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16 protocols using anti cd3 clone ucht1

1

Immunofluorescence Staining of Antigen-Presenting Cells

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PSC-ATOs were fixed in 4% Formaldehyde (Sigma-Aldrich, St. Louis, MO) for 30 minutes at room temperature followed by
3× 10 min. washes in PBST (0.3% Triton X-100) and a 1 hour block in PBST/BSA (2% BSA). ATOs were stained with anti-GFP
(clone FM264G; Biolegend, San Diego, CA) at a 1:100 dilution and anti-CD3 (clone UCHT1; Biolegend, San Diego, CA) at a 1:50
dilution overnight at 4ºC. Secondary antibodies AlexaFluor-594-conjugated anti-mouse IgG (H+L) (Jackson ImmunoResearch,
West Grove, PA) and AlexaFluor-488-conjugated anti-rat IgG (H+L) (Jackson ImmunoResearch West Grove, PA) were added at a 1:200
dilution for 2 hours at room temperature. Each ATO was mounted individually in Vectashield Antifade Mounting Medium (Vector
Laboratories, England) on a concavity microscope slide (ThermoFisher Scientific, Grand Island, NY). Immunofluorescence images
were acquired on a Zeiss LSM 880 confocal microscope equipped with Airyscan and Zen software (Zeiss, Jena, Germany).
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2

Histological and Immunofluorescent Analysis of Organoids

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For hematoxylin and eosin (H&E) images, ATOs were embedded in Histogel (ThermoFisher Scientific, Grand Island, NY) and fixed overnight in 10% neutral-buffered formalin (ThermoFisher Scientific, Grand Island, NY). 5 μm sections and H&E staining were performed by the UCLA Translational Pathology Core Laboratory (TPCL). For immunofluorescence imaging, ATOs were isolated by cutting the culture insert around each ATO with a scalpel, followed by embedding the membrane and ATO in Tissue-Tek OCT (VWR Radnor, PA) and freezing on dry ice. 5 μm frozen sections were fixed in 10% neutral-buffered formalin and stained with anti-CD3 (clone UCHT1; Biolegend, San Diego, CA) at a 1:50 dilution overnight at 4°C followed by incubation with AlexaFluor 594-conjugated anti-mouse IgG (H+L) (Jackson ImmunoResearch, West Grove, PA) at room temperature. H&E and immunofluorescence images were acquired on a Zeiss AzioImager M2 with AxioCam MRM and AxioVision software (Zeiss, Jena, Germany).
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3

Activation and Metabolic Regulation of Naive T Cells

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Naïve CD4+ T cells were isolated from fresh human blood samples with a negative selection isolation kit from Miltenyi Biotec as per protocol. The purity of naïve CD4+ T cells was evaluated with staining of anti-CD3 (Clone UCHT1, BioLegend, San Diego, USA), anti-CD4 (clone RPA-T4, BioLegend, San Diego, USA), and anti-CD45RA (HI100, BioLegend, San Diego, USA). Isolated cell purities were over 95% (Supplementary Figure S1). Cells were cultured in RPMI 1640 media (GE Health Care Life Sciences, Marlborough, USA) supplemented with 10% FBS (Life Technologies, Carlsbad, USA). Cells were stimulated overnight with anti-CD3 (10 μg/mL, pre-coated on plate, Clone UCHT1, BD Biosciences, San Jose, USA) and anti-CD28 (2.5 μg/mL, Clone CD28.2, BD Biosciences, San Jose, USA), with and without glycolysis inhibitor 2-deoxy-d-glucose (2-DG, 2 mg/mL, Acros Organics, New Jersey, USA), mTOR inhibitor rapamycin (100 Nm, Alfa Aesar, Ward Hill, USA) or H2O2 (50 μM, Sigma-Aldrich, St. Louis, USA). The next day the antibodies were removed and fresh media (RPMI and 10% FBS) were added with and without 2-DG, rapamycin, or H2O2. The cells were cultured for a total of 3 days before harvesting.
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4

Comprehensive Immunophenotyping of iNKT Cells

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Data were acquired with a BD LSR II Flow Cytometer (BD Biosciences) and
analyzed with FCS Express V3 (De Novo Software, Los Angeles, CA). Doublets were
excluded with FSC-A and FSC-H linearity. Human antibodies were as follows:
anti-TCR Vα24-Jα18 (referred to as iNKT; clone 6B11), anti-CD3
(clone UCHT1), anti-CD4 (clone RPA-T4), anti-CD8 (clone RPA-T8), anti-CD34
(clone 561), anti-CD38 (clone HIT2, Biolegend) and anti-TCR
γ/δ(clone B1) from Biolegend, anti-TCR Vβ11 (Beckman
Coulter), anti-iNKT (BD Biosciences), CD1d tetramers loaded with PBS57, an
analog of α-GalCer (National Institutes of Health Tetramer Core
Facility, Atlanta, GA).
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5

Flow Cytometric Quantification of ABC Transporters

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On some occasions, DCV/ABC drug transporter costainings were performed [13 (link), 19 (link)]. To this end, DCV-prestained cells were washed in >10x volume ice-cold PBS and stained for 30 min at 4°C with APC-conjugated monoclonal antibodies directed against ABCG2 (clone 5D3) (BioLegend, Catalog number 332020) or ABCB1 (clone UIC2) (eBioscience, Catalog number 17-2439-42). Thereafter, excessive antibody was washed away in >10x volume ice-cold PBS, and the cells were stained with 7-AAD as described above. Antibodies were added at optimized concentrations and staining specificity was controlled using an irrelevant antibody (anti-CD3, clone UCHT1) (BioLegend, Catalog number 300412).
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6

Multispectral Imaging of T-Cell Subsets

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The Amnis ImageStream X Mark II multispectral imaging system was used. 1×106 unmanipulated CB-CD8+ cells and eTCR−/− CD8+ T cells were washed and stained with antibodies against CD3 (clone OKT3, ref. 317306, Biolegend), CD8-PE (clone RPA-T8, ref. 301008, Biolegend), and TCR-pan-αβ (clone IP6, ref. 17-9986-42, eBioscience) to detect membrane expression. Subsequently, cells were fixed, permeabilized, and stained with anti-CD3 (clone UCHT1, ref. 300420, Biolegend) to determine cytoplasmatic expression of the coreceptor.
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7

Vγ9Vδ2 T cell proliferation assay

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Vγ9Vδ2 T cells were labeled with 2 μM CTV (Life Technologies, Grand Island, NY) and treated with IL-12, IL-18, or both for 16 h. After extensive washing, Vγ9Vδ2 T cells were further cultured with medium alone or with medium supplemented with IL-2, IL-7 (BioLegend), or IL-15 for an additional 3 days. CD3+Vδ2 TCR+ cells were gated, and CTV-diluted cells were counted as dividing cells. In some experiments, labeled Vγ9Vδ2 T cells were stimulated with plate bound anti-CD3 (clone UCHT1) and soluble anti-CD28 (clone CD28.2) (both from BioLegend) and used for positive control.
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8

Quantification of HIV-infected BLT Mouse Immune Response

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At the end of week 16 –end of the four treatments–the percentage of human CD3+ and CD45+ cells in blood of HIV-infected BLT mice was quantified and isolated by FACS. CD45+ cells were isolated by EasySep Human CD45+ Cell Enrichment Kit (STEMCELL Technologies). Isolated human CD45+ cells (100,000) (Clone HI100, BioLegend) were stimulated ex vivo for 24 h with anti-CD3 (clone UCHT1, BioLegend) (200 ng/mL) and anti-CD28 (Clone CD28.2, BioLegend) (500 ng/mL) antibodies and the percentage of IFNγ+ CD8+ cells from gated total CD8+ cells (Clone RPA-T8, BioLegend) was quantified by FACS. Intracellular IFNγ staining (Clone 4S.B3, BioLegend) was performed according to the manufacturer’s instructions using Cytofix/Cytoperm Kit (BD Biosciences), which saponin-permeabilized and fix cells prior to staining.
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9

Histological and Immunofluorescent Analysis of Organoids

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For hematoxylin and eosin (H&E) images, ATOs were embedded in Histogel (ThermoFisher Scientific, Grand Island, NY) and fixed overnight in 10% neutral-buffered formalin (ThermoFisher Scientific, Grand Island, NY). 5 μm sections and H&E staining were performed by the UCLA Translational Pathology Core Laboratory (TPCL). For immunofluorescence imaging, ATOs were isolated by cutting the culture insert around each ATO with a scalpel, followed by embedding the membrane and ATO in Tissue-Tek OCT (VWR Radnor, PA) and freezing on dry ice. 5 μm frozen sections were fixed in 10% neutral-buffered formalin and stained with anti-CD3 (clone UCHT1; Biolegend, San Diego, CA) at a 1:50 dilution overnight at 4°C followed by incubation with AlexaFluor 594-conjugated anti-mouse IgG (H+L) (Jackson ImmunoResearch, West Grove, PA) at room temperature. H&E and immunofluorescence images were acquired on a Zeiss AzioImager M2 with AxioCam MRM and AxioVision software (Zeiss, Jena, Germany).
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10

Multiparameter Flow Cytometry of Murine and Human Immune Cells

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Anti-CD3 (clone 17A2, catalog # 100227), anti-CD138 (clone 281-2, catalog # 142523), anti-CD317 (clone 927, catalog # 127023), anti-I-Ab (clone M5/114.15.2, catalog # 107631), anti-IgD (clone 11-26c.2a, catalog # 405725), anti-CD4 (clone RM4-5, catalog # 100539), anti-CD5 (clone 53-7.3, catalog # 100623), anti-CD8a (clone 53-6.7, catalog # 100733), anti-CD93 (clone AA4.1, catalog # 136511), anti-IgM (clone RMM-1, catalog # 406511), anti-B220 (clone RA3-6B2, catalog # 103235), anti-F4/80 (clone BM8, catalog # 123127), anti-CD1d (clone 1B1, catalog # 123521), anti-CD11b (clone M1/70, catalog # 101211), anti-CD11c (clone N418, catalog # 117309), anti-CD19 (clone 6D5, catalog # 115512), anti-Siglec H (clone 551, catalog # 129611), anti-Blimp-1 (clone 5E7, catalog # 150003) and anti-Bcl6 (clone 7D1, catalog # 358507) Abs were purchased from BioLegend and used for flow cytometric analyses of murine cells.
Anti-CD24 (clone ML5, catalog # 311105), anti-CD19 (clone HIB19, catalog # 302229), anti-CD27 (clone M-T271, catalog # 356411), anti-CD38 (clone HB-7, catalog # 356605), anti-CD20 (clone 2H7, catalog # 302357), anti-CD3 (clone UCHT1, catalog # 300433), and anti-IgD (clone IA6-2, catalog # 348220) Abs were purchased from BioLegend and used for flow cytometric analyses of human cells.
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