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10 protocols using p pras40 thr246

1

Western Blot Analysis of AKT/mTOR Pathway

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Western blots were performed as described previously [52 (link)]. Briefly, cells were lysed in RIPA buffer supplemented with phosphatase (Sigma–Aldrich) and protease inhibitors (Sigma–Aldrich) and equal amounts of protein were loaded and separated by SDS-PAGE and transferred onto a PVDF membrane. Membranes were probed with primary antibody then with appropriate horseradish peroxidase-conjugated secondary and incubated with ECL. Antibodies obtained from Cell Signalling: AKT-T (#9272), pAKT-Ser473 (#4060), pAKT-Thr308 (2965), S6 (#2217), pS6-Ser235/236 (#2111), PRAS40 (#2691), pPRAS40-Thr246 (#13175), TSC2 (#4308), PARP (#9532, #9542), MCL1 (#9429), BAD-T (#9239), BAD-P Ser 136 (#4366), Bcl-XL (#2764), Bcl-w (#2724), BAX (#5023, #2772), BAK (#12105, #6947), Bim (#2933), BID (#2002), Puma (#4976), SHIP2 (#2839). Other antibodies used were Bcl-2 (ab32124, Abcam), and HRK (#ab45419, Abcam) Actin (A2228, Sigma), Vinculin (#V9132, Sigma) PIK3R2 (#A302-593A, Bethyl Laboratories), Caspase-3 (#14220). Secondary antibodies used were HRP-linked anti-rabbit IgG (CST#7074,1:2000) and HRP-linked anti-mouse IgG (CST#7076, 1:2000).
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2

Immunohistochemical Analysis of Tumor Biomarkers

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IHC of pPRAS40 (Thr246), pAKT (Ser473), and cleaved PARP were conducted on 5-mm tissue sections of FFPE tumor biopsy cores as described previously using the EnVision + Single Reagents HRP-Rabbit (Dako, cat. no. K4003) and REAL substrate buffer (REAL DAB + chromogen, Dako, cat. no. K3468; ref. 30 (link)). The primary antibodies and dilutions are as follows: pAKT (Ser473; 1:200, Cell Signaling Technology, cat. no. 4060), pPRAS40 (Thr246; 1:200, Cell Signaling Technology, cat. no. 2997), and cleaved PARP (Asp214; 1:200, Cell Signaling Technology, cat. no. 9541). Abreast cancer xenograft model treated with either vehicle or MK-2206 was used as positive/negative control for staining. Allred score was used to quantify pAKT and pPRAS40 tumor staining (31 (link)). Briefly, based on reviewing the entire immunostained slide, a proportion score (PS) was assigned representing the estimated proportion of positive staining target cells (0 = none; 1 = ≤ 1%; 2 = 1%–10%; 3 = 11%–33%; 4 = 34%–66%; 5 = 67%–100%). Then, an intensity score (IS) was assigned representing the estimated average intensity of positive target cells (0 = none; 1 = weak; 2 = intermediate; 3 = strong). The PS and IS were then added to obtain a total score (TS, i.e., the Allred score), ranging from 0 to 8.
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3

Immunoblot Analysis of AKT Pathway

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All antibodies were purchased from Cell Signaling Technology: p-AKT Ser473 (#4060, 1:1000), p-AKT Thr308 (#2965, 1:1000), AKT (#4691, 1:1000), p-PRAS40 Thr246 (#2997, 1:1000), PRAS40 (#2691, 1:1000), PARP (#9542, 1:1000), p-S6 Ser240/244 (#2215, 1:1000), p-RxxS/T (#9614, 1:1000); HA-tag (#2367, 1:1000); xCT/SLC7A11 (#12691, 1:1000); β-actin (#4970, 1:5000); conformation specific mouse anti-rabbit IgG HRP conjugate (#5127, 1:3000).
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4

Phospho-Kinase Array Analysis of Cell Signaling

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Protein kinase activity was analyzed using a human phospho-kinase array (R&D systems; catalog number ARY003B) to identify signaling pathways that were especially active in the KLA cells compared to LEC. Cell lysates (375μg protein) were prepared from confluent cells cultured in EGM-2MV media. Array assays were performed according to manufacturer’s protocol and imaged using Kodak X-ray film. Films were imaged on a scanner and signals quantitated by densitometry. Results from the array were confirmed by performing western blot analysis on cell lysates with antibodies for phospho-AKT (Cell Signaling Technology; Ser473 catalog number 4060 and Thr308 catalog number 2965), phospho-Proline-Rich AKT Substrate of 40 kDa (Cell Signaling Technology; p-PRAS40 Thr246; catalog number 22997), phospho-p44/42 MAPK (ERK1/2)(Cell Signaling Technology; catalog number 9101). Total AKT (Cell Signaling Technology; catalog number 9272), PRAS40 (Cell Signaling Technology; catalog number 2691), ERK-1/2 (Cell Signaling Technology; Cell Signaling Technology; catalog number 9102), and C4 actin (Chemicon; catalog number MAB1501) were also assessed.
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5

PI3K/AKT/mTOR Signaling Pathway

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PI3 Kinase (p85), PI3 Kinase (p110), p-AKTSer473, p-AKTThr308, p-mTORSer2448, p-4EBP1Ser65, p-eIF4ESer209, p-p70S6K, p-AMPKαThr172, p-PRAS40Thr246, Rictor, Raptor, GβL and vinculin antibodies were obtained from Cell Signaling Technology (Danvers, MA). Antimouse and antirabbit secondary antibodies conjugated to horseradish peroxidase were obtained from Amersham Life Science Inc. (Arlington Height, IL). Fisetin and 5-FU were purchased from Sigma Chemical Co. (St. Louis, MO). Novex precast Tris-glycine gels were from BioRad (Hercules, CA). BCA Protein assay kit was obtained from Pierce (Rockford, IL). The Annexin-V-FLUOS staining kit was purchased from Roche Diagnostics GmbH, Mannheim, Germany.
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6

Protein Expression Analysis by Western Blot

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Boiled whole cell lysates were run on a precast Tris-acetate (Thermo Fisher Scientific) or Mini-PROTEAN TGX protein gel (Bio-Rad) and then transferred to a nitrocellulose membrane (Bio-Rad). The membrane was incubated overnight at 4 °C with primary antibodies against Cas9 (1:1,000; Active Motif 61577), Pten (1:1,000; Cell Signaling Technology 9188), ERG (1:1,000; Abcam ab92513), p53 (1:1,000; Cell Signaling Technology 2524), Apc (1:1,000; Millipore MABC202), AKT1 (1:2,000, Cell Signaling Technology 4060L), AKT2 (1:1,000, Cell Signaling Technology 5239S), pPRAS40-Thr246 (1:1,000, Cell Signaling Technology 2997S), Actin-HRP (horseradish peroxidase) (1:10,000; Abcam ab49900), Cyclophilin B (1:10000; Cell Signaling Technology 43603S) and Vinculin (1:10,000; Cell Signaling Technology 13901). Signal was visualized with secondary HRP-conjugated antibodies and chemiluminescent detection.
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7

Western Blot Protein Analysis Protocol

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Frozen xenograft samples or pelleted cells were lysed using a buffer of Mammalian Protein Extraction Reagent (Thermo Scientific, Tewksbury, MA) supplemented with kinase, protease and phosphatase inhibitors (Sigma-Aldrich, St. Louis, MO). Protein lysates were resolved on 10% Bis-Tris gels (NuPAGE Novex, Life Technologies) and transferred to PVDF membranes (Millipore, Billerica, MA). After blocking, membranes were incubated overnight with the primary antibody at 4°C. Primary antibodies directed against phospho-Akt (p-Akt, Thr308), Akt, phospho-Erk1/2 (p-Erk1/2, Thr202/Tyr204), Erk1/2, phospho-PRAS40 (p-PRAS40, Thr246), PRAS40, phospho-p70S6K (p-p70S6K, Thr389) and p70S6K (all Cell Signaling, Danvers, MA) were used. The dilution for all primary antibodies was 1:1000. The blots were then probed with a horseradish peroxidase conjugated goat anti-rabbit secondary antibody (Santa Cruz Biotechnology, Dallas, TX) and developed using a chemiluminescent detection reagent (ECL Prime, GE Healthcare Life Sciences, Pittsburgh, PA). Each blot was stripped with 1 M glycine when the same membrane was used to re-probe with another primary antibody. Finally, all membranes were stripped and re-probed with either a mouse anti-Pan-actin antibody (1:10000, NeoMarkers, Fremont, CA) or a rabbit anti-GAPDH antibody (1:1000, Cell Signaling) to verify equal protein loading.
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8

Western Blot Analysis of Cellular Proteins

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Cells and lungs from dissected animals of all genotypes and cell lines were homogenized and lysed in 50 nM Tris, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% NP-40, 1 mM sodium orthovanadate (Na3VO4), 10 mM NaF, and protease inhibitor cocktail (Roche) and cleared by centrifugation; concentrations were determined by protein assay (Bio-Rad Laboratories), and samples were combined with SDS sample loading buffer followed by brief sonication and centrifugation. The supernatant was collected for Western blotting. Western blotting was done using the following polyclonal antibodies from Cell Signaling Technology: Myc-tag (#2272), p-Akt Ser473 (#4051), p-S6 ribosomal protein Ser235/236 (#4856), and p-PRAS40 Thr246 (#2997), as published. Other polyclonal antibodies used were IPO11 (AP9661b; Thermo Fisher Scientific), UBE2E1, UBE2E3, NEDD4-1 (07-049; EMD Millipore), Ndfip1 (HPA009682; Sigma-Aldrich), and Ub (P4D1; Santa Cruz Biotechnology, Inc.). mAbs used were HA-tag (12CA5; homemade), β-actin (A5441; Sigma-Aldrich), γ-tubulin (T6199; Sigma-Aldrich), GFP (JL-8; Takara Bio Inc.), and c-Myc (ab32072; Abcam). Western blots were developed using the enhanced chemiluminescence detection reagent (EMD Millipore) or the Odyssey Infrared Imaging System (LI-COR Biosciences). Quantification was done using the LI-COR system or densitometry using ImageJ 1.38X software (National Institutes of Health).
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9

Comprehensive Molecular Profiling of Cellular Signaling

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The monoclonal antibodies against ADCY5, pmTOR(S2448), mTOR, pPRAS40 (Thr246), PRAS40, FoxO3a, LC3B, GSK-3β (S9P), IR, PCDNA and pJNK, senescence β-gal staining kit, and SimpleChIP chromatin IP kit were obtained from Cell Signaling (Beverly, MA, USA). Polyclonal antibodies against MKP7, RGS2, pEGFR, EGFR, pERK, ERK2, pMEK1, MEK1, IRS1, Cav2, cyclin D1, and c-myc were obtained from Santa Cruz Biotechnology (Dallas, TX, USA). The monoclonal antibodies against HIF1α, pAKT, and β-actin were obtained from Abcam (San Francisco, CA, USA). Horseradish peroxidase-conjugated goat anti-mouse IgG and horseradish peroxidase-conjugated goat anti-rabbit IgG were obtained from Bio-Rad (Hercules, CA, USA). Immunoblotting was performed using the ECL western blot detection kit (enhanced chemiluminescence; Amersham Biosciences, Amersham, UK). miRNA RT and PCR kits were obtained from Qiagen (Valencia, CA, USA). cAMP assay kit was obtained from R&D (Minneapolis, MN, USA).
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10

Intracellular Signaling Pathway Analysis

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FACS sorted CD15+ or CD15- cells were treated with different concentrations of inhibitors or DMSO for 30 minutes and then stimulated with IGF 50 ng/ml for 30 minutes. Cells were lysed with RIPA lysis buffer (Pierce) containing protease inhibitor cocktail. Proteins were quantitated by the BCA protein assay (Pierce) and equal amounts of protein were resolved by polyacrylamide gels, transferred to nitrocellulose membrane and probed with following primary antibodies: p-AKT(Ser473) (cat no. 9271), p-AKT(Thr308) (cat no. 9275), AKT(cat no. 9272), p-p70S6K(Thr389) (cat no. 9205), p70S6K (cat no. 2708), p-4EBP1(Thr37/46) (cat no. 2855), 4EBP1(cat no. 9452), pERK(Thr202/Tyr204) (cat no. 9101), p-PRAS40(Thr246) (cat no. 2997), PRAS40 (cat no. 2610), p27 Kip1 (cat no. 2552), p-MDM2(S166) (cat no. 3521), Bad (cat no. 9292) and PARP(cat no. 9542) (all from Cell Signaling Technologies); p21 Cip1/Waf1 (sc-397), Bax (sc-493) and β-actin (sc-47778) from Santacruz.
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