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21 protocols using ultraview universal dab kit

1

Comprehensive Immunohistochemical Analysis of HCC

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Immunohistochemical staining was used to detect the expression patterns of GPC3, CK19, vimentin, p53, AFP, EGFR, RRM1, BRCA1, VEGF, TS, Ki 67, ARG and GS in HCC tissues. The staining procedure was performed according to the instructions of the Roche benchmark XT Ventana (Roche Diagnostics, USA) automatic staining instrument, and the paraffin sections were detected by automatic immunohistochemistry. The slices were dewaxed, pretreated with cleaning buffer for 30 min, and then washed with reaction buffer. Subsequently, the following primary antibodies were added: GPC3, CK19, vimentin, mutant p53, AFP, EGFR, VEGF (all sourced from Santa Cruz Biotechnology, USA), RRM1, and BRCA1 (both sourced from Abcam, UK), After incubation for 30 min, the cells were stained with ultraView Universal DAB Kit (Roche Diagnostics, GER).
Positive criteria: All immunohistochemical staining results were judged independently by two senior pathologists, and unanimous interpretations are made in the event of a disagreement. The agreement between the two experts on the positive results of immunohistochemical staining was 97.15% (2526/2600). Furthermore, 74 immunohistochemical stained sections with inconsistent judgments were agreed upon after consultation.
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2

Immunohistochemical Profiling of FFPE Tumor Samples

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Formalin-fixed and paraffin-embedded (FFPE) archival tumour blocks were analysed by immunohistochemistry by collecting 4 μm sections on Superfrost charged slides (ThermoScientific). After drying overnight at 37 °C, samples were processed using a Ventana Benchmark immunohistochemistry platform (Roche) with antibodies against p53 (Agilent cat#7001, RRID: AB_2206626, 1:50), CK7 (Agilent cat#7018, RRID: AB_2134589, 1:250), PAX8 (Roche cat#760–4618, 1:100). Heat induced epitope retrieval was performed using CC1 (Roche), incubating samples at 95 °C for 36, 52, and 40 min for p53, CK7 and PAX8, respectively. Antibodies were incubated at 37 °C for 32, 40 and 32 min for p53, CK7 and PAX8, respectively. p53 and CK7 were detected using Ultraview universal DAB kit (Roche), while PAX8 was detected using Optiview universal DAB kit (Roche), all as per manufacturer’s instructions. Sections were counterstained using Haematoxylin II (Roche) for 12 min and bluing reagent (Roche) for 8 min. Slides were imaged using the EVOS FL Auto 2 Imaging System (Invitrogen), using a × 10 or × 40 objective lens under bright field, and processed using Adobe Photoshop.
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3

Immunohistochemical Staining of IR-β

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Staining was performed using a Ventana Benchmark XT (Roche Diagnostics, Basel, Switzerland) automatic immunostaining machine. The sections were deparaffinized in xylene, rehydrated in graded alcohols, and subjected to pretreatment with CC1 (Roche Diagnostics). The sections were washed with reaction buffer followed by incubation with primary IR-β antibody (Abcam, Cambridge, MA, USA) at a 1:100 dilution for 60 min at 42℃. Bound antibody was detected with the Ultra View Universal DAB kit (Roche Diagnostics) and sections were counterstained with hematoxylin (Roche Diagnostics) according to the manufacturer's instructions. Positive and negative control stains were also performed.
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4

Immunohistochemical Analysis of GBM Markers

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Immunohistochemical (IHC) analyses were carried out for CD4, CD8, and p53 markers via Ventana Benchmark Ultra (Ventana Medical System—Roche). Briefly, 4 μm-lick FFPE sections were immunostained with CD4 antibody (SP35, rabbit monoclonal); CD8 antibody (SP57, rabbit monoclonal), and p53 (DO-7 mouse monoclonal), and developed in diaminobenzidine (DAB)–hydrogen peroxide for 10 min (ultraView Universal DAB kit, Ventana Medical System—Roche). Finally, sections were counterstained with hematoxylin and mounted. Positive controls were included for the current analysis (tonsil, testis, liver, and kidney).
Slide scanning was performed via Ventana DP 200 Slide Scanner (Roche Diagnostics International, Rotkreuz, Switzerland). Imaging analyses were carried out through QuPath (v0.3.0, Belfast, XI) platform; a semiautomatic approach was applied and the number of total positive cells for each core and the average number of positive cells per high power field (HPF) were assessed. TP53 was considered mutated if no expression or a strong and diffuse expression was present in GBM cells.
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5

Multiplex IHC Analysis of Immune Markers

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The IHC staining was performed on the Ventana Benchmark XT from Roche with the Ultra View Universal DAB Kit using a rabbit antibody against CD3 and mouse antibodies against CD8, pan-cytokeratin and Foxp3. Briefly, the slides were deparaffinized using deparaffinization solution. For pan-cytokeratin staining, the antigen retrieval was performed by pre-treating the tissue with Protease1 (from Roche) for 8 min while for other stainings, CC1 (Cell Conditioning 1 from Roche) was used for 60 min. All antibodies were incubated for 32 min Counterstaining was done with hematoxylin. Slides were scanned in an Aperio AT2 slide scanner (Leica) at magnification of 40X. The immunohistochemical expression was analyzed with Aperio ImageScope software (V12.4.0.7018). “Positive Pixel Count v9” algorithm was used for quantifying pan-cytokeratin expression. The total positive pixel was normalized to the total area of the annotated regions on tissue section (pixel/mm2). “Nuclear v9” algorithm was used for CD3 and CD8 positive cell count. The default set of parameters of the algorithms was modified according to the stain contrast and intensity of the scanned images.
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HER2 Immunohistochemistry Protocol for Paraffin Sections

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TMAs paraffin blocks were sectioned into 4 µm slices, deparaffinized, and antigens demasked in EDTA buffer, pH 8.4. HER2 immunohistochemistry (IHC) was performed using PATHWAY anti-HER2/neu (4B5; rabbit monoclonal; pre-dilution; Ventana Medical Systems, Tucson, AZ, USA) antibody and ultraView Universal DAB kit (Ventana Medical Systems) on an automatic immunostainer (BenchMark XT, Ventana Medical Systems), according to the manufacturer's instructions. Primary antibody omission was used for the negative control and breast cancer previously confirmed by HER2-IHC showing 3+ immunopositivity was used for positive control. IHC scoring was independently performed by two pathologists without prior knowledge of clinicopathological information or molecular results obtained via other methods. The scoring was first semiquantitatively analyzed and grouped into 4 categories as follows: 0, no staining; 1+, faint/barely partial membrane staining less than 50% of tumor area; 2+, variable weak-to-moderate complete membrane staining in ≥50% of tumor area; 3+, strong complete membrane staining in all tumor area. The two pathologists completely agreed on all the IHC scoring and IHC 2+ and 3+ were considered to indicate HER2-IHC positive group for statistical reason.
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7

Immunohistochemical Detection of B7-1 in Tissues

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We performed immunohistochemical staining for B7-1 by using a BenchMark XT automated immunostaining system (Ventana Medical Systems, Inc., Tucson, AZ, USA). Briefly, the paraffin blocks were cut into 4-μm-thick sections, deparaffinised in xylene, and then hydrated by using alcohol (3×). After microwave antigen retrieval, the samples were incubated with a monoclonal mouse anti-human B7-1 antibody (diluted 1:20; catalogue No. MAB140; R&D Systems, Minneapolis, MN, USA) and subsequently treated with the UltraView Universal DAB kit (Ventana Medical Systems, Inc.). Harris haematoxylin was used as a counterstain. Two independent specialists blinded to the patients’ clinical data evaluated the stained slides. If the interpretation of the staining results was not consistent, the two specialists discussed conflicting findings. The intensity of the signal was rated 0 (negative), 1 (weak), or 2 (strong). Staining results for the glomerulus and tubular epithelium were recorded separately. Normal tonsillar tissue was used as a positive control for B7-1.
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8

Immunohistochemical Analysis of Androgen Receptor in Breast Cancer

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The expression of the AR on BC tissues was evaluated using IHC analysis. Surgical specimens were fixed in formalin and included in paraffin. For each sample, 3 µm sections were obtained. The IHC analysis was performed using VENTANA BenchMark Ultra (Ventana Medical Systems, Tucson, AZ, USA) with ultraView Universal DAB kit (Ventana Medical System).
A primary monoclonal rabbit antibody directed versus AR (SP107 Cell Marque, Ventana Medical System) and pre-diluted by the supplier was used. After immunostaining, the slides were counterstained with Harris hematoxylin de-hydrated and mounted for microscopic reading. Nuclear staining was expressed as the percentage of stained cells (0−100%) over the total number of viable cells. Two expert pathologists in BC (LV and MA) assessed the expression of AR together, and disagreement was resolved through consensus.
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9

HER2 Immunohistochemical Evaluation Protocol

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Sections of FFPE tissue (4 um thick) were obtained. HER2 immunostaining was performed using a PATHWAY anti-HER2/neu (4B5; rabbit monoclonal; predilution; Ventana Medical Systems, Tucson, AZ, USA) antibody and an ultraView Universal DAB Kit (Ventana Medical Systems) on an automatic immunostainer (BenchMark XT, Ventana Medical Systems), according to the manufacturer’s instructions. HER2 immunoreactivity was evaluated by two pathologists according to the scoring system described by Josef Ru¨ schoff et al.24 (link) as follows: 0, no reactivity or membrane staining in <10% of tumor cells; 1+, faint/barely perceptible membranous reactivity in ≥10% of tumor cells; 2+, weak-to-moderate complete, basolateral, or lateral membranous reactivity in ≥10% of tumor cells; and 3+, strong basolateral, or lateral membranous reactivity in ≥10% of tumor cells.
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10

Immunostaining for Tumor PD-L1 Expression

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We performed immunostaining with antibodies targeting PD-L1 (E1L3N, 1:50, Cell Signaling Technology, Danvers, MA) on tissue slides using the Ventana BenchMark XT auto-stainer (Ventana Medical Systems, Tucson, AZ) with the ultraView Universal DAB kit (Ventana Medical Systems) according to the manufacturer’s standard recommendations. Experienced pathologists (J.H.C. and K.S.L.) determined the percentage of tumor cells with membranous PD-L1 staining of any intensity (tumor proportion score) and grouped the scores into four categories based on cutoffs used in previous studies (0, < 1%; 1, 1%-5%; 2, 5%-50%; and 3, ≥ 50%) [6 (link),21 (link),22 (link)].
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