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6 protocols using odyssey version 3

1

Protein Abundance Detection Protocol

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Protein extractions were performed as previously described44 (link),49 . Primary antibodies HAS2 (Santa Cruz Biotechnology, sc-34068) (1:200 dilution), HSL (Santa Cruz Biotechnology, sc-74489) (1:200 dilution), α Tubulin (Santa Cruz Biotechnology, sc-53030) (1:200 dilution), Actin (Sigma #A4700) (1:1000 dilution), Adiponectin (homemade) (1:1000 dilution) were used. Protein abundance was detected using the one of the following secondary antibodies: Goat anti-Mouse IRDye 680RD (Li-cor 926-68070), Goat anti-rabbit IRDye 800CW (Li-cor 925-32211) or Goat anti-Rat DyLight 800 (Thermo Fisher SA5-10024) at 1:10,000 dilutions. Antibody decorated membranes were then visualized on a Li-Cor Odyssey infrared scanner (Li-Cor Bioscience). The scanned data were analyzed using Odyssey Version 3.0 software (Li-Cor Bioscience).
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2

Protein Extraction and Western Blot Analysis

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Protein extractions were performed as previously described (18 (link),23 ). Primary antibodies phospho-Akt (Ser473) (catalog no. 4060; Cell Signaling Technology) and total Akt (catalog no. 2920; Cell Signaling Technology), GALE (catalog no. ab155997; Abcam), tubulin (catalog no. sc-53030; Santa Cruz Biotechnology), O-linked glycosylation (catalog no. ab2739; Abcam), and actin (catalog no. A4700; Sigma-Aldrich) were used at 1:1,000 dilutions and detected using a secondary immunoglobulin G labeled with infrared dyes emitting at 680 nm (catalog no. 926-68070 and 926-68076; LI-COR Bioscience) or 800 nm (catalog no. 926-32211; LI-COR Bioscience) (both at 1:10,000 dilutions) and then visualized on a LI-COR Odyssey infrared scanner (LI-COR Bioscience). The scanned data were analyzed using Odyssey version 3.0 software (LI-COR Bioscience).
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3

Protein Expression Analysis of 4T1 Cells

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After exposure to the test compounds (450 μg/mL GYII; 200 μg/mL DR2 and DR3; or 40 μg/mL fucoidan) for 36 h, the 4T1 cells were harvested and lysed with RIPA lysis buffer (Beyotime Biotechnology, Beijing, China) containing Protease Inhibitor Cocktail Set III (Calbiochem, San Diego, CA, USA). The cell lysates were centrifuged at 12,000 rpm for 15 min at 4 °C, and the supernatants were collected. The protein concentration was determined using the Pierce BCA Assay Kit (Thermo Scientific, Rockford, IL, USA). Equal amounts (45 μg/lane) of total protein were separated by 12% SDS-PAGE and transferred onto PVDF membranes. The membranes were blocked with 5% BSA (Amresco, Solon, OH, USA) at room temperature for 1 h and incubated overnight at 4 °C with the following primary antibodies: anti-heparanase (1:500), anti-FGF-2 (1:500), anti-VEGF (1:1000), anti-ERK/p-ERK (1:1000), anti-PI3K/p-PI3K (1:1000), anti-AKT/p-AKT (1:1000), and β-actin (1:1000). After washing the membranes in Tris-buffered saline with 0.1% Tween-20 (TBST), the membranes were probed with secondary antibodies (1:10,000) for 1 h at room temperature. The signals were detected using an Odyssey Infrared Imaging System (Li-cor Biosciences, Lincoln, NE, USA). The relative density of the protein bands was measured by Odyssey version 3.0 software (LI-COR Biosciences). The experiments were repeated three times.
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4

Western Blot Protein Analysis Protocol

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Protein extractions were done as previously described. Primary antibodies phospho- HSL (catalog no.4139; Cell Signaling Technology), tubulin (catalog no. sc-53030; Santa Cruz Biotechnology), and actin (catalog no. A4700; Sigma-Aldrich) were used at 1:1,000 dilutions and detected using a secondary immunoglobulin G labeled with infrared dyes emitting at 680 nm (catalog no. 926–68070 and 926–68076; LI-COR Bioscience) or 800 nm (catalog no. 926–32211; LI-COR Bioscience) (both at 1:10,000 dilutions) and then visualized on a LI-COR Odyssey infrared scanner (LI-COR Bioscience). The scanned data were analyzed using Odyssey version 3.0 software (LI-COR Bioscience).
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5

Western Blot Analysis of A375 Cell Proteins

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Protein samples from cultured A375 cells were harvested with RIPA lysis buffer (Beyotime Institute of Biotechnology) containing 1% protein inhibitor and 10% phosphatase inhibitor. After being centrifuged at 12,000 × g at 4°C for 15 min, the supernatant was transferred and protein concentrations were assessed using a BCA assay kit (Bio-Rad Laboratories, Inc.). Equal amounts of protein (80 µg/lane) were loaded onto a 8–15% gel, resolved using SDS-PAGE and blotted onto a nitrocellulose membrane. After blocking with 5% non-fat milk at 4°C for 2 h, the membranes were incubated with primary antibodies at 4°C overnight. The primary antibodies were anti-p-STAT3 (Y705, #9131, 1:1,000), anti-STAT3 (#4904, 1:1,000), anti-p-AMPK (Thr172, #2535, 1:1,000), anti-AMPK (#2532, 1:1,000), anti-p62 (#88588, 1:1,000), anti-Bcl-2 (ab196495, 1:1,000) and anti-LC3 (L7543, 1:1,000). After being rinsed with TBS-0.1% Tween 20 (5 min for 3 times), the membranes were subsequently incubated with fluorescence-conjugated goat anti-mouse IgG or goat anti-rabbit IgG secondary antibody (1:10,000;LI-COR Biosciences) for 1 h at room temperature. Images were captured using an Odyssey infrared imaging system and Odyssey version 3.0 software (LI-COR Biosciences).
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6

Quantitative Protein Profiling in Cells

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Protein extractions were performed as previously described28 (link),29 (link). Primary antibodies p-ERK (Thr202/Tyr204, Cell Signaling, #4370S; 1:1000 dilution), ERK1/2 (C-9, Santa Cruz Biotechnology, SC-514302; 1:200 dilution), tyrosine hydroxylase (Abcam, ab75875; 1:1000 dilution), adiponectin (rabbit polyclonal, home-made), Connexin43 (Santa Cruz Biotechnology, SC-6560-R) and α-tubulin (DM1A, Cell Signaling, #3873S) were used. Protein abundance was detected using one of the following secondary antibodies: goat anti-mouse IRDye 680RD (LI-COR Biosciences, 926-68070), goat anti-rabbit IRDye 800CW (LI-COR Biosciences, 925-32211) at 1:10,000 dilutions. Antibody decorated membranes were then visualized on a LI-COR Odyssey infrared scanner (LI-COR Biosciences). The scanned data were analyzed using Odyssey Version 3.0 software (LI-COR Biosciences).
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