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16 protocols using cd8 clone 4b11

1

Immunohistochemical Profiling of Skin Biopsies

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Four micrometer sections, cut from a 4-mm punch biopsy that were fixed in 10% buffered formalin and embedded in paraffin, were stained with hematoxylin and eosin (H&E) or labeled immunohistochemically with antibodies against CD4 (clone EP204, Epitomics, Cambridge, MA), CD8 (clone 4B11, Leica Biosystems Inc., Buffalo Grove, IL), CD56 (clone 56C04 Thermo-Scientific, Waltham, MA), CD68 (clone PG-M1, Dako, Carpinteria, CA) and CD138 (clone B-A38 Cell Marque, Rocklin, CA) using an automated immunohistochemistry staining platform (Bond Max, Leica-Microsystems, Buffalo Grove, IL). IHC detection of Tp was performed manually as previously described (10 (link)) using a rabbit polyclonal anti-Tp Ab (Biocare, Concord, CA, USA). Skin specimens from healthy volunteers of the same socioeconomic background and conditions were not available for analysis. Tissue known to contain Tp were used for the positive control of Tp IHCs. Additionally, secondary alone controls were used to assess any non-specific Ab binding for each Ab used.
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2

Immunohistochemical Profiling of Carcinomatous and Sarcomatous Samples

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4 µm FFPE sections were used for immunohistochemical (IHC) staining on the Leica BOND III Autostainer (Leica Biosystems) using IHC protocol F. CD3 and CD8 IHC was performed using Leica ready-to-use CD3 (clone LN10, pre-diluted, Leica Biosystems #PA0553) and CD8 (clone 4B11, pre-diluted, Leica Biosystems, #PA0183) mouse monoclonal antibodies. Vimentin and pan-cytokeratin IHC was performed with Leica ready-to-use vimentin (clone V9, pre-diluted, Leica Biosystems #PA0640) and multi-cytokeratin (clone AE1/AE3, pre-diluted, Leica Biosystems #PA0909) monoclonal mouse antibodies as previously described [1 (link)]. CD3, CD8, vimentin and multi-cytokeratin staining were performed on carcinomatous and sarcomatous samples from all 12 cases.
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3

Comprehensive Immunohistochemical Profiling of Tumor Microenvironment

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Immunohistochemistry (IHC) analysis was used to detect the MMR-related proteins MSH2, MSH6, MLH1, and PMS2. To assess the TIME, CD3, CD8, and PD-L1 expression were evaluated. IHC was performed using our laboratory protocol as described previously [22 (link), 23 (link)]. Briefly, 3-μm-thick TMA serial sections were deparaffinized and subjected to heat-induced epitope retrieval with 10 mM sodium citrate (pH 6.0) at 95°C for 20 min. Endogenous peroxidase activity was quenched using a 0.3% hydrogen peroxide solution.
TMA sections were incubated with primary antibodies against MLH1 (clone ES05, ready to use; Leica Biosystems), PMS2 (clone MOR4G, ready to use; Leica Biosystems), MSH2 (clone 25D12, ready to use; Leica Biosystems), MSH6 (clone PU29, ready to use; Leica Biosystems), CD3 (clone LN10, ready to use; Leica Biosystems), CD8 (clone 4B11, ready to use; Leica Biosystems), and PD-L1 (SP142, 1: 100, ZSGB-BIO, China). Human tonsils treated with primary antibodies were used as positive controls, while the same tissues without primary antibodies comprised the negative controls. After the reactions, all sections were counterstained with hematoxylin. All slides except those used for manual PD-L1 staining were stained using an automatic IHC staining instrument (BOND-III; Leica Biosystems, Wetzlar, Germany) according to the manufacturer's instructions.
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4

Immunohistochemical Profiling of Thymic Tumors

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CD8, FOXP3, PD‐1, CD117 and CD5 immunohistochemistry was performed in the eight MNT and three MNCA cases. PD‐L1 immunohistochemistry was performed in all the 35 thymic epithelial neoplasm cases. Antigen retrieval for CD8, FOXP3 and PD‐L1 was performed with the buffer preheated to 95°C for 40 min (pH 9.0). Antigen retrieval for PD‐1, CD117 and CD5 was conducted with preheating to 120°C for 15 min (pH 6.0). The antibodies against these antigens were as follows: CD8 (clone 4B11, 1:40; Leica Biosystems, Wetzlar, Germany), FOXP3 (clone 236 A/E7, 1:100; Abcam, Cambridge, UK), PD‐1 (clone NAT105, 1:50; Abcam), PD‐L1 (clone E1L3N, 1:100; Cell Signaling Technology, Danvers, MA, USA), CD117 (polyclonal, 1:500; DakoCytomation, Carpinteria, CA, USA) and CD5 (clone 4C7, 1:400; Leica Biosystems). All sections were incubated with primary antibodies for 30 min. They were then incubated with peroxidase‐labeled goat anti‐mouse/rabbit IgG antibody (Nichirei Biosciences, Tokyo, Japan) for 30 min. The immune response was visualized using 3,3′‐diaminobenzidine (DakoCytomation) and counterstained with hematoxylin. Two board‐certified pathologists (HY and TI) examined the hematoxylin and eosin and immunohistochemical stains for CD5 and CD117.
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5

Multiplex IHC Profiling of Tumor-Infiltrating Immune Cells

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Immunohistochemical (IHC) staining using whole section FFPE tissues was performed with the following primary antibodies: CD8 (clone 4B11, 1:400, Cat#NCL-L-CD8-4B11, Leica Biosystems, Newcastle, UK), granzyme B (clone 11F1, 1:128, Cat#NCL-L-GRAN-B, Leica Biosystems, Newcastle, UK), CD68 (clone KP1, 1:2000, Cat#M0814, Dako, Glostrup, Denmark), and PD-L1 (clone 22C3, 1:50, Cat#M3653, Dako, Glostrup, Denmark). PD-L1 expression was evaluated as the tumor proportion score (TPS), which was defined as the percentage of tumor cells with PD-L1 expression, and the combined positive score (CPS), which was defined as the number of PD-L1-expressing tumors and immune cells (lymphocytes and macrophages) divided by the number of all tumor cells and multiplied by 100. To quantify CD8-, CD68-, and granzyme B-positive immune cells, up to 10 representative images of each IHC slide were acquired and analyzed by two expert genitourinary pathologists (S.H. and G.Y.K.) using the inForm 2.6 software (Akoya Biosciences, Marlborough, MA, USA). Positive cells were scored out of the total number of cells counted in representative images.
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6

Immunohistochemical Analysis of Tumor-Infiltrating Lymphocytes

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Immunohistochemistry (IHC) was performed on representative full tissue sections of formalin-fixed paraffin-embedded tumor blocks using monoclonal antibodies against Foxp3 (clone 236A/E7, dilution 1:200; Abcam, Cambridge, UK), CD4 (clone 4B12, dilution 1:60; Novocastra, Newcastle, UK), and CD8 (clone 4B11, dilution 1:80; Novocastra). Staining procedure was conducted using a Leica-BOND III automated IHC system (Leica Microsystems, Wetzlar, Germany) according to a modified manufacturer protocol. The Bond Polymer Refine Detection Kit (Leica Microsystems) was used following antigen retrieval with Solution 1 (Leica Microsystems). Briefly, tissue sections on adhesive glass slides were deparaffinized, hydrated in serially diluted alcohol, and immersed in 3% hydrogen peroxide to remove endogenous peroxidase activity. Sections were subsequently processed in EDTA buffer (pH 9.0) for CD4 or CD8, and citrate buffer (pH 6.0) for Foxp3 for 15 minutes in the microwave for antigen retrieval. After incubation with the primary antibodies, immuno-detection was performed according to the manufacturer's guidelines. We used 3'-diaminobenzidine chromogen as the substrate. The primary antibody incubation step was omitted in the negative control. Slides were counterstained with Mayer's hematoxylin.
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7

Immunohistochemical Detection of MMR Proteins

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Immunohistochemistry was performed on 2 μm paraffin sections by using monoclonal antibodies specific for MLH1 (clone G168-15, dilution 1:25, BD Pharmingen, Heidelberg, Germany), MSH2 (clone FE11, dilution 1:200, Calbiochem, Darmstadt, Germany) or MSH6 (clone44, dilution 1:50, Cell Marque, Rocklin, USA) for detecting loss of MMR protein as described previously [12 (link)]. An immunoperoxidase method was used to visualise the antibodies by labelling them with a chromogen (3-amino-9-ethylcarbazole, Dako, Glostrup, Denmark). The amount of mucosal length and surface analysed was calculated as described previously [12 (link)].
For immunohistochemical staining of immune cells in the vicinity of MMR-DCF the following antibodies were used: CD4 (clone RPA-T4, dilution 1:50, BD Pharmingen, Heidelberg, Germany), CD8 (clone 4B11, dilution 1:50, Novocastra, Wetzlar, Germany) and FoxP3 (clone 236A/E7, dilution 1:50, eBioscience, Frankfurt, Germany).
Immune cell infiltration was qualitatively assessed by two independent observers.
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8

Immunohistochemical Analysis of Immune Markers

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Immunohistochemical staining (IHC) was performed according to the manufacturer’s instruction using an autostainer (Dako autostainer Link 48 and Omnis staining platform; Dako, Glostrup, Denmark) and the following monoclonal antibodies: PD-L1 (PD-L1 IHC [22C3] pharmDx; Agilent), CD4 (clone 4B12; Novocastra), CD8 (clone 4B11; Novocastra), CD20 (L26; Thermo) and FOXP-3 (236 A/E7; Abcam).
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9

Immunohistochemical Profiling of Immune Markers

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Formalin-fixed, paraffin-embedded specimens were stained with hematoxylin and eosin, CD4 (clone EP204, Sigma-Aldrich, St. Louis, MO), and CD8 (clone 4B11, Leica, Wetzlar, Germany) using standard automated protocols. Immunohistochemistry (IHC) for PD-1 (clone NAT105, Abcam, Cambridge, U.K.)16 (link) and PD-L1 (clone SP142, Spring Bioscience, Pleasanton, CA)17 (link) were performed as previously described, including the use of an isotype control for PD-L1 to control for potential false-positive staining.18 (link) Eight patient samples from the control and iLTS cohorts were stained for CD4, CD8, PD-1, and PD-L1. Eight iSGS patient samples were stained for only CD4, PD-1, and PD-L1 due to limited sample supply.
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10

Automated Immunohistochemistry Staining Protocol

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Briefly, 4 μm tissue slices were prepared from cryopreserved tissues and mounted on glass slides. Immunohistochemistry was performed according to the manufacturer’s instructions using an automated staining facility (Bond Max, Leica, Wetzlar, Germany). The following mouse monoclonal antibodies were utilized: CD3ϵ (clone ab16669, 1:100, Abcam, Cambridge, UK; RRID: AB_443425), CD4 (clone 4B12, 1:150, Leica, Wetzlar, Germany; RRID: AB_563559), CD8 (clone 4B11, 1:100, Leica, Wetzlar, Germany; RRID: AB_442068), CD20 (clone L26, 1:100, Leica, Wetzlar, Germany; RRID: AB_442055), CD163 (clone EPR19518, 1:500, Abcam, Cambridge, UK; RRID: AB_2753196), NKp46 (clone 195314, 1:175, R&D Systems, Minneapolis, MN, USA; RRID: AB_2149153) and FoxP3 (clone 236A/E7, 1:100, Thermo Fisher Scientific, Waltham, MA, USA; RRID: AB_467555).
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