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12 protocols using cyclin a1

1

Western Blot Analysis of RA-FLS Proteins

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A RIPA (radioimmunoprecipitation) lysis buffer from Beyotime (Shanghai, China) was used to isolate total proteins from cultured RA-FLSs. The determination of the concentration of total protein was carried out employing a BCA protein assay kit procured from Pierce (Rockford, IL, U.S.A.). Proteins in equal, and measured amounts were electrophoretically separated on SDS-PAGE (10%) and transferred to PVDF membranes (polyvinylidene fluoride; Millipore, U.S.A.). After the blocking procedure with nonfat milk (5%), antibodies against TLR4 (1:2000), CyclinA1(1:1000), CyclinB1(1:1000), CyclinD2(1:2000), and GAPDH (1:5000) (all from Santa Cruz, U.S.A.) were added to the membrane, followed by secondary antibodies (1:6000, Santa Cruz) conjugated with horseradish peroxidase. The internal loading control was GAPDH. The chemiluminescent substrate kit from Millipore Company (Bedford, MA, U.S.A.) was used to observe protein bands as per instructions of the manufacturer. Gray analysis was performed using software Gel-Pro Analyzer 4 (United States Biochemical, Cleveland, OH, U.S.A.).
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2

CDK4/6 Inhibitor Palbociclib Protocol

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PD-0332991 (palbociclib), a selective CDK4/6 inhibitor, was purchased from Sigma Aldrich (St. Louis, MO, USA). Anti-phospho-H2AX (Ser139) antibodies were purchased from Millipore (Billerica, MA, USA). RB1, phospho-RB1 (Ser780; Ser807/811), E2F1, cyclin B1, cyclin D1, cyclin E1, CDK4, and CDK6 antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA). Anti-β-actin antibodies were purchased from Sigma Aldrich (St. Louis, MO, USA). Anti-RAD51, cyclin A1, and CDKN2A antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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3

Western Blot Analysis of Cellular Proteins

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Total protein or nuclear/cytoplasmic protein fractions were extracted from cells using lysis buffer (Beyotime Biotechnology Shanghai, China) supplemented with protease inhibitor. Western blot was performed with a standard method as previously described (Chen et al., 2018b) using the following antibodies: RDM1 (1 : 500; Proteintech, Rosemont, IL, USA), p53 (1 : 2000; Santa Cruz Biotechnology, Dallas, TX, USA, β‐actin (1 : 2000; Santa Cruz), 14‐3‐3σ (1 : 1000; Santa Cruz), p21 (1 : 2000; CST, Boston, MA, USA), Cyclin A1 (1 : 1000; Santa Cruz), Cyclin B1 (1 : 1000; CST), VEGFB (1 : 1000; CST), BAX (1 : 1000; CST), RAD51 (1 : 1000; CST), hTERT (1 : 500; Abcam, UK), c‐myc (1 : 1000; Proteintech), METTL3 (1 : 1000; Abcam), METTL14 (1 : 1000; Abcam), Ras (1 : 500; CST), p‐cRaf (1 : 500; CST), ERK (1 : 1000; CST), and p‐ERK (1 : 1000; CST).
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4

Comprehensive Protein Analysis Protocol

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Antibodies and sources: CDK9, pCDK9, RNAPII, phospho-RNAPII, TGM2, Cyclin B1, Cyclin E1, and NUP98 (Cell Signaling Technology); CDC37, SPT5, Stomatin, PLK1, Cyclin A1 (Santa Cruz Biotechnology); BRD4, Cyclin T1 and GFP (Abcam); Caspase-8 (Enzo Life Sciences); β-Actin, pCDK9, Vimentin, and Flag (Sigma-Aldrich).
Reagents and sources: CellTiter-Blue Cell Viability assay and Caspase-Glo 3/7 assay (Promega); BrdU kit (Roche); Thymidine, 5-ethynyl uridine (EU), Azide-fluor 488 (Sigma-Aldrich); AnnexinV and 7AAD (BD); [γ-32P] ATP (3000Ci/mmol, Amersham Pharmacia); Trail, FasL (Enzo Life Sciences); PLA assay kit (Olink Biosciences); BAY1251152, Cisplatin, and Carboplatin (Selleckchem); BioCoat Matrigel invasion chamber (Corning); Migration chamber (Ibidi); RNeasy Plus kit (Qiagen), active GST-CDK9/Cyclin K (SRP5012, Sigma-Aldrich).
The following vectors were used: pCas9(BB)-2A-Puro (PX459) V2.0 (62988, Addgene); p3xFlag-CMV-7.1 (E7533, Sigma); pGEX-5X-3 (28–9545-55, GE Healthcare) and pEGFP-C2 (6083-1, Clontech). All siRNAs and primers were from Sigma-Aldrich.
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5

Rhein Modulates PI3K/Akt/mTOR Pathway

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Rhein (purity: >98% assessed by HPLC) was purchased from Harvey Biotech Co., Ltd. (Beijing, China). For in vitro experiments, rhein was dissolved in dimethyl sulfoxide (DMSO). CNBr Sepharose 4B beads were obtained from GE Healthcare (Piscataway, NJ, USA). The primary antibodies PI3K, p-Akt, Akt, p-mTOR, mTOR, cleaved caspase3, p53, p-p53, Bax, p70 S6 Kinase (p70S6K), p-p70 S6 Kinase (p-p70S6K), cyclin-dependent kinase (CDK) 2, cyclin D1, cyclin E1, E-cadherin, N-cadherin, Heat shock protein 90 (HSP90), 4EBP1, and p-4EBP1 were purchased from Cell Signaling Technology (Beverly, MA, USA). β-Actin, Heat shock factor 1 (HSF1), and cyclin A1 were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Ki-67 and vimentin were purchased from Abcam (Cambridge, MA, USA).
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6

Immunofluorescence Analysis of EMT Markers

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The expression of FoxM1, EMT markers and β-tubulin were observed by immunostaining and imaging. After transfection with si-FoxM1 or si-NC for 48 h, cells were seeded on coverslips, which were pre-placed in a 24-well plate and fixed with 4% paraformaldehyde after 24 h adherent growth. After 40 min, cells were washed with 1X PBS and blocked in Immunol Staining Blocking Buffer (#P0102; Beyotime Institute of Biotechnology) for 2 h at room temperature. Cells were incubated with primary antibodies against FoxM1 (1:100; Bioworld Technology), cyclin A1 (#sc-751, 1:100; Santa Cruz Biotechnology), PCNA (#ab2426, 1:100; Abcam), E-cadherin (#RLT1453, 1:100; Suzhou Ruiying Biological Technology) vimentin (#RLT4879, 1:100; Suzhou Ruiying Biological Technologyl) and β-tubulin (#RLM3030, 1:100; Suzhou Ruiying Biological Technology) for 20 h, and then incubated with Alexa Fluor-conjugated secondary antibodies (1:1000; Invitrogen/Thermo Fisher Scientific) and Hoechst stain (Sigma-Aldrich, St. Louis, MO, USA) for 2 h at room temperature in the dark. The images were viewed and recorded with a fluorescence microscope (Leica Microsystems, Wetzlar, Germany).
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7

Histological Analysis of Mouse Intestinal Tissues

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Small intestine and colon from sacrificed mice were placed immediately into 10% neutral buffered formalin (NBF). Intestines were opened longitudinally, cleaned, and swiss-rolled. Swiss rolls were fixed for ~24 hr in 10% NBF at room temperature (RT). Fixed tissues were embedded in paraffin and stained with H&E. Adenomas were graded by inspection of H&E-stained sections.
For immunohistochemistry (IHC), primary antibodies (Abs) recognized were β-catenin (Cell Signaling Technology, #2677), c-Myc (Santa Cruz, #SC764, N-262), lysozyme (#A0099), ephrinB1 (R&D Systems, clone AF473), EphB2 (R&D Systems, clone AF467), EphB3 (R&D Systems, clone AF432), cleaved caspase-3 (Cell Signaling Technology, #9661), Ki67 (Dako, Tec3 clone), chromogranin A (Immunostar, #20085), p21 (Santa Cruz Biotechnology, clone M19), GFP (Novus, 100–1678), cyclin D1 (Cell Signaling Technology, #2978), cyclin E1 (Abcam, ab7959), cyclin A1 (Santa Cruz Biotechnology, sc-751), and B23 (Sigma, B0556). Anti-LFABP antibody was the kind gift of Dr. Jeffrey Gordon (Washington University, St. Louis).
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8

Molecular Mechanisms of Anticancer Therapy

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Chemicals: AdipoRon (#SML0998; Sigma-Aldrich), gemcitabine (#G6423, Sigma-Aldrich), trypan blue (#T8154; Sigma-Aldrich), propidium iodide (#P4864; Sigma-Aldrich), crystal violet (#C0775; Sigma-Aldrich), PD98059 (#P215; Sigma-Aldrich), dimethyl sulfoxide (DMSO) (A3672; AppliChem), and ethanol absolute anhydrous (308603; Carlo Erba). Antibodies: α-Tubulin (#3873; Cell Signaling Technology), cyclin E1 (#4129; Cell Signaling Technology), p44/42 MAPK (#9102; Cell Signaling Technology), phospho-p44/42 MAPK (#9101; Cell Signaling Technology), cyclin A1 (sc-751; Santa Cruz Biotechnology), vinculin (sc-73614; Santa Cruz Biotechnology), and p27KIP1 (ab3203; Abcam).
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9

Quantitative Western Blot Analysis of Pluripotency Factors

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Western Blot was carried out as previously described [12 (link)]. Cells for analysis were harvested by trypsinization, centrifuged at 1000 rpm and washed once with ice-cold PBS buffer. Cells were then lysed using the Total Protein Extraction Kit (EMD Millipore, MA)) based on protocol provided by the manufacturer. Cell lysates were then subjected to Western blot analyses using specific antibodies to various cyclins. Cell lysates were prepared from wild type and CDK2AP1 knockdown WA09 hESCs and analyzed for CDK2AP1, OCT4, NANOG, p53, Cyclin A1 expression by Western blot using specific antibodies. The CDK2AP1, OCT4, NANOG and Cyclin A1 antibodies were obtained from Santa Cruz, CA, USA, while p53 antibody was obtained from Cell Signaling, MA, USA. Details of antibodies and sources are provided in S2 Table. Appropriate infrared emitting-conjugated secondary antibodies were obtained from Invitrogen, CA. Detection was then carried out using the Odyssey Infrared Imaging System (Li-Cor Biosciences, NE). The quantitative analysis of the Western Blot bands was carried out using the ImageJ software [13 (link)].
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10

Western Blotting Analysis of Cell Signaling

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Western blotting analysis used in this study was performed as previously described (24 (link)). Antibodies against human HK2, cyclin A1, p27, p-Raf-1, MEK1/2, p-MEK1/2, ERK1/2, c-myc, GAPDH were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Anti-p-ERK1/2 was purchased from CST (Littleton, CO, USA). The horseradish peroxidase-conjugated anti-rabbit or anti-mouse IgG was purchased from Thermo Fisher Scientific (New York, NY, USA). The antibodies used were as follows: anti-HK2 (1:500 dilution, sc-374091, Santa Cruz, USA), anti-cyclin A1 (1:1,000 dilution, sc-239, Santa Cruz, USA), anti-p27 (1:300 dilution, sc-1641, Santa Cruz, USA), anti-MEK1/2 (1:500 dilution, sc-81504, Santa Cruz, USA), anti-p-MEK1/2 (1:500 dilution, sc-81503, Santa Cruz, USA), anti-ERK1/2 (1:500 dilution, sc-135900, Santa Cruz, USA), anti- p-Raf-1 (1:500 dilution, sc-271919, Santa Cruz, USA), anti-c-myc (1:500 dilution, sc-40, Santa Cruz, USA), anti-GAPDH (1:500 dilution, sc-47724, Santa Cruz, USA), anti-p-ERK1/2 (1:200 dilution, #4370, Cell Signaling Technology). GAPDH was used as the control and for quantification.
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