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7 protocols using apc cy7 anti human cd4

1

Multiparameter Flow Cytometry for T Cell Phenotyping

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The following antibodies were used in this study: anti-human CD45RA-PERCPCy5.5 (Clone HI100, Lot# B213966, Cat# 304107, Biolegend), anti-human CD127-Brilliant Violet 510 (Clone A019D5, Lot# B197159, Cat# 351331, Biolegend), anti-human CD4-APC-Cy7 (Clone OKT4, Lot# B207751, Cat# 317417, Biolegend), anti-human CCR6-PE (Clone G034E3, Lot# B203239, Cat# 353409, Biolegend), anti-human CD25-FITC (Clone BC96, Lot# B168869, Cat# 302603, Biolegend), anti-human CXCR3-Brilliant Violet 421 (Clone G025H7, Lot# B206003, Cat# 353715, Biolegend), anti-human CXCR5-AlexaFluor647 (Clone RF8B2, Lot# 5302868, Cat# 558113, BD Pharmingen), anti-human CD26-PE (Clone 2A6, Lot# 4301881, Cat# 12-0269-42, Thermo Fisher), and anti-human CD3E-Pacific Blue (Clone UCHT1, Lot# 4341657, Cat# 558117, BD Biosciences). All antibodies were validated by the manufacturer in human peripheral blood samples, used at a 1:200 dilution, and compared to isotype and no staining control samples.
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2

Isolation and Analysis of Immune Cells from Tumor Tissues

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Thirty-two fresh tumor tissues and 11 distant normal lung tissues were collected and stored in Tissue Storage Solution (Miltenyi Biotec), and processed on the same day of sample collection. The tissues were washed with PBS until there was no visible blood on the surface, and then minced into a homogenate. Subsequently, 10 mL of type IV collagenase (Gibco) was used for digestion at 37 °C for 1 h with agitation. The resulting single-cell suspension was filtered through 70 μm cell strainer (BD Bioscience), and the supernatant was discarded after centrifugation at 500g for 10 min. After resuspension in PBS buffer, the suspension was centrifuged at 800g for 2 min, and the supernatant was discarded. This washing process was repeated twice. Fixable Viability Dye eFluor780 (eBioscience) and Zombie Yellow Viability Kit (BioLegend) were used to distinguish dead cells. Anti-human CD3 BUV395 (BD Bioscience), Anti-human CD4 APC/Cy7 (BioLegend), Anti-human CD8a Alexa Fluor700 (BioLegend), Anti-human Perforin FITC (BioLegend), and Anti-human FOXP3 PE/Cy5 (eBioscience) were used to stain cell membrane surface proteins and intracellular proteins. Samples were acquired on the BD LSR Fortessa (BD Bioscience). Flow cytometry data were analyzed using FlowJo (TreeStar). The representative gating strategies for Tregs, CD8+ T cells, and CD8+Perforin+ T cells were shown in Supplementary Figure S1.
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3

Multiparameter Flow Cytometry for T Cell Phenotyping

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The following antibodies were used in this study: anti-human CD45RA-PERCPCy5.5 (Clone HI100, Lot# B213966, Cat# 304107, Biolegend), anti-human CD127-Brilliant Violet 510 (Clone A019D5, Lot# B197159, Cat# 351331, Biolegend), anti-human CD4-APC-Cy7 (Clone OKT4, Lot# B207751, Cat# 317417, Biolegend), anti-human CCR6-PE (Clone G034E3, Lot# B203239, Cat# 353409, Biolegend), anti-human CD25-FITC (Clone BC96, Lot# B168869, Cat# 302603, Biolegend), anti-human CXCR3-Brilliant Violet 421 (Clone G025H7, Lot# B206003, Cat# 353715, Biolegend), anti-human CXCR5-AlexaFluor647 (Clone RF8B2, Lot# 5302868, Cat# 558113, BD Pharmingen), anti-human CD26-PE (Clone 2A6, Lot# 4301881, Cat# 12-0269-42, Thermo Fisher), and anti-human CD3E-Pacific Blue (Clone UCHT1, Lot# 4341657, Cat# 558117, BD Biosciences). All antibodies were validated by the manufacturer in human peripheral blood samples, used at a 1:200 dilution, and compared to isotype and no staining control samples.
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Isolation and Staining of Human and Murine Tregs

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Fresh human PBMCs were stained with monoclonal antibodies, such as PercP-Cy5.5-anti-human CD3, APC/Cy7-anti-human CD4, PE-anti-human CD25, and Brilliant Violet 510-anti-human CD127 (all purchased from BioLegend, San Diego, CA, USA), in 0.5% BSA + 2 mM EDTA in PBS. Splenocytes were obtained from the spleens of mice by mechanical disruption and through a 200-gauge steel mesh. Splenocytes were lysed with 1X red blood cells (RBCs) lysis buffer to remove RBCs. First, magnetic microbeads (Miltenyi Biotec) bead-based enrichment of CD4+T cells was performed. Then, cells were stained with monoclonal antibodies, such as PE-anti-mice CD4, APC/Cyanine7-anti-mice CD25, and Alexa-Fluor647-anti-mice CCR6 (all purchased from BioLegend), in 0.5% BSA + 2 mM EDTA in PBS. Human Treg cells and murine Treg cells were sorted using a SH800S cell sorter (SONY, Japan) and analyzed with the SH800 software (SONY, Japan). Human Treg cells were gated as CD3+CD4+CD25+CD127- within the lymphocyte gate, which excluded cell debris, doublets, and dead cells (Supplementary Figure 2). Mice Treg cells were gated as CD4+CD25+ within the lymphocyte gate which excluded cell debris, doublets, and dead cells (Supplementary Figure 2). The purity of the sorted cell population was above 95% for human and 91% for mice, which was verified using post-sorting flow cytometry.
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Multicolor Flow Cytometry for Peptide-Specific CD4+ T-Cell Profiling

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For multicolor flow cytometry–based phenotyping of peptide-specific CD4+ T-cell responses, cells were stimulated with the pool of HLA class II–restricted AML/LSC-associated peptides (10 μg/mL of each peptide) and incubated with 10 μg/mL Brefeldin A and 10 μg/mL GolgiStop for 12-16 hours. Staining was performed using Cytofix/Cytoperm, PE/Cy7 anti-human CD8 (BioLegend, catalog no. 344711, RRID: AB_2044007, clone SK1), APC/Cy7 anti-human CD4 (BioLegend, catalog no. 300518, RRID: AB_314086, clone RPA-T4), Pacific Blue anti-human TNF (BioLegend, catalog no. 502920, RRID: AB_528965, clone MAb11), PE anti-human IFNγ (BioLegend, catalog no. 506507, RRID: AB_315440, clone B27), APC anti-human CD45RO (BioLegend, catalog no. 304210, RRID: AB_314426), PE-Dazzle 594 anti-human IL4 (BioLegend, catalog no. 500832, RRID: AB_2564036), and Brilliant Violet 650 anti-human CD62 L (BioLegend, catalog no. 304831, RRID: AB_2561461) mAbs. Zombie Aqua (BioLegend, catalog no. 423101) was used as viability marker. PMA and ionomycin served as positive control. The peptide ETVITVDTKAAGKGK (FLNA_HUMAN) was used as negative control. Samples were analyzed on a LSR Fortessa cytometer (BD Biosciences).
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Characterizing Peptide-Specific T Cells

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Peptide-specific T cells were characterized by intracellular cytokine and cell surface marker staining. PBMCs were incubated with 10 μg/mL per peptide of EC or negative control peptide, 10 μg/mL Brefeldin A (Sigma-Aldrich), and a 1:500 dilution of GolgiStop (BD Biosciences) for 12 - 14 hours. Staining was performed using Cytofix/Cytoperm solution (BD Biosciences), APC/Cy7 anti-human CD4 (1:100 dilution, BioLegend, Cat# 300518, RRID: AB_314086), PE/Cy7 anti-human CD8 (1:400 dilution, Beckman Coulter, Cat# 737661, RRID: AB_1575980), Pacific Blue anti-human TNF (1:120 dilution, BioLegend, Cat# 502920, RRID: AB_528965), FITC anti-human CD107a (1:100 dilution, BioLegend, Cat# 328606, RRID: AB_1186036), and PE anti-human IFN-γ monoclonal antibodies (1:200 dilution, BioLegend, Cat# 506507, RRID: AB_315440). T cells exposed to phorbol myristate acetate (PMA, 5 μg/mL, Sigma-Aldrich) and ionomycin (1 μM, Sigma-Aldrich) served as positive controls. Viable cells were determined using Aqua live/dead (1:400 dilution, Invitrogen). All samples were analyzed on a FACS Canto II cytometer (BD Biosciences) and evaluated using FlowJo software version 10.0.8 (BD Biosciences). The gating strategy applied for the analyses of flow cytometry-acquired data is provided in fig. S14.
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7

Characterization of SARS-CoV-2 Peptide-Specific T Cells

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Peptide-specific T cells were characterized by intracellular cytokine and cell surface marker staining as previously described (24) . In brief, PBMCs were incubated with SARS-CoV-2 peptide/EC or negative control peptide Brefeldin A (Sigma-Aldrich), and GolgiStop (BD Biosciences). Staining was performed using Cytofix/Cytoperm solution (BD), Aqua live/dead (1:400 dilution; Invitrogen), APC/ Cy7 antihuman CD4 (1:100 dilution; BioLegend, cat. 300518, RRID: AB_314086), PE/Cy7 antihuman CD8 (1:400 dilution; Beckman Coulter, cat. 737661, RRID: AB_1575980), Pacific Blue antihuman TNF (1:120 dilution; BioLegend, cat. 502920, RRID: AB_528965), FITC antihuman CD107a (1:100 dilution; BioLegend, cat. 328606, RRID: AB_1186036), and PE antihuman IFNγ monoclonal antibodies (1:200 dilution; BioLegend, cat. 506507, RRID: AB_315440). PMA and ionomycin (Sigma-Aldrich) served as positive control. All samples were analyzed on a FACS Canto II cytometer (BD).
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