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50 protocols using fgfr1

1

Synthesis and Evaluation of Small Molecule Inhibitors

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ISJ and its intermediate, compound 7, were synthesized in our laboratory. GF 109203X (GFX) and Go 6976 (GO) were purchased from Tocris Bioscience (Ellisville, MO). 5-Fluorouracil (5-Fu) was obtained from Sigma (St. Louis, Mo). Primary antibodies were purchased from Cell Signaling Technology (Beverly, MA), including those specific for β-actin (#4970), MMP-9 (#2270), E-Cadherin (#3195), FGFR-1 (#9740), PKCε (#2683), c-Raf (#9422), MEK1/2 (#9122), ERK1/2 (#9102), Phospho-c-Raf (#9427), Phospho-MEK1/2 (#9154), and Phospho-ERK1/2 (#4370). The PKC Isoform Antibody Sampler Kit (#9960) and the Apoptosis Antibody Sampler Kit (#9915) were also purchased from Cell Signaling Technology. Antibodies to p53 (AP062) and p21 (AP021) were purchased from Beyotime (Shanghai, China).
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2

Western Blot Analysis of Protein Signaling Pathways

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Lysates were made using RIPA lysis buffer (1X RIPA lysis buffer consists of 50 mM Tris HCl, 150 mM NaCl, 1.0% (v/v) NP-40, 0.5% (w/v) sodium deoxycholate, 1.0 mM EDTA, 0.1% (w/v) SDS, and 0.01% (w/v) sodium azide at a pH of 7.4) with 0.5M EDTA and proteases and phosphatases. Sixty micrograms of protein were loaded onto SDS-PAGE gels and then transferred onto Immobilon-FL Transfer Membranes (Millipore cat. no. IPFL00010). The antibodies used were p-4EBP1 (Cell Signaling Technology cat. no. 2855L), 4EBP1 (Cell signaling Technology 9644S), FGFR1 (cat. no. ab10646), HK1 (cat. no 2804S), HK2 (cat. no 2867S), GAPDH (Cell signaling Technology cat. no 5174), and β-actin (Sigma cat. no A5316). Quantification of the protein expression was carried out using ImageJ software. Each protein was normalized to β-actin and fold change was compared to the untreated samples or the FGFR1-4EBP1 wild-type cell line, as indicated in each figure.
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3

Histological and Immunohistochemical Analysis of Lung Tissues

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For histological analysis, lungs were inflated and fixed for 24 h with ethanol–acetic acid–formalin (EAF). Fixed tissues were subsequently dehydrated, embedded in paraffin and sections of 2-4 μm were prepared, and stained with hematoxylin and eosin (H&E) for subsequent histopathological analyses. For IHC, tissue sections were rehydrated, blocked in BSA containing PBS, and sequentially incubated with specific primary antibodies and with biotinylated secondary antibodies (DAKO).
The following primary antibodies were applied: CGRP (Sigma, C8198),
E-cadherin/CDH1 (Cell signaling, 3195), FGFR1 (Cell signaling, 9740), GFP (Abcam, ab6556), ALDH1A1 (Abcam, ab23375), EGFR (Abcam, ab52894), SOX2 (Millipore, AB5603), SOX9 (Millipore AB5535), TTF1 (Agilent M357501-2), Synaptophysin/SYP (Abcam, ab32127).
The sections were reviewed with a Zeiss Axioskop2 Plus microscope (Carl Zeiss Microscopy, Jena, Germany) and images were captured with a Zeiss AxioCam HRc digital camera and processed with AxioVision 4 software (both from Carl Zeiss Vision, München, Germany).
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4

Western Blot Analysis of Protein Expression

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Protein samples (20 μg) were separated using a 10% sodium dodecyl sulfate-polyacrylamide electrophoresis gel and transferred to polyvinylidene fluoride (PVDF) membranes by using a Bio-Rad Mini-Protein electro-transfer system (Bio-Rad Laboratories, Inc., CA, USA). Next, the PVDF membranes were blocked in 5% nonfat milk in Tris-buffered saline with Tween 20 for 1 h. After blocking, the membranes were incubated at 4 °C overnight with primary antibodies against FGFR1 (#9740; 1:1000, Cell Signaling Technology Inc., Danvers, MA, USA), PARP (#9532; 1:1000, Cell Signaling Technology), cleaved PARP (#5625; 1:1000, Cell Signaling Technology), caspase-9 (#9508; 1:1000, Cell Signaling Technology), caspase-3 (#9668; 1:1000, Cell Signaling Technology), Bcl-xL (#2764; 1:1000, Cell Signaling Technology), and β-actin (sc-69879; 1:500, Santa Cruz Biotechnology, Santa Cruz, CA, USA). All the antibodies used are listed in Supplementary Table S1. The membranes were then incubated with appropriate horseradish peroxidase (HRP)-conjugated secondary antibodies at room temperature for 1 h and washed carefully with PBS three times. Next, protein band detection was performed using the enhanced chemiluminescence detection system (Thermo Fisher Scientific Inc., Waltham, MA, USA). The protein bands were quantified using ImageJ (https://imagej.nih.gov/ij/).
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5

Western Blot Analysis of Signaling Proteins

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Indicated cells were lysed with RIPA buffer. Protein lysates were electrophoresed through SDS polyacrylamide gel, followed by transferring to PVDF membranes (Millipore, USA). The membranes were blocked with non-fat dry milk at room temperature and then incubated with primary antibodies at 4°Covernight. The primary antibodies included: FGFR1, PDHK1, P-PDHK1, LDHA, P-LDHA, MMP-1 and β-actin (Cell Signaling Technology). Membranes were then washed and incubated with secondary antibodies. Proteins were visualized by the electrochemiluminescence (ECL) western blot substrate detection (Pierce).
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6

Western Blot Analysis of Signaling Proteins

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Cells were lysed for 20 min in ice-cold RIPA lysis buffer supplemented with 1 mM phenylmethylsulfonyl fluoride (PMSF) and a cocktail of protease inhibitors. Western blotting was performed using antibodies against FGFR1 (#9740, Cell Signaling Technology), Akt (#2920, CST), phospho-Akt (#4060, CST), β-Actin (#3700, CST), mTOR (#2983, CST), and phospho-mTOR (#5536, CST). Goat anti-rabbit and goat anti-mouse immunoglobulin horseradish peroxidase-linked F(ab’)2 fragments (Millipore) were used as secondary antibodies.
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7

Comprehensive Phosphoprotein Analysis

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Antibodies against p-AKT(Ser473), p-AKT(Thr308), p110α, p110β, p-GSK3α/β, p-PRAS40, p-ATP citrate lyase, p-ERBB3, p-HER2, HER2, PARP, ACTIN, IR, IGFR, FGFR1, p-RPS6 (Ser240–244), p-Tyrosine, and PTEN were from Cell Signaling Technology. Antibodies against AKT and ERBB3 were purchased from Santa Cruz Biotechnology. GAPDH, IRS1, and p85 antibodies were from Millipore.
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8

Immunohistochemical Analysis of Subcutaneous PCa PDX Models

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For subcutaneous PCa PDXs, tumor samples were prepared as previously described (13 (link)). IHC analysis was done at described elsewhere (29 (link)), using antibodies against FGFR1 (Epitomics, rabbit monoclonal clone ID EPR806Y), FGFR1 (Cell Signaling, rabbit monoclonal), FRS2α (Santa Cruz Biotechnology, rabbit polyclonal sc83138), p-FRS2α (Cell Signaling, rabbit polyclonal (Tyr196)), p-p44/42 MAPK (Erk1/2) (Cell Signaling, rabbit monoclonal (Thr202/Tyr204)), p-AKT (Dako, rabbit monoclonal), p-S6K (p-S434) (AbCam, ab47379), androgen receptor (Dako, rabbit polyclonal) and cleaved caspase 3 (Cell Signaling, rabbit polyclonal [Asp175]).
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9

Liver Tissue Protein Expression Analysis

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Liver tissues were homogenized and determined as described previously (Wang et al., 2019 (link)). The blots were incubated with primary antibodies: cleaved caspase-3, Bax, Bcl-2, ATF6, GRP78, Nrf2, SOD2, collagen IA1, ATG5, p62 and LC3 (Abcam, USA), HO-1 (Santa Cruz Biotechnology, CA, USA), CHOP, P-IRE1α, P-eIF2α, P-PERK, PERK, FGFR1, P-AMPK and AMPK (Cell Signaling Technology, Danvers, MA, US), and α-SMA, TGF-β, and GAPDH (Proteintech, China) followed by incubation with their corresponding secondary antibodies: anti-rabbit and anti-mouse (Proteintech, China).
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10

Protein Analysis of Dissected Liver Tissues

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The dissected liver tissues were stored in liquid nitrogen until analyses (n = 6 per group). Otherwise, insulin (0 and 10 U/kg) was intraperitoneally administrated 15 min prior to tissue collection in certain rats (n = 6 per group). The tissues were homogenized in tissue-protein extraction reagent (T-PER, Pierce Biotechnology, Rockford, IL, USA). After sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) separation and transfer, the polyvinylidene fluoride (PVDF) membranes reacted with primary antibodies, horseradish peroxidase-labeled IgG, subsequently followed by Enhanced Chemiluminescence (ECL) detection reagents. The intensity of recognized protein was quantified through densitometry. The primary antibodies recognized included GLP-1R (1:1000, sc-390774), Klotho (1:500, sc-515939), Akt (1:2000, sc-8312), phospho-Akt (1:1000, sc-7985-R), ERK1/2 (1:2000, sc-514302), phospho-ERK1/2 (1:1000, sc-7383), PERK (1:1000, sc-9479), phospho-PERK (1:1000, sc-32577), FGF-21 (1:500, sc-16842), glyceraldehyde-3-phosphate dehydrogenase (GAPDH, 1:2000, sc-32233) (Santa Cruz Biotechnology, Santa Cruz, CA, USA), FGFR1 (1:1000, #9740), phospho-FGFR1 (1:1000, #3471) (Cell Signaling, Danvers, MA, USA).
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