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114 protocols using lc3 1 2

1

Protein Analysis by Western Blotting

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Western blotting was performed as described previously. 16 (link),17 (link) Antibodies used were as follows: Ampk, p-Ampk (Thr172), LC3-I/II, ACC, p-ACC (Ser79), p4EBP1 (Ser65), 4EBP1, LC3-I/II (Cell Signaling), and PARP and GAPDH (Santa Cruz). Cytosolic and nuclear proteins were isolated as described previously.16 (link)
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Western Blotting Signaling Protein Analysis

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Western blotting was performed as described previously.16 (link), 17 (link) Antibodies used were as follows: Ampk, p-Ampk (Thr172), LC3-I/II, ACC, p-ACC (Ser79), p4EBP1 (Ser65), 4EBP1, LC3-I/II (Cell Signaling), and PARP and GAPDH (Santa Cruz). Cytosolic and nuclear proteins were isolated as described previously.16 (link)
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In vivo Protein Analysis after SCI

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For in vivo protein analysis, a spinal cord segment at the lesion epicentre was dissected at 7 and 14 days and immediately stored at −80°C. Proteins from animal tissue or PC12 cells were first quantified by the BCA reagent method. We separated the proteins on 8% (w/v) or 12% (w/v) gels and transferred the proteins onto polyvinylidene fluoride membrane (Bio‐Rad, Hercules, CA, USA). Membranes were blocked with 5% (w/v) milk (Bio‐Rad) in TBS with 0.05% Tween 20 (TBST) for 2 hours at room temperature and then were incubated overnight at 4°C with primary antibodies of FGF1 (1:1000; Abcam), ace‐tubulin (1:2000; Cell Signaling Technology), Tau (1:1000; Abcam), GAP43 (1:1000; Abcam), MBP (1:1000; Abcam), p‐mTOR (1:1000; Cell Signaling Technology), mTOR (1:1000; Cell Signaling Technology), ATG7 (1:1000; Bio‐world), Beclin1 (1:1000; Abcam), LC‐3 I/II (1:1000; Cell Signaling Technology), PRDX1 (1:1000; Cell Signaling Technology) and GAPDH (1:10000; Bio‐world). Next, the membranes were washed with TBST 3 times and treated with horseradish peroxidase‐conjugated secondary antibodies for 60 minutes. All signals were detected by ChemiDocXRS + Imaging System (Bio‐Rad). All experiments were repeated 3 times for accuracy.
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4

Carfilzomib Modulates Apoptosis Pathways

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Carfilzomib (CFZ) was purchased from Onyx Pharmaceuticals (San Francisco, CA, USA). Resveratrol (RSV), N-Acetylcysteine (NAC), methyl-thiazolyl tetrazolium (MTT), 2′, 7′-dichlorofluorescein diacetate (DCFH-DA) fluorescent probe, and dimethyl sulfoxide (DMSO) were from Sigma-Aldrich (St. Louis, MO, USA). 3-methyladenine (3-MA) was obtained from Abmole inhibitor leader (Houston, TX, USA). The CFZ and NAC were dissolved in double-distilled water, and the RSV and 3-MA were dissolved in DMSO, respectively. Primary antibodies of SIRT1 (Cat. 2310), Smac (Cat.15107), survivin (Cat.2808), p-p38 (Cat.4511), p53 (Cat.2527), PARP (Cat.9542), caspase 3 (Cat.9662), LC3-I/II (Cat. 3868), and tubulin (Cat. 2144) were purchased from Cell Signaling Technology (Beverly, MA, USA). Antibody against tubulin was from Wuhan Boster Biological Technology (Wuhan, Hubei, China). Scrambled siRNA AND SMARTpool: ON-TARGETplus DIABLO (Smac) siRNA were purchased from Dharmacon.
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5

Sorafenib and Autophagy Modulation in Cancer

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Sorafenib (Sf) (Selleckchem, Houston, TX) was used at different concentrations at micromolar scale. Doxercalciferol (1-hydroxyvitamin D2; D2) (Sigma-Aldrich, St. Louis, MO) was used at the final concentration of 100 nM. Carnosic acid (CA) (Enzo Life Sciences Inc., Farmingdale, NY) was used at the final concentration of 10 μM (7 (link),27 (link)). Autophagy inhibitor chloroquine (Sigma) was used at 10 μM and caspase 3 inhibitor Z-DEVD-FMK (Selleckchem) at final concentration of 1 μM. The following antibodies were used for Western blotting: Beclin1 (#3738), Cleaved Caspase 3 (#9661), Capase 9 (#9502), Atg3 (#3415), p62 (Cat#39749S), LC3I/II (#12741) and HRP-linked anti-rabbit (#7074) antibodies were purchased from Cell Signaling Technologies (Danvers, MA). The loading control for Western blotting β-actin antibody was purchased from Sigma-Aldrich. Propidium Iodide Nucleic Acid Stain kit was purchased from Invitrogen (Carlsbad, CA).
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Apoptosis and Autophagy Signaling Pathways

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GC cells were treated with drugs for 12, 24 or 48 hr. Proteins from the cell cultures were extracted and western blot analysis was performed as described previously [29 (link)]. Apoptotic proteins were detected with the antibodies reported previously [28 (link)]. Histone acetylation was detected with acetyl-histone H4 rabbit polyclonal antibodies (1:2000; Millipore, Temecula, CA). Expression of autophagic proteins was detected with Beclin-1, Atg12 and LC3-I/II rabbit polyclonal antibodies, respectively (1:1000; Cell Signaling Technology). Expression of phosphorylated JNK1/2 isoforms, phosphorylated c-Jun, phosphorylated ERK1/2 and phosphorylated p38 was detected with p-JNK, p-c-Jun, p-ERK1/2 and p-p38 rabbit polyclonal antibodies, respectively (1:1000; Cell Signaling Technology). Expression of human α-tubulin was detected with α-tubulin antibody (1:5000; Sigma-Aldrich) as a loading control.
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7

Mitochondrial Protein Analysis by Western Blot

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Fibroblasts were lysed in RIPA buffer containing 1 × complete protease inhibitor (Roche). Western blot analysis was performed with antibodies against Miro1 (WH0055288M1; Sigma–Aldrich, Munich, Germany), LC3-I/II (2775; Cell Signaling), Hsp60 (4870; Cell Signaling), Tom20 (sc-17764; Santa Cruz Biotechnologies), Rab9 (sc-74482; Santa Cruz Biotechnologies), MnSOD (ab13533; Abcam), anti-V5 (R960-25; Novex, R96125; Sigma–Aldrich), and β-actin (MA1-744; Thermo Scientific). Mitochondrial fractionation was performed as described previously (12 (link)).
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8

Autophagy and Apoptosis Signaling Pathway

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Trypan blue solution (prod. no. T8154), phosphatase inhibitor cocktails 2 and 3 (prod. no. P5726 and P0044, respectively), and furazolidone (prod. no. V900742) were from Sigma-Aldrich (St. Louis, MO, USA). A protease inhibitor cocktail (ref. no. 11836 153 001) was from Roche Diagnostics (Basel, Switzerland). Primary antibodies anti-Atg5 (#2630), anti-beclin-1 (#3738), cleaved caspase-3 (#9661), Bcl-2 (#3498S), PARP (#46D11), H2AX (#2595S), LC3I/II (#4180S), BAX (#2772), and P53 (#9282) were purchased from Cell Signaling Technology (Danvers, MA USA), and anti-actin was purchased from Sigma-Aldrich (prod. no. A3853). Secondary antibodies goat anti-rabbit IgG- (H+L) HRP conjugate (cat. no. 170-6515) and goat anti-mouse IgG- (H+L) HRP conjugate (cat. no. 170-6516) were obtained from Bio-Rad Laboratories (Mississauga, Ontario, Canada).
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9

Protein Extraction and Western Blot Analysis

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Protein samples were extracted from the heart/cells as previously described [25 (link)]. For heart/cellular samples, proteins were lysed using the radioimmunoprecipitation assay lysis buffer (Beyotime, Shanghai, China). After concentration determination using a bicinchoninic acid kit (Beyotime, Shanghai, China), proteins (80 μg/lane) were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels (12.5%) (EpiZyme, Shanghai, China), transferred to a nitrocellulose filter membrane (Millipore Corporation, Billerica, MA, USA), and blocked with 5% skimmed milk in PBS for 2 h. Samples were incubated in primary antibodies overnight at 4 °C, followed by incubation with fluorescence-labeled secondary antibody (1:10,000, Invitrogen, Carlsbad, CA, USA) for 1 h. Fluorescence was detected using the Odyssey Imaging System (LI-COR, Lincoln, NE, USA). Primary antibodies against p62 (1:1000, Cell Signaling Technology, Boston, MA, USA, Cat#5114S), LC3 I/II (1:500, Cell Signaling Technology, Cat#12741S), ATG4B (1:500, Sigma-Aldrich, Saint Louis, MO, USA, Cat#A2981), ATG3 (1:1000, Cell Signaling Technology, Boston, MA, USA, Cat#3415S), and ATG7 (1:500, Cell Signaling Technology, Boston, MA, USA, Cat#2631S) were used. Glyceraldehyde 3-phosphate dehydrogenase (1:1000, Zhongshanjinqiao, Beijing, China, TA-08) was used as an internal control.
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10

Protein Expression Analysis in Lung Tissue

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We used immunoblotting techniques to measure lung protein levels of the autophagy-related Beclin-1, Atg5-Atg12 and LC3-II/LC3-I, apoptosis-related caspase 3 and poly-(ADP-ribose)-polymerase (PARP), and PI3K/AKT/m-TOR signaling. In brief, proteins (20 μg) were separated on 10% polyacrylamide gels and electrophoretically transferred to nitrocellulose membranes (Amersham Biosciences, Buckingham, England, UK). The membranes were blocked and then incubated overnight, at 4 °C, with antibodies raised against Beclin-1 (Cell Signaling Technology, Inc., Danvers, MA, USA), Atg5-Atg12 (Gene Tex, Alton Parkway, Irvine, CA, USA), and LC3-II/I (Cell Signaling Technology); the activation fragments (32 kDa of proenzyme and 17 kDa of cleaved product) of caspase 3 (CPP32/Yama/Apopain, Upstate Biotechnology, Lake Placid, NY), PARP (Cell Signaling Technology), p-PI3K (Cell Signaling Technology), p-Akt (Cell Signaling Technology), p-mTOR (Cell Signaling Technology), and β-actin (Sigma) were used. The density of the band with the appropriate molecular mass was determined semi-quantitatively by densitometry, using an image-analyzing system (Alpha Innotech, San Leandro, CA, USA).
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