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8 protocols using anti cd8 clone rpa t8

1

Monitoring Donor Chimerism via Multimodal Analysis

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Donor chimerism was monitored by molecular chimerism analysis-based divergent microsatellite markers as previously described30 (link),31 (link), as well as by flow cytometry using a discriminatory anti-Mamu A01 antibody34 (link). Flow cytometric analysis was performed with FlowJo (Tree Star) using the following analysis pipeline: (1) Doublets were excluded on the basis of FSC-H vs. FSC-A and SSC-H vs. SSC-A gating, (2) Neutrophils cells were identified as high SSC, CD11b + CD3- cells, (3) T cells as CD3 + CD20- CD11b- cells present in the lymphocyte gate (then sub-gated for CD4 or CD8 positivity), and (4) B cells as CD3- CD20 + lymphocytes. The following antibody clones were used for this analysis: anti-Mamu A01 clone P1234 (link) (Anti-Mamu A01-PE, NHP Reagent Resources,1:50 dilution), anti-CD11b clones ICRF44 and D12 (BD Biosciences, catalog numbers 557918 and 340936, 1:100 dilution), anti-CD3 clone SP34–2 (BD Biosciences, catalog number 557757, 1:50 dilution), anti-CD4 clone OK-T4 (Biolegend, catalog number 317442, 1:100), anti-CD8 clone RPA-T8 (BD Biosciences, catalog number 563795, 1:50 dilution), anti-CD20 clone 2H7 (ThermoFisher, catalog number 45-0209-42, 1:50 dilution).
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2

Multiparametric Flow Cytometry Immunophenotyping

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After thawing, PBMC were washed and immediately stained with the following panel: anti-CD3 (clone UCHT1; #IM2467, Beckman Coulter, Brea, CA, USA), anti-CD4 (clone SFCI12T4D11; #737660, Beckman Coulter), anti-CD8 (clone RPA-T8; #558207, BD Biosciences, Franklin Lakes, NJ, USA), anti-CD14 (cloneMφP9; #641394, BD Biosciences), anti-CD16 (clone3G8; #555406, BD Biosciences), anti-CD56 (clone N901; #A07788, Beckman Coulter), anti-CD11c (clone B-ly6; #561352, BD Biosciences), anti-CD19 (clone SJ25C1; #563036, BD Biosciences), anti-CD123 (clone 6H6; #45-1239-42, eBioscience, Affymetrix, Santa Clara, CA, USA), anti-HLA-DR (clone Immu-357; #IM3636, Beckman Coulter), and Zombie UV (#77474, Biolegend, San Diego, CA, USA). The samples were acquired on an BD Fortessa instrument equipped with the FACS Diva software. The analysis was performed with the FlowJo (FLOWJO, LLC, Ashland, OR, USA).
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3

Multiparametric Flow Cytometry for Immune Profiling

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Single cell suspensions isolated from PB, SN and tumour were stained for surface and intracellular markers for flow cytometry analysis. Briefly, cells were stained with fixable live/dead dye (Life Technologies), followed by surface marker staining using anti‐CD8 (clone RPA‐T8; BD Biosciences), anti‐CD56 (clone B159; BD Biosciences), anti‐CD103 (clone Ber‐ACT8; BioLegend), anti‐CCR7 (clone 150503; BD Biosciences), anti‐CD45RA (clone HI100; BD Biosciences) and anti‐PD‐1 (clone EH12.2H7; BioLegend) antibodies. The cells were then fixated and permeabilized using the forkhead box P3 (FOXP3) transcription factor kit (eBioscience, San Diego, CA, USA). Next, the cells were stained for intracellular marker using: anti‐perforin (clone δG9; BD Biosciences), anti‐granzyme B (clone GB11; BD Biosciences), anti‐T‐bet (clone 4B10; BioLegend) and anti‐Ki‐67 (clone 20Raj1; eBioscience) antibodies. Isotype control was used to ascertain the correct gating for the following markers: perforin, granzyme B, T‐bet, Ki‐67 and PD‐1. Flow cytometry data were acquired using an LSR Fortessa instrument (BD Biosciences) and analysed with FlowJo version 10 (TreeStar, Inc., Ashland, OR, USA).
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4

Immune Checkpoint Blockade Assay Protocol

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NECA, adenosine and LPS were purchased from Sigma-Aldrich. Oxaliplatin, CPI-444, AZD4635 and AB928 were purchased from MedChemExpress, DZD2269 was designed and synthesized by Dizal Pharmaceuticals. All the compounds were dissolved in DMSO to prepare a 10 mM stock solution and stored in a nitrogen cabinet before use. Anti-PD-1 (BE0146) and Isotype control antibodies were purchased from Bioxcell. Anti-mouse CD45 PE (clone 30-F11), anti-mouse CD4 PerCP (clone RM4-5), anti-mouse CD8a FITC (clone 53 − 6.7), anti-CD45 FITC (clone HI30), anti-human CD8 PE (clone RPA-T8), anti-human CD4 FITC (clone PRA-T4), anti-CD14 PE (clone M5E2), anti-HLA-DR APC-H7 (clone G155-178), anti-CD83 APC (clone HB15e), anti-CD4 (clone, RPA-T4) and anti-CD8 (clone RPA-T8) were purchased from BD Bioscience. Anti-pCREBSer133 Alexa Fluor 647 (clone 87G3) and anti-mouse CD8 (clone D4W2Z) were purchased from Cell Signaling Technology. Anti-human CD3 antibody (clone OKT3) and anti-human CD28 antibody (clone CD28.2) were purchased from eBioscience. Anti-mouse CD3 antibody (clone 145-2C11) and anti-mouse CD28 antibody (clone E18) were purchased from BioLegend. Anti-mouse CD4 (EPR19514) was purchased from Abcam.
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5

Isolation and Purification of Naive CD8+ T Cells

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Human PBMCs were isolated from the whole blood of healthy donors with Ficoll-Hypaque Solution (Hao Yang, China); human CD8+ T lymphocytes were then purified with human CD8+ T-cell isolation kit according to the manufacturer’s instructions (BD IMag). Cells were then labeled with anti-CD8 (clone RPA-T8; BD Pharmingen, San Diego, CA), anti-CD45RO (clone UCHL1; BD Pharmingen), and anti-CD62L (clone DREG56; eBioscience, San Diego, CA) fluorescent antibodies and Fluorescence-activated cell sorting (FACS)-purified into naive CD8+ T cells on a FACSAria cell sorter (Becton, Dickinson and Company, Franklin Lakes, NJ). Postsorting analysis of purified subsets revealed >98% purity.
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6

BTLA Regulation in T Cell Activation

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Murine OT-1 BTLA KO cells overexpressing BTLA WT or mutants constructs were re-stimulated with either 10 ng/ml anti-mouse CD3 (Clone 145-2C11, BD Pharmingen™) alone or with recombinant mouse HVEM Fc (R&D systems) plate-bound for 8 h prior to harvest with the cell lysis buffer (kindly provided by RPPA core facility at The University of Texas M.D. Anderson Cancer Center). The cell lysates were centrifuged at 14,000 rpm for 10 minutes at 4°C. The protein supernatant was quantified using protein assay kit (Thermo scientific). RPPA was processed and normalized as previously described (20 (link)). Differential fold expression of protein was analyzed using Linear models and empirical Bayes methods(21 (link)). Volcano plots were generated using R system. For human TIL, four TIL lines were stained with anti-CD8 (clone RPA-T8, BD Pharmingen™), anti-BTLA (clone J168, BD Pharmingen™), and Sytox blue (Molecular Probe™) under aseptic condition. The cells were sorted based on expression of CD8+BTLA+ using FACSAria (BD Biosciences). On the next day, sorted TIL were re-stimulated with anti-human CD3 (clone OKT-3, eBioscience) with or without recombinant human HVEM-Fc (R&D systems) plate-bound for 8 h prior to harvest with the cell lysis buffer. The protein samples were processed, normalized, and analyzed as similar to the mouse experiment described above.
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7

Peripheral Blood Immune Cell Phenotyping

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Peripheral blood monocytes (PBMC) were isolated from peripheral blood by Ficoll-Hypaque (GE Healthcare, Uppsala, Sweden) density centrifugation. The phenotypes of immune cells in the peripheral blood were identified by flow cytometry after stained with fluorescence-conjugated monoclonal antibodies. The surface monoclonal antibodies included anti-CD4 (RPA-T4 clone; PharMingen, San Diego, CA), anti-CD8 (RPA-T8 clone; PharMingen), anti-CD33 and anti-HLA-DR. The intracellular foxp3 was stained by fluorescence-conjugated rat anti-human foxp3 (eBioscience,San Diego, CA). The expression of these molecules was analyzed by cytofluorography employing a Beckman Coulter NAVIOS flow cytometer (Beckman Coulter Co., Indianapolis, IN). Regulatory T-cells were identified as positive for CD4 and foxp3. MDSC was identified as positive for CD33 and negative for HLA-DR.
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8

Sorafenib-Induced Changes in Immune Cells

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Ten milliliters of peripheral blood was drawn prior to sorafenib treatment and 1 month after sorafenib administration. Peripheral blood monocytes (PBMC) were isolated by Ficoll‐Hypaque (GE Healthcare, Uppsala, Sweden) density centrifugation. The phenotypic analysis of immune cells was performed by flow cytometry after the cells were stained with fluorescence‐conjugated monoclonal antibodies. The surface monoclonal antibodies included anti‐CD4 (RPA‐T4 clone; PharMingen, San Diego, California) anti‐CD8 (RPA‐T8 clone; PharMingen), anti‐CD33 (WM 53 clone, PharMingen), anti‐HLA‐DR (TU36 clone, PharMingen), anti‐CD40 (5C3 clone, PharMingen) and anti‐CD86 (FUN‐1 clone, PharMingen). The intracellular Foxp3 was stained by fluorescence‐conjugated rat anti‐human foxp3 (eBioscience, San Diego, California). The expression of these molecules was analyzed by cytofluorography employing a Beckman Coulter NAVIOS flow cytometer (Beckman Coulter Co., Indianapolis, Indiana). Regulatory T‐cells were identified as positive for CD4 and foxp3. MDSC was identified as positive for CD33 and negative for HLA‐DR.
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