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4 protocols using fixable viability dye efluor 450

1

Immune Phenotyping of PBMC Samples

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Cryopreserved peripheral blood mononuclear cell (PBMC) samples from baseline and post-treatment (cycles 1–12) were thawed and rested overnight at 37°C. Then cells were stained with a viability dye (eBioscience Fixable Viability Dye eFluor 450) and a master mix of antibodies for surface stains including CD4-BV605 (BioLegend Cat# 317438, RRID:AB_11218995), CD3-PE-Cyanine5.5 (Invitrogen Cat# 35-0036-42, RRID: AB_11220085), CD8a-PE-Cyanine7 (Invitrogen Cat# 25-0088-42, RRID: AB_1659702), PD1-APC (BioLegend Cat# 329908, RRID: AB_940475), CD152-PE-Cy5 (BD Biosciences Cat# 555854, RRID:AB_396177). Cells were next fixed and permeabilized with the eBioscience Foxp3/Transcription Factor Staining Buffer Set (ThermoFisher) and subsequently stained intracellularly with Alexa Fluor 700 antihuman Ki67 antibody (BioLegend Cat# 350530, RRID: AB_2564040). Stained cells were acquired on a BD Canto RUO and analyzed with FlowJo software (FlowJo, RRID:SCR_008520).
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2

Comprehensive Immune Cell Profiling

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A panel of monoclonal antibodies was developed to enable phenotypic characterization of B and T lymphocyte subpopulations: CD3-FITC, CD4-APC, CD25-BV421, FoxP3-PE, CD19-PeCy7, CD9-BB700 (BD Bioscience, France), CD24-BV510, and CD38-APC-Cy7 (Sony Biotechnology, UK); hematopoietic stem and progenitor cells: CD34-BV421 (Biolegend, France), cKit-APC-H7, CD135-PE, lineage-FITC, Sca-1-BV510, CD16/32-PerCPCy5.5, CD127-APC (BD Bioscience), and TLR-4-PeCy7 (Biolegend); and dendritic cells: CD11c-PeCy7 (eBioscience, France), CMH-II-FITC, Siglec-H-BV510, CD11b-APC-H7, and CD103-PerCP5. For intracellular staining, cells were fixed and permeabilized using a Cytofix/Cytoperm kit (BD Biosciences). For in vitro human B cell differentiation experiments, cells were stained with Fixable Viability Dye eFluor 450 to identify dead cells, followed by staining with CD25-BV605 (Biolegend), CD19-BUV395, CD9-FITC, CD27-BUV737, CD38-BV711 and intracellular IL-10-PE (BD Bioscience). Cells were analyzed on a Canto II flow cytometer (BD Biosciences). Data were acquired using Diva 8.0 software and analyzed with FlowJo X (TreeStar, Williamson Way, Ashland, USA). Fluorescence minus one staining controls were used for all panels, and dead cells were removed using viability staining.
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3

Splenocyte Immunophenotyping and Flow Cytometry

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Single-cell suspensions of splenocytes were prepared as described (34 (link)). The removed tumors were dissected with a gentleMACS dissociator (Miltenyi, Bergisch Gladbach, Germany) and then treated with collagenase I and DNase (Roche, Basel, Switzerland) for 45 min at 37°c. The cells were filtered and stained with antibodies. The following antibodies were used in this study: anti-mouse CD11c, anti-mouse/human CD11b, anti-mouse Ly6G, anti-mouse F4/80, anti-mouse CD69, anti-mouse CD8a, anti-mouse CD4 anti-mouse Ly6C, anti-mouse I-A/I-E, anti-mouse CD25, anti-mouse CD40, Fixable Viability Dye eFluor® 450 (BioLegend, CA, USA). Cell apoptosis, CFSE, H2DCFDA, and MitoTracker Green staining were measured under the manufacturer protocols (Life Technologies, USA). BD FACS Canto flow cytometer (BD, NJ, USA) and FlowJo software were used for flow cytometry analysis (TreeStar, OR, USA). Antibodies used in this set of experiments are listed in Supplementary Table 1.
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4

Single-Cell Analysis of TNBC Biopsies

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Freshly isolated TNBC biopsies were digested with collagenase IV (40 mg/mL, Gibco, #17104-019) and filtered through a 100 μm stainless strainer to obtain single-cell suspensions. The cells were resuspended in PBS containing 0.5% BSA and 2 mM EDTA. The prepared single-cell suspensions were blocked with an Fcγ receptor blocker and then incubated with fluorescence-labelled antibodies on ice for 15 min for surface staining. After washing twice with PBS, the cells were fixed and permeabilised with a Cytofix/Cytoperm Kit (BD, #554717) and then incubated with fluorescence-labelled antibodies for intracellular staining. After washing twice with PBS containing 0.5% BSA, the cells were resuspended in PBS containing 0.5% BSA and 2 mM EDTA. A flow cytometer (Thermo Fisher Attune NxT) was used to measure the events. The antibodies used in this study included PE anti-CD31 (Biolegend, #303106), Fixable Viability Dye–eFluor 450 (Biolegend, #65-0863-14), 7-AAD (Invitrogen, #A1310), APC anti-human CD298/ATP1B3 (Biolegend, #341706), FITC anti-HSPA1B (Cusabio, #CSB-PA28047C0Rb), Alexa Fluor anti-KRT7 (Novus, #NBP2-47944 AF700), APC anti-CD93 (Biolegend, #336120), and FITC anti-CDH5 (LSBio, #LS-C467144-100).
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