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All mouse experiments were authorized by the Animal Ethics Committee at West China Hospital, Sichuan University (Approval Nos. 20250814006, 20211212A). All mice used in this experiment were on a C57BL/6 genetic background.
1. Preparation of solutions
- Prepare fluorescence-activated cell sorting (FACS) buffer: 1× PBS containing 0.5% bovine serum albumin (BSA).
- Prepare magnetic-activated cell sorting (MACS) buffer: 1× PBS containing 0.5% BSA and 2 mM ethylenediamine tetraacetic acid (EDTA).
- Prepare cell culture medium: RPMI 1640 medium containing 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 2 mM L-glutamine, 10 mM HEPES, 55 µM β-mercaptoethanol, 100 U/mL penicillin, and 100 µg/mL streptomycin.
2. Preparation of C57BL/6 mouse lymphocytes
- Take the spleen and peripheral lymph nodes (LNs) of a 6–8-week-old C57BL/6 mouse (either male or female) under sterile conditions and place them in a 50 mL centrifuge tube with 5 mL of FACS buffer.
NOTE: The dissection of the spleen and LNs should be performed according to standard procedures.
- Place a 70 µm cell strainer on a 50 mL centrifuge tube, then place the spleen and LNs on the strainer, and use a 5 mL syringe piston to grind the tissue gently for 1 min. During grinding, rinse the strainer 3x with FACS buffer. Make sure to grind all the tissue completely and rinse the cells into the centrifuge tube. After grinding, remove the strainer.
- Centrifuge at 4 °C, 350 × g for 7 min.
- Remove the supernatant, resuspend the cell pellet in 3 mL of red blood cell lysis buffer, and leave the suspension at room temperature for 3–5 min.
- Immediately add FACS buffer to the centrifuge tube to a volume of 15–20 mL to terminate the lysis, and centrifuge at 4 °C, 350 × g for 7 min.
- Remove the supernatant, add 10 mL of FACS buffer, and gently resuspend the cell pellet.
- Take 10 µL of cell suspension and use trypan blue staining to count the total live lymphocytes.
NOTE: These cells are CD45.2+ lymphocytes.
3. Preparation of CD45.1 mouse lymphocytes
- Take the spleen and LNs of a 6–8-week-old CD45.1 mouse (either male or female) under sterile conditions and place them in a 50 mL centrifuge tube with 5 mL of FACS buffer.
- Prepare lymphocytes from the CD45.1 mouse by following the same steps described above.
NOTE: These cells are CD45.1+ lymphocytes.
4. Preparation of CD45.2+CD4+CD62L+ naïve T cells
NOTE: The entire process uses the CD4+CD62L+ T Cell Isolation Kit for MACS. The MACS buffer is pre-cooled at 4 °C, and all centrifugation conditions are 4 °C, 350 × g for 7 min.
- Collect the cell suspension from C57BL/6 mice, centrifuge and discard the supernatant, add 400 µL of MACS buffer and 100 µL of CD4+ T Cell Biotin-Antibody Cocktail to the centrifuge tube per 1 × 108 initial total cells. Mix gently and incubate at 4 °C for 5 min in the dark.
- Add 300 µL of MACS buffer and 200 µL of Anti-Biotin Microbeads to the centrifuge tube from step 4.1 per 1 × 108 initial total cells. Mix gently and incubate at 4 °C for 10 min in the dark.
- Add 10 mL of MACS buffer, centrifuge, and discard the supernatant. Resuspend the cell pellet in 2 mL of MACS buffer.
- Place the LS column on the appropriate MACS sorting magnetic separator. Use 3 mL of MACS buffer to rinse the column. Wait until the buffer in the column completely drains before proceeding to the next step.
NOTE: The maximum cell loading capacity of the LS column is 2 × 109 cells, including both positive and negative cells, and the maximum number of positive cells it can capture is 1 × 108. Usually, a single mouse only requires one LS column here.
- Load the cell suspension from step 4.3 onto the LS column. When the cell suspension completely flows into the column, use 3 mL of MACS buffer to wash the column. Collect all the flowthrough liquid in a new 15 mL centrifuge tube.
NOTE: These are the total CD4+CD25– T cells.
- Centrifuge the total CD4+CD25– T cells obtained in step 4.5, discard the supernatant, and obtain the cell pellet.
- Add 800 µL of MACS buffer and 200 µL of CD62L Microbeads to the cell pellet per 1 × 108 initial total cells. Mix gently and incubate at 4 °C for 10 min in the dark.
- Add 10 mL of MACS buffer to the centrifuge tube, centrifuge and discard the supernatant, and resuspend the cell pellet in 500 µL of MACS buffer.
- Place the MS column on the appropriate MACS sorting magnetic separator and use 1 mL MACS buffer to rinse the column.
- Load the cell suspension onto the MS column. When the suspension completely flows into the column, use 1 mL of MACS buffer to wash the column 2x.
- Remove the MS column from the magnetic separator and place it on a new 15 mL centrifuge tube. Add 1 mL of MACS buffer to the column and immediately push the plunger firmly to elute the cells labeled with magnetic beads.
- Count the cells, centrifuge and discard the supernatant, resuspend the cells in an appropriate volume of culture medium, and keep the tube on ice.
NOTE: These cells are CD45.2+CD4+CD62L+ naïve T cells. Usually, approximately 8 × 106 to 1 × 107 CD4+CD25–CD62L+ naive T cells can be purified from one mouse; inclusion of peripheral lymph nodes can increase the yield.
- Determine the purity of the isolated cells: Take 5 × 104 isolated CD4+CD62L+ T cells and resuspend them in 50 µL of antibody solution in a 1.5 mL centrifuge tube.
NOTE: Prepare the antibody solution by adding the anti-mouse CD4 PerCP-Cy5.5 antibody, anti-mouse CD62L FITC antibody, and anti-mouse CD25 PE antibody into the FACS buffer at a 1:100 ratio.
- Following the 20 min incubation at 4 °C in the dark, add 1 mL of FACS buffer to wash the cells. Centrifuge the cells, remove the supernatant, and resuspend the pellet in 200 µL of FACS buffer.
- Detect the purity of the samples by flow cytometry.
NOTE: For details of flow cytometer analysis, refer to the user manual of the instrument or the previously reported protocol14. The purity of CD4+CD25–CD62L+ naive T cells should be greater than 95% in the isolated T cell sample (Figure 2).
5. Preparation of CD45.1+CD4+CD25+ Treg-enriched cells and antigen-presenting cell-enriched non-CD4+ cells
NOTE: The entire process uses the CD4+CD25+ Regulatory T Cell Isolation Kit for MACS, and the instructions in the kit have been optimized to simultaneously obtain antigen-presenting cell (APC)-enriched non-CD4+ cells and CD4+CD25+ Treg-enriched cells. The MACS buffer is precooled at 4 °C, and all centrifugation conditions are 4 °C, 350 × g for 7 min.
- Collect the cell suspension from CD45.1 mice, centrifuge, and discard the supernatant, add 400 µL of precooled MACS buffer and 100 µL of CD4+CD25+ Regulatory T Cell Biotin-Antibody Cocktail to the centrifuge tube per 1 × 108 initial total cells. Mix gently and incubate at 4 °C for 10 min in the dark.
- Without washing, directly add 380 µL of precooled MACS buffer, 200 µL of Anti-Biotin Microbeads, and 20 µL of CD25-PE antibody per 1 × 108 initial total cells to the centrifuge tube from step 5.1. Mix gently and incubate at 4 °C for 15 min in the dark.
- Add 10 mL of MACS buffer to the centrifuge tube, centrifuge, and discard the supernatant, then resuspend the cell pellet in 500 µL of MACS buffer per 1 × 108 initial total cells.
- Place the LD column on the appropriate MACS sorting magnetic separator and rinse the column with 2 mL of MACS buffer. Wait until the buffer in the column completely drains before proceeding to the next step.
- Slowly load the cell suspension from step 5.3 onto the LD column. When the cell suspension completely flows into the column, wash the column 2x with 2 mL MACS buffer. Collect all the flowthrough liquid in a new 15 mL centrifuge tube.
- Remove the LD column from the magnetic separator and place it on a new 15 mL centrifuge tube. Add 3 mL of MACS buffer to the LD column, immediately push the plunger firmly to expel the Microbeads-labeled non-CD4+ cells. Count the cells, centrifuge, resuspend the cells in an appropriate volume of cell culture medium to achieve a cell concentration of 1 × 107 cells/mL, and keep the tube on ice.
NOTE: These non-CD4+ cells mainly consist of APCs such as macrophages, dendritic cells, and B cells. In this protocol, these cells are used as an APC-enriched non-CD4+ fraction.
- Centrifuge the total CD4+ T cells collected from step 5.5, discard the supernatant, and obtain the cell pellet.
- Add 900 µL of MACS buffer and 100 µL of Anti-PE Microbeads to the cell pellet per 1 × 108 initial total cells. Mix gently and incubate at 4 °C for 15 min in the dark.
- Place the MS column on the appropriate MACS sorting magnetic separator and rinse the column with 500 µL of precooled MACS buffer. Wait until the buffer in the column completely drains before proceeding to the next step.
- Slowly load the cell suspension from step 5.8 onto the MS column. When the cell suspension completely flows into the column, wash the column 2x with 1 mL MACS buffer. Collect the flowthrough liquid in a new 15 mL centrifuge tube.
NOTE: The cells in the flowthrough liquid at this time are CD4+CD25– T cells.
- Detach the MS column from the magnetic separator and position it over a fresh 15 mL centrifuge tube. Add 1 mL of MACS buffer to the column, then promptly depress the plunger to recover the magnetic bead-labeled CD4+CD25+ Treg-enriched cells.
- After counting the cells, centrifuge the suspension and remove the supernatant. Resuspend the pellet in enough culture medium to obtain a final concentration of 2 × 106 cells/mL, and keep the tube on ice.
NOTE: These cells are CD45.1+CD4+CD25+ Treg-enriched cells. Usually, approximately 8 × 105 to 1 × 106 CD4+CD25+ cells can be purified from one mouse; inclusion of peripheral lymph nodes can increase the yield.
- Determine the purity of the isolated CD4+CD25+ Treg-enriched cells: Take 5 × 104 isolated CD4+CD25+ Treg-enriched cells and 5 × 104 isolated APC-enriched non-CD4+ cells, respectively, and resuspend them in 50 µL of antibody solution.
NOTE: Prepare the antibody solution by adding the anti-mouse CD4 PerCP-Cy5.5 antibody and anti-mouse CD25 PE antibody into the FACS buffer at a 1:100 ratio. Use the same anti-mouse CD25 PE antibody here to confirm that the CD4+CD25+ cells are adequately labeled and that there are no CD4+CD25+ T cells in the non-CD4+ fraction. For more stringent identification of Treg cells, intracellular staining with an anti-mouse Foxp3 PB antibody can also be carried out.
- Following the 20 min incubation at 4 °C in the dark, add 2 mL of FACS buffer to wash the cells. Centrifuge the cells, remove the supernatant, and resuspend the pellet in 200 µL of FACS buffer.
- Detect the purity of the samples by flow cytometry.
NOTE: The frequency of CD4+CD25+ cells should be ≥ 95% to ensure that the purity of the Treg-enriched cell population meets the experimental requirements (Figure 2). Non-CD4+ cells used as the APC-enriched fraction should contain no more than 5% CD4+ T cells (Figure 2).
6. Labeling of naïve CD4+ T cells with cell proliferation dye
NOTE: All centrifugation conditions are 4 °C, 350 × g for 7 min. The PBS buffer is preequilibrated to room temperature before use. The labeling process is conducted under light protection to avoid dye quenching.
- Take the naïve CD4+ T cell suspension, centrifuge, discard the supernatant, and obtain the cell pellet.
- Dilute the Cell Proliferation Dye eFluor 450 in PBS to obtain a concentration of 20 µM at room temperature.
- Add 0.5 mL of PBS per 1 × 107 cells. Keep the tube tilted at approximately 45° and gently resuspend the cells by pipetting up and down 50x.
- Add an equal volume of cell proliferation dye solution quickly into the cell suspension, so that the final concentration of the cell proliferation dye is 10 µM. Keep the tube tilted at approximately 45° and mix the cells by pipetting up and down 50x to ensure full contact between the cells and the cell proliferation dye.
- Immediately wrap the centrifuge tube with aluminum foil to avoid light exposure. Incubate at room temperature for 20 min. Gently vortex the cells every 5 min to prevent cell aggregation.
- Add 10 mL of precooled cell culture medium to the centrifuge tube, gently vortex to terminate the staining, then centrifuge, and discard the supernatant.
- Add 5 mL of precooled cell culture medium to the cell pellet, centrifuge, and discard the supernatant to wash the cells.
- Add 5 mL of precooled cell culture medium to the cell pellet again and resuspend the cells.
- Count the cells, centrifuge and discard the supernatant, resuspend the cells in an appropriate volume of culture medium to achieve a cell concentration of 2 × 106 cells/mL, and keep the tube on ice.
7. Setting up the in vitro functional analysis of Treg cells
- Calculate the number of samples required for the cell culture, prepare an appropriate amount of cell culture medium containing 2.5 µg/mL anti-mouse CD3 antibody or the indicated induction cytokines, and gently vortex the prepared CD45.2+CD4+CD62L+ naïve T cells, CD45.1+CD4+CD25+ Treg-enriched cells, and APC-enriched non-CD4+ cells.
NOTE: Use CD45.2+CD4+CD62L+ naïve T cells as responder T (Tresp) cells. This example experiment studies the effect of Treg cells on the differentiation and proliferation of Th1 and Th17 cells. Therefore, there are a total of four samples for the cell culture: Tresp cells cultured under Th1 or Th17 induction conditions, in the absence or presence of Treg-enriched cells.
- Add 100 µL of CD45.2+CD4+ naïve T cells (2 × 105 cells per well) to the 48-well plate.
- Add 100 µL of CD45.1+ APC-enriched non-CD4+ cells (1 × 106 cells per well) to the 48-well plate.
- Add 100 µL of CD45.1+CD4+CD25+ Treg-enriched cells (2 × 105 cells per well) to the experimental wells, and add 100 µL of cell culture medium to the control wells. The Treg-enriched cell:Tresp ratio in the experimental samples is 1:1.
NOTE: The ratio of Treg cells to Tresp cells can be set as needed, or a panel of multiple ratios can be designed. The number of Tresp cells is fixed in the co-culture, while the number of Treg cells can be changed as needed. Typically, the ratios of Treg to Tresp in the experimental samples include 1:1, 1:2, 1:4, 1:8, 1:16, and 0:1. Furthermore, each experimental condition can be prepared in triplicate to minimize random experimental error. Here, for the sake of clarity, based on previous research experience15,16, a 1:1 ratio is used as an example.
- Add 100 µL of cell culture medium containing 2.5 µg/mL anti-mouse CD3 antibody to each well.
NOTE: The final concentration of anti-mouse CD3 antibody is 0.5 µg/mL. In addition to the experimental samples, set a blank control sample without anti-mouse CD3 antibody. In this sample, add 100 µL of T cell culture medium without anti-mouse CD3 antibody to determine the fluorescence intensity of the non-proliferated T cells, or the intensity of peak 0. This allows accurate calibration of the proliferation distribution.
- Add 100 µL of cell culture medium containing the indicated cytokines to each well to make the final volume of each well 500 µL.
NOTE: In this experiment, recombinant mouse IL-12 p70 at a final concentration of 10 ng/mL is used to induce Th1 cells, and recombinant human TGF-β1 at a final concentration of 2 ng/mL and recombinant mouse IL-6 at 50 ng/mL are used to induce Th17 cells.
- Add PBS to the remaining empty wells (500 µL/well) to maintain the humidity of the plate and reduce edge effects.
- Incubate the 48-well plate in a 5% CO2 incubator at 37 °C for 3 days.
NOTE: In this co-culture system, soluble anti-mouse CD3 antibody provides the primary T cell receptor (TCR) signal for T cell activation, and APC-enriched non-CD4+ cells provide costimulatory signals to fully activate T cells. TCR and costimulatory signals can also be triggered by plate-coated anti-mouse CD3 antibody and soluble anti-mouse CD28 antibody. Researchers can choose the stimulation method as needed.
8. In vitro functional analysis of Treg cells
NOTE: All centrifugation conditions are 4 °C, 350 × g for 7 min.
- Gently pipette the cultured cells to resuspend them and transfer the suspension to a 1.5 mL centrifuge tube. Centrifuge the cells and remove the supernatant.
- Add 500 µL of cell culture medium containing 5 ng/mL PMA, 1 µg/mL ionomycin, and 1:1,000 diluted GolgiPlug Protein Transport Inhibitor to each tube, gently vortex to resuspend the cells, and incubate them in a 5% CO2 incubator at 37 °C for 3 h.
- Centrifuge, discard the supernatant, add 50 µL of PBS containing one test of Zombie Yellow dye and 1:100 diluted anti-mouse CD16/32 antibody to each sample, vortex, and incubate at room temperature in the dark for 15 min to label dead cells and block Fc receptors.
- Centrifuge, discard the supernatant, add 50 µL of surface antibody cocktail, vortex, and incubate at 4 °C in the dark for 20 min.
NOTE: Add anti-CD4 PerCP-Cy5.5 antibody, anti-CD45.1 FITC antibody, and anti-CD45.2 APC-eFluor 780 antibody to the FACS buffer at a 1:200 ratio to prepare the surface antibody cocktail.
- Add 1 mL of FACS buffer to each centrifuge tube, centrifuge, and discard the supernatant.
- Add 300 µL of Fixation and Permeabilization Solution to each centrifuge tube, vortex, and incubate at 4 °C in the dark for 20 min.
- Add 1 mL of 1× Permeabilization/Wash (Perm/Wash) Buffer to each centrifuge tube, centrifuge, and discard the supernatant; then repeat this wash step once to ensure complete removal of residual fixative.
- Add 50 µL of cytokine antibody cocktail, vortex, and incubate at 4 °C in the dark for 40 min.
NOTE: Add anti-IFN-γ PE antibody and anti-IL-17A PE-Cy7 antibody to the Perm/Wash Buffer at a 1:100 ratio to prepare the cytokine antibody cocktail.
- Wash each sample with 1 mL of Perm/Wash buffer, centrifuge the cells, and remove the supernatant. Resuspend the pellet in 300 µL of FACS buffer.
- Measure the proliferation and differentiation of Tresp cells by flow cytometry. Use the following gating strategy (Figure 3): first, gate the lymphocyte population among the total cells and exclude cell debris and impurities; second, gate the single-cell population among the lymphocytes based on scatter signals; third, gate the live cell population among the single cells; fourth, gate the CD4+ T cell population among the live cells; fifth, gate the CD45.1+ Treg-enriched cell population and CD45.2+ Teff cell population among the CD4+ T cells; sixth, gate CD45.2+CD4+IFN-γ+ Th1 cells, CD45.2+CD4+IL-17A+ Th17 cells, and non-proliferated CD45.2+CD4+ T cells among the CD45.2+ T cells.
- Perform flow cytometry data acquisition and analyze the flow cytometry data.
- Use cultured T cells labeled with cell proliferation dye eFluor 450 as the cell proliferation dye single-stained control. Prepare the Zombie Yellow dye single-stained control with cultured T cells that were not labeled with cell proliferation dye. Prepare the other single-stained controls with compensation beads for every fluorophore used.
- Use T cells labeled with cell proliferation dye eFluor 450 and cultured without anti-mouse CD3 antibody to define the gate of non-proliferated cells.
- Use cultured T cells labeled with cell proliferation dye and stained with Zombie Yellow dye, all cell surface antibodies, and isotype controls of anti-mouse IFN-γ PE antibody and anti-mouse IL-17A PE-Cy7 antibody to define gates of IFN-γ+CD4+ and IL-17A+CD4+ T cells.