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6 protocols using ab169197

1

GSK-J4 Inhibitor Effects on JMJD3, Rb, and p21

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GSK-J4, a UTX-specific pharmacological inhibitor (SML0701, Sigma-Aldrich, St. Louis, Missouri, USA), reconstituted in DMSO, with different concentrations (0, 2, 4, 8 µM) were given to these cells for 48 h. Whole-cell lysates of GSK-J4 treated cells were extracted using the fixture of RIPA lysis buffer (50 mM Tris, 150 mM NaCl, 1% NP40, 0.5% sodium deoxycholate, and 0.1% sodium dodecyl sulfate (SDS)) and subjected to western blot analyses. The membranes were incubated with primary antibodies against JMJD3 (ab169197, 1:2000, Abcam, Cambridge, MA, USA), Rb (#9309, 1:1000, cell signaling, Danvers, Massachusetts, USA), phosphorylated Rb (pRb) (ab173289, 1:1000, Abcam, Cambridge, UK), p21 (#2947, 1:1000, Cell Signaling, Danvers, Massachusetts, USA) and β-actin (A5441, 1:10000, Sigma-Aldrich, St. Louis, Missouri, USA) at 4 °C overnight. After that, the membranes were incubated with secondary antibodies for one hour at room temperature to reveal the immune detection. The protein signals were detected with Western Lightning Chemiluminescence Reagent Plus (Amersham Biosciences). All the experiments were repeated at least three times with similar results.
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2

AMPK and TRIM11 Pathway Analysis

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Tissue or cells samples were lysed with ice‐cold RIPA buffer with complete protease and phosphatase inhibitors. The protein concentrations were measured using BCA protein assay kit. Total proteins were separated by SDS–PAGE and transferred onto polyvinylidene difluoride (PVDF) membranes. The membranes were incubated with primary antibodies: AMPK (1:1000, ab169197, abcam) and p‐AMPK (1:1000, 3934, Cell Signaling Technology, Inc.), TRIM11 (1:1000, ab191217, abcam), GPX4 (1:1000, ab267373, abcam), and β‐Actin (1:5000, Santa Cruz Biotechnology) after blocking with 5% BSA in TBS, followed by incubation with peroxidase‐conjugated secondary antibodies (Santa Cruz Biotechnology). The signals were detected with the ECL system and exposed by the ChemiDoc XRS system with Image Labsoftware (Bio‐rad).
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3

Western Blot Analysis of Signaling Proteins

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Cell lysates were obtained by extraction with protein lysis buffer supplemented with protease inhibitors. Lysates were then resolved using SDS-PAGE. The protein gel is then transferred to a PVDF membrane and closed with 5% skim milk powder and incubated overnight at 4 °C with the primary antibody. The PVDF membrane is then incubated with the appropriate secondary antibody. Signals were analyzed using ECL detection reagents (Millipore, St. Louis, MO, USA). The antibodies used in this study are as follows: anti-KDM6B (ab169197, Abcam), anti-β-actin (60008-1, Proteintech, Wuhan, PR China), anti-CXCR4 (ab181020, Abcam), anti-E-Cadhrein (3195, Cell Signaling Technology), anti-N-Cadhrein (13116, Cell Signaling Technology), anti-AKT (4691, Cell Signaling Technology), anti-p-AKT (4064, Cell Signaling Technology), anti-ERK (4695, Cell Signaling Technology), and anti-p-ERK (4370, Cell Signaling Technology).
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4

Comprehensive Protein Expression Analysis

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RIPA cell lysate was used to extract cellular proteins, and the BCA Protein Assay Kit (Abcam) was used to quantify the proteins. The SDS-PAGE gel was prepared, and 6 μL of denatured protein was added to each well for electrophoresis and transferred to a PVDF membrane. The primary antibodies were as follows: rabbit anti-β-actin (4970, Cell Signaling), rabbit anti-cleaved CASP-3 (ab32042, Abcam), rabbit anti-BIRC5 (ab196495, Abcam), rabbit anti-CASP-9 (ab2324, Abcam), rabbit anti -EZH2 (49–1043, Invitrogen), rabbit anti-SMYD3 (ab187149, Abcam), rabbit anti-KDM6A (ab253183, Abcam), rabbit anti-KDM6B/JMJD3 (ab169197, Abcam), rabbit anti-ESET (2196, Cell Signaling), and rabbit anti-histone H3 (tri methyl K27) (ab192985, Abcam). Goat anti-rabbit IgG H&L (HRP) (ab6721, Abcam) was used as the secondary antibody. Immobilon Western Chemiluminescent HRP Substrate (Millipore) was used for exposure; images were acquired using a gel imaging system, and quantitative analysis was performed by ImageJ.
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5

Protein Extraction and Western Blot Analysis

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Total protein extractions were performed using RIPA buffer with 1% protease inhibitor and 1% phosphatase inhibitor cocktails (Sigma-Aldrich) according to the manufacturer's instructions. Protein concentrations were determined by the Bradford method (Bio-Rad Laboratories, Hercules, CA, USA). 35 μg of all protein samples were separated on 4–15% Mini-PROTEAN® TGX™ Precast Protein Gels (Bio-Rad Laboratories) and transferred to nitrocellulose membranes (Bio-Rad Laboratories).
Membranes were blocked for 1 h at room temperature with 5% milk in TBST buffer (1X Tris-buffered saline, 0.1% Tween). Primary antibodies used were: anti-EZH2 (1:500, #C15410039, Diagenode, Seraing, Belgium) anti-JMJD3 (1:750, #ab169197, Abcam, Cambridge, UK) and anti-GAPDH (1:5000, #sc-25778, Santa Cruz Biotechnologies, Dallas, TX, USA). After three washes, membranes were blocked with secondary antibody anti-rabbit ads-HRP (1:5000, #4050-05, Southern Biotech, Birmingham, AL, USA).
Membranes were incubated in ECL Clarity Western Substrate (Bio-Rad Laboratories) and detection was performed on a ChemiDoc™ Touch Imaging System (Bio-Rad Laboratories) coupled with Image Lab™ Touch Software; quantification was expressed as the ratio of proteins over GAPDH densities.
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6

Chromatin Immunoprecipitation (ChIP) Protocol

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For ChIP analysis, cells were fixed with 1% formaldehyde for 15 min at room temperature, and then quenched with 2.5 M glycine. Subsequently, the cells were lysed on ice for 10 min in SDS buffer containing protease inhibitors, and then sonicated with Sonics Vibra CellTM (Sonics & Materials Inc., CT, USA; 7 min: 10 s pulse, 10 s interval) on ice. The fragmented chromatin samples were centrifuged at 8000 ×g at 4 °C for 5 min and the supernatant was collected. The samples were pre-cleared, and then incubated overnight at 4 °C with the appropriate antibodies and protein-coated A/G agarose beads (Santa Cruz) with gentle shaking. The immunoprecipitated eluates were reverse cross-linked and recovered through DNA purification for PCR. Anti-H3K4me3 (ab1012; Abcam), anti-H3K9ac (ab12179; Abcam), anti-H3K27me3 (ab6002; Abcam), anti-EZH2 (#5246S; Cell Signaling), anti-SUZ12 (#3737; Cell Signaling), anti-EED (ab96801; Abcam), anti-UTX (ab36938; Abcam), anti-JMJD3 (ab169197; Abcam), and non-immune mouse IgG (sc2025; Santa Cruz) antibodies were used. ChIP-PCR primers are listed in Table 2.
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