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8 protocols using facs symphony cytometer

1

Cryopreserved PBMC Immunophenotyping

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Peripheral blood mononuclear cells (PBMCs) were separated by Ficoll density gradient (Axis-Shield, Oslo, Norway) and cryopreserved in freezing medium (10% DMSO, 90% fetal calf serum; Lonza, CA, USA) in liquid nitrogen until used. PBMCs were thawed, washed twice with phosphate-buffered saline (PBS, Lonza, CA, USA), and stained at room temperature for 15 min with the following antibodies: BV570-CD3 (clone UCHT1), APC-Cy7-CD4 (clone A161A1), and Alexa Fluor 700-CD8 (clone RPA-T8) (BD Biosciences, San Jose, CA, USA). Viability was determined using live/dead aqua fluorescent reactive dye (Thermo Fisher Scientific, CA, USA). Cells were washed and fixed in 300 μl of 1% paraformaldehyde (Sigma-Aldrich, St. Louis, MO, USA) and acquired immediately in a FACS Symphony cytometer (BD, Biosciences). Fluorescence minus one stained tubes were used as gating controls. Data were analyzed using FlowJo v.10 software (FlowJo LLC, Ashland, OR, USA) (Supplementary Figure S1).
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2

Comprehensive Tumor Immune Cell Profiling

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Tumors were chopped into small pieces that were then transferred into gentleMACS Tubes (MACS Miltenyi Biotec), containing 10 mL of DMEM media and 1 mg/mL collagenase D (Sigma-Aldrich, COLLD-RO Roche, #11088866001). The tubes were placed on a gentleMACS Dissociator (MACS Miltenyi Biotec, #130-095-937) using the program 37_m_TDK2. After incubation, cells were filtered using 70 µm cell strainer and recovered by centrifugation. Cells were stained for live/dead with either LIVE/DEAD Fixable Violet Dead Cell Stain Kit, for 405 nm excitation (Thermo Fisher, cat#L34963) or Zombie NIR (BioLegend, cat#423105) then stained with a cocktail of surface mAbs Panel 1: BV711 anti-CD45 (BioLegend, cat#103147), PE anti-NK1.1 (BioLegend, cat#108707) and PE/Cy7 anti-CD8 (eBioscience, cat# 25-0083), APC anti-CD4 (eBioscience, cat#14-0042-81), BV421 anti-F4/80 (BioLegend, cat#123137) and PE/Dazzle 594 anti-CD183 (CXCR3) (BioLegend, cat#155914); Panel 2: BV711 anti-CD45 (BioLegend, cat#103147), APC anti-IFNg (BioLegend, cat#505810) and PE/Dazzle 594 anti-T-bet (BioLegend, cat#644828), PE/Cy7 anti-CD4 (BioLegend, cat#100422). After 30 min of staining, cells were washed and samples were run on FACS Symphony Cytometer (BD Biosciences). FlowJo V.10 was used for the analysis, cells were manually gated on size and granularity. Dead cells and doublets were excluded, and CD45 + cells were selected.
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3

Cellular Lipid Oxidation Assay

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Briefly, 1.5 × 105 cells were treated as indicated and harvested at the indicated time points. Then, cells were pelleted, washed with PBS, resuspended in BODIPY C11 (2 μM in PBS; Invitrogen), incubated at 37 °C for 15 min in the dark, and 10.000 events were acquired by using a FACS Symphony cytometer (Becton-Dickinson). Data analysis was performed using the Flowing Software.
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4

Comprehensive T-cell Immunophenotyping

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T-cell subsets were analysed for the expression of surface markers, transcription factors and cytokines by staining with various combinations of fluorochrome-conjugated monoclonal antibodies (Supplementary Table 1). For intracellular cytokine detection, T cells were incubated for 4 hours in the presence or absence of phorbol 12-myristate 13- acetate (PMA), ionomycin in complete RPMI (10% FBS, 1 mmol/L sodium pyruvate, 10 mmol/L nonessential amino acids, and 1% penicillin/streptomycin), and with BrefeldinA (Sigma, St Louis, Mo) for an additional 2 hours. After fixation with Intracellular Fixation & Permeabilization Buffer Set (Thermo Fisher Scientific, Waltham, Massachusetts) cells were permeabilized with Permeabilization Buffer (BD Biosciences). Analysis was performed with a FACSSymphony™ cytometer (Becton Dickinson, Franklin Lakes, NJ) and analysed using FlowJo software (BD Biosciences).
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5

Assessment of Anti-PGLALA Binding in PBMCs

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Freshly prepared PBMCs (1 × 105/condition) were incubated with 10 μg of rituximab (Roche), pembrolizumab IgG4 (InvivoGen, 375939001), pembrolizumab‐PGLALA (for comparison reasons, Roche), or isotype controls IgG1 LEAF (BioLegend, 400166), IgG4 LEAF (BioLegend, 403702) or DP47 (Roche) for 30 min on ice, then washed twice with PBS. Anti‐PGLALA binding was assessed by flow cytometry after incubation with a PBS based staining master mix (50 μl/condition) containing CD45‐PerCPCy5.5 (1:100, HI30, BioLegend, 304028), CD3‐APC‐Cy7 (1:100, UCHT1, BD, 300426), CD4‐AF647 (1:100, RPA‐T4, BioLegend, 300520), CD8‐AF488 (1:100, BD, RPA‐T8, 557696), CD19‐BV421 (1:100, HIB19, BioLegend, 302220 and anti‐PGLALA‐PE (Roche, 1:160), for 30 min on ice. Cells were then acquired on a BD FACS‐Symphony cytometer (five lasers: 355, 405, 488, 561, 637 nm). Compensation was performed using VersaComp antibody capture beads (Beckman, B22804). PGLALA‐PE expression was assessed on CD3+ T cells and CD19+ B cells. Refer to Supporting Information for details on anti‐PGLALA‐PE generation.
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6

Comprehensive Immune Cell Profiling

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Cells from each tissue were resuspended in PBE 1x (PBS supplemented with 0.5% BSA + 1 mM EDTA) and incubated for 30 min on ice with fluorescently labeled antibodies: CD45-AF700 (BioLegend Cat. No. 103127), CD4-BUV495 (BD Biosciences Cat. No. 565974), CD8α-BUV805 (BD Biosciences Cat. No. 612898), TCRβ-BUV395 (BD Biosciences Cat. No. 742485), NK1.1-BV785 (BioLegend Cat. No. 108749), CD11b-BV711 (BioLegend Cat. No. 101241), CD11c-BUV496 (BD Biosciences Cat. No. 750483), I-A/I-E-BUV395 (BD Biosciences Cat. No. 743876), Ly6G-BV605 (BioLegend Cat. No. 127639), F4/80-BV785 (BioLegend Cat. No. 123141), IFN-δ-PerCP-Cy5.5 (BD Biosciences Cat. No. 560660), TNF-α-PE-Cy7 (BioLegend Cat. No. 506323), IL-17α-BV421 (BioLegend Cat. No. 506925), B220-BV785 (BioLegend Cat. No. 103245), FAS-PE-Cy7 (BioLegend Cat. No. 152617), CD38- PerCP-Cy5.5 (BioLegend Cat. No. 102721) and CD138-BV650 (BioLegend Cat. No. 142517). WA-1 RBD and Omicron RBD biotinylated were purchased from Sino Biological and conjugated with streptavidin. LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, L-34965, was purchased from Life Technologies. Cells were filtered and washed with PBE 1x again before analysis on BD FACS Symphony cytometer. Analyses were performed using FlowJo v. 10 software.
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7

Immune Checkpoint Inhibitor Binding Assay

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Fresh PBMCs (1x105/condition) were incubated with nivolumab (InvivoGen, 375938995), pembrolizumab (InvivoGen, 375939001) or IgG4 LEAF isotype (BioLegend, 403702) in 96‐well round‐bottom plates (GreinerBioOne) in a total of 100 μl of PBS containing 10 pg/ml to 100 μg/ml. After 30 min at 4°C, cells were washed three times with PBS (150 μl/well), then incubated with RG7769 (10 μg/well in PBS). After 30 min at 4°C, cells were again washed three times with PBS (150 μl/well), then stained with 50 μl of master mix containing CD45‐PerCPCy5.5 (1:100, HI30, BioLegend, 304028), CD4‐V500 (1:100, RPA‐T4, BD Horizon, 560768), CD56‐APC (1:100, HCD56, BioLegend, 318310), CD16‐APC (1:100, 3G8, BD PharMingen, 561248), CD8‐BV421 (1:100, RPA‐T8, BioLegend, 301036) and CD3‐AF488 (1:100, SP34‐2, BD PharMingen, 557705) and anti‐PGLALA‐PE (M.1.7.24, 1:160). Cells were analyzed on a BD FACS‐Symphony cytometer (five lasers: 355, 405, 488, 561, 637 nm). Compensation was performed using VersaComp antibody capture beads (Beckman, B22804).
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8

Immunophenotyping Peripheral B Cells

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For flow cytometry of peripheral B cells, blood was collected in microtubes with EDTA to prevent coagulation and treated with ACK buffer (Lonza) to lyse red-blood cells. For lymph node samples, cell suspensions were obtained by mechanical disassociation with disposable micropestles (Axygen). Spleens were homogenized by filtering through a 70-μm cell strainer and treated with ACK buffer. Bone-marrow cells were extracted by centrifugation of punctured tibiae and femurs at up to 10,000 xG for 10 s, then treated with ACK buffer. Cells from each tissue were resuspended in PBS supplemented with 0.5% BSA and 1 mM EDTA and incubated first with FC-block (rat anti-mouse CD16/32, clone 2.4G2, Bio X Cell) for 30 min on ice and subsequently with various fluorescently-labeled antibodies (see Table S1) for 30 min. Cells were filtered and washed with the same buffer before analysis on a BD FACS Symphony cytometer. Data were analyzed using FlowJo v.10 software.
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