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13 protocols using pparg

1

Western Blot Analysis of Adipogenic Markers

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Proteins 5–35 μg were loaded onto a 7%−14%
poly-acrylamide for gel electrophoresis and transferred to polyvinylidene
difluoride (Pvdf) membranes. After the membranes were immersed in a blocking
buffer (3% milk in TBST) for 30+ minutes at room temperature on a shaker, the
membranes were treated with primary antibody overnight at 4°C.
Antibodies: Pparg, (Cell Signaling); lamin B1, lamin A/C, Arp3 (Abcam); mDia1
(BD); mDia2 (ECM Biosciences, Versailles, Kentucky); Fabp4 (ProSci, Poway,
California); actin, (Santa Cruz); Adipoq (Affinity Bioreagents, Golden,
Colorado). Secondary antibody conjugated with horseradish peroxidase was
detected with Super Signal West Pico Plus chemiluminescent substrate (Thermo
Fischer Scientific, Waltham, Massachusetts).
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2

Immunohistochemical Analysis of Breast Tumors

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Tissue microarrays (1.0 mm cores, 4 μm sections) were analyzed with antibodies against CCNB1 (Y106, Epitomics), EGFR (3C6, Ventana), FOXA1 (2F83, Abcam), FOXM1 (C-20, Santa Cruz), GATA3 (D13C9, Cell Signaling), phospho-HISTH3 (Ser10) (#9701, Cell signaling), KRT5 (EP1601Y, Thermo Scientific), LAMA5 (4C7, Dako), PLK1 (208G4, Cell signaling), PPARG (C26H12 Cell Signaling), RXRA (F-1, Santa Cruz), STAT3 (124H6, Cell signaling), phospho-STAT3 (Tyr705) (D3A7, Cell signaling). Cores were evaluated as blinded digitalized image files. For quantitatively staining markers (EGFR, FOXA1, GATA3, KRT5, PPARG, RXRA, STAT3) a tumor cell score (TCS) was defined as described in Sjödahl et al. [4 (link)]. For discrete cellular labeling (CCNB1, FOXM1, PLK1, p-STAT3), fractions of positive tumor cells was recorded. The mean tumor cell score of core pairs from the same sample was calculated. The number of cores evaluated for each marker ranged from 480 to 524. Mitotic figures were identified by the phospho-HISTH3 (Ser10) antibody and basal lamina by anti-Laminin α-5 staining. When possible, lines were drawn through the plane of the mitotic figure (in the direction of the cell division), and tangentially along the nearest basal lamina (Photoshop CS5 version 12.1), and the distance, in cell layers, to the basal membrane recorded. A total of 416 mitoses from 112 different tumors were analyzed.
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3

Multimodal Analysis of Adipose Tissue

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qPCR and western blotting were done according to standard methods. For qPCR from whole tissues or TRAP samples, all values were normalized by the ΔΔCt method to Tbp or to Actb, respectively. RNA-Seq was performed by the Dana-Farber Cancer Institute Center for Cancer Computational Biology Sequencing Facility (see Supplemental Experimental Procedures for details). The following antibodies were used: UCP1 (catalog #ab10983, Abcam), GFP (catalog #ab290, Abcam, for immunoaffinity purifications and Western blotting), GFP (catalog #NB-100–1678, Novus, for immunohistochemistry), perilipin (catalog #ab61682, Abcam) β-actin (catalog #ab20272, Abcam), and PPARG (catalog #2435, Cell Signaling).
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4

Western Blot Analysis of Cell Proteins

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Whole cell lysates were prepared with lysis buffer (150 mM NaCl, 50 mM Tris HCl, 1 mM EGTA, 0.24% sodium deoxycholate, 1% Igepal, pH 7.5) containing 25 mM NaF and 2 mM Na3VO4, aprotinin, leupeptin, pepstatin, and phenylmethylsulfonyl fluoride were added before each lysis. Fractionated or whole lysate proteins of 5–20 μg were loaded onto a 7%–10% poly-acrylamide gel for chromatography and transferred to polyvinylidene difluoride membrane. After blocking, primary antibody was applied overnight at 4°C including antibodies against Bglap, Pparg, PARP1 (Cell Signaling, Danvers Mass); Runx2, mDia2, MKL-1, importin-9, Arp3 (Abcam), mDia1 (BD), LDHA (Millipore, St Louis, Mo), Fabp4 (ProSci, Poway, CA), actin, beta-tubulin (Santa Cruz, Dallas TX), Adipoq (Affinity Bioreagents, Golden, CO). Secondary antibody conjugated with horseradish peroxidase was detected with ECL plus chemiluminescence kit (Amersham Biosciences, Piscataway NJ). The images were acquired with an HP Scanjet and densitometry determined using NIH ImageJ, 1.37v.
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5

Caspase-1 Expression in Developing Mouse Limbs

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Mouse front limbs (CD1 strain) were collected as fresh post mortem samples. Stages E12, E15, and E18 were examined. Histological sections were deparaffinized in xylene and rehydrated in a gradient series of ethanol. Sections were pre-treated in citrate buffer (10 min/98 °C) for antigen retrieval and then incubated with Caspase-1 p20 (Cleaved Asp296) Antibody (PA5-99390, Thermo Fisher Scientific) overnight. The primary antibody was followed by incubation with secondary anti-rabbit antibody Alexa Fluor® 488 (Thermo Fischer Scientific, Waltham, MA, USA) for 40 min at RT. Nuclei were detected by ProLong® Gold Antifade reagent with DAPI (Thermo Fischer Scientific).
For immunocytofluorescence, micromass cultures were grown on culture glass and fixed by 4% paraformaldehyde. Primary antibodies for Caspase-1 p20 (PA5-99390, Thermo Fisher Scientific), Cd36 (PA1-16813, Thermo Fisher Scientific), Pparg (2443, Cell Signaling Technology, Danvers, MA, USA), and Rankl (PA5-110268, Thermo Fisher Scientific) were diluted in the range 1:50–1:200 and were applied overnight/4 °C. Alexa Fluor® 488 or 568 (A11034, A10037, Thermo Fischer Scientific) was diluted at 1:200 and then applied for 40 min/RT. The cytoskeleton was visualized by ActinGreenTM 488 ReadyProbesTM Reagent (Thermo Fischer Scientific), and nuclei were detected by ProLong® Gold Antifade reagent with DAPI (Thermo Fischer Scientific).
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6

Chromatin Immunoprecipitation of PPARG

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RF24 cells were cultured in a hypoxic condition for 16 h. After hypoxic culture, ChIP assays were performed by using an EZ ChIPTM kit (Millipore, Temecula, CA) according to the manufacturer’s instructions. In brief, cross-linked cells were collected, lysed, sonicated, and subsequently subjected to immunoprecipitation with PPARG (Cell Signaling) antibody or IgG control. Immunocomplexes were collected with protein G agarose beads and eluted. Cross-links were reversed by incubating at 65 °C. DNA was then extracted and purified for subsequent PCR amplification with the use of gene-specific primers. Negative control forward: GCAGTGAGAAAGCAGGTTTG, negative control reverse: CATAATCCAGGGTCATGGTG. PPARG binding region forward: TCCTTTCCTCTGGAACATGC, PPARG binding region reverse: TAAGAGGAGGGACAAAGACAGG.
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7

Antibody-based Signaling Pathway Analysis

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Antibodies against mTOR, phospho-mTOR, IRS2, AKT, phospho-AKT-308, NF-kappaB, phospho-NF-kappaB, JNK, phospho-SAPK/JNK (Thr183/Tyr185), PPAR-g, F4/80, SREBP, and GAPDH were purchased from Cell Signaling Technology (USA).
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8

Protein Expression Analysis in Placenta

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Total protein from both the placental samples and trophoblast cells was extracted using RIPA lysis buffer, and quantified using the Bradford method (Thermo Fisher Scientific, Waltham, MA, USA). A total of 20 μg protein of each sample was electroblotted onto PVDF membranes (Millipore, Burlington, MA) after sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separation [12 (link)]. Protein signals were developed using an enhanced chemiluminescence kit (Bio-Rad, Irvine, CA) and quantified with a ChemiDoc system (Bio-Rad, Irvine, CA). The primary antibodies and dilutions are listed as following: rabbit polyclonal antibodies against adiponectin (1:500, Proteintech, Wuhan, China), fatty acid binding protein 4 (FABP4) (1:1000, Abcam, Cambridge, UK), peroxisome proliferator activated receptor gamma (PPARg) (1:1000, Cell Signaling Technology, Boston, MA, USA), acetyl-CoA carboxylase (ACC) (1:1000, Cell Signaling), ERK1/2 (1:1000, Cell Signaling), phospho-ERK1/2 (1:1000, Cell Signaling), low density lipoprotein receptor (LDLR) (1:1000, Thermo Fisher), mouse monoclonal antibodies against sterol regulatory element-binding protein 2 (SREBP2) and sterol regulatory element-binding protein 1 (SREBP1) (1:1000, Santa Cruz Biotechnology, Santa Cruz, CA, USA), β-actin (1:5000, Sigma-Aldrich) and sortilin 1 (SORT1) (1:1000, BD Bioscience, Ann Arbor, MI, USA).
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9

Western Blot Analysis of Metabolic Regulators

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Whole cell lysates were electrophoretically separated on denaturing polyacrylamide gels and transferred to polyvinylidene difluoride membranes. Proteins were detected with USF1 (sc-229, Santa Cruz Biotechnology), FLAG (F1804, Merck), PPARg (2443, Cell Signaling Technology), SREBP1 (sc-365514, Santa Cruz Biotechnology), FASN (3180 Cell Signaling Technology), and β-actin antibody (G043, abm).
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10

Protein Extraction and Immunoblotting

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Tissues were lysed on ice in lysis-buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 6 mM EGTA, 20 mM NaF, 1% Triton X-100, and protease inhibitors) for 15–20 min. After centrifugation at 13000 rpm for 15 min, supernatants were collected for protein determinations and SDS-PAGE analysis. The following antibodies were used: pS245-Hdac4 (#3443), Hdac4 (#7628), Sik2 (#6919), Cox4 (4850), Pparg (#2435), and phosphor-PKA substrate (#9624) antibodies (Cell Signaling Technology), Hsp90 (Santa Cruz Biotechnology, #SC-7947), Ucp1 (Sigma, U6382), mt-Co1 (Abcam, #ab110413), mt-Co2 (Proteintech, #55070–1-AP), Cox5b (Bethyl, #A-305–523A), Cox6b (Abgent, #AP20624a), Hsp60 (Bethyl, #A302–846A), Hk1 (Proteintch, #19662-1-AP). Immunoblots were quantified using Image J software.
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