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4 protocols using clone l200

1

Multiparametric Flow Cytometry for SARS-CoV-2-Specific T-Cell Detection

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Detection of AIM was performed as described previously (8 (link)). Briefly, cells were stained with the following antibodies in their respective dilutions: anti–CD3-PerCP (1:25, clone SK7, BD), anti–CD4-V50 (1:50, clone L200; BD), anti–CD8–fluorescein isothiocyanate (1:25, clone DK25; Dako), anti–CD45RA-phycoerythrin (PE)–Cy7 (1:50, clone L48; BD), anti–CCR7-BV711, anti–CD69-allophycocyanin (APC)-H7 (1:50, clone FN50; BD), anti–CD137-PE (1:50, clone 4B4-1; Miltenyi), and anti–OX40-BV605 (1:25, clone L106; BD). LIVE/DEAD Fixable Aqua Dead Cell staining was included (1:100, AmCyan; Invitrogen) and acquired on a FACSLyric (BD Biosciences). After setting a time gate, LIVE CD3+ T-cells were gated, singlets were selected, and T-cells were subtyped into CD3+CD4+ and CD3+CD8+ cells. Within the CD4+ and CD8+ T-cells, Tnaive were defined as CD45RA+CCR7+, TCM as CD45RA-CCR7+, TEM as CD45RA-CCR7-, and TEMRA as CD45RA+CCR7-. S-specific T-cells were detected by co-expression of AIM on CD4+ (OX40 and CD137) or CD8+ (CD69 and CD137) T-cells in the combination of memory subsets (Fig. 3A). The DMSO-stimulated sample was used to set the cutoff gate for activation markers. On average, 500,000 cells were acquired per sample.
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2

Identifying SARS-CoV-2-specific T cells

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After ex vivo stimulation of PBMCs, cells were stained at 4°C for 15 min for phenotypical lymphocyte markers and AIM expression. Surface staining was performed with the following antibodies in their respective dilutions: anti–CD3-PerCP (1:25, clone SK7, BD), anti–CD4-V50 (1:50, clone L200; BD), anti–CD8–fluorescein isothiocyanate (1:25, clone DK25; Dako), anti–CD45RA-phycoerythrin (PE)–Cy7 (1:50, clone L48; BD), anti–CCR7-BV711, anti–CD69-allophycocyanin (APC)-H7 (1:50, clone FN50; BD), anti–CD137-PE (1:50, clone 4B4-1; Miltenyi), and anti–OX40-BV605 (1:25, clone L106; BD). LIVE/DEAD Fixable Aqua Dead Cell staining was included (1:100, AmCyan; Invitrogen). Cells were first gated for LIVE CD3+ T cells and then subdivided into CD3+CD4+ T helper cells and CD3+CD8+ T-cytotoxic cells (Fig. 4A). SARS-CoV-2–specific T cells were identified by gating the CD69+CD137+ cells (within CD4+ or CD8+ subsets). For N = 11 of 20 donors assessed, SARS-CoV-2 specificity in the CD4+ subset was confirmed by gating CD137+OX40+ cells. The DMSO-stimulated sample was used to set the cutoff gate for activation markers. On average, 500,000 cells were acquired per sample. Low-frequency samples (<10,000 cells in CD4 gate and <5000 cells in CD8 gate) were excluded from analysis.
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T cell phenotyping and analysis

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T cells were phenotyped with antibodies against surface markers CD4 (BD PharMingen, San Jose, CA, Clone L200), CD8 (BD PharMingen, Clone RPA-T8), CD195 (BD PharMingen, Clone 3A9), CD62L (BD Biosciences, Clone SK11), and CD45RA (BD Biosciences, Clone UCHL-1) according to manufacturers’ recommendations. Live/dead discrimination was performed using propidium iodide staining. Stained cells were processed on a FACSCanto II (BD Biosciences) and analyzed using FlowJo software (Tree Star, Ashland, OR).
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4

PBMC T cell allele presentation

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PBMC T cell cultures expanded with the dominant epitope for RV1196 or Rv0125 were tested for specific allele presentation, using RM3 cells transfected with MHC II alleles at a 1:1 or 2:1 ratio (i.e., T cell:transfected RM3 cell) (Fig. S1). Transfected RM3 cells were prepared for T cell testing via the addition of 1 μg/mL peptide to individual wells of a 96-well plate and were incubated for 90 min at 37°C and 5% CO2. Following the incubation, the prepared T cells were added to each well of a 96-well plate and incubated for another 12 h in the presence of a Golgi plug inhibitor, namely, BFA (BD Biosciences, catalog number 555029). Stimulation plates were spun down and washed with 1× PBS, following 12 h of incubation. Flow cytometry staining was performed for viability (Live/Dead Fixable Blue Dead Cell Stain Kit, Thermo Fisher, catalog number L34962) and surface marker expression for CD3 (BD, clone SP34-2), CD4 (BD, clone L200), CD8 (BD, clone RPA-T8), HLA DR/DP/DQ (Bio-Rad clone Bu26; Beckman clone I3; BioLegend, clone Tü39), and the intracellular cytokines IFN-γ (BD, clone B27) and TNF (BD, clone Mab11), using standard flow cytometry and intracellular staining protocols. The samples were run on a BD LSRII or a Cytek Aurora (Cytek, Bethesda, MD, USA) and were analyzed using the FlowJo software package (BD, version 10).
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