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13 protocols using anti cxcr4

1

Purification and Characterization of B Cells

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Peripheral B cells were purified from the blood of patients and HD by Ficoll density gradient purification followed by positive selection using CD20 magnetic beads (Miltenyi Biotec). Bone marrow and splenic B cells from humanized mice were enriched using anti-human CD19 magnetic beads (Miltenyi Biotec). Purified B cells were then stained with the following antibodies: anti-CD10 (clone: HI10A), anti-CD19 (clone: HIB19), anti-CD21 (clone: B-LY4), anti-CD27 (clone: O323), anti-CD34 (clone: 581), anti-CD45 (clone: HI30), anti-CD69 (clone: FN50), anti-CD86 (clone: IT2.2), anti-CXCR4 (clone: 12G5), anti-IgM (clone: MHM88), anti-IgD (clone: IA6–2), anti-PD-1 (clone: EH12.2H7), anti-RANKL (clone: MIH24) (all from Biolegend), anti-CD3 (clone: OKT3) and 7AAD (eBioscience), and annexin V (AF488 conjugated) (ThermoFisher Scientific). Intracellular staining was performed with anti-p-ATM (clone: 10H11.E12) and anti-γ-H2AX (clone: 2F3) (Biolegend) after staining for surface markers using a fixation-permeabilization solution kit (eBioscience). Flow cytometry was performed using a BD LSRII, and the data were analyzed using Flow Jo software (Treestar).
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2

Transwell-based Chemotaxis Assay

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Using a transwell system (Corning, NY, USA), migration in response to stimuli, SDF-1 (R&D systems, Minneapolis, MN, USA) or supernatants from CS or PS cell cultures was assessed after 3 h. Migration was also assessed in the presence of blocking anti-CXCR4 (Biolegend, San Diego, CA, USA). The transmigration assays using endothelial cells, the upper chamber of the transwell was covered with attachment factor (Gibco, Thermo Scientific, MA, USA) during 1 h/37°. Human umbilical vein endothelial cells were cultured for 1–2 days (with supplemented EGM-2 medium, Lonza, Switzerland) in the previous covered well to promote monolayer formation. The monolayer was subsequently washed with PBS 1× and used for the migration assay. 2 × 106 PBMCs per milliliter were placed in the upper chamber in the presence or absence of SDF-1 as stimuli to assess migration after 4 h. Cells from the upper and lower chambers were counted using a microscope and were analyzed by flow cytometry.
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3

Multiparametric Flow Cytometry Immune Profiling

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Cell suspensions were stained with: anti-CD45 (30-F11); anti-CD45.1 (A20); anti-CD45.2 (104); anti-CD11c (N418); anti-CD11b (Mi/70); anti-CD127 (IL7Rα; A7R34); anti-CD27(LG.7F9); anti-CD8α (53-6.7); anti-CD19 (eBio1D3); anti-CXCR4(L276F12); anti-NK1.1 (PK136); anti-CD3ε (eBio500A2); anti-TER119 (TER-119); anti-Gr1 (RB6-8C5); anti-CD4 (RM4-5); anti-CD25 (PC61); anti-CD117 (c-Kit; 2B8); anti-CD90.2 (Thy1.2; 53-2.1); anti-TCRβ (H57-595); anti-TCRγδ (GL3); anti-B220 (RA3-6B2); anti-KLRG1 (2F1/KLRG1); anti-Ly-6A/E (Sca1; D7); anti-CCR9 (CW-1.2); anti-IL-17 (TC11-18H10.1); anti-rat IgG1k isotype control (RTK2071); anti-streptavidin fluorochrome conjugates from Biolegend; anti-α4β7 (DATK32); anti-Flt3 (A2F10); anti-NKp46 (29A1.4); anti-CD49b (DX5); anti-Ki67 (SolA15); anti-rat IgG2ak isotype control (eBR2a); anti-IL-22 (1H8PWSR); anti-rat IgG1k isotype control (eBRG1); anti-EOMES (Dan11mag); anti-Tbet (eBio4B10); anti-FOPX3 (FJK-16s); anti-GATA3 (TWAJ); anti-CD16/CD32 (93); 7AAD viability dye from eBiosciences; anti-CD196 (CCR6; 140706) from BD Biosciences; anti-RORγt (Q31-378) and anti-mouse IgG2ak isotype control (G155-178) from BD Pharmingen. LIVE/DEAD Fixable Aqua Dead Cell Stain Kit was purchased from Invitrogen.
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4

Flow Cytometry Analysis of DE and CGRP+ Cells

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FACS with anti-c-Kit (Invitrogen; cat. no. CD11705), anti-CXCR4 (BioLegend; clone 12G5, cat. no. 306506), and anti-EpCAM (Invitrogen; clone G8.8, cat. no. 17-5791-80) was used to detect DE cells. Basically, cells were incubated with antibodies for 30 min at 4°C, followed by being washed and suspended in 0.1% BSA/PBS buffer. PE and APC filters were then used to detect cells double positive for Kit and CXCR4 or EpCAM and CXCR4 by signal intensity gating. FACS with anti-CGRP antibody (Abcam; clone 4902, cat. no. ab81887) was used to detect CGRP+ cells. Cells were first incubated with anti-human CGRP antibody for 30 min at room temperature followed with incubation of secondary antibody conjugated with R-PE for 30 min at room temperature. Then cells were washed and suspended in 0.1% BSA/PBS buffer. PE filter was then used to separate cells into CGRP+ and CGRP subgroups by signal intensity gating. Negative controls stained with control IgG instead of primary antibodies were always performed with sample measurements. Flow cytometry machine of BD FACSAria II and software of Flowjo were mainly used to collect and analyze the flow cytometry data.
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5

Comprehensive PBMC Immunophenotyping Protocol

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Human peripheral blood mononuclear cells (PBMCs) were isolated using density-gradient centrifugation as previously described (Ahmad et al., 2017). Flow cytometric analysis was performed to assess Ki-67 production in CD3+, CD4+, CD8+, CXCR4+, CXCR7+, CD45R+, HLA-DR+, GATA3+, Helios+, and FOXP3+ cells. Briefly, PBMCs were stimulated for 4 h with PMA/ionomycin (Sigma-Aldrich, St. Louis, MO, USA) in the presence of GolgiStop ((BD Biosciences, San Jose, CA, USA)) as previously described [10 (link),29 (link)]. PBMCs were washed, and anti-CD3, anti-CD4, anti-CD8, anti-CXCR4, anti-CXCR7, anti-CD45R, and anti-HLA-DR (BioLegend, San Diego, CA, USA) staining was performed. Cells were fixed and permeabilized for staining with anti-Ki-67, anti-GATA3, anti-Helios, and anti-FOXP3 (BioLegend) antibodies. Forward scatter/side scatter and single-cell gating were used to exclude dead cells from all analyses. Data were acquired and analyzed with an FC 500 flow cytometer Beckman Coulter (Indianapolis, IN, USA) using CXP software (Beckman Coulter, USA).
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6

Colonic Leukocyte Phenotyping by Flow Cytometry

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Colonic LP cells were incubated with anti-mouse CD16/CD32 (BioLegend) to block non-specific Fc receptors, followed by a cell surface staining with the corresponding mixture of fluorescently-labelled monoclonal antibodies. Seven-amino actinomycin D (BioLegend) was used to discriminate live and dead cells. The following antibodies conjugated with biotin, PE, peridinin chlorophyll-Cy5.5, PE-Cy7, APC, APC-Cy7, brilliant violet (BV) 421, BV510, BV650, BV711, or BV785 were used for flow cytometry: anti-B220, anti-CD4, anti-IA/IE, anti-Ly6G, anti-Siglec F (all from BD Biosciences), anti-CD3e, anti-CD8a, anti-CD11b, anti-CD11c, anti-CD45, anti-CD45.2, anti-CXCR4, anti-F4/80, anti-TER119 (all from BioLegend), anti-Ly6C, anti-NK-1.1, anti-Siglec F (all from Miltenyi Biotec, Auburn, CA) and anti-CCR2 (R&D Systems). Following extracellular staining, the cells were fixed and permeabilised with Cytofix/Cytoperm (BD Biosciences) and sequentially incubated with rabbit anti-collagen type I (Rockland, Limerick, PA), followed by Alexa Fluor 647-conjugated goat anti-rabbit IgG (Invitrogen). Data were acquired on LSRFortessa and processed using FlowJo software (Tree Star, Ashland, OR) with appropriate isotype controls to determine gating. Cell sorting was performed using FACSAria II (BD Biosciences).
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7

Characterizing Monocyte Subsets by Flow Cytometry

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The expression of chemokine receptors was determined on the surface of fresh monocytes or cultured monocytes53 (link), 54 (link). Cells were incubated for 20 min at room temperature in the dark with anti-CD14, anti-CD163 (BDBioscience) anti-CD16 (Immunotools, Friesoythe, Germany), anti-CCR2 (R&D Systems, Weisbaden, Germany), anti-CCR5 (Clone:HEK/1/85a), anti-CXCR4, anti-CX3CR1, anti-CD206, and anti-HLA-DR (Biolegend, San Diego, CA) monoclonal-antibodies. Red blood cells were then lysed using RBC lysis buffer (1X) (Biolegend). Cells were washed twice with staining buffer (PBS, supplemented with 0.5% BSA; Calbiochem Merck, Darmstadt, Germany) and resuspended in 200 μl of staining buffer to be analyzed by flow cytometry.
The surface expression of different markers was analyzed on gated CD14+ monocytes and on gated monocyte subsets (identified as CD14+ CD16- (classical), CD14+ CD16+ (intermediate) and CD14lowCD16++ (non-classical)) using a MACSQuant® Instrument (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). The percentage of positive cells (% cells) and mean fluorescence intensity (MFI) of each individual marker were calculated using © FlowJo, LLC 2013-2016 data analysis software.
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8

Silencing TSHZ2 with siRNA

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The following 21-nucleotide duplex siRNAs against human TSHZ2 (siTSHZ2-1, siTSHZ2-2), as well as a control (siControl), were synthesized: siTSHZ2-1, 5′-caauuugguaaugaaguaudTdT-3′ and 5′-auacuucauuaccaaauugdTdT-3′; siTSHZ2-2, 5′-guagaagaauuauuaaguudTdT-3′ and 5′-aacuuaauaauucuucuacdTdT-3′; and siControl, 5′-acacauuacaucuauguaadTdT-3′ and 5′-uuacauagauguaaugugudTdT-3′. The following antibodies were used: anti-TSHZ2 antibody (LS Bioscience), anti-GLI1 (Novus), anti-CtBP2 (BD Biosciences), anti-CXCR4 (BioLegend), anti-AEBP1 (LSBio), anti-GAPDH (Santa Cruz Biotechnology), anti-myc tag, anti-HA tag (Cell Signaling), and anti-DYKDDDDK (FLAG) tag (Transgenic, Japan). Immunoprecipitation was performed as previously reported [30 (link)].
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9

Stem Cell Identity and Purity Analysis

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Cells were analyzed by flow cytometry for identity and purity markers using the following antibodies: anti-A2B5 (1:20; Miltenibiotec), anti-GLAST (1:20; Miltenibiotec), anti-CD44 (1:20; BD Pharmingen), anti-CXCR4 (1:20; Biolegend), anti-TRA-1-60 (1:50; Biolegend), anti-EPCAM (1:50; Biolegend), anti-SSEA4 (1:50; Biolegend), anti-GFAP (1:2000; Sigma), Nestin (1:500; BD Pharmingen) and anti-AQP-4 (1:2000; Abcam). The Flow Cytometer FACS Canto II (BD) was operated with FACSDIVA software (BD). At least 10,000 events were collected per sample.
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10

Comprehensive B Cell Immunophenotyping

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Bone marrow, spleen, mesenteric lymph node (mLN) and Peyer’s Patch (PP) cells were isolated as described previously (26 (link)). In brief, cells were stained with anti-B220 (BioLegend), anti-CD11b (BD Biosciences), anti-CD43 (eBioscience), anti-CD24 (BioLegend), anti-BP1 (eBioscience), anti-IgD (BioLegend), anti-IgM (BioLegend), anti-CD93 (eBioscience) and anti-CD23 (BioLegend) for B cell development staining. For B1 and B2 cell development staining, cells were stained with anti-B220 (BioLegend), anti-CD19 (BioLegend), anti-CD43 (eBioscience), anti-CD23 (BioLegend) and anti-CD5 (BioLegend). For FOB and MZB cell staining, cells were stained with anti-B220 (BioLegend), anti-CD19 (BioLegend), anti-CD21 (BD Biosciences) and anti-CD23 (BioLegend).Cells were stained with anti-B220 (BioLegend), anti-Gl7 (BioLegend), anti-CD95 (Fas) (BD Biosciences), anti-CD86 (BioLegend), and anti-CXCR4(BioLegend) for GC B cell staining and cells were stained with anti-B220 (BioLegend), anti-MHC II (eBioscience) and anti-CD86 (BioLegend) for B cell activation staining.
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