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11 protocols using pmet tyr1234 1235

1

Antibody Validation for Protein Analysis

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The antibodies used for western blot analysis and immunohistochemistry were pAKT
Ser473 (Cell Signaling Technology, 1:1000 dilution), pAKT Thr308 (Cell Signaling
Technology 1:500 dilution), AKT (Cell Signaling Technology, 1:1000 dilution), pS6
Ser240/244 (Cell Signaling Technology, 1:1000 dilution), pERK Thr202/Tyr204 (Cell
Signaling Technology, 1:1000 dilution), ERK (Cell Signaling Technology, 1:1000 dilution),
pMET Tyr1234/1235(Cell Signaling Technology, 1:1000 dilution), MET (Cell Signaling
Technology, 1:1000 dilution), MET (Santa Cruz Biotechnology, 1:200 dilution) and Actin
(Cell Signaling Technology, 1:1000 dilution). All immunohistochemical analyses were
conducted by the MSKCC Molecular Cytology core.
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2

Signaling Pathway Protein Analysis

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Proteinase, saline, dimethyl sulphoxide (DMSO), and MG132 were purchased from Sigma-Aldrich. Poly(I:C), mainly consisting of low molecular weight species (100b–500b > 90%), and LPS was purchased from Sigma-Aldrich. HGF recombinant human protein was purchased from Thermo Fisher Scientific (Waltham, MA). SHP099 was purchased from Cayman Chemical (Ann Arbor, MI). Primary antibodies to RIG-I (#3743), MDA5 (#5321), p-IRF3 (#83611), IRF3 (#4302), p-MET (Tyr1234/1235) (#3077), p-MET (Tyr1349) (#3121), MET (#3127), p-GAB1 (#12745), GAB1 (#3232), p-SHP2 (#5431), SHP2 (#3397), p-ERK (#9101), ERK1/2 (#9102), DC-SIGN (#13193), DYKDDDDK Tag (FLAG) (#14793), Myc (#2276), GAPDH (#2118) and β-actin (ACTB; #4970) were purchased from Cell Signaling Technology (Beverly, MA); phosphotyrosine (05-321) and K48-ubiquitin (05-1307) were from Merck Millipore (Burlington, MA); PRL-1 (PTP4A1) (ab168643) and LECT2 (ab119429) were from Abcam (Cambridge, UK); and p-MET (Tyr1356) (PA5-40218) was from Thermo Fisher Scientific. All antibodies were used at a 1:1000 dilution.
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3

Antibody Characterization for SOCS1 Signaling

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The polyclonal SOCS1 antibody that was raised in rabbit against the carboxyl-terminus peptide of human SOCS1 was purchased from Abcam (Toronto, ON, Canada). The β-Actin and Flag monoclonal antibodies were purchased from Sigma-Aldrich Canada (Oakville, ON, Canada). The p53, pp53 (Ser15, equivalent to Ser18 in mouse), pSTAT1 (Tyr701) and pMet (Tyr1234/1235) antibodies were acquired from Cell Signaling Technology (Danvers, MA, USA). The STAT1 antibody was obtained from Santa Cruz Technology (Santa Cruz, CA, USA). The E-cadherin antibody was purchased from BD Transduction Labs (Lexington, KY, USA). The Met 148 antibody was kindly provided by Morag Park (McGill University, Montreal, QC, Canada). Anti-mouse IgG HRP-linked and Protein A HRP-linked were used as secondary antibodies and were purchased from GE Healthcare (Piscataway NJ, USA). Murine HGF and IFNγ were purchased from PeproTech (Rocky Hill, NJ, USA) and etoposide was obtained from Sigma Aldrich Canada. Preparation of TCLs, SDS-PAGE and IB analysis were performed as previously described31 (link)48 (link).
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4

Immunoblot Analysis of Signaling Proteins

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Total protein was extracted from the cell lines following the standard protocol, and 20–40 μg of protein was used for immunoblotting27 (link). The blots were cut prior to hybridization with antibodies during blotting. The primary antibodies purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA) were as follows: pHER2-Tyr1221/1222 (#2249), pEGFR-Tyr1173 (#4407), EGFR (#2232), pHER3-Tyr1289 (#4791), pMET-Tyr1234/1235 (#3077), pIGF1R-Tyr1135/1136 (#3024), IGF1R (#9750), ERK (#4695), pAKT-Ser473 (#4060), pAKT-Thr308 (#4056), AKT (#9272), pH2A.X-Ser139 (#9718), cleaved PARP (#9541), and PCNA (#2586). Other primary antibodies [HER3 (sc-285), MET (sc-514148), pERK-Tyr204 (sc-7383), and PTEN (sc-6818)] were purchased from Santa Cruz Biotechnology, Inc. Anti-HER2 (ab16901) and anti-α-tubulin (T6199) antibodies were purchased from Abcam Inc. and Sigma-Aldrich, Inc., respectively. After incubation with peroxidase-conjugated secondary antibodies for 1 h at 20 °C, the protein blots were developed using an enhanced chemiluminescent reagent (Amersham Inc., Amersham, UK). Total protein visualized on the ChemiDoc™ XRS + System (Bio-Rad) and analysed on Image Lab software (Image Lab 6.0, Bio-Rad).
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5

Protein Extraction and Western Blot Analysis

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Total protein was extracted using a lysis buffer (Pierce, Rockford, IL, USA) and quantified with the Bradford method [40 (link)]. Fifty μg of the total protein samples were separated by 10% SDS-PAGE and transferred onto polyvinylidene fluoride membranes (PVDF; Millipore, Billerica, MA, USA). Immunoprecipitation assays were performed as described previously [41 (link)]. Membranes were incubated overnight at 4°C with the following primary antibodies: Lasp1 (1:100, Abcam, Cambridge, UK); GAPDH (1:5000, Sigma, St. Louis, MO, USA); Myc-tag, CyclinD1, CyclinB1, CyclinA2, CyclinE1, Snail, p-ERK, ERK, p-AKT-Ser473, AKT, p-p38, p38, p-FAK-Tyr397, p-FAK-Tyr925, p-FAK-Tyr576/577, FAK, p-Met-Tyr1234/1235, p-Met-Tyr1349, p-Met-Tyr1003, Met, p-Gab1-Tyr307, Gab1 (1:1000; Cell Signaling Technology, Danvers, MA, USA); E-cadherin(1:1000; BD Transduction Laboratories, Lexington, KY, USA); Zo-1 and Occludin(1:500; Proteintech, Chicago, IL, USA). PF-562271 was purchased from Selleck Chemicals (Houston, TX, USA), LY294002 was purchased from Cell Signaling Technology. Membranes were washed and subsequently incubated with peroxidase-conjugated anti-mouse or anti-rabbit IgG (Santa Cruz Biotechnology) at 37 °C for 2 hours. Bound proteins were visualized using electrochemiluminescence (Pierce, Rockford, IL, USA) and detected with a bio-imaging system (DNR Bio-Imaging Systems, Jerusalem, Israel).
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6

Western Blot Analysis of Protein Targets

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Total cellular protein was extracted using RIPA lysis buffer supplemented with phosphatase and protease inhibitor cocktail and EDTA (Sigma-Aldrich, St. Louis, MO, USA). The protein samples (20–40 µg each) were subjected to SDS-PAGE and transferred to a PVDF membrane (Millipore, Bedford, MA, USA). Immunoblotting was performed using antibodies against MET (#4250S, Cell Signaling Technology, Danvers, MA, USA; diluted at 1:1000 in 5% skim milk), phospho-MET (p-MET) (Tyr1234/1235) (#3126S, Cell Signaling Technology, Danvers, MA, USA; 1:500 in 5% bovine serum albumin), PD-L1 (#1368S, clone E1L3N, Cell Signaling Technology, Danvers, MA, USA; 1:1000 in 5% skim milk), PD-L2 (#MAB1224-100, clone 176611, R&D systems, Minneapolis, MN, USA; 1:500 in 5% skim milk), or β-actin (#sc-47778, Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:5000 in 5% skim milk). The bound antibody was visualized using a chemiluminescence kit (Amersham Pharmacia Biotech, Uppsala, Sweden).
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7

Esophageal Squamous Cell Lines Cultivation

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Esophageal squamous cell lines ECA-109 and TE-13 were purchased from KeyGEN Biotechnology (Nanjing, China) and maintained in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 10% fetal bovine serum (Gibco). Cells were cultured at 37°C in an environment of 5% carbon dioxide. Foretinib was obtained from Selleck Chemicals. The antibodies were as follows: GAPDH (Cell Signaling Technology), Akt (Cell Signaling Technology), p-Akt (Cell Signaling Technology), c-Met (Bioworld Technology), p-Met (Tyr 1234/1235) (Cell Signaling Technology), γH2AX (Cell Signaling Technology).
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8

Paroxetine HCl Modulates Receptor Signaling

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Paroxetine HCl, an anti‐depressant agent, was obtained from APExBIO (Houston, TX, USA). Antibodies for cleaved caspase‐8, cleaved caspase‐3, PARP, p‐EGFR (Tyr1068), p‐ERBB3 (Tyr1289 and Tyr1328), ERBB3, p‐ERBB2 (Tyr1248), ERBB2, p‐MET (Tyr1234/1235), MET, p‐AXL (Tyr702), AXL, p‐IGF‐1Rb (Tyr1131), IGF‐1Rb, p‐AKT (Ser437), AKT, p‐ERK (Thr202/Tyr204), ERK, p‐p38 (Thr108/Tyr182), p38, p‐JNK (Thr183/Tyr185), and JNK were purchased from Cell Signaling Technology (Beverly, MA, USA). Antibodies specific for Bcl‐2, GAPDH, and EGFR and the secondary antibody were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Halt protease and phosphatase inhibitor cocktail (100×), EDTA (100×), and bicinchoninic acid (BCA) protein assay kit were obtained from Thermo Fisher Scientific (Rockford, IL, USA). MTT and DMSO were obtained from Sigma‐Aldrich (St. Louis, MO, USA). PVDF membranes were purchased from Bio‐Rad (Hercules, CA, USA). SuperSignal West Dura Extended Duration Substrate was purchased from Thermo Scientific (Waltham, MA, USA). A human phospho‐RTK array kit was purchased from R&D Systems (Minneapolis, MN, USA).
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9

Western Blot Analysis of Protein Expression

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Tissue were homogenized with a Polytron and cells were washed in PBS and lysed in M-PER™ Mammalian Protein Extraction Reagent (ThermoFisher Scientific) containing the Halt™ Protease Inhibitor Cocktail (ThermoFisher Scientific). Protein concentration was quantified using the Pierce™ Microplate BCA Protein Assay Kit (ThermoFisher Scientific). Membranes were blocked in in 5% non-fat milk for 1 h and incubated with the following primary antibodies: β-catenin (1:2000; BD Transduction Laboratories™), p-β-catenin (Ser45; 1:1000; Cell Signaling Technology), Myc-tag (1:2000; MMCRI), Glutamine Synthetase (1:5000; BD Transduction Laboratories), c-Met (1:400, Invitrogen), p-Met (Tyr1234/1235; 1:1000; Cell Signaling Technology), cyclin D1 (1:10000; Abcam, Cambridge, UK), β-actin (1:5000; Sigma-Aldrich) and GAPDH (1:10000; EMD Millipore). Each primary antibody was followed by incubation with secondary antibody (1:5000; Jackson ImmunoResearch Laboratories Inc., West Grove, PA) for 1 h. After appropriate washing, bands were revealed with the Super Signal West Dura Kit (ThermoFisher Scientific).
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10

Immunofluorescence Staining of Brain Sections

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Formalin-fixed, paraffin-embedded brain sections were deparaffinized, re-hydrated, and stained using standard protocols, as described previously (30 (link)). Briefly, antigen retrieval was performed at 98°C for 20 min, at 15psi, in 10mM citrate buffer (pH 6) in a commercial pressure cooker for all antibodies. Tissue sections were blocked in Goat Serum (Vector Laboratories) for 30 minutes in TBS prior to overnight incubation in primary antibody, following which sections were incubated with Alexa 488/568- conjugated secondary antibodies (Invitrogen) for 1 hour prior to mounting in Vectashield with 4',6-diamidino-2-phenylindole (DAPI; Vector Laboratories). The following primary antibodies were used: p21 (Abcam, Cat. No. 1888224), Lamin B1 (Abcam, Cat. No. 16048), pMET Tyr1234/1235 (Cell Signaling, Cat. No. 3077S), GFAP (Biocare, Cat. No. CP040A). Immunofluorescence images were acquired with a Zeiss Axio Imager 2 motorized inverted microscope with an Axiocam camera and ZEN imaging software (Carl Zeiss). The percentage of p21+/GFAP+, Lamin B1+/GFAP+, or Lamin B1+/DAPI+ cells was calculated by counting the number of GFAP− or DAPI-positive cells that also co-stained with p21 or Lamin B1 per visual field (40X).
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