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16 protocols using mhc 1

1

Flow Cytometric Immune Profiling

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Murine cells were incubated with a Ghost Dye Red 780 (Tonbo Biosciences) viability marker and anti-mouse CD16/32 (Tonbo Biosciences) in FACS buffer for 30 minutes on ice to block murine Fc receptors. Cells were then stained with the following fluorophore-conjugated anti-mouse monoclonal antibodies: CD45, CD3, CD4, CD8, ICOS [C398.4A], CD11c, CD11b, GR1 [RB6-8C5], F4-80, CD206 [C068C2], B7-1, MHC-I [34-1-2S & 28-8-6], MHC-II [M5/114.15.2], PD-1, Tim3, PD-L1, and B7x [HMH4-5G1] (all from Biolegend); and SPSYVYHQF/H-2Ld Alexa-647 conjugated tetramer [NIH Tetramer Core Facility]. All antibodies were stained for an additional 45 minutes on ice. Human cells were incubated with the Ghost Dye Red 780 viability marker for 30 minutes on ice and immediately stained with the following fluorophore-conjugated anti-human monoclonal antibodies: MHC-I, MHC-II, PD-L1, and B7x [MIH43] (all from Biolegend) on ice for 45 minutes.
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2

Comprehensive Immunophenotyping Protocol

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The following monoclonal antibodies (mAb) were obtained from BioLegend (San Diego, CA, USA): MHC-I (Alexa Fluor 647, clone AF6-88.5), CD40 (PE/Cy5, clone 3/2.3), PD-L1 (PE/Cy7, clone MIH5), IDO (clone mIDO-48) and an ELISA MAX standard set for mouse IFN-γ, IL-12 (p70), IL-10, and TNF-α. From Tonbo Biosciences (San Diego, CA. USA) mAb to CD11c (PE, clone N418); MHC-II (APC, clone APC 114.15.2); CD80 (FITC, clone 16-10A1); CD86 (APC, clone GL-1); CD25 (PE/Cy7, clone PC61.5); CD4 (PE, clone GK1.5). From eBioscience (San Diego, CA, USA): anti-CD25 (Clone 61.5) and anti-CD25 biotin (clone eBio7D4).
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3

Comprehensive Tumor Immunophenotyping by FACS

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FACS analysis was performed using 200-μL tumor or splenocyte single-cell suspensions per antibody panel. Cells were first incubated at 4°C for 30 minutes in PBS with anti-CD16/CD32 Fc block (BD Biosciences) at 1: 100 and live/death staining (Zombie Aqua, BioLegend) at 1: 1,000, or Live/Dead fixable blue dead cell stain (Invitrogen). Next, cells were washed and stained at 4°C for 30 minutes in PBS with antibodies against CD45 (clone 30-F11), B220 (clone RA3–6B2), CD3 (clone 17A2), CD8 (clone 53–6.7), MHC-I (clone AF6–88.5), PD-1 (clone RPM1–30), PD-L1 (clone 10F.9G2), NK1.1 (clone PK136), CD11b (clone M1/70), Ly6G (clone 1A8) and F4/80 (clone BM8), all from BioLegend, at 1 μg/mL. PE-labeled H-2Kb - SIINFEKL pentamer (ProImmune) was used at 2.5 μL per staining. In some sets of experiments, absolute cell numbers were calculated by adding 10 μL counting beads (1 × 106 beads/mL, Spherotech) to each sample before acquisition.
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4

Endothelial Cell Surface Marker Analysis

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After cold storage, ECs were warm-reperfused with/without 1μM NIM811 for 6 or 24 hours. ECs were detached, washed, and resuspended in PBS supplemented with 1% BSA (Fisher Scientific, NH) and 10μg/mL DNAse I (Sigma-Aldrich, MO). ECs were then FcR-blocked at 10μL/mL (eBioscience, CA) and stained with fluorophore-conjugated antibodies against ICAM-1, VCAM-1, PD-L1, MHC-I (BioLegend, CA), E-selectin, CD80 (BD Biosciences, NJ), and CD86 (eBioscience, CA). Mean fluorescence intensity (MFI) was determined by Guava easyCyte 8HT flow cytometer (Merck Millipore, MA). Data were processed with FCS Express 4 (De Novo Software, CA).
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5

Comprehensive Immune Cell Profiling

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Antibodies specific for the mouse cell surface markers CD19, CD3, CD11b, CD11c, F4/80, Gr-1, Ly6C, Ly6G, MHCI, MHCII, CD80, CD86, PD-L1, IL-4Ra, IL-10R, CD45, CD4, CD8, CD69, CD126, CD130, HLA-DR, CD33, CD14, and CD66b were purchased from BioLegend (all antibodies shown in Table S2). For intracellular staining of IL-6, IL-10 and TGF-β, tumor MDSCs were isolated and stimulated with LPS (1 µg/ml; Sigma-Aldrich) for 6 h, and then stained with the cell surface marker antibodies, followed by fixation, permeabilization with Intracellular Fixation & Permeabilization Buffer Set (eBioscience), and intracellular staining with IL-6, IL-10, and TGF-β antibodies (BioLegend). Flow cytometry data were acquired using Beckman Coulter CytoFLEX or BD FACSCanto II flow cytometer and analyzed with FlowJo software (TreeStar).
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6

Interferon-gamma Induced MHC-I Expression

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Usp22-WT and Usp22-KO tumor cells were treated with 100ng/mL of IFNγ (Peprotech) in DMEM with 10% FBS and Glutamax (Thermo 35050061) for 24 hours. Tumor cells were trypsinized from culture plates and re-suspended in PBS with 5% FBS for staining of antibodies. Single-cell suspensions were stained with antibodies on ice for 30 minutes and washed twice with PBS with 5% FBS for flow cytometric analysis. Samples were stained for MHCI (Biolegend 114612) and then analyzed by flow cytometry using BD FACS LSR machine (BD Biosciences) and FlowJo software (Treestar).
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7

Bone Marrow-Derived Dendritic Cell Maturation and Migration

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BMDCs were extracted from the femurs and tibias of 7-week-old C57BL/6 mice and cultured for 8 days. Briefly, bone marrow cells were incubated in RPMI-1640 medium with 10% FBS and recombinant granulocyte-macrophage colony-stimulating factor (GM-CSF, 20 ng/mL, PeproTech). On the 5th day, the medium was replaced with fresh medium with GM-CSF, and after 2 days the BMDCs were harvested for future use.
For the BMDC maturation assay, TC-1 cells (vector, NT-GSDMD) and BMDCs were cocultured in a 6-well plate at a ratio of 1:10 for 24 h, and doxy was added to induce pyroptotic cell death. The positive control BMDCs were cocultured with LPS (100 ng/mL). Next, the cocultured cells were harvested and stained with CD11c, CD86, CD80, MHC-I and MHC-II (Biolegend). Finally, flow cytometry was used to analyze the percentage of mature BMDCs.
For the BMDC migration assay using Transwells, GSDMD-NT-TC-1 cells were untreated or induced to undergo pyroptotic cell death with doxy for 24 h. Then, the supernatant was collected and placed in the bottom chambers of a 24-well Transwell plate and BMDCs were added to the upper chamber. The migration rate of the BMDCs was measured by optical microscopy after incubation for 6 h.
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8

Western Blot Analysis of Macrophage and Exosome Proteins

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Total proteins were isolated from fresh macrophages cells (5.5 × 106) or frozen exosomes (100 μg) were lysed using RIPA peptide lysis buffer (Beyotime Institute of Biotechnology, Haimen, China). Proteins (30 μg) were loaded on 10% SDS-PAGE gels, electrophoresed, and then transferred to PVDF membranes (MilliporeSigma, Burlington, MA, United States). Subsequently, the membranes were incubated with primary antibodies against CD81 (at 1:2,000 dilution, ProteinTech Group, Inc., Chicago, United States), HSP70 (at 1:3,400 dilution, Biolegend, Inc., San Diego, CA, United States), LBP (at 1:2,400 dilution, ProteinTech Group, Inc.), CD36 (at 1:2,000 dilution, Biolegend, Inc.), MHC-I (at 1:3,000 dilution, Biolegend, Inc.) and TSG101 (at 1:2,000 dilution, ProteinTech Group, Inc.) at 4°C overnight. Then, PVDF membranes were washed three times with TBS-T under shaking. Finally, the membranes were incubated with secondary antibody solution (mouse anti-rabbit IgG-HRP at a 1:10,000) for 60 min at room temperature with gentle shaking, and washed with TBS-T under shaking three times again. Protein bands were imaged and analyzed using the Chemiluminescent Substrate System (Thermo Fisher Scientific, Inc., Waltham, MA, United States).
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9

Analyzing T Cell Activation in Tumor Microenvironment

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B16-OVA tumor cells infected with scramble sgRNA or sgRAD21 were stained with MHC-I (BioLegend, catalog 116525) and MHC-I SIINFEKL (eBioscience, catalog 17-5743-82). The B16-OVA or ID8-OVA tumor cells were cocultured with T cells (B3Z or OT-I cells) for 24 hours. The LacZ activity and supernatant levels of IL-2 and IFN-γ were examined as previously described (40 (link)). For intracellular cytokine staining, GolgiStop reagent (1,000×; BD Biosciences) was added to the coculture system for 3 hours before staining. First, OT-I cells were stained with fluorescence-labeled antibodies against CD8 (BioLegend, catalog 100706) for 1 hour at 4°C. Next, the cells were fixed and permeabilized using an intracellular fixation and permeabilization buffer kit (eBioscience) and stained with anti–IFN-γ (eBioscience, catalog 17-7311-82) or anti-GZMB (eBioscience, catalog 12-8898-82). The stained cells were then analyzed using flow cytometry.
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10

IFNγ-Induced MHC-I Expression in PDA Tumor Cells

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Kdm3a-WT and Kdm3a -KO PDA tumor cells were treated with 100ng/mL of IFNγ (Peprotech) in cell culture medium for 24 hours. Tumor cells were then trypsinized from culture plates and re-suspended in PBS with 5% FBS for staining of antibodies. Tumor cells were then stained with MHCI (Biolegend 114612) antibody on ice for 40 minutes and washed twice with cold PBS with 5% FBS for flow cytometric analysis using BD FACS LSR machine (BD Biosciences) and FlowJo software (Treestar).
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