R.W. was supported by National Natural Science Foundation of China (82002130), Beijing Natural Science Foundation of&#160;China (7222059). ZD.X. was supported by the CAMS Innovation Fund for Medical Sciences (2019-I2M-5-026).

Ethical approval for the present study was obtained by the Ethics Committee of Beijing Children&#39;s Hospital, Capital Medical University (Approval Number: 2020-k-85). Volunteers were recruited from Beijing Children&#39;s Hospital, Capital Medical University. Peripheral venous blood samples were obtained from apparently healthy children (2 years old) who had previously received a prime and boosted vaccination with live-attenuated JE SA14-14-2 vaccine for less than half a year (JE-vaccinated children, n = 5) and unvaccinated children (6 months old, n = 5). Informed consent of human subjects was waived as only the residual samples, after being clinically tested, were used in this study. To protect the privacy of the volunteers, all data were fully anonymized and de-identified.
1. Isolation of PBMCs from peripheral venous blood
<ol>
	<li>Collect peripheral venous blood samples (2 mL) from JE-vaccinated and unvaccinated children in EDTA-K2-anticoagulated tubes (see Table of Materials) by the standard venipuncture technique18.</li>
	<li>Add 2 mL of phosphate-buffered saline (1x PBS) to dilute the peripheral blood. 
	NOTE: The process is handled as soon as possible to maintain maximum survivability.</li>
	<li>Add 4 mL of the density gradient medium (see Table of Materials) to a 15 mL centrifuge tube, and slowly transfer the diluted blood to the upper layer of the separation medium. 
	NOTE: Do not mix the blood with the separation medium or destroy the contact surface formed by the two liquids; otherwise, the separation effect will not be achieved.</li>
	<li>Centrifuge at 800 &#215; g for 20 min at room temperature. Observe the significant layers after centrifugation.</li>
	<li>Transfer the PBMCs (the middle layer) to another 15 mL centrifuge tube, and wash the PBMCs with 10 mL of RPMI-1640 medium containing 10% fetal bovine serum (FBS, see Table of Materials).</li>
	<li>Centrifuge at 800 &#215; g for 10 min at room temperature and discard the supernatant with a pipette carefully.</li>
	<li>Resuspend the PBMCs with 1 mL of RPMI-1640 medium containing 10% FBS and count the cells with a trypan blue-based automated counter (see Table of Materials).</li>
</ol>
2. Stimulation of PBMCs by inactivated JEV particles to induce cytokine expression
<ol>
	<li>Set two subgroups of the JEV stimulation and control groups in the JE-vaccinated and unvaccinated samples, respectively.</li>
	<li>Adjust the number of PBMCs to 2 &#215; 106 cells/mL with RPMI-1640 medium containing 10% FBS, and seed the PBMCs in 24-well plates (2 &#215; 106 cells/1 mL medium per well); inoculate three wells for each group.</li>
	<li>Stimulate the PBMCs of the JEV stimulation group with concentrated inactivated JEV particles5 (2 &#215; 105 PFU) for 16 h at 37 &#176;C in the presence of monoclonal antibodies CD28 (1 &#181;g/mL, 1:1,000) and CD49d (1 &#181;g/mL), GolgiPlug (1 &#181;g/mL, 1:1,000), and monensin (1 &#181;g/mL, 1:1,000). For surface staining, use BV605-anti-CD107a (1 &#181;g/mL, 1:1,000) (see Table of Materials). 
	NOTE: The JEV was inactivated by UV irradiation as described previously19.</li>
	<li>Stimulate the PBMCs of the control group without concentrated virus particles for 16 h at 37 &#176;C in the presence of monoclonal antibodies CD28 (1 &#181;g/mL, 1:1,000) and CD49d (1 &#181;g/mL, 1:1,000), GolgiPlug (1 &#181;g/mL, 1:1,000), and monensin (1 &#181;g/mL, 1:1,000). Stain the surface with BV605-anti-CD107a (1 &#181;g/mL, 1:1,000).</li>
</ol>
3. Ex vivo intracellular staining
<ol>
	<li>Collect the cell suspension from each group in a 1.5 mL microcentrifuge tube, centrifuge at 500 &#215; g for 5 min at room temperature, and remove the supernatant with a pipette.</li>
	<li>Resuspend the cells in 1 mL of 1x PBS, add fixable viability dye (1 &#181;L/mL, 1:1,000, see Table of Materials) to the cell suspension, and incubate for 10 min at room temperature in the dark. Centrifuge at 500 &#215; g (at room temperature) for 5 min and remove the supernatant.</li>
	<li>Resuspend the cells in 1 mL of 1x PBS. Centrifuge at 500 &#215; g (at room temperature) for 5 min. Discard the supernatant carefully.</li>
	<li>Perform cell surface marker staining.
	<ol>
		<li>Resuspend the cells in 100 &#181;L of 1x PBS, and add 2 &#181;L of each surface markers antibody (BV650-anti-CD3, BUV395-anti-CD4, BV421-anti-CD8, BUV737-anti-CD27, and BV480-anti-CD45RO, dilution factor: 1:50, see Table of Materials) to the cell suspension in each tube. 
		NOTE: The color fluorescent antibody staining protocol is shown in Table 1.</li>
		<li>Incubate the tubes (step 3.4.1) for 30 min at room temperature, and protect them from light. Centrifuge at 500 &#215; g for 5 min and remove the supernatant. 
		NOTE: The antibody of BUV737-anti-CD27 and BV480-anti-CD45RO can be replaced with BUV737-anti-CCR7 and BV480-anti-CD45RA as the annotation of the memory T cells.</li>
	</ol>
	</li>
	<li>Resuspend the cells in 1 mL of 1x PBS. Centrifuge at 500 &#215; g for 5 min at room temperature. Discard the supernatant carefully.</li>
	<li>Perform fixation and membrane breaking.
	<ol>
		<li>Resuspend the cells with 500 &#181;L of membrane-breaking fixative solution (see Table of Materials) and fix the cells for 20 min in the dark at room temperature. Centrifuge at 500 &#215; g for 5 min and remove the supernatant.</li>
	</ol>
	</li>
	<li>Resuspend the cells in 1 mL of 1x PBS. Centrifuge for 5 min at 500 &#215; g at room temperature and remove the supernatant carefully.</li>
	<li>Perform intracellular cytokine staining.
	<ol>
		<li>Resuspend the cells in 100 &#181;L of 1x PBS, and add 2 &#181;L of each cytokine antibody (FITC-anti-IFN-&#947;, PE-anti-TNF-&#945;, BV785-anti-IL-2, and APC-anti-MIP-1&#945;, dilution factor: 1:50, see Table of Materials) to the cell suspension in each tube. 
		NOTE: The volumes and information on fluorophore conjugated antibodies are shown in Table 1.</li>
		<li>Incubate the tubes (step 3.8.1) for 30 min at room temperature in the dark. Centrifuge at 500 &#215; g for 5 min and remove the supernatant.</li>
	</ol>
	</li>
	<li>Resuspend the cells in 1 mL of 1x PBS. Centrifuge at 500 &#215; g for 5 min at room temperature, and remove the supernatant carefully. Add 500 &#181;L of 1x PBS to resuspend the cells.</li>
</ol>
4. Flow cytometry set-up
<ol>
	<li>Isolate the PBMC sample alone following the procedures described in step 1 as the control sample. Divide the cell suspension into 12 equal parts in 1.5 mL microcentrifuge tubes (100 &#181;L/tube) as mentioned below.
	<ol>
		<li>Set up unstained, APC-Cy7-live/dead fixable stained, BV650-anti-CD3 single-stained, BUV395-anti-CD4 single-stained, BV421-anti-CD8 single-stained, BUV737-anti-CD27 single-stained, BV480-anti-CD45RO stained, BV605-anti-CD107a, FITC-anti-IFN-&#947; stained, PE-anti-TNF-&#945; single-stained, BV785-anti-IL-2 single-stained, and APC-anti-MIP-1&#945; single-stained samples.</li>
	</ol>
	</li>
	<li>Add the cell surface markers and intracellular cytokine staining as described in step 3. For each single-staining sample, only add one of the fluorophores from the staining step. Add 500 &#181;L of 1x PBS to resuspend the cells and vortex with low velocity.</li>
	<li>Using an unstained sample, adjust the forward scatter (FSC), side scatter (SSC), and different fluorescent dye voltages. 
	NOTE: For the present study, the following voltages were set. FSC: 440 V, SSC: 233 V, BV650: 575 V, APC-Cy7: 449 V, BUV395: 500 V, BV421: 402 V, BUV737: 585 V, BV480: 444 V, BV605: 457 V, FITC: 475 V, PE: 469 V, APC: 623 V, and BV785: 725 V.</li>
	<li>Using the single-staining samples, adjust the flow cytometry compensation to eliminate the contamination signals between the different fluorophores. 
	&#8203;NOTE: The compensation parameters are shown in Table 2.</li>
</ol>
5. Gating strategy and data analysis
NOTE: In the present study, for this analysis, the central memory T cells (TCM of CD8+ or CD4+ T cells as CD27+ CD45RO+ or CCR7+ CD45RA- and the effector memory T cells (TEM) of CD8+ or CD4+ T cells as CD27- CD45RO+ or CCR7- CD45RA- were defined respectively16.
<ol>
	<li>Draw a polygon gate through the FSC-area (FSC-A)/SSC-area (SSC-A) dot plot to select the intact lymphocyte population while excluding the debris (Figure 1A).</li>
	<li>Draw a rectangular gate through the FSC-A/FSC-width (FSC-W) dot plot to select the single cells (Figure 1B).</li>
	<li>Draw a rectangular gate through the live/dead/SSC-A dot plot to select the live cells (Figure 1C).</li>
	<li>Draw a rectangular gate through the CD3/SSC-A dot plot to identify the CD3+ T cells (Figure 1D).</li>
	<li>Draw a quad gate through the CD4/CD8 dot plot to identify the CD4+ or CD8+ T cells (Figure 1E).</li>
	<li>Draw a quad gate through the CD45RO/CD27 dot plot to subdivide the CD4+ or CD8+ T cells into TCM (CD27+ CD45RO+) and TEM (CD27- CD45RO+) (Figure 1F-I).</li>
	<li>Draw the gates of CD107a, IFN-&#947;, TNF-&#945;, IL-2, and MIP-1&#945; from the TCM or TEM of the CD8+ or CD4+ T cells to determine the frequency of different response patterns, respectively.</li>
	<li>Load the samples onto the cytometry sequentially. Use a stopping gate20 to acquire 1 &#215; 106 lymphocytes. 
	NOTE: The individual user can collect more than 1 &#215; 106 cells. This number was a compromise between the time taken and the collection of enough cells to provide meaningful results.</li>
</ol>

<ol>
	<li>Vanden Eynde, C., Sohier, C., Matthijs, S., De Regge, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Japanese+encephalitis+virus+interaction+with+mosquitoes:+A+review+of+vector+competence,+vector+capacity+and+mosquito+immunity.">Japanese encephalitis virus interaction with mosquitoes: A review of vector competence, vector capacity and mosquito immunity.</a> Pathogens. 11 (3), 317 (2022).</li><li>Wang, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+epidemiology+and+disease+burden+of+children+hospitalized+for+viral+infections+within+the+family+Flaviviridae+in+China:+A+national+cross-sectional+study.">The epidemiology and disease burden of children hospitalized for viral infections within the family Flaviviridae in China: A national cross-sectional study.</a> PLoS Neglected Tropical Diseases. 16 (7), 0010562 (2022).</li><li>Wang, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Decreases+in+both+the+seroprevalence+of+serum+antibodies+and+seroprotection+against+Japanese+encephalitis+virus+among+vaccinated+children.">Decreases in both the seroprevalence of serum antibodies and seroprotection against Japanese encephalitis virus among vaccinated children.</a> Virologica Sinica. 34 (3), 243-252 (2019).</li><li>Wang, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neutralizing+antibody+rather+than+cellular+immune+response+is+maintained+for+nearly+20+years+among+Japanese+encephalitis+SA14-14-2+vaccinees+in+an+endemic+setting.">Neutralizing antibody rather than cellular immune response is maintained for nearly 20 years among Japanese encephalitis SA14-14-2 vaccinees in an endemic setting.</a> Infection, Genetics and Evolution. 85, 104476 (2020).</li><li>Wang, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=T+cell+immunity+rather+than+antibody+mediates+cross-protection+against+Zika+virus+infection+conferred+by+a+live+attenuated+Japanese+encephalitis+SA14-14-2+vaccine.">T cell immunity rather than antibody mediates cross-protection against Zika virus infection conferred by a live attenuated Japanese encephalitis SA14-14-2 vaccine.</a> Applied Microbiology and Biotechnology. 104 (15), 6779-6789 (2020).</li><li>Redant, V., Favoreel, H. W., Dallmeier, K., Van Campe, W., De Regge, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Japanese+encephalitis+virus+persistence+in+porcine+tonsils+is+associated+with+a+weak+induction+of+the+innate+immune+response,+an+absence+of+IFNgamma+mRNA+expression,+and+a+decreased+frequency+of+CD4(+)CD8(+)+double-positive+T+cells.">Japanese encephalitis virus persistence in porcine tonsils is associated with a weak induction of the innate immune response, an absence of IFNgamma mRNA expression, and a decreased frequency of CD4(+)CD8(+) double-positive T cells.</a> Frontiers in Cellular and Infection Microbiology. 12, 834888 (2022).</li><li>Jain, 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=CD8+T+cells+protect+adult+naive+mice+from+JEV-induced+morbidity+via+lytic+function.">CD8 T cells protect adult naive mice from JEV-induced morbidity via lytic function.</a> PLoS Neglected Tropical Diseases. 11 (2), 0005329 (2017).</li><li>Khakhum, N., Bharaj, P., Walker, D. H., Torres, A. G., Endsley, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Antigen-specific+antibody+and+polyfunctional+T+cells+generated+by+respiratory+immunization+with+protective+Burkholderia+DeltatonB+Deltahcp1+live+attenuated+vaccines.">Antigen-specific antibody and polyfunctional T cells generated by respiratory immunization with protective Burkholderia DeltatonB Deltahcp1 live attenuated vaccines.</a> NPJ Vaccines. 6 (1), 72 (2021).</li><li>Weaver, J. 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=Increase+in+IFNgamma(-)IL-2(+)+cells+in+recent+human+CD4+T+cell+responses+to+2009+pandemic+H1N1+influenza.">Increase in IFNgamma(-)IL-2(+) cells in recent human CD4 T cell responses to 2009 pandemic H1N1 influenza.</a> PloS One. 8 (-), 57275 (2013).</li><li>Boaz, M. J., Waters, A., Murad, S., Easterbrook, P. J., Vyakarnam, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Presence+of+HIV-1+Gag-specific+IFN-gamma+IL-2++and+CD28+IL-2++CD4+T+cell+responses+is+associated+with+nonprogression+in+HIV-1+infection.">Presence of HIV-1 Gag-specific IFN-gamma+IL-2+ and CD28+IL-2+ CD4 T cell responses is associated with nonprogression in HIV-1 infection.</a> Journal of Immunology. 169 (11), 6376-6385 (2002).</li><li>Gui, 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=IL-2,+IL-4,+IFN-gamma+or+TNF-alpha+enhances+BAFF-stimulated+cell+viability+and+survival+by+activating+Erk1/2+and+S6K1+pathways+in+neoplastic+B-lymphoid+cells.">IL-2, IL-4, IFN-gamma or TNF-alpha enhances BAFF-stimulated cell viability and survival by activating Erk1/2 and S6K1 pathways in neoplastic B-lymphoid cells.</a> Cytokine. 84, 37-46 (2016).</li><li>Terahara, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vaccine-induced+CD107a++CD4++T+cells+are+resistant+to+depletion+following+AIDS+virus+infection.">Vaccine-induced CD107a+ CD4+ T cells are resistant to depletion following AIDS virus infection.</a> Journal of Virology. 88 (24), 14232-14240 (2014).</li><li>Tanyi, J. 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=Personalized+cancer+vaccine+strategy+elicits+polyfunctional+T+cells+and+demonstrates+clinical+benefits+in+ovarian+cancer.">Personalized cancer vaccine strategy elicits polyfunctional T cells and demonstrates clinical benefits in ovarian cancer.</a> NPJ Vaccines. 6 (1), 36 (2021).</li><li>Ammirati, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effector+memory+T+cells+are+associated+with+atherosclerosis+in+humans+and+animal+models.">Effector memory T cells are associated with atherosclerosis in humans and animal models.</a> Journal of the American Heart Association. 1 (1), 27-41 (2012).</li><li>Rizk, N. M., Fadel, A., AlShammari, W., Younes, N., Bashah, 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+immunophenotyping+changes+of+peripheral+CD4++T+lymphocytes+and+inflammatory+markers+of+class+III+obesity+subjects+after+laparoscopic+gastric+sleeve+surgery+-+A+follow-up+study.">The immunophenotyping changes of peripheral CD4+ T lymphocytes and inflammatory markers of class III obesity subjects after laparoscopic gastric sleeve surgery - A follow-up study.</a> Journal of Inflammation Research. 14, 1743-1757 (2021).</li><li>Zhang, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Phenotypic+and+functional+characterizations+of+CD8(+)+T+cell+populations+in+malignant+pleural+effusion.">Phenotypic and functional characterizations of CD8(+) T cell populations in malignant pleural effusion.</a> Experimental Cell Research. 417 (1), 113212 (2022).</li><li>Shin, H., Iwasaki, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue-resident+memory+T+cells.">Tissue-resident memory T cells.</a> Immunological Reviews. 255 (1), 165-181 (2013).</li><li>Birnie, K. A., Noel, M., Chambers, C. T., Uman, L. S., Parker, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Psychological+interventions+for+needle-related+procedural+pain+and+distress+in+children+and+adolescents.">Psychological interventions for needle-related procedural pain and distress in children and adolescents.</a> Cochrane Database of Systematic Reviews. 10 (10), (2018).</li><li>Lin, R. J., Liao, C. L., Lin, Y. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication-incompetent+virions+of+Japanese+encephalitis+virus+trigger+neuronal+cell+death+by+oxidative+stress+in+a+culture+system.">Replication-incompetent virions of Japanese encephalitis virus trigger neuronal cell death by oxidative stress in a culture system.</a> Journal of General Virology. 85, 521-533 (2004).</li><li>Byford, E., Carr, M., Pinon, L., Ahearne, M. J., Wagner, S. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+CD4++T-cells+and+analysis+of+circulating+T-follicular+helper+(cTfh)+cell+subsets+from+peripheral+blood+using+6-color+flow+cytometry.">Isolation of CD4+ T-cells and analysis of circulating T-follicular helper (cTfh) cell subsets from peripheral blood using 6-color flow cytometry.</a> Journal of Visualized Experiments. (143), e58431 (2019).</li><li>Zheng, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immune+responses+and+protective+effects+against+Japanese+encephalitis+induced+by+a+DNA+vaccine+encoding+the+prM/E+proteins+of+the+attenuated+SA14-14-2+strain.">Immune responses and protective effects against Japanese encephalitis induced by a DNA vaccine encoding the prM/E proteins of the attenuated SA14-14-2 strain.</a> Infection, Genetics and Evolution. 85, 104443 (2020).</li><li>Zheng, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complete+protection+for+mice+conferred+by+a+DNA+vaccine+based+on+the+Japanese+encephalitis+virus+P3+strain+used+to+prepare+the+inactivated+vaccine+in+China.">Complete protection for mice conferred by a DNA vaccine based on the Japanese encephalitis virus P3 strain used to prepare the inactivated vaccine in China.</a> Virology Journal. 17 (1), 126 (2020).</li><li>Lam, J. K. P., 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=Emergence+of+CD4++and+CD8++polyfunctional+T+cell+responses+against+immunodominant+lytic+and+latent+EBV+antigens+in+children+with+primary+EBV+infection.">Emergence of CD4+ and CD8+ polyfunctional T cell responses against immunodominant lytic and latent EBV antigens in children with primary EBV infection.</a> Frontiers in Microbiology. 9, 416 (2018).</li><li>Meckiff, B. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Imbalance+of+regulatory+and+cytotoxic+SARS-CoV-2-reactive+CD4(+)+T+cells+in+COVID-19.">Imbalance of regulatory and cytotoxic SARS-CoV-2-reactive CD4(+) T cells in COVID-19.</a> Cell. 183 (5), 1340-1353 (2020).</li><li>Ning, R. J., Xu, X. Q., Chan, K. H., Chiang, A. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+carriers+generate+Epstein-Barr+virus+(EBV)-specific+CD4(+)+and+CD8(+)+polyfunctional+T-cell+responses+which+show+immunodominance+hierarchies+of+EBV+proteins.">Long-term carriers generate Epstein-Barr virus (EBV)-specific CD4(+) and CD8(+) polyfunctional T-cell responses which show immunodominance hierarchies of EBV proteins.</a> Immunology. 134 (2), 161-171 (2011).</li></ol>

The authors have nothing to disclose.

This protocol represents a feasible flow cytometry-based detection method for TPF profiles in the PBMCs of children vaccinated with the JEV vaccine SA14-14-2. This study used the venous blood PBMCs of both vaccinated and unvaccinated children as research materials. With the stimulation of PBMCs with the JEV antigen, those amplified antigen-specific TPFs can be characterized by multicolor flow cytometry antibody staining. Compared with the conventional enzyme-linked immunospot assay method, flow cyto...

Japanese encephalitis virus (JEV) is an important mosquito-borne virus belonging to the genus Flavivirus within the Flaviviridae&#160;family1. Many Asia-Pacific countries have long faced enormous public health challenges due to the huge disease burden caused by Japanese encephalitis (JE), but this has improved dramatically with the increasing availability of various types of vaccinations2. Adaptive protective immune responses evoked by natural infection or vaccination contribute to the prevention and antiviral regulation. Humoral immunity and cell-mediated immunity are classified as adaptive immunity, and the induction of the former has always been regarded as a key strategy in vaccine design, albeit with relatively limited understanding in the past3. However, the role of T cell-mediated immunity in limiting flavivirus dissemination and virus clearance has been increasingly focused on and extensively studied4. Furthermore, T cell immunity is not only indispensable in JEV-specific antiviral responses but also plays a prominent role in cross-protection from secondary infection with heterologous flaviviruses, which has been demonstrated in previous studies5. It is speculated that this effect may bypass potential antibody-mediated enhancement effects in infection5. Of note, such cross-reactive T cell immunity is important, especially in the absence of vaccines and antiviral drugs against flaviviruses. Although many studies have been performed to determine the contribution of T cells in JEV infection with respect to CD4+ and CD8+ T cells6,7, the respective lineages secreting cytokines and their functional diversification remain undetermined, which means the elucidation of the exact functions of helper and killer T cells is hindered.
The scale of their antiviral defenses determines the quality of T cell responses. CD4+ or CD8+ T cells that can compatibly confer two or more functions, including cytokine secretion and degranulation, are characterized as polyfunctional T cells&#160;(TPFs)&#160;upon specific stimulation at the single-cell level8. CD4+ T cells that produce single or multiple cytokines may have various effects and immune memories. For example, IL-2+ IFN-&#947;+ CD4+ T cells are more likely to form a long-term effective protective response than IL-2+ CD4+ T cells9, which can be used as an important parameter in evaluating the vaccination effect. The frequency of IL-2+ IFN-&#947;+ CD4+ T cells is increased in patients with long-term non-progression of acquired immune deficiency syndrome (AIDS), while CD4+ T cells in patients with AIDS progression are more inclined to produce IFN-&#947; alone due to the promoting effect of IL-2 on T cell proliferation10. Furthermore, a subset of IL-2+ IFN-&#947;+ TNF-&#945;+ was shown to survive long-term in vivo and synergistically promote the killing function11. Although CD8+ T cells are more likely to exhibit cytotoxic activity, some CD4+ T cells are also equipped with cytotoxic activity as an indirectly detected expression of surface CD107a molecules12. In addition, certain T cell subsets express the chemokine MIP-1&#945;, which is often secreted by monocytes to participate in T cell-mediated neutrophil recruitment13. Similarly, CD8+ TPFs can also be used to characterize the versatility of the above markers. Studies have shown that the prime-boost strategy can effectively induce a prolonged period of TPF protective effects13, which can enhance the protection elicited by vaccination. A central feature in examining the immune system is the ability of memory T cells to facilitate stronger, faster, and more effective responses to secondary viral challenges than na&#239;ve T cells. Effector memory T cells (TEM) and central memory T cells (TCM) are important T cell subsets that are often differentiated by the composite expression of CD27/CD45RO or CCR7/CD45RA14. TCM (CD27+ CD45RO+ or CCR7+ CD45RA-) tends to localize in secondary lymphoid tissues, while TEM (CD27- CD45RO+ or CCR7- CD45RA-) localizes in lymphoid and peripheral tissues15,16. TEM provides immediate but not sustained defense, whereas TCM sustains the response by proliferating in the secondary lymphoid organs and generating new effectors17. Thus, given that memory cells can mediate specific and efficient recall responses to viruses, questions arise about the contribution of this subset of polyfunctions.
With the development of flow cytometry technology, it has become common to simultaneously detect markers of more than 10 clusters, phenotypes, and differentiation antigens, which is beneficial to more abundantly annotate the functional immunological features on individual T cells to reduce misinterpretation and difficulties in understanding of T cell phenotypes. This study used ex vivo stimulation and flow cytometry to analyze TPF profiles in peripheral blood mononuclear cells (PBMCs) within JEV-vaccinated children. Applying this approach, the understanding of short- and long-term JEV-specific and even cross-reactive T cell immunity induced by vaccination will be expanded.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>anti-human CD28</td>
			<td>Biolegend</td>
			<td>302934</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>anti-human CD49d</td>
			<td>Biolegend</td>
			<td>304339</td>
			<td>Antibody</td>
		</tr>
		<tr>
			<td>APC anti-human MIP-1&#945;</td>
			<td>BD</td>
			<td>551533</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>Automated cell counter</td>
			<td>BIO RAD</td>
			<td>TC20</td>
			<td>Cell count</td>
		</tr>
		<tr>
			<td>BD FACSymphony A5</td>
			<td>BD</td>
			<td>A5</td>
			<td>flow Cytometry</td>
		</tr>
		<tr>
			<td>BUV395 anti-human CD4</td>
			<td>BD</td>
			<td>563550</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BUV737 anti-human CCR7</td>
			<td>BD</td>
			<td>741786</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BUV737 anti-human CD27</td>
			<td>BD</td>
			<td>612829</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BV421 anti-human CD8</td>
			<td>Biolegend</td>
			<td>344748</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BV480 anti-human CD45RA</td>
			<td>BD</td>
			<td>566114</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BV480 anti-human CD45RO</td>
			<td>BD</td>
			<td>566143</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BV605 anti-human CD107a</td>
			<td>Biolegend</td>
			<td>328634</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BV650 anti-human CD3</td>
			<td>BD</td>
			<td>563999</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>BV785 anti-human IL-2</td>
			<td>Biolegend</td>
			<td>500348</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>Centrifuge Tube</td>
			<td>BD Falcon</td>
			<td>BD-35209715</td>
			<td>15 mL centrifuge tube</td>
		</tr>
		<tr>
			<td>Cytofix/Cytoperm Fixation/Permeabilization Solution Kit</td>
			<td>BD</td>
			<td>554714</td>
			<td>Cell fixation and permeabilization</td>
		</tr>
		<tr>
			<td>Density gradient medium</td>
			<td>Dakewe</td>
			<td>DKW-KLSH-0100</td>
			<td>Ficoll-Paque, human lymphocyte separation medium</td>
		</tr>
		<tr>
			<td>FITC anti-human IFN-&#947;</td>
			<td>Biolegend</td>
			<td>502506</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>Gibco Fetal Bovine Serum</td>
			<td>Thermo Fisher Scientific</td>
			<td>16000-044</td>
			<td>Fetal Bovine Serum</td>
		</tr>
		<tr>
			<td>Gibco RPMI-1640 medium</td>
			<td>Thermo Fisher Scientific</td>
			<td>22400089</td>
			<td>cell culture medium</td>
		</tr>
		<tr>
			<td>High-speed&#160;centrifuge</td>
			<td>Sigma</td>
			<td>&#160;3K15</td>
			<td>Cell centrifugation for 15 mL centrifuge tube</td>
		</tr>
		<tr>
			<td>High-speed&#160;centrifuge</td>
			<td>Eppendorf</td>
			<td>5424R</td>
			<td>Cell centrifugation for 1.5 mL Eppendorf (EP) tube</td>
		</tr>
		<tr>
			<td>Microcentrifuge tubes</td>
			<td>Axygen</td>
			<td>MCT-150-C</td>
			<td>1.5 mL microcentrifuge tube</td>
		</tr>
		<tr>
			<td>PE anti-human TNF-&#945;</td>
			<td>Biolegend</td>
			<td>502909</td>
			<td>Fluorescent antibody&#160;</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline (PBS)</td>
			<td>BI</td>
			<td>02-024-1ACS</td>
			<td>PBS</td>
		</tr>
		<tr>
			<td>Protein Transport Inhibitor (Containing Brefeldin A, GolgiPlug)</td>
			<td>BD</td>
			<td>555029</td>
			<td>blocks intracellular protein transport processes</td>
		</tr>
		<tr>
			<td>Protein Transport Inhibitor (Containing Monensin)</td>
			<td>BD</td>
			<td>554724</td>
			<td>blocks intracellular protein transport processes</td>
		</tr>
		<tr>
			<td>Round-bottom test tube</td>
			<td>BD Falcon</td>
			<td>352235</td>
			<td>5 mL test tube</td>
		</tr>
		<tr>
			<td>Trypan Blue Staining Cell Viability Assay Kit</td>
			<td>Beyotime</td>
			<td>C0011</td>
			<td>Trypan Blue Staining</td>
		</tr>
		<tr>
			<td>Zombie NIR Fixable Viability Dye</td>
			<td>Biolegend</td>
			<td>423106</td>
			<td>Dead cell stain</td>
		</tr>
	</tbody>
</table>

detection of polyfunctional t cells in children vaccinated with japanese encephalitis vaccine via the flow cytometry technique

T cell-mediated immunity plays an important role in controlling flavivirus infection, either after vaccination or after natural infection. The "quality" of a T cell needs to be assessed by function, and higher function is associated with more powerful immune protection. T cells that can simultaneously produce two or more cytokines or chemokines at the single-cell level are called polyfunctional T cells (TPFs), which mediate immune responses through a variety of molecular mechanisms to express degranulation markers (CD107a) and secrete interferon (IFN)-&#947;, tumor necrosis factor (TNF)-&#945;, interleukin (IL)-2, or macrophage inflammatory protein (MIP)-1&#945;. There is increasing evidence that TPFs are closely related to the maintenance of long-term immune memory and protection and that their increased proportion is an important marker of protective immunity and is important in the effective control of viral infection and reactivation. This evaluation applies not only to specific immune responses but also to the assessment of cross-reactive immune responses. Here, taking the Japanese encephalitis virus (JEV) as an example, the detection method and flow cytometry color scheme of JEV-specific TPFs produced by peripheral blood mononuclear cells of children vaccinated against Japanese encephalitis were tested to provide a reference for similar studies.

Figure 1 shows&#160;the gating strategy used to divide the TCM or TEM of&#160;CD8+ or CD4+ T cells from a representative JEV stimulation group of JE-vaccinated children. The FSC-A/SSC-A dot plot is used to identify lymphocytes, and the FSC-A/FSC-W dot plot is used to identify single cells. Viable cells are selected on the live/dead/SSC-A dot plot. The CD3/SSC-A dot plot is used to identify the CD3+ T cells. The CD4/CD8 dot plot is used t...

Watch this Scientific Journal Video about Detection of Polyfunctional T Cells in Children Vaccinated with Japanese Encephalitis Vaccine via the Flow Cytometry Technique at JoVE.com

Detection of Polyfunctional T Cells in Children Vaccinated with Japanese Encephalitis Vaccine via the Flow Cytometry Technique

The present protocol combines ex vivo stimulation and flow cytometry to analyze polyfunctional T cell (TPF)&#160;profiles in peripheral blood mononuclear cells (PBMCs) within Japanese encephalitis virus (JEV)-vaccinated children. The detection method and flow cytometry color scheme of JEV-specific TPFs were tested to provide a reference for similar studies.

Detection of Polyfunctional T Cells in Children Vaccinated with Japanese Encephalitis Vaccine via the Flow Cytometry Technique

T cell-mediated immunity plays an important role in controlling flavivirus infection, either after vaccination or after natural infection. The "quality" ...

detection-polyfunctional-t-cells-children-vaccinated-with-japanese

Microsoft Bing

Research

JoVE Journal

Immunology and Infection

1.8K Views.  Capital Medical University, National Center for Children’s Health. The present protocol combines ex vivo stimulation and flow cytometry to analyze polyfunctional T cell (TPF) profiles in peripheral blood mononuclear cells (PBMCs) within Japanese encephalitis virus (JEV)-vaccinated children. The detection method and flow cytometry color scheme of JEV-specific TPFs were tested to provide a reference for similar studies.

Video: Detection of Polyfunctional T Cells in Children Vaccinated with Japanese Encephalitis Vaccine via the Flow Cytometry Technique

Cell-based Flow Cytometry Assay to Measure Cytotoxic Activity

Cytolytic activity of CD8+ T cells is rarely evaluated. We describe here a new cell-based assay to measure the capacity of antigen-specific CD8+ T cells to kill CD4+ T cells loaded with their cognate peptide. Target CD4+ T cells are divided into two populations, labeled with two different concentrations of CFSE. One population is pulsed with the peptide of interest (CFSE-low) while the other remains un-pulsed (CFSE-high). Pulsed and un-pulsed CD4+ T cells are mixed at an equal ratio and incubated with an increasing number of purified CD8+ T cells. The specific killing of autologous target CD4+ T cells is analyzed by flow cytometry after coculture with CD8+ T cells containing the antigen-specific effector CD8+ T cells detected by peptide/MHCI tetramer staining. The specific lysis of target CD4+ T cells measured at different effector versus target ratios, allows for the calculation of lytic units, LU30/106 cells. This simple and straightforward assay allows for the accurate measurement of the intrinsic capacity of CD8+ T cells to kill target CD4+ T cells.

This protocol describes a sensitive, cell-based cytotoxicity assay. By enumerating the decrease in frequency of live target CD4+ T cells in the presence of an increasing number of effector CD8+ T cells, this assay allows for the direct assessment of cytolytic activity of antigen-specific CD8+ T cells.

Cytolytic activity of CD8+ T cells is rarely evaluated. We describe here a new cell-based assay to measure the capacity of antigen-specific CD8+ T cells ...

Detection of Fluorescent Nanoparticle Interactions with Primary Immune Cell Subpopulations by Flow Cytometry

Engineered nanoparticles are endowed with very promising properties for therapeutic and diagnostic purposes. This work describes a fast and reliable method of analysis by flow cytometry to study nanoparticle interaction with immune cells. Primary immune cells can be easily purified from human or mouse tissues by antibody-mediated magnetic isolation. In the first instance, the different cell populations running in a flow cytometer can be distinguished by the forward-scattered light (FSC), which is proportional to cell size, and the side-scattered light (SSC), related to cell internal complexity. Furthermore, fluorescently labeled antibodies against specific cell surface receptors permit the identification of several subpopulations within the same sample. Often, all these features vary when cells are boosted by external stimuli that change their physiological and morphological state. Here, 50 nm FITC-SiO2 nanoparticles are used as a model to identify the internalization of nanostructured materials in human blood immune cells. The cell fluorescence and side-scattered light increase after incubation with nanoparticles allowed us to define time and concentration dependence of nanoparticle-cell interaction. Moreover, such protocol can be extended to investigate Rhodamine-SiO2 nanoparticle interaction with primary microglia, the central nervous system resident immune cells, isolated from mutant mice that specifically express the Green Fluorescent Protein (GFP) in the monocyte/macrophage lineage. Finally, flow cytometry data related to nanoparticle internalization into the cells have been confirmed by confocal microscopy.

Analysis of nanoparticle interaction with defined subpopulations of immune cells by flow cytometry.

Engineered nanoparticles are endowed with very promising properties for therapeutic and diagnostic purposes. This work describes a fast and reliable ...

The Use of Flow Cytometry to Assess the State of Chromatin in T Cells

During a proper immune response, quiescent T cells become activated upon antigen presentation to their antigen-specific T cell receptor. This leads to clonal proliferation of only those T cells that bear a receptor that recognizes the antigen. Chromatin decondensation is a hallmark of T cell activation and is required for T cells to acquire the ability to proliferate after antigen engagement. This change in chromatin condensation can be detected using antibodies raised against histone proteins. These antibodies cannot bind to their epitopes in na&#239;ve T cells as well as they can in activated T cells. We describe how to simultaneously stain T cell-specific surface markers, track viability with a fixable dead cell stain, and measure chromatin status via intracellular staining of Histone H3 proteins. Stained cells are analyzed by flow cytometry and chromatin condensation status is measured as the mean fluorescence intensity (MFI) of the Histone H3 stain. Chromatin decondensation during T cell activation is demonstrated as an increase in the MFI

Flow cytometry can be utilized to assess the state of chromatin within T cells. This protocol allows scientists to interpret evidence of chromatin decondensation during T cell activation demonstrated by an increase in the mean florescence intensity (MFI) of fluorescent Histone H3 antibodies

During a proper immune response, quiescent T cells become activated upon antigen presentation to their antigen-specific T cell receptor. This leads to ...

Fluorescence-activated Cell Sorting for Purification of Plasmacytoid Dendritic Cells from the Mouse Bone Marrow

Fluorescence-activated cell sorting (FACS) is a technique to purify specific cell populations based on phenotypes detected by flow cytometry. This method enables researchers to better understand the characteristics of a single cell population without the influence of other cells. Compared to other methods of cell enrichment, such as magnetic-activated cell sorting (MCS), FACS is more flexible and accurate for cell separation due to the ability of phenotype detection by flow cytometry. In addition, FACS is usually capable of separating multiple cell populations simultaneously, which improves the efficiency and diversity of experiments. Although FACS has some limitations, it has been broadly used to purify cells for functional studies in both in vitro and in vivo settings. Here we report a protocol using fluorescence-activated cell sorting to isolate a very rare population of immune cells, plasmacytoid dendritic cells (pDC), with high purity from the bone marrow of lupus-prone mice for in vitro functional studies of pDC.

We report a protocol using fluorescence-activated cell sorting to isolate plasmacytoid dendritic cells (pDC) with high purity from the bone marrow of lupus-prone mice for functional studies of pDC.

Fluorescence-activated cell sorting (FACS) is a technique to purify specific cell populations based on phenotypes detected by flow cytometry. This method ...

Measurement of T Cell Alloreactivity Using Imaging Flow Cytometry

The measurement of immunological reactivity to donor antigens in transplant recipients is likely to be crucial for the successful reduction or withdrawal of immunosuppression. The mixed leukocyte reaction (MLR), limiting dilution assays, and trans-vivo delayed-type hypersensitivity (DTH) assay have all been applied to this question, but these methods have limited predictive ability and/or significant practical limitations that reduce their usefulness. Imaging flow cytometry is a technique that combines the multiparametric quantitative powers of flow cytometry with the imaging capabilities of fluorescent microscopy. We recently made use of an imaging flow cytometry approach to define the proportion of recipient T cells capable of forming mature immune synapses with donor antigen-presenting cells (APCs). Using a well-characterized mouse heart transplant model, we have shown that the frequency of in vitro immune synapses among T-APC membrane contact events strongly predicted allograft outcome in rejection, tolerance, and a situation where transplant survival depends on induced regulatory T cells. The frequency of T-APC contacts increased with T cells from mice during acute rejection and decreased with T cells from mice rendered unresponsive to alloantigen. The addition of regulatory T cells to the in vitro system reduced prolonged T-APC contacts. Critically, this effect was also seen with human polyclonally expanded, naturally occurring regulatory T cells, which are known to control the rejection of human tissues in humanized mouse models. Further development of this approach may allow for a deeper characterization of the alloreactive T-cell compartment in transplant recipients. In the future, further development and evaluation of this method using human cells may form the basis for assays used to select patients for immunosuppression minimization, and it can be used to measure the impact of tolerogenic therapies in the clinic.

This paper describes a method for measuring alloreactivity in a mixed population of T cells using imaging flow cytometry.

The measurement of immunological reactivity to donor antigens in transplant recipients is likely to be crucial for the successful reduction or withdrawal ...

Isolation and In Vitro Culture of Murine and Human Alveolar Macrophages

Alveolar macrophages are terminally differentiated, lung-resident macrophages of prenatal origin. Alveolar macrophages are unique in their long life and their important role in lung development and function, as well as their lung-localized responses to infection and inflammation. To date, no unified method for identification, isolation, and handling of alveolar macrophages from humans and mice exists. Such a method is needed for studies on these important innate immune cells in various experimental settings. The method described here, which can be easily adopted by any laboratory, is a simplified approach to harvesting alveolar macrophages from bronchoalveolar lavage fluid or from lung tissue and maintaining them in vitro. Because alveolar macrophages primarily occur as adherent cells in the alveoli, the focus of this method is on dislodging them prior to harvest and identification. The lung is a highly vascularized organ, and various cell types of myeloid and lymphoid origin inhabit, interact, and are influenced by the lung microenvironment. By using the set of surface markers described here, researchers can easily and unambiguously distinguish alveolar macrophages from other leukocytes, and purify them for downstream applications. The culture method developed herein supports both human and mouse alveolar macrophages for in vitro growth, and is compatible with cellular and molecular studies.

Isolation and In Vitro Culture of Murine and Human Alveolar Macrophages

This communication describes methodologies for isolation and culture of alveolar macrophages from humans and murine models for experimental purposes.

Alveolar macrophages are terminally differentiated, lung-resident macrophages of prenatal origin. Alveolar macrophages are unique in their long life and ...

Multicolor Flow Cytometry-based Quantification of Mitochondria and Lysosomes in T Cells

T cells utilize different metabolic programs to match their functional needs during differentiation and proliferation. Mitochondria are crucial cellular components responsible for supplying cell energy; however, excess mitochondria also produce reactive oxygen species (ROS) that could cause cell death. Therefore, the number of mitochondria must constantly be adjusted to fit the needs of the cells. This dynamic regulation is achieved in part through the function of lysosomes that remove surplus/damaged organelles and macromolecules. Hence, cellular mitochondrial and lysosomal contents are key indicators to evaluate the metabolic adjustment of cells. With the development of probes for organelles, well-characterized lysosome or mitochondria-specific dyes have become available in various formats to label cellular lysosomes and mitochondria. Multicolor flow cytometry is a common tool to profile cell phenotypes, and has the capability to be integrated with other assays. Here, we present a detailed protocol of how to combine organelle-specific dyes with surface markers staining to measure the amount of lysosomes and mitochondria in different T cell populations on a flow cytometer.

This article illustrates a powerful method to quantify mitochondria or lysosomes in living cells. The combination of lysosome- or mitochondria-specific dyes with fluorescently conjugated antibodies against surface markers allows the quantification of these organelles in mixed cell populations, like primary cells harvested from tissue samples, by using multicolor flow cytometry.

T cells utilize different metabolic programs to match their functional needs during differentiation and proliferation. Mitochondria are crucial cellular ...

Isolation of Mouse Kidney-Resident CD8+ T cells for Flow Cytometry Analysis

Tissue-resident memory T cell (TRM) is a rapidly expanding field of immunology research. Isolating T cells from various non-lymphoid tissues is one of the key steps to investigate TRMs. There are slight variations in lymphocyte isolation protocols for different organs. Kidney is an essential non-lymphoid organ with numerous immune cell infiltration especially after pathogen exposure or autoimmune activation. In recent years, multiple labs including our own have started characterizing kidney resident CD8+ T cells in various physiological and pathological settings in both mouse and human. Due to the abundance of T lymphocytes, kidney represents an attractive model organ to study TRMs in non-mucosal or non-barrier tissues. Here, we will describe a protocol commonly used in TRM-focused labs to isolate CD8+ T cells from mouse kidneys following systemic viral infection. Briefly, using an acute lymphocytic choriomeningitis virus (LCMV) infection model in C57BL/6 mice, we demonstrate intravascular CD8+ T cell labeling, enzymatic digestion, and density gradient centrifugation to isolate and enrich lymphocytes from mouse kidneys to make samples ready for the subsequent flow cytometry analysis.

Isolation of Mouse Kidney-Resident CD8+ T cells for Flow Cytometry Analysis

Following viral infection, kidney harbors a relatively large number of CD8+ T cells and offers an opportunity to study non-mucosal TRM cells. Here, we describe a protocol to isolate mouse kidney lymphocytes for flow cytometry analysis.

Tissue-resident memory T cell (TRM) is a rapidly expanding field of immunology research. Isolating T cells from various non-lymphoid tissues is one of the ...

A DNA/Ki67-Based Flow Cytometry Assay for Cell Cycle Analysis of Antigen-Specific CD8 T Cells in Vaccinated Mice

The cell cycle of antigen-specific T cells in vivo has been examined by using a few methods, all of which possess some limitations. Bromodeoxyuridine (BrdU) marks cells that are in or recently completed S-phase, and carboxyfluorescein succinimidyl ester (CFSE) detects daughter cells after division. However, these dyes do not allow identification of the cell cycle phase at the time of analysis. An alternative approach is to exploit Ki67, a marker that is highly expressed by cells in all phases of the cell cycle except the quiescent phase G0. Unfortunately, Ki67 does not allow further differentiation as it does not separate cells in S-phase that are committed to mitosis from those in G1 that can remain in this phase, proceed into cycling, or move into G0.
Here, we describe a flow cytometric method for capturing a &#34;snapshot&#34; of T cells in different cell cycle phases in mouse secondary lymphoid organs. The method combines Ki67 and DNA staining with major histocompatibility complex (MHC)-peptide-multimer staining and an innovative gating strategy, allowing us to successfully differentiate between antigen-specific CD8 T cells in G0, in G1 and in S-G2/M phases of the cell cycle in the spleen&#160;and draining lymph nodes of mice after vaccination with viral vectors carrying the model antigen gag of human immunodeficiency virus (HIV)-1.
Critical steps of the method were the choice of the DNA dye and the gating strategy to increase the assay sensitivity and to include highly activated/proliferating antigen-specific T cells that would have been missed by current criteria of analysis. The DNA dye, Hoechst 33342, enabled us to obtain a high-quality discrimination&#160;of the G0/G1 and G2/M DNA peaks, while preserving membrane and intracellular staining. The method has great potential to increase knowledge about T cell response in vivo and to improve immuno-monitoring analysis.

Clonal expansion is a key feature of antigen-specific T cell response. However, the cell cycle of antigen-responding T cells has been poorly investigated, partly because of technical limitations. We describe a flow cytometric method to analyze clonally expanding antigen-specific CD8 T cells in spleen and lymph nodes of vaccinated mice.

The cell cycle of antigen-specific T cells in vivo has been examined by using a few methods, all of which possess some limitations. Bromodeoxyuridine ...

Analysis of SAMHD1 Restriction by Flow Cytometry in Human Myeloid U937 Cells

Sterile &#945;-motif/histidine-aspartate domain-containing protein 1 (SAMHD1) inhibits replication of HIV-1 in quiescent myeloid cells. U937 cells are widely used as a convenient cell system for analyzing SAMHD1 activity due to a low level of SAMHD1 RNA expression, leading to undetectable endogenous protein expression. Based on similar assays developed in the Stoye laboratory to characterize other retroviral restriction factors, the Bishop lab developed a two-color restriction assay to analyze SAMHD1 in U937 cells. Murine Leukaemia Virus-like particles expressing SAMHD1, alongside YFP expressed from an IRES, are used to transduce U937 cells. Cells are then treated with phorbol myristate acetate to induce differentiation to a quiescent phenotype. Following differentiation, cells are infected with HIV-1 virus-like particles expressing a fluorescent reporter. After 48 h, cells are harvested and analyzed by flow cytometry. The proportion of HIV-infected cells in the SAMHD1-expressing population is compared to that in internal control cells lacking SAMHD1. This comparison reveals a restriction ratio. SAMHD1 expression leads to a five-fold reduction in HIV infection, corresponding to a restriction ratio of 0.2. Our recent substitution of RFP for the original GFP as the reporter gene for HIV infection has facilitated flow cytometry analysis.
This assay has been successfully used to characterize the effect of amino acid substitutions on SAMHD1 restriction by transducing with viruses encoding altered SAMHD1 proteins, derived from site-directed mutagenesis of the expression vector. For example, the catalytic site substitutions HD206-7AA show a restriction phenotype of 1, indicating a loss of restriction activity. Equally, the susceptibility of different tester viruses can be determined. The assay can be further adapted to incorporate the effect of differentiation status, metabolic status, and SAMHD1 modifiers to better understand the relationship between SAMHD1, cell metabolic state, and viral restriction.

Described here is an established method to determine the extent of HIV-1 restriction by the cellular inhibitory protein SAMHD1. Human myeloid lineage U937 cells are transduced with a SAMHD1 expression vector co-expressing YFP, differentiated and then challenged with HIV-RFP. The level of restriction is determined by flow cytometry analysis.

Sterile &#945;-motif/histidine-aspartate domain-containing protein 1 (SAMHD1) inhibits replication of HIV-1 in quiescent myeloid cells. U937 cells are ...