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6 protocols using p p38α

1

Protein Fractionation and Immunoblotting

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Total protein was fractionated by 9% SDS–PAGE, transferred
onto nitrocellulose and then blocked blots with Tris-buffered saline and Tween
20 (0.1%) containing 5% BSA before incubation overnight
with primary antibodies (1:1,000) to S100A9 (ab73987 Abcam), PCNA (ab2426
Abcam), Cyclin D1 (ab16663 Abcam), p105/p50 (ab7971 Abcam), RelA (ab7970 Abcam),
c-Rel (sc71 Santa Cruz), CyP2E1 (ab28146 Abcam) or GAPDH (Abcam), total
p38α (9218 Cell Signaling), P-p38α (9216 Cell Signaling), HA
or Flag-HRP conjugate (Sigma). Next day, membranes were washed in T-TBS and then
incubated with horseradish peroxidase-conjugated mouse anti-rabbit IgG. Blots
were washed and antigen was detected using enhanced chemiluminescence (Amersham
Biosciences). Images have been cropped for presentation. Full-size images are
presented in Supplementary Fig.
10
.
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2

Immunofluorescent Analysis of Cartilage Markers

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The sectioned samples were washed 3 times with PBS, and permeabilized with 0.25% Triton X-100 (Sigma). Samples were then incubated in 1% BSA, 22.5 mg/ml glycine in PBST (1 × PBS and 0.1% Tween 20) at room temperature for 1 hour to block non-specific binding, followed by overnight incubation at 4 °C with primary antibodies (pGSK-3β, Santa Cruz Biotechnology; sc-373800, pP38α, Cell Signaling Technologies, 9211S, collagen type II, abeam, ab34712, aggrecan, abeam, ab3778, collagen type V1, sc-20649). The samples were then washed 3 times with PBS and incubated in the dark at room temperature for 1 hour with secondary antibodies (such as goat anti-mouse IgG Dylight 488, goat anti-rabbit IgG Dylight 594 in 1:200 dilution). All the antibodies were diluted in 1% BSA in PBST. Finally, samples were washed and stained for nuclei using DAPI and/or F-actin using phalloidin (1:40 dilution). Samples were imaged using Zeiss LSM 880 laser scanning confocal microscope. The obtained images were analyzed using FIJI-imageJ v1.52i software.
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3

Analyzing EGFR Pathway Modulation

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GEO-CR cell lines were treated with cetuximab (2.5 μg/mL) and 4-IPP (25 μM) for 24 h. Equal amounts of total proteins (25 μg) were incubated with the following primary polyclonal antibodies: p-AKT, p-MEK, p-p70S6, p-p38α and p-GSK-3β purchased from Cell Signaling and anti-MIF antibody (1:500; Sigma). The monoclonal anti-α-tubulin antibody (Sigma-Aldrich) was used as loading control antibody. After incubation with the secondary antibody, membranes were developed using an enhanced chemi-luminescence (ECL) detection system (BioRad). Densitometry readings/intensity ratios normalized with tubulin along with the whole blot showing all the bands with all molecular weight markers of Western blot sections of Figure 2D and Figure 5C are reported in the Figures S9–S11.
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4

Molecular Signaling Pathway Analysis

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All the chemicals used in this study were obtained from Invitrogen, Carlsbad, USA. The β-actin, AKT, and p38α were purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA). The p-AKT, p-p38α, and p-ERK were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA). Rabbit polyclonal antibodies against p38α, p-p38α, p-Akt, and p-ERK were purchased from DAKO (Glostrup, Denmark). Goat polyclonal antibodies against Akt and β-actin were purchased from DAKO.
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5

Profiling EGFR Signaling Pathways in Lung Cancer Cells

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All chemicals were purchased from Sigma unless stated otherwise. Antibodies directed to EGFR, ERBB2, ERBB3, ERBB4, MET, p-EGFR (Y-1068), and scrambled shRNA and JUN shRNA were purchased from Santa Cruz Biotechnology. The antibodies to MAPK, pMAPK, AKT, pAKT, PTEN, YES, pYES, FOS, p-FOS, JUN-B, JUN-D, CREB, pCREB, CHK2, pCHK2, p38α, p-p38α, p-JUN, and SRC as well as EGF Receptor (D38B1) XP® rabbit mAb (Sepharose® Bead Conjugate) were obtained from Cell Signaling. HCC827 (exon 19 del, E746-A750) and H3255 (exon 21 substitution, L858R), PC9 (exon 19 del), H4006 (exon 19 del), A431 (WT EGFR) cell lines were obtained from the ATCC and tested for mycoplasma (PCR) every 30 days. These cells were authenticated by ATCC utilizing Short Tandem Repeat (STR) profiling and used within 6 months of purchase. Gefitinib, AS601245, JNK-IN-8, canertinib, and erlotinib were obtained from LC Labs. The CellTiter96® AQeous Non-Radioactive Cell Proliferation Assay (MTS) was purchased from Promega. The receptor and kinase array were obtained from R&D Systems and used according to the manufacturer’s instructions.
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6

Characterization of Murine and Human Cell Lines

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All cells were maintained in RPMI 1640 culture medium supplemented with 10% fetal calf serum. Murine cell lines were derived in-house [4 (link), 6 (link), 14 (link)] and constantly monitored for the expression of their definitive chimeric kinases. Human KG1 cells were obtained from ATCC and similarly charcterized for the expression of the FGFR1OP2-FGFR1 fusion kinase. Cell proliferation was assessed using Trypan blue exclusion assays over a time course and cell viability was measured using the CellTitre Glow assay according to the manufacturer’s instructions (Promega). Western blot, genomic DNA preparation, plasmid transfection, quantitative RT-PCR, miR146b overexpression, cell cycle and cell apoptosis assays followed standard procedures that have been described extensively previously [9 (link), 15 (link)]. Antibodies used for western blotting (dilution 1:1000): β-Actin (Cell signaling, #5125), IRAK1 (Cell signaling, # 4504), p-IRAK1 (Sigma-Aldrich, SAB4504246), IFN-γ (Abclonal, # A12450), CXCL9 (Abclonal, # A19135), p-AKT (Cell Signaling, # 9272), AKT (Cell Signaling, # 9271), p- p38α (Cell Signaling, # 9211), p38α (Cell Signaling, # 9218), p-Stat3 (Cell Signaling, # 9134), Stat3 (Cell Signaling, # 4904).
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