tr><tr><td>PBS, 1x</td><td>Corning</td><td>21040CV</td><td></td></tr><tr><td>RPMI-1640</td><td>Corning</td><td>10040CV</td><td></td></tr><tr><td>RXDX-106</td><td>Selleck Chemicals</td><td>CEP-40783</td><td></td></tr><tr><td>Staurosprine (100mg)</td><td>Fisher Scientific</td><td>BP2541-100</td><td>Add 214.3 ml of DMSO into 100mg to make 1mM stocking solution</td></tr><tr><td>Thioglycolate Medium Brewer Modified</td><td>BD Biosciences</td><td>243010</td><td>Prepare 3% thioglycolate buffer in 1&amp;acute;PBS, autoclaved, and store in the dark for 3 months.</td></tr></tbody></table>

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.

Analysis of peritoneal macrophage-mediated engulfment of apoptotic thymocytes. Peritoneal macrophages and apoptotic cells were prepared and co-cultured as described in the protocol. Macrophages were detached and stained with PE conjugated anti-CD11b antibody for 20 min on ice. Macrophages were then washed and processed in a flow cytometer. As seen, there is no CFSE positive macrophage in the bottom right quadrant when no apoptotic cells were added into the culture (Figure 1<...

Watch this Scientific Journal Video about Experimental Analysis of Apoptotic Thymocyte Engulfment by Macrophages at JoVE.com

Experimental Analysis of Apoptotic Thymocyte Engulfment by Macrophages

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 ...

experimental-analysis-of-apoptotic-thymocyte-engulfment-by-macrophages

Research

JoVE Journal

Immunology and Infection

6.9K Views.  University of Cincinnati. 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.

Video: Experimental Analysis of Apoptotic Thymocyte Engulfment by Macrophages

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

Modified Annexin V/Propidium Iodide Apoptosis Assay For Accurate Assessment of Cell Death

Studies of cellular apoptosis have been significantly impacted since the introduction of flow cytometry-based methods. Propidium iodide (PI) is widely used in conjunction with Annexin V to determine if cells are viable, apoptotic, or necrotic through differences in plasma membrane integrity and permeability1,2. The Annexin V/ PI protocol is a commonly used approach for studying apoptotic cells3. PI is used more often than other nuclear stains because it is economical, stable and a good indicator of cell viability, based on its capacity to exclude dye in living cells 4,5. The ability of PI to enter a cell is dependent upon the permeability of the membrane; PI does not stain live or early apoptotic cells due to the presence of an intact plasma membrane 1,2,6. In late apoptotic and necrotic cells, the integrity of the plasma and nuclear membranes decreases7,8, allowing PI to pass through the membranes, intercalate into nucleic acids, and display red fluorescence 1,2,9. Unfortunately, we find that conventional Annexin V/ PI protocols lead to a significant number of false positive events (up to 40%), which are associated with PI staining of RNA within the cytoplasmic compartment10. Primary cells and cell lines in a broad range of animal models are affected, with large cells (nuclear: cytoplasmic ratios &lt;0.5) showing the highest occurrence10. Herein, we demonstrate a modified Annexin V/ PI method that provides a significant improvement for assessment of cell death compared to conventional methods. This protocol takes advantage of changes in cellular permeability during cell fixing to promote entry of RNase A into cells following staining. Both the timing and concentration of RNase A have been optimized for removal of cytoplasmic RNA. The result is a significant improvement over conventional Annexin V/ PI protocols (&lt; 5% events with cytoplasmic PI staining).

An accurate method for the assessment of cell death is described. The protocol improves upon conventional Annexin V/ propidium iodide (PI) protocols, which display up to 40% false- positive events in cell lines and primary cells from a broad range of animal models.

Studies of cellular apoptosis have been significantly impacted since the introduction of flow cytometry-based methods. Propidium iodide (PI) is widely ...

Biology

Phagocytosis Assay for Apoptotic Cells in Drosophila Embryos

The molecular mechanisms underlying the phagocytosis of apoptotic cells need to be elucidated in more detail because of its role in immune and inflammatory intractable diseases. We herein developed an experimental method to investigate phagocytosis quantitatively using the fruit fly Drosophila, in which the gene network controlling engulfment reactions is evolutionally conserved from mammals. In order to accurately detect and count engulfing and un-engulfing phagocytes using whole animals, Drosophila embryos were homogenized to obtain dispersed cells including phagocytes and apoptotic cells. The use of dispersed embryonic cells enables us to measure in vivo phagocytosis levels as if we performed an in vitro phagocytosis assay in which it is possible to observe all phagocytes and apoptotic cells in whole embryos and precisely quantify the level of phagocytosis. We confirmed that this method reproduces those of previous studies that identified the genes required for the phagocytosis of apoptotic cells. This method allows the engulfment of dead cells to be analyzed, and when combined with the powerful genetics of Drosophila, will reveal the complex phagocytic reactions comprised of the migration, recognition, engulfment, and degradation of apoptotic cells by phagocytes.

Phagocytosis Assay for Apoptotic Cells in Drosophila Embryos

We herein describe a phagocytosis assay using the dispersed embryonic cells of Drosophila. It enables us to easily and precisely quantify in vivo phagocytosis levels, and to identify new molecules required for the phagocytosis of apoptotic cells.

The molecular mechanisms underlying the phagocytosis of apoptotic cells need to be elucidated in more detail because of its role in immune and ...

Time-lapse 3D Imaging of Phagocytosis by Mouse Macrophages

Phagocytosis plays a key role in host defense, as well as in tissue development and maintenance, and involves rapid, receptor-mediated rearrangements of the actin cytoskeleton to capture, envelop and engulf large particles. Although phagocytic receptors, downstream signaling pathways, and effectors, such as Rho GTPases, have been identified, the dynamic cytoskeletal remodeling of specific receptor-mediated phagocytic events remain unclear. Four decades ago, two distinct mechanisms of phagocytosis, exemplified by Fc&#947; receptor (Fc&#947;R)- and complement receptor (CR)-mediated phagocytosis, were identified using scanning electron microscopy. Binding of immunoglobulin G (IgG)-opsonized particles to Fc&#947;Rs triggers the protrusion of thin membrane extensions, which initially form a so-called phagocytic cup around the particle before it becomes completely enclosed and retracted into the cell. In contrast, complement opsonized particles appear to sink into the phagocyte following binding to complement receptors. These two modes of phagocytosis, phagocytic cup formation and sinking in, have become well established in the literature. However, the distinctions between the two modes have become blurred by reports that complement receptor-mediated phagocytosis may induce various membrane protrusions. With the availability of high resolution imaging techniques, phagocytosis assays are required that allow real-time 3D (three dimensional) visualization of how specific phagocytic receptors mediate the uptake of individual particles. More commonly used approaches for the study of phagocytosis, such as end-point assays, miss the opportunity to understand what is happening at the interface of particles and phagocytes. Here we describe phagocytic assays, using time-lapse spinning disk confocal microscopy, that allow 3D imaging of single phagocytic events. In addition, we describe assays to unambiguously image Fc&#947; receptor- or complement receptor-mediated phagocytosis.

Here we describe methods using spinning disk confocal microscopy to image single phagocytic events by mouse resident peritoneal macrophages. The protocols can be extended to other phagocytic cells.

Phagocytosis plays a key role in host defense, as well as in tissue development and maintenance, and involves rapid, receptor-mediated rearrangements of ...

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 ...

In vitro Quantitative Imaging Assay for Phagocytosis of Dead Neuroblastoma Cells by iPSC-Macrophages

Microglia orchestrate neuroimmune responses in several neurodegenerative diseases, including Parkinson&#39;s disease and Alzheimer&#39;s disease. Microglia clear up dead and dying neurons through the process of efferocytosis, a specialized form of phagocytosis. The phagocytosis function can be disrupted by environmental or genetic risk factors that affect microglia. This paper presents a rapid and simple in vitro&#160;microscopy protocol for studying microglial efferocytosis in an induced pluripotent stem cell (iPSC) model of microglia, using a human neuroblastoma cell line (SH-SY5Y) labeled with a pH-sensitive dye for the phagocytic cargo. The procedure results in a high yield of dead neuroblastoma cells, which display surface phosphatidylserine, recognized as an &#34;eat-me&#34; signal by phagocytes. The 96-well plate assay is suitable for live-cell time-lapse imaging, or the plate can be successfully fixed prior to further processing and quantified by high-content microscopy. Fixed-cell high-content microscopy enables the assay to be scaled up for screening of small molecule inhibitors or assessing the phagocytic function of genetic variant iPSC lines. While this assay was developed to study phagocytosis of whole dead neuroblastoma cells by iPSC-macrophages, the assay can be easily adapted for other cargoes relevant to neurodegenerative diseases, such as synaptosomes and myelin, and other phagocytic cell types.

Neurodegenerative diseases are associated with dysregulated microglia functions. This article outlines an in vitro assay of phagocytosis of neuroblastoma cells by iPSC-macrophages. Quantitative microscopy readouts are described for both live-cell time-lapse imaging and fixed-cell high-content imaging.

Microglia orchestrate neuroimmune responses in several neurodegenerative diseases, including Parkinson&#39;s disease and Alzheimer&#39;s disease. ...

Neuroscience

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.

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 ...

Analysis of Efferocytosis of Apoptotic Thymocytes by Peritoneal Macrophages

Source: Zhen, Y. et al., <a href="https://app.jove.com/v/59731">Experimental Analysis of Apoptotic Thymocyte Engulfment by Macrophages.</a> J. Vis. Exp. (2019)
This video demonstrates a procedure for analyzing peritoneal macrophage-mediated efferocytosis of apoptotic mouse thymocytes by fluorescence microscopy.

Source: Zhen, Y. et al., Experimental Analysis of Apoptotic Thymocyte Engulfment by Macrophages. J. Vis. Exp. (2019)
This video demonstrates a procedure ...

JoVE Encyclopedia of Experiments

Immunology

Immunodiagnostics

Cellular Immunodiagnostics

An In Vitro Assay for Studying the Cytotoxicity of Pre-Activated CD8+ T Cells against Cancer Cells

Source: Kitamura, T., et al. <a href="https://app.jove.com/v/58841">Real Time Detection of In Vitro Tumor Cell Apoptosis Induced by CD8+ T Cells to Study Immune Suppressive Functions of Tumor-infiltrating Myeloid Cells.</a> J. Vis. Exp. (2019)
This video showcases an apoptosis assay in cancer cells induced by pre-activated effector T cells. By co-culturing these cells with cancer cells marked with fluorescent nuclei, a caspase-cleavable fluorogenic substrate is added. Apoptotic cancer cells will display a different color in their nuclei, leading to dual fluorescence. This dual fluorescence is indicative of cancer cells undergoing apoptosis.

1. Preparation of target cells that express red fluorescent protein in their nuclei

	Obtain a target mouse cancer cell line from an appropriate source.
	...

Specialized Assays

Fixed Cell Efferocytosis Assay: A Method to Study Efferocytic Uptake of Apoptotic Cells by Macrophages Using Fluorescence Microscopy

Source: Taruc, K., et al. <a href="https://app.jove.com/v/58149">Quantification of Efferocytosis by Single-cell Fluorescence Microscopy.</a> J. Vis. Exp. (2018).
In this video, we demonstrate the efferocytosis assay to study the clearance of apoptotic cells using confocal microscopy. Efferocytosis is a multi-step process where apoptotic cells are engulfed by phagocytes and degraded within vesicles called efferosomes. This protocol provides a method to visualize internalized and non-internalized portions of individual apoptotic cells and quantify efferocytosis.

Source: Taruc, K., et al. Quantification of Efferocytosis by Single-cell Fluorescence Microscopy. J. Vis. Exp. (2018).
In this video, we demonstrate the ...

Experimental Analysis of Apoptotic Thymocyte Engulfment by Macrophages

Summary

Explore More Videos

Chapters in this video

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

Modified Annexin V/Propidium Iodide Apoptosis Assay For Accurate Assessment of Cell Death

Phagocytosis Assay for Apoptotic Cells in Drosophila Embryos

Time-lapse 3D Imaging of Phagocytosis by Mouse Macrophages

Quantification of Efferocytosis by Single-cell Fluorescence Microscopy

In vitro Quantitative Imaging Assay for Phagocytosis of Dead Neuroblastoma Cells by iPSC-Macrophages

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

Analysis of Efferocytosis of Apoptotic Thymocytes by Peritoneal Macrophages

An In Vitro Assay for Studying the Cytotoxicity of Pre-Activated CD8⁺ T Cells against Cancer Cells

Fixed Cell Efferocytosis Assay: A Method to Study Efferocytic Uptake of Apoptotic Cells by Macrophages Using Fluorescence Microscopy