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4 protocols using clone 10d6

1

Quantifying Tumor-Infiltrating Lymphocytes in FFPE Samples

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Paraffin‐embedded tumor sections were dewaxed in xylene and ethanol and autoclaved for 15 min in an antigen retrieval solution to retrieve their antigen epitopes, and endogenous peroxidase activity was blocked with 3% H2O2. Tissue sections were incubated overnight at 4°C with primary antibodies, including rabbit polyclonal anti‐CD3 (1:200 dilution; ab4055, Abcam, Cambridge, UK) for CD3+ T lymphocytes, mouse monoclonal anti‐CD8 (1:300 dilution; clone G10F5, BD Pharmingen, San Diego, CA, USA) for CD8+ T lymphocytes, anti‐CD4 (1:300 dilution; clone 10D6, Novocastra, Newcastle, UK) for CD4+ T lymphocytes, and anti‐FOXP3 (1:300 dilution; clone 10D6, Novocastra) for FOXP3+ T lymphocytes. The secondary antibody was incubated in a ready‐for‐use EnVision–peroxidase system (Dako Japan, Tokyo, Japan). Sections were incubated with horseradish peroxidase‐labeled polymer (EnVision1kit, Dako, Carpinteria, CA, USA) for 30 min at 25°C and incubated with 3,30‐diaminobenzidine tetrahydrochloride (applied as a 0.02% solution containing 0.005% H2O2 in 0.05 M Tris–HCl; pH 7.6) at 25°C for 5–15 min and counterstained with hematoxylin. We counted each positive lymphocyte in the invasive tumor margin using a BZ‐X700 digital microscope at a magnification of 200× (Keyence) using hybrid cell count software (BZ‐H3C; Keyence; Figure S1).
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2

Evaluating Allograft Rejection Through Biopsy and MRI

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Patients with allografts underwent routine biopsies either (a) on the same day as the MRI (n = 12), (b) before the MRI (n = 3; mean 18 days prior), or (c) after the MRI (n = 5; mean 10 days later). The biopsy specimens were dissected parasagittally, kept in formalin overnight, dehydrated through graded alcohol washes (70, 95, and 100 %), embedded in paraffin and sliced on a microtome. Five-micrometer thick tissue slices on glass slides were stained with hematoxylin and eosin (HE) and Periodic acid-Schiff (PAS) stains. In addition, the samples were stained with antisera against CD163 (Novocastra, Clone 10D6, 1:50 dilution, performed on the Ventana XT using HIER solution CC1, pH 8.0). The histological and immunohistochemical analysis was performed under a light microscope (Olympus BX51). The biopsy samples were evaluated for cellular and antibody-mediated rejection as per the Banff 2013 criteria [29 (link)]. Evidence for other disease processes affecting the allograft was also sought. The CD163 stained slides were scored blinded as follows: no stained cells = 0, <10 positive cells/hpf present in <25 % of biopsy = 1, >10 positive cells/hpf in 26–50 % of biopsy = 2, and >10 positive cells in >50 % of biopsy = 3.
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Multiplexed Immunohistochemistry for Tumor Profiling

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An automated slide staining machine BOND RX (Leica Biosystems, Nußloch, BW, Germany) and an Opal 7-color Automation IHC kit (Perkin Elmer, Waltham, MA, USA) were used for mIHC staining. The following primary antibodies were used: CD68 (1:2000, clone KP-1, Agilent, Tokyo, Japan), CD163 (1:100, clone 10D6, Leica Biosystems), PD-L1 (1:100, clone SP142, abcam, Cambridge, MA, USA), CD20 (1:1, clone L26, Agilent, Tokyo, Japan), HLA class I (1:800, clone EMR8-5, abcam, Cambridge, MA, USA), and pan-cytokeratin (CK) (1:4, clone AE1/AE3, Agilent, Tokyo, Japan). Staining was performed using the Opal 7-color Automation IHC kit and BOND research detection kit (Leica Biosystems Nußloch, BW, Germany), according to the manufacturer’s instructions. Primary antibodies were incubated for 30 min at 25 °C. Slides were mounted using a ProLong Diamond Antifade Mountant (Thermo Fisher Scientific, Waltham, MA, USA).
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4

Immunohistochemical Analysis of CD163 in ATC

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Immunohistochemical analyses were performed on 6 µm thick sections prepared from 4 paraffin-embedded ATC tissues (4 of the 11 ATC studied by microarrays) and from 1 normal thyroid tissue, with the primary antibody directed against CD163 (Leica Biosystems, UK, Clone 10D6). The sections were deparaffinized, pretreated with CC1 (EDTA, pH 8.4) and incubated with the antibody at a 1∶100 dilution. The revelation was performed with a detection kit (Roche, ref. 760-501).
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