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9 protocols using d6h2l

1

Immunofluorescence and Western Blot Analysis of MSCs

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For immunofluorescence staining, MSCs were grown in cover slips, washed with PBS, fixed with methanol, permeabilized with 0.1% Triton X- and blocked with 5% BSA in TBST. The samples were incubated with the following antibodies overnight at 4 °C: glucocorticoid receptor (D6H2L, 1:200, Cell Signaling), HDAC6, Runx2 (SC-5258 and SC-390715, 1:50 Santa Cruz). The appropriate secondary antibodies used are: Alexa Fluor 488-conjugated goat anti-rabbit, Alexa Fluor 586-conjugated goat anti-mouse, Alexa-fluor 688- conjugated donkey anti-goat (Life technologies) at a 1:250 dilution in PBS and counterstained with DAPI (1:2,000; Invitrogen Corporation, NY, USA). Images were acquired from at least 50 cells per treatment using Olympus Ax80 microscope. For co-localization detection, images were obtained using a confocal microscope (Zeiss LSM 700) and processed using LSM Image Browser (Zeiss).
For western blot, cells were harvested and lysed using RIPA buffer, and immunoblots were probed with glucocorticoid receptor (D6H2L, Cell Signaling) and Runx2 (SC-390715, Santa Cruz) antibodies.
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2

Immunohistochemical Staining of Tumor Samples

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Serial tissue sections of 4-μm thickness, containing the deepest area of the tumor invasion, were deparaffinized in xylene, rehydrated in graded alcohol, and immersed in 3.0% hydrogen peroxide in methanol for 10 min at room temperature to inhibit endogenous peroxidase activity. For antigen retrieval, the tissue slides for GR, Sgk1, and NDRG1 immunohistochemistry were heated in an autoclave at 121 °C for 5 min in 0.01 M citrate buffer (pH 6.0). After washing three times for 5 min each in phosphate-buffered saline (PBS), the reacted slides were incubated in 1% normal goat serum for 30 min at room temperature to reduce nonspecific antibody binding and then incubated at 4 °C overnight with rabbit monoclonal antibody against GR (D6H2L, Cell Signaling Technology, Danvers, MA, USA, diluted 1/400), Sgk1 (Y238, Abcam, Cambridge, UK, diluted 1/200), or NDRG1 (EPR5593, Abcam, diluted 1/400). The reacted sections were then washed three times for 5 min each in PBS, incubated with biotinylated anti-rabbit immunoglobulin (Nichirei Biosciences, Inc., Tokyo, Japan), washed three times for 5 min each in PBS, and incubated with peroxidase-labeled streptavidin (Nichirei Biosciences, Inc.) for 30 min at room temperature. Immunoreactivity was visualized with 3,3-diaminobenzidine, and the slides were counterstained with Mayer’s hematoxylin, dehydrated in graded alcohol, and cleared in xylene.
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3

Immunoprecipitation of GR and HDAC6 from MSCs

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Mouse MSCs at day 0, 3 and 5 of osteogenic induction under 10−7 M dexamethasone were lysed with PierceTM IP lysis buffer (87787) with protease inhibitor cocktail. An estimated 350 μg of the pre-cleared lysate (total protein) was incubated with 1 μl of total GR antibody (D6H2L, Cell Signaling) or HDAC6 antibody (ab12173, Abcam), and incubated overnight at 4 °C under rotation. The complex was pulled down by 100 μl of Protein A- coupled separose beads (Millipore) PierceTM Protein A/G Agarose (20421) slurry for 2 hours at room temperature under rotation. The complex was centrifuged at 3000 rpm and the supernatant was discarded (unbound protein). The beads with the bound complex was washed 3x with 1 ml IP lysis buffer, centrifuged and the supernatant was discarded. Finally, the Ag-Ab complex was eluted from the beads by adding 50 μl of 2x SDS loading buffer and heated at 95 °C for 5 minutes. The samples, together with 20% input were analyzed by western blot.
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4

Immunoprecipitation of Steroid Receptors

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Whole brains from 12-month-old males were lysed by homogenization in cold PBS supplemented with 0.5% NP-40 and complete Protease/Phosphatase Inhibitor cocktail (Sigma). The lysate was cleared by centrifugation (10 min, 25.000 × g, 4 °C). 2 mg of lysate was incubated overnight at 4 °C with the GR affinity resin (sc-393232 AC, Santa Cruz Biotechnology), anti-AR agarose affinity resin (sc-7305 AC, Santa Cruz Biotechnology) or with empty agarose beads (Sigma Aldrich) respectively. The next day, the beads were washed 3 times with Lysis Buffer without detergent and samples were eluted with 0.1 M acetic acid for 10 min and neutralized with concentrated NaOH. One-tenth of the brain lysates and immunoprecipitates were separated by SDS-PAGE, blotted to nitrocellulose membrane (Millipore) and probed with respective antibodies for GR (D6H2L, Cell Signaling), AR (sc-7305, Santa Cruz Biotechnology), Hsp90 (37-9400, Invitrogen), FKBP51 (GTX66429, GeneTex), FKBP52 (sc-100758, Santa Cruz Biotechnology), PP5 (sc-271816, Santa Cruz Biotechnology). Signals were developed using IRDye 800CW donkey anti-rabbit IgG or IRDye 680RD anti-mouse IgG (Li-Cor Biosciences) and quantified by Odyssey imaging system (Li-Cor Biosciences).
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5

Immunohistochemical Analysis of Tumor Samples

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Hematoxylin and eosin staining of paraffin-embedded tissues was used to identify viable tumor cells in the tissues. Two cores (5–8 tumors per group) were punched and placed in tissue microarrays. The tissue microarray slides were stained for AR (F39.4.1, 1:100, BioGenex, Fremont, CA), GR (D6H2L, 1:100, Cell Signaling, Danvers, MA), chromogranin A (DAK-A3, 1:100, DAKO, Carpinteria, CA), and synaptophysin (D-4, 1:200, Santa Cruz Biotechnology, Dallas, TX) using standard procedures as described previously (19 (link)–21 (link)). All evaluations were performed in a blinded fashion and a quasi-continuous immunohistochemical (IHC) score was calculated by multiplying each intensity level (0 for no stain, 1 for faint stain, and 2 for intense stain) by the corresponding percentage of cells (0–100%) at the corresponding intensity and totaling the results. IHC scores ranged from 0 (no staining in any cell) to 200 (intense staining in 100% of the cells).
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6

Chromatin Immunoprecipitation and Sequencing

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Chromatin immunoprecipitations were performed as previously described104 (link). Nuclear lysates were incubated with 7.5 μl of GR antibody (D6H2L, Cell Signalling Technology) pre-bound to 50 μl of protein A beads per samples. Immunoprecipitated DNA was processed for library preparation (0801-0303, KAPA biosystems kit). Samples were sequenced using an Illumina Hiseq2500 genome analyser (65 bp reads, single end), and aligned to the Human Reference Genome (hg19, February 2009). Reads were filtered based on MAPQ quality ((samtools v1.8); quality ≥20) and duplicate reads were removed (Picard MarkDupes v2.18). Peak calling over input control was performed using MACS2 (v2.1.1) peak caller. MACS2 was run with the default parameters. Genome browser snapshots, heatmaps and density plots were generated using EaSeq (http://easeq.net)105 (link).
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7

Immunohistochemical Analysis of Tumor Markers

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Serial tissue sections of 4-μm thickness, containing the deepest area of the tumor invasion, were depara nized in xylene, rehydrated in graded alcohol, and immersed in 3.0% hydrogen peroxide in methanol for 10 min at room temperature to inhibit endogenous peroxidase activity. For antigen retrieval, the tissue slides for GR, Sgk1, and NDRG1 immunohistochemistry were heated in an autoclave at 121 °C for 5 min in 0.01 M citrate buffer (pH 6.0). After washing three times for 5 min each in phosphate-buffered saline (PBS), the reacted slides were incubated in 1% normal goat serum for 30 min at room temperature to reduce nonspeci c antibody binding and then incubated at 4 °C overnight with rabbit monoclonal antibody against GR (D6H2L, Cell Signaling Technology, Danvers, MA, USA, diluted 1/400), Sgk1 (Y238, Abcam, Cambridge, UK, diluted 1/200), or NDRG1 (EPR5593, Abcam, diluted 1/400). The reacted sections were then washed three times for 5 min each in PBS, incubated with biotinylated anti-rabbit immunoglobulin (Nichirei Biosciences, Inc., Tokyo, Japan), washed three times for 5 min each in PBS, and incubated with peroxidaselabeled streptavidin (Nichirei Biosciences, Inc.) for 30 min at room temperature. Immunoreactivity was visualized with 3,3 ′ -diaminobenzidine, and the slides were counterstained with Mayer's hematoxylin, dehydrated in graded alcohol, and cleared in xylene.
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8

Immunohistochemical Analysis of Tumor Markers

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Serial tissue sections of 4-μm thickness, containing the deepest area of the tumor invasion, were depara nized in xylene, rehydrated in graded alcohol, and immersed in 3.0% hydrogen peroxide in methanol for 10 min at room temperature to inhibit endogenous peroxidase activity. For antigen retrieval, the tissue slides for GR, Sgk1, and NDRG1 immunohistochemistry were heated by autoclave at 121°C for 5 min in 0.01 M citrate buffer (pH 6.0). After washing three times for 5 min each in phosphate-buffered saline (PBS), the slides were incubated in 1% normal goat serum for 30 min at room temperature to reduce nonspeci c antibody binding and then incubated at 4°C overnight with rabbit monoclonal antibody against GR (D6H2L, Cell Signaling Technology, Danvers, MA, USA, diluted 1/400), Sgk1 (Y238, Abcam, Cambridge, UK, diluted 1/200), or NDRG1 (EPR5593, Abcam, diluted 1/400). The reacted sections were then washed three times for 5 min each in PBS, incubated with biotinylated anti-rabbit immunoglobulin (Nichirei Biosciences, Inc., Tokyo, Japan), washed three times for 5 min each in PBS, and incubated with peroxidase-labeled streptavidin (Nichirei Biosciences, Inc.) for 30 min at room temperature. Immunoreactivity was visualized with 3,3 ′ -diaminobenzidine, and the slides were counterstained with Mayer's hematoxylin, dehydrated in graded alcohol, and cleared in xylene.
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9

Immunohistochemical Analysis of Tissue Samples

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Serial tissue sections of 4-μm thickness, containing the deepest area of the tumor invasion, were deparaffinized in xylene, rehydrated in graded alcohol, and immersed in 3.0% hydrogen peroxide in methanol for 10 min at room temperature to inhibit endogenous peroxidase activity. For antigen retrieval, the tissue slides for GR, Sgk1, and NDRG1 immunohistochemistry were heated in an autoclave at 121 °C for 5 min in 0.01 M citrate buffer (pH 6.0). After washing three times for 5 min each in phosphate-buffered saline (PBS), the reacted slides were incubated in 1% normal goat serum for 30 min at room temperature to reduce nonspecific antibody binding and then incubated at 4 °C overnight with rabbit monoclonal antibody against GR (D6H2L, Cell Signaling Technology, Danvers, MA, USA, diluted 1/400), Sgk1 (Y238, Abcam, Cambridge, UK, diluted 1/200), or NDRG1 (EPR5593, Abcam, diluted 1/400). The reacted sections were then washed three times for 5 min each in PBS, incubated with biotinylated anti-rabbit immunoglobulin (Nichirei Biosciences, Inc., Tokyo, Japan), washed three times for 5 min each in PBS, and incubated with peroxidase-labeled streptavidin (Nichirei Biosciences, Inc.) for 30 min at room temperature. Immunoreactivity was visualized with 3,3 ′ -diaminobenzidine, and the slides were counterstained with Mayer's hematoxylin, dehydrated in graded alcohol, and cleared in xylene.
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