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14 protocols using pher3

1

Comprehensive Protein Analysis of Cellular Responses

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Whole-cell extracts of untreated and treated cells were used in Western blot analysis as described previously [53 (link)]. Antibodies against p-EGFR (cat no. 3777; 1 : 1000), EGFR (cat no. 2232; 1 : 1000), p-MET (cat no. 3077; 1 : 1000), MET (cat no. 8198; 1 : 1000), p-HER3 (cat no. 4791; 1 : 1000), HER3 (cat no. 12708; 1 : 1000), p-AKT (cat no. 9271; 1 : 1000), AKT (cat no. 9272; 1 : 1000), GAPDH (cat no. 5174; 1 : 1000), vimentin (cat no. 5741; 1 : 1000), snail (cat no. 3879; 1 : 1000), and MMP-9 (cat no. 13667; 1 : 1000) were from Cell Signaling Technology (Danvers, Massachusetts, USA). P-ERK1/2 (cat no. sc7383; 1 : 1000) and ERK2 (cat no. sc1647; 1 : 1000) antibodies were purchased from Santa Cruz Biotechnology (Dallas, Texas, USA).
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2

Assessing Receptor Tyrosine Kinase Activation

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Cells were seeded into 24-well plates and treated with compounds for 2 h on the following day. Growth medium was removed and cells were lysed. Protein was resolved by SDS-PAGE and transferred to polyvinylidene fluoride membranes. The antibodies used in this study were specific for EGFR (#2232), HER2 (#2242), pHER2 (Tyr1248; #2247), pHER3 (Tyr1289; #4791), pAkt (Ser473; #9271, Cell Signaling Technology), HER3 (C-17, Santa Cruz Biotechnology), and GAPDH (ab9484-100, Abcam).
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3

Western Blot Protein Analysis

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Western blotting was carried out as described previously [24 (link)]. Antibodies used included p-AKT S473, total AKT, p-4EBP1, total 4EBP1, p-S6RP, total S6, p-HER3, p-ERK, and p-PDK1 (all from Cell Signaling), and tubulin (Invitrogen) and actin (Santa Cruz) as controls. Images were captured using Bioluminescent imaging (Invitrogen) and x-ray film (Kodak) or with Alexa dyes and an Odyssey imaging system.
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4

Immunohistochemical Profiling of FFPE Tissues

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5 μm sections from FFPE tissue were mounted on glass slides, air dried at 56°C overnight and subjected to immunostaining using an automated platform (Ventana Discovery XT, Tucson, AZ, USA). The following primary antibodies and dilutions were used: pERK1/2 1:300, pAkt(Ser473) 1:30, pEGFR 1:110, pmTOR 1:130, pHer3 1:70 (all from Cell Signaling Technology Inc., Danvers, MA, USA). After staining, sections were treated with ascending ethanol concentrations and xylene and were finally covered with Pertex (Medite GmbH, Burgdorf, Germany). Sections were examined under a light microscope by a pathologist. Tumor cell staining was classified as absent, weak, moderate, or strong and a staining score was calculated based on the extent of staining according to the formula: score = 3 × percentage of strongly stained tumor cells + 2 × percentage of moderately stained tumor cells + 1 × percentage of weakly stained tumor cells. All IHC staining protocols used within this study are “fit for purpose” and validated according to FDA guidelines, and staining procedures were also conducted according to standard operating procedures. Therefore, assays are controlled in terms of specificity and accuracy.
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5

Western Blot Analysis of Signaling Pathways

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Cells were harvested after indicated treatment and suspended in RIPA lysis buffer (Solarbio, Beijing, China) with protease inhibitor and phosphatase inhibitors (1 mM sodium fluoride and 2 mM sodium orthovanadate and 1 mM phenylmethylsulfonyl fluoride [PMSF]) on ice for 30 min, centrifuged at 13 500 g for 10 min to collect the whole cell lysates. The proteins (20 μg for most proteins and 40–50 μg for ErbB receptors) were separated on an 8% SDS–PAGE and transferred onto a polyvinylidene fluoride (PVDF) membrane (Milipore, Bedford, MA, USA). Specific antibodies were used in the immunoblotting process. HSP70, HSP90, ER, EGFR, HER2, HER3, HER4, pEGFR(Tyr1068), pHER2(Tyr1221/1222), pHER3(Tyr1289), pHER4(Tyr1284), p110α, AKT, p‐AKT(Ser473), p‐AKT(Thr308), p‐p70S6(Thr389), p‐S6(Ser235/236), ERK1/2 were purchased from Cell Signaling Technology (Danvers, MA, USA), p70S6 and β‐actin were purchased from Immunoway (Plano, TX, USA). p‐ERK1/2 (Thr202/Tyr204) was purchased from Santa Cruz Biotechnology (CA, USA). Proteins were detected using an ECL kit according to the manufacturer's protocol.
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6

Western blot analysis of cellular proteins

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Whole cell lysates were prepared from floating and adherent cells using RIPA or AZ lysis buffer according to standard protocols. Total protein (30–50 μg/sample) was resolved by SDS-PAGE. Proteins were detected by a standard immunoblot protocol using the following primary antibodies: PARP, cleaved PARP, cleaved caspase 3, γH2AX, XPD, p53, HER2, pHER2 (Y11221/1222), HER3, pHER3 (Y1289), HER4, pHER4 (Y1284), EGFR, pEGFR (Y1068), Chk1, pChk1(S345), pChk2 (T68), and Chk2 (Cell Signaling Technology); pH2AX (tyrosine 142; EMD Millipore); tubulin (clone B-512; Sigma), γH2AX (Santa Cruz Biotechnology) and GAPDH-HRP (Proteintech). Each experiment was repeated with independent sample preparation a minimum of three times, and representative western blots are shown.
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7

Western blot analysis of cellular proteins

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Whole cell lysates were prepared from floating and adherent cells using RIPA or AZ lysis buffer according to standard protocols. Total protein (30–50 μg/sample) was resolved by SDS-PAGE. Proteins were detected by a standard immunoblot protocol using the following primary antibodies: PARP, cleaved PARP, cleaved caspase 3, γH2AX, XPD, p53, HER2, pHER2 (Y11221/1222), HER3, pHER3 (Y1289), HER4, pHER4 (Y1284), EGFR, pEGFR (Y1068), Chk1, pChk1(S345), pChk2 (T68), and Chk2 (Cell Signaling Technology); pH2AX (tyrosine 142; EMD Millipore); tubulin (clone B-512; Sigma), γH2AX (Santa Cruz Biotechnology) and GAPDH-HRP (Proteintech). Each experiment was repeated with independent sample preparation a minimum of three times, and representative western blots are shown.
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8

Gefitinib Cytotoxicity and Apoptosis

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Gefitinib (Iressa, TOCRIS, UK) was dissolved in dimethyl sulfoxide (DMSO, Sigma) prior to the experiments. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT, Amresco, USA) and propidium iodide (PI) were dissolved in PBS to final concentrations of 5 mg/ml and 50 μg/ml, respectively. The Annexin V-APC apoptosis detection kit was obtained from BD Biosciences (BD, NY, USA). Antibodies against HER3, p-HER3, HER2, p-HER2, AKT, p-AKT, ERK, p-ERK and Cyclin B1 were purchased from Cell Signalling Technology (Beverly, MA, USA), and the antibody against β-actin was obtained from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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9

Immunohistochemical Analysis of Xenograft Samples

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Xenografts were fixed in 4% paraformaldehyde, dehydrated in ethanol, and embedded in paraffin. Sections were cut 10 μm in thickness. Immunohistochemistry was done with antibodies against P-AKT (1:200; Cell Signaling Technology, Cat# 9271), P-HER3 (1:100; Cell Signaling Technology, Cat# 2842), human Ki67 (1:200, Cell Signaling Technology, Cat# 9449T). Isotype-matched immunoglobulin was used as a control. The HRP-conjugated anti-rabbit secondary antibody (Cell Signaling Technology, Cat# 8114p) were used with the DAB substrate kit (Vector Laboratories, Newark, CA, SK-4800) for staining. Stained sections were examined under a microscope (Keyence BZ-X810). The intensity of the staining was quantified by the QuPath software (NIH), and presented as density relative to control groups with PDAC CM.
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10

Analysis of Tumor Signaling Pathways

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KPL-4 tumor xenograft tumors were collected 4 days after the initiation of treatment and immediately frozen in liquid nitrogen and stored at −80°C. Tumor samples were homogenized with Cell Lysis Buffer (Cell Signaling Technology, Inc., Beverly, MA, USA) including 10 mM NaF, 1 µg/ml aprotinin, and 1 mM phenylmethylsulfonyl fluoride (PMSF). After centrifugation, the resultant supernatant was used for the assays. The lysate was separated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel and transferred onto polyvinylidene fluoride (PVDF) membrane. The membrane was primarily treated with antibodies against p-EGFR, EGFR, p-HER2, HER2, p-HER3, p-ERK, ERK, p-AKT, AKT (Cell Signaling Technology, Inc.), HER3 (Santa Cruz Biotechnology, Inc., Dallas, TX, USA), and β-actin (Sigma-Aldrich Co. LLC., St. Louis, MO, USA). These proteins were detected by horseradish peroxidase (HRP)-conjugated secondary antibodies (Santa Cruz Biotechnology, Inc.). For HER3, HRP-conjugated anti-rabbit IgG (Cell Signaling Technology, Inc.) was used as the secondary antibody.
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