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42 protocols using axin1

1

Cell Line Characterization and Assays

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The cell lines where obtained from ATCC or the Japanese Collection of Research Bioresources (JCRB) in 2014 and culturing was performed as described previously (7 (link)). The cell cultures were kept below 20 passages (∼10 weeks) and routinely monitored (upon thawing and monthly) for Mycoplasma infections with MycoAlert Mycoplasma Detection Kit (Lonza). All cell lines were authenticated by short tandem repeat profiling to confirm their identity (Eurofins). TNKS1/2 and PARP1 biochemical assays (27, 32 (link)), luciferase-based WNT/β-catenin signaling pathway reporter assay (22, 27, 32 (link)), anti-proliferative assays, and NCI-60 tumor cell line panel screen (7 (link)), immunoblot analyses (7, 32, 39 (link)), RNA isolation, and real-time qRT-PCR (7, 27, 39, 40 (link)) were performed as previously described. Structured illumination microscopy (SIM) was performed as previously described (7, 39 (link)) using the following additional primary antibody: AXIN1 (2087, RRID: AB_2274550, Cell Signaling Technology) and displayed as maximum intensity projections rendered from 20 Z planes spanning 3.68 μm in total.
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2

Western Blot Analysis of Wnt Signaling

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As we previously described [10 (link)], primary antibodies including RXRα (Abcam), Frizzled-7(Millipore), CK1α(Santa Cruz), β-catenin, GSK3β, LRP6, phosphorylated-LRP6 (Ser1490), Dvl2, Dvl3, Axin1 (Cell Signaling Technology, Danvers, MA) were used. Signal was detected by enhanced chemoluminescence techniques (Millipore). GAPDH or Lamin B1 (Cell Signaling Technology) was used as the loading control. After washing, the membranes were incubated with secondary antibody HRP-conjugated goat anti-rabbit (Cell Signalling Technology) for 1h at room temperature and visualised by enhanced chemiluminescence detection kit (Millipore).
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3

Bone Morphogenetic Pathway Signaling Assay

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The Human Phospho-Kinase Array Kit and recombinant human BMP-2/ BMP-9 were purchased from R&D Systems (Minneapolis, MN, USA). The primary antibodies against anti-human Phospho-p53 (Ser6, 9, 15, 46, 392, and Thr81), Wnt5a/b, LRP6, Phospho-LRP6, Dvl2, Dvl3, Axin1, GSK3β, Phospho-GSK3β, PI3K, Phospho-PI3K, AKT, Phospho-AKT, MDM2, and β-actin were purchased from Cell Signaling Technology (Danvers, MA, USA). The iScript cDNA Synthesis Kit was purchased from Bio-Rad Laboratories, Inc. (Hercules, CA, USA). All primers and probes (RUNX2 #Hs00231692_m1; ALPL #Hs010291444_m1; BGLAP #Hs01587814_g1; NOG #Hs00271352_s1; GAPDH #Hs99999905-m1) were purchased from Applied Biosystems, Inc. (Bedford, MA, USA). Moreover, the TaqMan MicroRNA Reverse Transcription Kit and TaqMan Universal Master mix were from Applied Biosystems, Inc.
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4

Western Blot Analysis of Dental Proteins

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The total protein was extracted from the cells by protein lysate. On 10% SDS-PAGE gels, equal quantities of proteins were isolated and then transferred to 0.22 m polyvinylidene fluoride membranes (Millipore Corporation, Billerica, MA, USA). After being blocked with 5% skim milk for 1 h, the membranes were incubated with the following antibodies overnight at 4 °C: GAPDH (Proteintech, 10,494–1-AP), DSPP (Bioword, BS71212), DMP-1 (Affinity, DF8825, RRID: AB_2842022), ALP (Abcam, ab95462), Axin1 (Cell Signaling Technology, #2087), β-catenin (Cell Signaling Technology, #8480), Active β-catenin (Cell Signaling Technology, #19,807). The membranes were incubated secondary antibody for 1 h at room temperature and then exposed using the Immobilon Western Chemiluminescent HRP substrate (Millipore Corporation, Billerica, MA, USA). The protein bands were subsequently quantified with Image J software.
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5

Antibody Validation for Western Blotting

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The following antibodies were used at the indicated dilutions: c‐Myc (9E10, sc‐40, 1:1,000, Santa Cruz Biotechnology), Separase (A302‐215A, 1:2,000, Bethyl Laboratories), KIF4A (A301‐074A, 1:1,000, Bethyl Laboratories), Axin1 (#2087, 1:1,000, Cell Signaling Technology), B56α (610615, 1:3,000, BD Biosciences), BubR1 (A300‐995A,1:1,000, Bethyl Laboratories), PP2A catalytic subunit (05‐421, 1:2,000, Millipore), PP2A scaffold subunit (#2041, 1:1,000, Cell Signaling Technology) GFP (ab290, 1:4,000, Abcam), FoxO3 pS413 (#8174, 1:1,000, Cell Signaling Technology), FoxO3 rabbit polyclonal α‐pS253 (Raised against peptide CAPRRRAV(pS)MDNS; 1:500, Moravian Biotechnology), Anti‐RFP (1:1,000; MBL, FM005), Anti‐GFP (1:1,000; Roche, 11814460001), Rabbit anti‐ADAM17 (1:1,000, Abcam, 2051), Rabbit anti‐ADAM17 (1:1,000, Abcam, 39162), Rabbit anti‐EGFR (1:1,000, cell signaling, 2232), Rabbit anti‐pEGFR Y1068 (1:1,000, cell signaling, 2234), Mouse anti‐Transferrin receptor (1:1,000, Invitrogen, 136800), Mouse anti‐GAPDH (1:5,000, Sigma, G8795), rabbit Anti‐GFP (1:3,000, Takara Bio Clontech, 632592), Donkey anti‐rabbit‐HRP (1:2,000, GE Healthcare, NA934), Sheep anti‐mouse‐HRP (1:2,000, GE Healthcare, NXA931), and H3pS10 (06‐570, 1:1,000, Millipore).
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6

Antibody Acquisition Protocol

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Anti-β-catenin (BD Bioscience), Twa1, lamin B (Proteintech), GSK3β, TCF4, Axin1 (Cell Signal Technology), Myc, GAPDH, GST, His, HA, Flag (Santa Cruz), actin and α-tubulin (Sigma) antibodies were acquired commercially.
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7

Wnt Pathway Protein Expression Analysis

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Whole cell lysates were obtained from DPSCs cultured under control conditions or stimulated with ferutinin (10 μg/mL in αMEM) or CHIR-98014 (50 nM) for 12, 24, and 48 h. Protein was quantified by colorimetric assay using the Bradford method (Bio-Rad, Hercules, CA) and the proteins were separated in a polyacrylamide gel. Briefly, a polyacrylamide gel was cast and denatured proteins (20 µg) were loaded and separated through the gel by electrophoresis; a protein ladder was loaded as a marker (Sigma, St. Louis, MO). The proteins were transferred from the gel to a 0.45 µm nitrocellulose membrane (Bio-Rad) at 4 °C. The membrane was blocked for 1 h at room temperature (RT) with a blocking buffer composed of 5% nonfat milk in TBS-Tween-20 (TBST) (Boston BioProducts, Ashland, MA). The membrane was washed and incubated with primary antibody against LRP6, Dvl3, Axin1, Naked1, β-catenin, GAPDH (Cell Signaling, Danvers, MA), and GSK3 (Santa Cruz Biotechnology, Dallas, TX) (1:1000 diluted in a solution of 5% BSA in TBST) for 2 h. The membrane was washed, then incubated in secondary antibody (1:3000 in a solution of 5% milk in TBST) (Cell Signaling). The membrane was then washed, placed in the cassette holder and incubated briefly in chemiluminescent substrate (Sigma). Films were then exposed and developed. Densitometric quantification of bands was performed using ImageJ software (NIH).
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8

Isolation and Sonication of Intestinal Tissues

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Intestinal tissues from mice were isolated and sonicated in lysis buffer (1% Triton X-100, 150 mmol/L NaCl, 10 mmol/L Tris pH 7.4, 1 mmol/L EDTA, 1 mmol/L EGTA pH 8.0, 0.2 mmol/L sodium ortho-vanadate, and protease inhibitor cocktail), as previously described [12 (link)]. MEFs, HCT116, and HT29 cells rinsed twice with ice-cold PBS, were lysed and sonicated in protein loading buffer (50 mmol/L Tris, pH 6.8, 100 mmol/L dithiothreitol, 2% SDS, 0.1% bromophenol blue, and 10% glycerol). Primary antibodies to mouse VDR, β-actin (Sigma-Aldrich, Milwaukee, WI, USA), and Axin1 (Cell Signal, Beverly, MA, USA) were used, and were visualized by ECL Relative abundance of protein was determined using Quantity One software (Bio-Rad, Hercules, CA).
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9

Analysis of Nuclear and Cytosolic Proteins

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Protein lysates were separated by SDS-PAGE electrophoresis for western blotting. Nuclear and cytosolic proteins were extracted using the Qproteome Nuclear Protein Kit (Qiagen). The following antibodies were detected by chemiluminesence: PHB1 (PA5–17325, ThermoFisher) Axin1 (2087T, Cell Signaling), β-catenin (9581, Cell Signaling), Cleaved Caspase 3 (9661, Cell Signaling), PCNA (ab29, Abcam), TBP (ab818, Abcam), β-actin (A1978; Sigma-Aldrich). Densitometric units were measured using Photoshop CC and target proteins were normalized to TBP (nuclear extracts) or β-actin (cytosolic extracts) as loading controls. Whole membrane scans of western blots are shown in Supplementary Figures S7S10.
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10

Western Blot Analysis of Cellular Proteins

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Proteins from cells were extracted using
Pierce IP Lysis Buffer supplemented with protease inhibitors (Life
Technologies, 87786) followed by centrifugation to remove insoluble
material, and clarified supernatant was measured using a BCA protein
assay kit (Bio-Rad). Thirty micrograms of protein was resolved by
NuPAGE 4–12% Bis-Tris gels and transferred to PVDF membranes
(Bio-Rad) according to the manufacturer’s instructions. Membranes
were blocked in 5% non-fat dry milk in PBS buffer and then incubated
with the indicated antibodies including FTO (Cell Signaling Technology,
14386), GAPDH (Proteintech, HRP-60004), Axin1 (Cell Signaling Technology,
2087), β-catenin (Cell Signaling Technology, 8480), Akt (Cell
Signaling Technology, 4691), Phospho-Akt (Ser473) (Cell Signaling
Technology, 4060) and E-cadherin (Cell Signaling Technology, 3195)
overnight at 4 °C. After being washed, the membranes were incubated
with HRP-conjugated secondary antibodies at room temperature (RT)
for 15 min and then washed 3 times as before (Thermo Scientific, Pierce
Fast Western Blotting Blot Kit). Protein was visualized on autoradiography
film (Genesee Scientific Inc., 30-100) using the enhanced chemiluminescence
(ECL) detection system (Thermo Scientific).
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