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6 protocols using m3562

1

Immunohistochemical Analysis of AR-V7 in Breast Tissue

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Immunohistochemical staining for AR-V7 was done on serial 4 μm breast tissue sections as described previously [62 (link)] using the AR-V7 EPR15656 antibody (1:200), biotinylated anti-rabbit antibody (1:400, DAKO Corp., Carpinteria, CA), streptavidin-horseradish peroxidase complex (1:500, DAKO), and diaminobenzidine tetrahydrochloride. To analyze 22Rv1 cells (Supplementary Figure S4), a standard cytospin protocol was utilized [63 (link)] followed by immunohistochemistry as above.
Preparation of formalin-fixed, paraffin-embedded tissue sections for immunofluorescence was done as described previously [64 (link)]. For all antigens, retrieval was performed in 600 mL of 10 mM Tris base and 1 mM Na-EDTA (pH 9.0) by heating in a 1100W microwave at full power for 5 min and subsequently heating at 50% power for an additional 5 min. Primary antibodies used for immunofluorescence were AR-441 (M3562, 1:50, DAKO) and AR-V7 (EPR15656, 1:400). Primary antibodies were detected using secondary antibodies conjugated to either Alexa-Fluor 488 (A11029; Life Technologies) or Alex-Fluor 568 (A11036; Life Technologies). Images were acquired sequentially on a Zeiss 700 confocal microscope with a pinhole aperture of 2 airy units.
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2

Prostate Cancer Immunohistochemical Analysis

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Prostate cancer microarray slides immunostained for NEK6 were scanned and scored by automated spectral imaging analysis per the Supplemental Methods. Paraffin embedded subcutaneous tumor sections were immunostained using anti-AR (Dako # M3562, dilution 1:200, 1 hr incubation, citrate and microwave retrieval, EnVision detection. BioGenex platform); anti beta-catenin (Santa Cruz sc-1496, dilution 1:100, T3 H1(30 (link)), Leica platform), anti-KRT13 (GeneTex EPR3671), anti-NEK6 (as for TMAs but at 1:100 dilution).
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3

Immunohistochemistry and FISH Analysis

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IHC was performed according to the standard indirect immuno-peroxidase procedures. The primary antibody was omitted for negative controls. All slides were read manually by an experienced pathologist (LB). Data from AR and Ki67 were available from a previous study on the same TMA block.18 (link) Briefly, the antibodies M3562 and M7240 (both DAKO, Carpinteria, CA, USA) were used for AR and Ki67 staining, respectively. The anti-ERG mouse monoclonal antibody 9FY was from Biocare Medical (Concord, CA, USA).19 (link) FISH analysis for detection of ERG rearrangement was performed as previously reported.13 (link) Images were obtained by usage of the AXIO Imager.A1 microscope equipped with an AxioCam and the AxioVision 4.6 software (all from Zeiss, Jena, Germany).
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4

Tumor Cell Marker Analysis via TMA

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A human tissue microarray (TMA) was constructed to assess tumor cell positivity for markers of interest. TMAs were constructed using H&E stained slides, marked to identify tumor area by an expert pathologist (CSH), to guide tissue coring. Three 0.8 mm tissue cores were taken per EnOC case.
IHC for PR was performed using 1:50 mouse anti-human PR antibody M3569 (DAKO, clone PgR-636). ER staining was performed using 1:50 dilution of rabbit anti-human ER antibody M3643 (DAKO, clone EP1). AR staining was performed using 1:50 dilution of mouse anti-human AR antibody M3562 (DAKO, clone AR441). IHC was performed using the Leica BOND III Autostainer with epitope retrieval solution 2 for 20 min. Normal human breast tissue was used as a positive control for ER and PR, while normal human prostate tissue was used as a positive control for AR. Negative controls were performed using further sections without the addition of primary antibody.
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5

Comprehensive Immunostaining of FFPE Tumors

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FFPE patient tumors and PDX blocks were sectioned and slides immunostained with the following antibodies: cytokeratin cocktail AE1AE3 (M3515, Agilent), androgen receptor (M3562, Agilent), hCD45 (IR751, Agilent), PSA (M0750, Agilent), ERG (AC-0105, Clinisciences), NKX3.1 (AC-0314, Clinisciences), PTEN (ab228466, Abcam), Ki67 (M7240, Agilent), P53 (GA616, Agilent), synaptophysin (IR660, Agilent) and chromogranin A (M0869, Agilent). After heat antigen retrieval as specified by provider, experiments were performed using Dako Omnis Instrument, EnVision FLEX, High pH kit for revelation (GV800, Agilent) for hCD45, cytokeratin cocktail AE1AE3, PSA, P53, synaptophysin, ERG and chromogranin A, or Leica Bond III Instrument for androgen receptor, Ki67 and NKX3.1 and on Autostainer 480S instrument for PTEN. The conditions are described in the Supplementary Table 3.
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6

Prostate Cancer Organoid Culture Protocol

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Fresh PDX tissue was chopped, digested with collagenase II (R&D) on advanced DMEM/F-12 (Gibco) with 1% PenStrep (Sigma-Aldrich), 10 mmol/L HEPES (Gibco), and 1X GlutaMAX (Gibco) on an orbital shaker (37°C, 2 hours), and passed sequentially through a 100- and 70-μm strainer. After centrifugation, cells were incubated for 5 minutes with ammonium–chloride–potassium (ACK) lysis solution (Quality Biological). Cells were plated in PCM media for 2 to 4 days and then plated in Cultrex Basement Membrane Extract (Cell density: 1 × 106 in 100 μL) in PCM medium. For histology, organoids were fixed with 10% formalin ON, transferred to 70% ethanol, and paraffin embedded. Hematoxylin and eosin and IHC using anti-AR antibody (Agilent, M3562, RRID:AB_2060174) were performed using standard techniques (11 (link)).
PCM medium was prepared as in ref. 12 (link) with these modifications: Noggin conditioned medium 10%, R-spondin 1 conditioned medium 5%. N-acetyl-L-cysteine and SB202190 were not added.
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