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17 protocols using ki 67 clone 30 9

1

Histological Characterization of Lens Capsule

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Immediately after samples were removed from culture, they were placed in 4% paraformaldehyde for fixation for at least one week and then embedded in paraffin. Once all samples were in paraffin, they were sectioned along the sagittal plane and stained on the same day. Tissue were stained with hematoxylin and eosin for morphological analysis, α-smooth muscle actin α-SMA (clone 14A, Cell Marque) for myofibroblast formation and intercapsular adhesion28 (link)–30 (link), Ki-67 (clone 30–9, Ventana) for proliferation31 (link) and vimentin (clone V9, Ventana) a marker of both undifferentiated lens epithelium as well as differentiating fiber cells32 (link). All immunostainings were done with the BenchMark® ULTRA device (Ventana Medical Systems, Inc.). We also included negative immunostain controls to support the validity of our stains and identify possible experimental artefacts or background noise. These controls were processed in the same manner with the automated staining device but without the primary antibodies. Capsular adhesion, cellular morphology and the degree of staining of α-SMA, Ki-67 and vimentin were studied at the equatorial region of the capsule and at the center of the posterior capsule.
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2

Ki-67 Immunohistochemical Staining Protocol

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Sections were cut at 3 to 4μm intervals and immuno-stained using the monoclonal antibody Ki-67 (clone 30-9, pre-diluted, Ventana-Roche, Arizona, USA). Immunohistochemical stains were subsequently performed using Bench Mark GX with the iView DAB Detection kit (Ventana-Roche, Arizona, USA).
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3

Immunohistochemical Analysis of Phyllodes Tumors

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One representative formalin-fixed paraffin-embedded tissue block from each case (31 low-grade phyllodes tumor, 30 fibroadenoma, and 10 high-grade phyllodes tumor) was selected to generate 4 μm thick unstained slides for immunohistochemical staining for the following antibodies: Ki-67 (clone 30-9, prediluted, Ventana), p53 (clone Bp53-11, prediluted, Ventana), β-catenin (clone 14, prediluted, Ventana), and E-cadherin (clone EP700Y, prediluted, Ventana). The immunohistochemistry staining was performed on Ventana Benchmark automated immunostainer (Ventana Medical Systems, Inc., Tucson, AZ) according to standard protocols with appropriate positive and negative controls. The immunohistochemistry staining results were interpreted individually by two pathologists (C.Y. and L.Z.) blinded of the diagnosis. The percentage of cells positive was visually estimated and recorded and the average of the two results were used for analysis. Only nuclear staining for Ki-67, p53, and β-catenin in the stromal tumor cells were considered as positive. In contrast, cytoplasmic and membranous staining in the stromal tumor cells for E-cadherin was interpreted as positive. The percentage of staining was estimated relative to total number of stromal cells.
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4

Tissue Preparation and Staining Protocol

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Upon completion of the experimental protocols, animals were euthanized by CO2 and eyes were enucleated. Whole P14, P28, and P63 eyes or CAM tumors were fixed in 4% paraformaldehyde overnight, dehydrated, paraffin‐embedded, and 5 μm sections were obtained using a microtome. Sections were deparaffinized and rehydrated in an ethanol series of descending concentration. Subsequently, sections were stained using Mayer's hematoxylin. Besides, immunohistochemical detection was performed using a ready‐to‐use rabbit monoclonal antibody against Ki67 (clone 30‐9; Roche Ventana, Basel, Switzerland) or CRX red (dilution 1 : 50; clone A‐9; Santa Cruz Biotechnology, Heidelberg, Germany) with the OptiView DAB IHC detection kit (Thermo Fisher, Darmstadt, Germany) for visualization. Images were captured using a slide scanner (Leica, Wetzlar, Germany) and subsequently analyzed by am aperio image scope Software (Leica).
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5

Comprehensive Breast Cancer Biomarker Profiling

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ER, PR, HER2, and Ki67 status were tested by immunohistochemical staining and the following antibodies were applied: monoclonal ER antibody (clone SP1; Ventana, Tucson, AZ), monoclonal PR (clone 1E2; Ventana), Ki-67 (clone 30–9; Ventana), and HER2 (clone 4B5; Roche, Sandhofer, Mannheim, Germany). The cut-off value for positive ER or PR was ≥1% of immunoreactive tumor cell nuclei, and for Ki-67 was ≥14%. The immunohistochemical staining for HER2 was scored as 0, 1+, 2+, or 3+; and 0 or 1+ was defined as HER2 negative, whereas 3+ was reported as positive. Fluorescence in situ hybridization was performed to explicate the HER2 gene amplification status in case of a 2+ score. Molecular subtypes were classified according to the St. Gallen expert consensus of 2011.[15 (link)]
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6

Immunohistochemical Staining Protocols

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Immunohistochemical stainings were performed as described previously [52] (link), using the monoclonal primary anti-NUT antibody (clone C52B1, 1:200, Cell Signaling Technology, Danvers, MA, USA) and the monoclonal anti-NR4A3 (NOR-1) antibody (clone H-7, 1:25, Santa Cruz Biotechnology, Inc, Dallas, TX, USA), applying the automated Leica Bond III staining system (Leica Biosystems, Nussloch, Germany). The Ventana Benchmark staining system (Oro Valley, AZ, USA) was applied for the following primary antibodies: p63 (clone 4A4, prediluted, Ventana, Oro Valley, AZ, USA), p40 (clone BC24, 1:100, Zytomed Systems, Berlin, Germany), panTRK (clone EPR17341, 1:100, Abcam, Cambridge, UK), CD117 (clone YR145, 1:200, Cell Marque Lifescreen Ltd., Rocklin, CA, USA), Ki-67 (clone 30-9, prediluted, Ventana, Oro Valley, AZ, USA), S100 (polyclonal, 1:2000, DAKO A/S, Jena, Germany), DOG-1 (clone SP31, 1:50 Invitrogen, Carlsbad, CA, USA).
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7

Immunohistochemical Breast Cancer Profiling

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IHC primary antibodies used were: ERα (clone SP1, Ventana), PR (clone 1E2, Ventana), Ki67 (Clone 30–9, Ventana), Her2 (clone 4B5, Ventana). Tumors were considered positive for ER and PR when at least 1% of tumor cells showed unequivocal nuclear staining according to American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guidelines. PR expression was considered high in the presence of nuclear staining in 20% or more cells. We set a cut-off point to distinguish low versus high Ki67 expression at 20%. The original HER2/neu immunostained glass slides were concurrently reviewed by pathologists at a multiheaded microscope, and the consensus HER2/neu immunoreactivity was manually scored by conventional microscopy as 0, 1+, 2+, or 3+ according to the proposed HER/neu scoring system for breast cancer. According to the percentage of stained malignant cells, criteria for HER2/neu score assignment were: 0, no staining or staining in <10% of cells; 1, faint staining in ≥10% of cells; 2, moderate staining in ≥10% of cells; and 3, strong staining in ≥10% of cells. Tumors classified as 0, 1+, and 2+ were considered “negative” and those scored as 3+ were classified as “positive”.
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8

Immunohistochemical Analysis of Tumor Samples

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The original tumor tissue and the explant of the tumor tissue were fixed in 10% neutral-buffered formalin and embedded in paraffin. Four microm sections were stained with H&E for the histological evaluation. For immunohistochemical analysis four micron paraffin sections were prepared, deparaffinized in xylene, and rehydrated with graded ethanol. Antigen retrieval was performed by microwave pretreatment. The following antibodies were employed for the analysis: Ki67 (clone 30-9, dilution, Ventana Medical Systems), p53 (clone DO-7, dilution 1:100, DAKO), p16ink4a (clone E6H4, dilution 1:50, MTM Laboratories), RB (clone 1F8, dilution 1:50, Thermoscientific), EGFR (clone 5B7 prediluted, Ventana Medical Systems) and cleaved caspase 3 (clone 5A1E, dilution 1:300, Cell Signaling). All stains were performed using the BenchMark XT Slide Preparation System (Ventana Medical Systems).
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9

Routine Histopathological SFT Analysis

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Routine histopathological processing, including immunohistochemistry (IHC), of the patients’ tumor tissues was performed at the Department of Pathology of the Medical University of Vienna. The antibody panels used for immunohistochemistry included bcl-2 (clone 124; DAKO Agilent, Santa Clara, CA, USA), CD34 (clone QBend/10; Leica, Wetzlar, Germany), CD99 (clone EP8, Biocare, Pacheco, CA, USA), STAT6 (anti-Stat 6 polyclonal antibody; Sigma-Aldrich, St. Louis, MO, USA), and Ki67 (clone 30-9; Ventana, Oro Valley, AZ, USA). In addition, all cases were re-reviewed by the author LM to confirm pathologic SFT diagnosis.
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10

Immunohistochemical Evaluation of Cell Markers

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Immunohistochemistry for part 2 and 3 was performed at Johns Hopkins Immunopathology Laboratory; to assess the expression levels of p53 (clone Bp53–11, cat # 760–2542; Ventana Medical Systems, Tucson, AZ) and Ki-67 (clone 30–9, cat # 760–4286; Ventana Medical Systems, Tucson, AZ) in formalin fixed paraffin-embedded tissue sections. All sections were immunostained automatically using either Ventana Benchmark Ultra or XT (Ventana Medical Systems, Inc.). Immunoreactivity was detected by iView (cat # 760–091, Ventana Medical Systems, Inc.). Immunohistochemistry to assess laminin γ1 polyclonal antibody (cat # HPA001909, Sigma-Aldrich, St Louis, MO) was performed manually in the Shih laboratory in accordance to manufacturer’s instructions (diluted 1:400) and immunoreactivity was detected by the Dako Liquid DAB+ Substrate Chromogen System (cat # K3468, DAKO North America, Inc., Agilent Technologies).
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