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96 protocols using cyclin d3

1

Western Blot Analysis of Protein Expression

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Cells were lysed in RIPA buffer [137 mM NaCl, 20 mM Tris-HCl (pH 7.4), 10% glycerol, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 2 mM EDTA] including protease inhibitor cocktail (Millipore, #539137) on ice followed by short sonication. Sample supernatants were collected after centrifugation at 14,000 rpm for 10 min. Forty micrograms of protein were separated on a 10% SDS-polyacrylamide gel before being transferred to nitrocellulose using a Bio-Rad Mini-Blot transfer apparatus (Richmond, CA). Membranes were blocked in Tris-buffered saline (TBS) containing 5% non-fat milk powder (Lab Scientific, Livingston, NJ) for 1 h.
Immunoblotting was performed at 4 °C overnight using antibodies against ACSL3 (ab151959), ACSL4 (ab205197), CD34 (ab81289) from Abcam (Cambridge, MA), AR (N-20) from Santa Cruz Biotechnology (Dallas, TX), CDK4 (Cat# 12790T), cyclin D1 (Cat# 2978), cyclin D3 (Cat# 2936T), GAPDH (Cat# 2118) from Cell Signaling (Boston, MA), or NMT1 (HPA022949) from Sigma (St. Louis, MO). The membranes were incubated with a secondary antibody at room temperature for 1 h after washing with TBS containing 0.5% Tween-20. Protein bands were visualized using the Pierce ECL Western Blotting substrate (Rockford, IL) and quantified by Image J software.
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2

Luteolin and BMS-5 Cellular Assays

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Luteolin (purity ≥ 98%) was purchased from Sichuan Weikeqi Biological Technology CO., Ltd (CAS#: 491‐70‐3). BMS‐5 (purity ≥ 98%) was purchased from Enzo Life Sciences (CAS#:1338247‐35‐0). CNBr‐activated SepharoseTM 4B (Lot# 10265330) was purchased from GE Healthcare. Thiazolyl blue tetrazolium bromide (MTT) powder was purchased from Solarbio Technology Co., Ltd. Dimethylsulfoxide (DMSO) was purchased from Sigma. Cyclin D1 (catalog# 2922), cyclin D3 (catalog# 2936), Bax (catalog# 5023), cleaved‐PARP (catalog# 5625), caspase‐3 (catalog# 9662), cleaved caspase‐3 (catalog# 9664), caspase‐7 (catalog# 9492), cleaved caspase‐7 (catalog# 8438), ROCK1 (catalog# 4035) and ROCK2 (catalog# 9029) were purchased from Cell Signaling Technology. Phospho‐LIMK‐1/2 (Thr 508/505)‐R (catalog# sc‐28409‐R), LIMK‐1(catalog# sc‐28370), cofilin (catalog# sc‐33779) and phospho‐cofilin (mSer3)‐R (catalog# sc‐21867‐R) were purchased from Santa Cruz Technology.
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3

Evaluating Apoptotic and Cell Cycle Markers

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Cells were treated with DMSO, TA, VCR or combination for 24 and 48 h. Total cellular protein extracts and western blotting was then done using the previously described method (Abdelrahim et al., 2006 (link)). Proteins of interest were probed by specific primary antibodies of apoptotic markers, cleaved poly-ADP-ribose polymerase (c-PARP, Cell Signaling Technology, Danvers, MA) and survivin (R&D Systems, Minneapolis, MN), and cell cycle markers cyclin A, cyclin D3 (Cell Signaling Technology), cyclin B1 and cyclin dependent kinases 4/6 (CDK4/6, Santa Cruz Biotechnology, Santa Cruz, CA). The expression of β-actin (Sigma) was used as a loading control.
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4

Protein Extraction and Western Blotting

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Protein extraction and Western blotting experiments were performed as described previously [12 (link)]. Primary antibodies used were as follow: anti-TGF-β1, CDK4, c-Myc, CyclinD3, p27, phospho-Akt, Akt, phospho-Erk1/2, Erk1/2, phospho-JNK, JNK, phospho-p38, p38, phospho-Smad 2, Smad 2/3, Smad 4, and Histone H3 (Cell Signaling, Danvers, MA); anti-CD63, CD81, and CD9 (Santa Cruz, Santa Cruz, CA); and anti-β-actin (Sigma-Aldrich). HRP-conjugated horse anti-mouse and goat anti-rabbit IgG (Cell Signaling) were used as secondary antibodies.
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5

Western Blot Analysis of Cell Signaling

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The protein extraction and western blot analysis protocol were described in our previous study [20 (link)]. The primary antibodies detected IGF2BP3 (#07-104) was from Merck Millipore. Other primary antibodies were from Cell Signaling (Danvers, MA) including p21 (#2946), p27 (#2552), p-Rb (Ser807/811) (#9308), cleaved-PARP (Asp214) (#9541), Cyclin D3 (#2936), CDK4 (# 12790), CDK6 (#3136) and GAPDH (#2118). The secondary antibodies were anti-Mouse IgG-HRP (Dako, 00049039, 1:30000) and anti-Rabbit IgG-HRP (Dako, 00028856, 1:10000).
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6

In vitro and in vivo Bladder Cancer Models

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Human bladder cancer cell lines (T24, J82, 5637, TCCSUP) were obtained from the American Type Culture Collection (Manassas, VA), and were cultured with the recommended medium at 37 °C with 5% CO2. Mouse bladder cancer cell line BBN963 was a general gift from Dr. William Kim at University of North Carolina. Palbociclib (LC Laboratories, Woburn, MA) was dissolved in dimethyl sulfoxide (DMSO) to 10 mM stock concentrations for cell culture experiments and in phosphate-buffered solution (PBS) at 4 mg/ml for in vivo experiments. Gemcitabine (Eli Lilly, Indianapolis, IN) was diluted in PBS to 15 mg/ml stock concentrations. Anti-mouse PD-1(CD279) antibody was purchased from BioXCell (West Lebanon, NH). MTS reagent was purchased from Promega (Madison, WI). Propidium iodide and Annexin V were purchased from BioLegend (San Diego, CA). The following antibodies were used for this paper: CDK4, GAPDH, total AKT, p-AKT, total ERK, p-ERK, E2F1, total RB, p-RB(Ser780), cyclin D3, cleaved caspase3, Ki-67 and CD8 (Cell Signaling Technology, Danvers, MA); Cyclin D1 (NeoMarkers, Fremont, CA); and actin (Sigma-Aldrich, St. Louis, MO). IHC kits were purchased from BioGenex (Fremont, CA).
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7

Immunoblotting and Immunohistochemistry Protocols

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The following primary antibodies were used in this study for immunoblotting: pRBser780 (CST-3590), pRBser807 (CST-8516), total-RB (CST-9309), cyclin D1 (CST-2922), cyclin D3 (CST-2936), pAKTser473 (CST-9271), pAKTThr308 (CST-9275), total-AKT (CST-9272), pEGFRTyr1068 (CST-3777), total-EGFR (CST-2232), pERBB2Tyr1248 (CST-2243), total-ERBB2 (CST-4290), pERBB3Tyr1222 (CST-4784), pIGF1RTyr1135 (CST-3918), pS6KSer235/236 (CST-2211), total-S6K (CST-2217), Raptor (CST-2280), RheB (CST-13879), p4EBP1Thr37/46 (CST-2855), 4EBP1 (CST-9452), pSIN1Thr86 (CST-14716), SIN1 (CST-12860), pERser167 (CST-5587), Rictor (CST-2114) and Deptor (SCT-11816) were purchased from Cell Signaling Technology. p107 (sc-318), p130 (sc-317), total-ER (sc-8002, F-10), ERBB3 (sc-415) and IGF1R (sc-713) were purchased from Santa Cruz Biotechnology. β-tubulin (T-9026) were from Sigma-Aldrich and Ki67 from Clinisciences. The following antibodies were used for immunohistochemistry: pERK1/2Thr202/4 (CST-4370), pAKTser473 (CST-4060), pS6KSer235/6 (CST-4858), pmTORSer2448 (CST-2976) and p4EBP1Thr37/46 (CST-2855) were purchased from Cell Signaling Technology. Ki67 was purchased from Clinisciences. Reagents were obtained from the following sources: 17-β-oestradiol (E2) and 4-hydroxytamoxifen (4-OHT) from Sigma-Aldrich, fulvestrant from Tocris, and neratinib and vistusertib from SelleckChem.
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8

Immunoblotting Analysis of Cellular Proteins

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Cells were lysed either in CelLytic M (Millipore Sigma) with Protease/Phosphatase Inhibitor Cocktail (Cell Signaling Technology) or in 1% SDS buffer. Immunoblotting was performed following standard procedures. PVDF membranes were blocked with 5% Milk in TBST and probed with primary antibodies overnight on a rotating platform at 4°C. The following antibodies were used: c-Myc (D84C12), cyclin D2 (D52F9), cyclin D3 (DCS22), FOXO1 (C29H4), phospho-FOXO1T24, phospho-AktS473 (D9E), β-actin (13E5) (Cell Signaling Technology) and cyclin D2 (Santa Cruz Biotechnology). The following horseradish-peroxidase-coupled antibodies were used as secondaries: donkey anti-rabbit IgG and goat anti-mouse IgG (Jackson ImmunoResearch Labs). Protein signal was detected by film or on a ChemiDoc Imaging System (Bio-Rad).
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9

Cell Cycle Regulators Analysis

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All active reagents (e.g., arecoline hydrobromide, arecaidine hydrochloride, guvacine hydrochloride, and others) were purchased from Sigma Chemical (St. Louis, MO, USA), unless otherwise stated. BNAs were dissolved in sterile medium for cell treatment. RPMI-1640, Keratinocyte-SFM, fetal bovine serum (FBS), trypsin, and protein markers were purchased from Gibco-Invitrogen (Grand Island, NY, USA). The CDK4, CDK6, cyclin B1, cyclin D1, cyclin D3, p21, p27, and actin antibodies were obtained from Cell Signaling Technology (Billerica, MA, USA), while other antibodies (i.e., CDK1, CDK2, and all others) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA) (Table 1).
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10

Immunoblotting of Cell Cycle Regulators

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Cell monolayers were washed twice with PBS, harvested, and lysed with ice-cold assay buffer (Sigma-Aldrich) after which protein lysates (20 μg) were subjected to SDS-PAGE and Western blotting. The antibodies used for immunoblotting included those raised against cyclin D1, cyclin E2, cyclin D3 (1:500; Cell Signaling Technology), GAPDH (1:1000; Abcam) and horseradish peroxidase-conjugated anti-mouse/rabbit IgG antibody (1:10000; Santa Cruz Biotechnology). After a final wash, signals were detected with use of an enhanced chemiluminescence kit (Amersham Pharmacia, Buckinghamshire, United Kingdom). GAPDH levels were used as an internal standard.
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