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7 protocols using ab828

1

Quantifying T-Cell Populations in Tumor Samples

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Part of the selected n = 188 tumor samples could not be analyzed due to insufficient tumor material to obtain at least one microscopic image (n = 26). Triple immunofluorescent staining for CD3 (ab828, Abcam, Cambride, UK), FoxP3 (ab20034, Abcam) and IL-17 (AF-317-NA, R&D Systems, Abingdon, UK) was performed on 162 tumor samples as described before [29 (link)]. These comprised 86 p16 positive and 76 p16 negative tumors. Images were obtained using an LSM700 confocal laser scanning microscope containing an LCI Plan-Neofluar 25×/0.8 Imm Korr DIC M27 objective (Zeiss, Göttingen, Germany). One to four random images sampled a total vital tumor (epithelium + stroma) area of up to 1.0 mm2. Total tumor epithelium and stroma surface area and double or triple positivity of cells were determined in each image using LSM Image Browser (version 4.2.0.121, Zeiss). Single-, double- and triple-positive cells were scored separately in the tumor epithelial and stromal areas using ImageJ version 1.47 (http://rsb.info.nih.gov/ij). Cells within blood vessels and largely autofluorescent areas were not scored.
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2

Immunohistochemical Analysis of BAP1, T Cells, and Macrophages

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4-µm serial sections from paraffin-embedded tissue were cut and used for immunostaining. Immunohistochemistry (IHC) of BAP1 was performed on 74 tumors, as described previously [24 (link)]. Tumors were scored by two independent investigators as BAP1-positive or -negative based on nuclear staining. Immunofluorescence (IF) staining for T cells and macrophages was performed on 43 tumors as described previously [29 (link), 30 (link)]. T cell types were detected by primary antibodies: anti-CD3 (ab828, rabbit polyclonal; Abcam, Cambridge, MA, United States of America) and anti-CD8 (4B11, mouse monoclonal IgG2b; Novocastra, Valkenswaard, The Netherlands). To visualize the T cells, the following secondary antibodies were used: goat-anti-rabbit IgG Alexa 546 and goat-anti-mouse IgG2b Alexa 647 (Molecular Probes, Invitrogen, Breda, The Netherlands). Counts of intratumoral CD3+ and CD8+ T cells were represented as the number of cells per square millimeter. For IF staining of CD68+ macrophages, we used the primary mouse anti-human macrophage CD68 antibody (clone 514H12; ab49777; Abcam, Cambridge, United Kingdom), and as secondary antibody AlexaFluor IgG2a (488) goat-anti-mouse. The amount of CD68+ expression was determined in pixels per square millimeter.
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3

Immunohistochemical and Immunofluorescence Analyses

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Immunohistochemical staining for HLA class I (HLA-A, -B) and II (HLA-DR) was previously performed as described [4 (link)]. In short, immunohistochemical staining was carried out using the mouse monoclonal antibodies HCA2 (Produced by the Netherlands Cancer Institute, Amsterdam, the Netherlands) exclusively staining HLA-A heavy chains, HC10 (Produced by The Netherlands Cancer Institute, Amsterdam, the Netherlands) which binds to HLA-B and -C heavy chains [38 (link),39 (link)], and Tal.1B5 (DakoCytomation, Glostrup, Denmark) reacting with HLA-DR alpha chains. The number of tumor cells positive for each marker was counted at 100X magnification and expressed as percentage of the total number of tumor cells (S2 Table).
Immunofluorescence staining for infiltrating macrophages was performed and described previously, with antibodies against CD68 (clone 514H12; Abcam, Cambridge, UK) and CD163 (clone 10D6; Novocastra, Newcastle-upon-Tyne, UK), and expressed as pixels per millimeter squared [40 (link)]. T cells were identified and scored previously using an anti-CD3 antibody (ab828; Abcam), and expressed as numbers of cells per millimeter squared [12 (link)].
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4

Multiplex Immunofluorescence Staining of FFPE Tissues

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Triple immunofluorescent staining was performed on 4-μm-thick FFPE sections. After antigen retrieval using Tris–ethylenediaminetetraacetic acid (EDTA) buffer (10 mM Tris plus 1 mM EDTA pH 9.0), rabbit anti-CD3 (ab828, Abcam, Cambride, UK), mouse IgG1 anti-FoxP3 (ab20034, Abcam) and goat anti-IL-17 (AF-317-NA, R&D Systems, Abingdon, UK) diluted in 1 % w/v bovine serum albumin (BSA) in phosphate-buffered saline (PBS) were incubated at room temperature overnight. Alexa Fluor labeled donkey anti-rabbit-A546 (A10040), donkey anti-mouse-A647 (A31570) and donkey anti-goat-A488 (A11055; all from Invitrogen, Life Technologies, Carlsbad, USA) were incubated at room temperature for 1 h. Slides were mounted using VectaShield mounting medium containing DAPI (Vector Laboratories, Burlingame, USA). For negative controls, the primary antibodies were omitted and substituted with antibodies of the same isotype class with an unknown specificity.
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5

Immunohistochemical Analysis of Mammary Tumors

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Whole mounts were prepared as previously described [15 (link)]. Mammary tumors were fixed in formalin and embedded in paraffin. hematoxylin and eosin staining (H&E) was used to assess histology. Infiltration by CD3+ and perforin-positive cells was determined through immunohistochemistry with anti-CD3 (Ab828; Abcam, Cambridge, UK) and anti-perforin (Ab16074, Abcam) antibodies as previously described [16 (link)]. Immunostaining was developed using alkaline phosphatase-conjugated streptavidin (Thermo Fisher Scientific, Waltham, MA, USA) and vulcan fast red chromogen (Biocare Medical, Concord, CA, USA). Slides were counterstained with hematoxylin (BioOptica, Milan, Italy) and images were acquired by Leica DMRD optical microscope (Leica, Milton Keynes, UK).
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6

Immunohistochemical Analysis of Caecal Tissues

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The immunohistochemistry was carried out on formalin-fixed caeca collected at the hatching day. The specimens were processed, embedded in paraffin, and the tissue sections were cut at 4μm. The sections were treated with 10 mL MoL Tris buffer and 1 mL MoL ethylene-diamine tetra-acetic acid, pH 9.0 for 20 min at 90 °C. The block of endogenous peroxidase was done by incubation the sections with 3% H2O2, followed by preincubation overnight at 4 °C in 1% bovine serum albumin in PBS. The sections were stained for 30 min at 37 °C, using the following antibodies that showed reactivity in avian species: a rabbit polyclonal anti-CD3 (1:200; Abcam, Cambridge, UK, ab828), a mouse polyclonal anti-CD20 (1:200; Abcam, Cambridge, UK, ab88247), a rabbit polyclonal anti-S100 protein antibody (1:200, Thermo Fisher Scientific, Cat. RB-044-A0), and a rabbit polyclonal anti-SIgA (1:400; Abcam, Cambridge, UK, ab2411), according to the method described by Hsu and colleagues28 (link). The sections were counterstained with haematoxylin, and analysed using an Olympus microscope (Japan). In parallel, tissue specimens, in which the primary antibodies were omitted and replaced with buffer, served as negative controls.
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7

Immunohistology Antibody Staining Protocol

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The following polyclonal or monoclonal antibodies (mAbs) were used for immunohistology: anti-CD3 (for rats: clone 1F4, Bio-Rad, Oxford, UK; for dogs: Ab828, Abcam, Cambridge, UK; for minipigs: clone 8E6, WSU Monoclonal antibody center, Pullman, WA; for monkeys: clone CD3-12, Abcam), anti-CD4 (for rats: clone OX-35, Bio-Rad; for dogs: clone DH-29A, WSU Monoclonal antibody center; for minipigs: clone 74-12-4, WSU Monoclonal antibody center; for monkeys: clone BC/1F6, Abcam), anti-CD163 (for all species: clone AM-3K, Antibodies online, Paris, France), anti-CD172a (for rats: clone ED9, Bio-Rad; for dogs: clone DG-DH59B, WSU Monoclonal antibody center; for minipigs: clone BL1H7, Bio-Rad; for monkeys: Ab139698, Abcam), anti-MHC-II (for rats: clone OX-6, Bio-Rad; for dogs: clone DG-H42A, WSU Monoclonal antibody center; for minipigs: clone TH21A, WSU Monoclonal antibody center; for monkeys: clone L243, Abcam). Corresponding isotype-matched mAbs were used as controls in all experiments.
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