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44 protocols using cd133

1

Western Blot Analysis of Cellular Proteins

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Western blot assay was performed as described previously 20 (link). Briefly, total protein from cells was extracted using RIPA buffer (Beyotime, Shanghai, China) supplemented with complete EDTA-free Protease Inhibitor Cocktail (Roche Diagnostics, Basel, Switzerland). The extracted protein was separated on SDS polyacrylamide gels and transferred to the PVDF membranes. Western blotting was performed using antibodies against human COL6A1 (Abcam, Milton, Cambridge, UK), N-cadherin, E-cadherin, Vimentin, FAK, Src, p-FAK, p-Src, p-STAT1 (Tyr701), p-STAT1 (Ser727), p-STAT3 (Tyr705), STAT1, STAT3, CD133, ABC2G, SOX2, Nanog, CD63, CD9, TSG101, SOCS5, Flag, GFP, HA, Ubiqution (Ub), GAPDH, p300, c-Jun were purchased from Cell Signaling Technology (CST, USA).
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2

Stemness and EMT Markers in Cancer

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CD24, CD44, CD133, Nanog, Oct4, Sox2, KLF4, c‐Myc, Gli1, Gli2, Patched1, Patched2, Smoothened, Bcl‐2, Cyclin D1, E‐cadherin, N‐cadherin, Snail, Slug and Nanog antibodies were obtained from Cell Signaling Technology (Danvers, MA). Shh protein and anti‐β‐actin antibody were purchased from Santa Cruz Biotechnology Inc (Santa Cruz, CA). α‐Mangostin (98% pure) was obtained from the LKT (St. Paul, MN). Accutase was purchased from Innovative Cell Technologies, Inc (San Diego, CA). Matrigel was purchased from BD Bioscience (San Jose, CA). Crystal violet was purchased from Sigma‐Aldrich (St. Louis, MO). TRIZOL was purchased from Invitrogen (Grand Island, NY). Luciferase assay kit was purchased from Promega.
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3

RCC cell line cultivation and molecular analysis

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RCC cell lines Ketr-3, 786-O, and ACHN as well as normal renal tubular epithelial cell HK-2 were all cultured in DMEM (high glucose) medium supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and streptomycin. All the cultures were maintained in humidified incubator with 5% CO2 at 37 °C. The antibodies against β-actin, CD133, Nanog, Oct4, GAPDH, phosphorylated (Serine-311) and total NF-κB p65, PARP were obtained from Cell Signaling Technology (Danvers, MA, USA). The antibody against LC3B was purchased from Novus (Shanghai, China), and Ki-67 was purchased from Abcam (Shanghai, China). All the secondary antibodies labeled with HRP were purchased from Beyotime (Nanjing, China). B-27 supplement (B-27) was purchased from Thermo Fisher Scientific (Shanghai, China). Epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) were purchased from PeproTech (Rocky Hill, NJ, USA). Insulin was purchased from Sigma (Shanghai, China). Bay 11–7082 (inhibitor of NF-κB) was purchased from MCE (Shanghai, China). Sorafenib tosylate tablets were purchased from Bayer (Shanghai, China). 3-Methyladenine (3-MA, an inhibitor of PI3K) was purchased from TargetMol (Shanghai, China). YOYO-1 dye was purchased from Invitrogen (Carlsbad, CA, USA).
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4

Western Blot Analysis of Cellular Proteins

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Protein lysates (30 µg/lane) were separated on 10% SDS-PAGE gels and transferred to PVDF membrane. Following blocking, target proteins were detected by probing overnight at 4°C with antibodies against: NFIB, Bin1 and p19ARF (Abcam); PARP, cleaved PARP, cleaved caspase-3, caspase-3, cyclin D1, CDK4, CDK6, p-Akt-ser473, β-catenin, and CD133 (Cell Signaling Technologies); and total Akt, p-Erk and ERK (Santa Cruz Biotechnology). Then, membranes were washed and incubated with anti-mouse/rabbit IgG secondary antibody (Invitrogen) conjugated with horseradish peroxidase (HRP) at room temperature. Specific proteins were visualized using an enhanced chemiluminescence detection reagent (Pierce; ThermoFisher Scientific, Inc.).
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5

Western Blot Analysis of Stem Cell Markers

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Western blot analysis was conducted as previously described (He et al., 2015). The primary antibodies were Nanog (1 : 1000, Cell Signaling Technology, Beverly, MA, USA, #4548), OCT4 (1 : 1000, Cell Signaling Technology, #2750), CD133 (1 : 1000, Cell Signaling Technology, #5741), HIF‐1α (1 : 1000, Abcam, Cambridge Science Park, Cambridge, USA, ab39266), HIF‐2α (1 : 1000, Abcam, ab72130), β‐actin (1 : 500, Abcam, ab92611), and BCRP (1 : 800, Abcam, ab26056). The bands were visualized by enhanced chemiluminescence. The band intensities were quantitatively analyzed using imagej Software (National Institutes of Health, Bethesda, MD, USA).
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6

Hypoxia Regulates Stemness Markers in Cells

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For Western blot analysis of HIF-1α, cells were incubated in 21% oxygen or 1% oxygen for 24 hrs. Samples were collected in RIPA buffer (Sigma-Aldrich) containing Complete Protease Inhibitor Cocktail (Roche, Indianapolis, IN, USA), and protein concentration was determined by Bio-Rad Protein Assay (Bio-Rad, Hercules, CA, USA). Western blot analysis was performed for HIF-1α using the following antibodies: HIF-1α (C-Term) Polyclonal Antibody (10006421, Cayman Chemical, Ann Arbor, MI, USA), anti-CD31 (rat monoclonal antibody, DIA-310, Dianova), CD133 (MBS46020, USA), Nanog (#8822, Cell Signaling Technology), Oct-4 (#83932, Cell Signaling Technology), Sox-2 (#2748, Cell Signaling Technology), CD271 (orb224643, Biocompare), TNAP (sc-23430, Santa Cruz Biotechnology, INC.), CD44 (#3570, Cell Signaling Technology) and β-actin (A5441, Sigma-Aldrich).
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7

Colorectal Cancer Stem Cell Marker Expression

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Evaluation of expression of the colorectal cancer stem cell (CrCSC)-associated markers, CD133, CD44 and ALDH1 (Cell Signaling Technology, USA), was done using immunofluorescence analysis. The passage 5 (P5)-derived spheroid cells were fixed with 4% paraformaldehyde and embedded in parafilm wax for sectioning. After blocking with 5% bovine serum albumin, the cells were stained overnight with anti-CD133, -CD44 or -ALDH1 antibodies conjugated with Alexa Fluor 488 (Invitrogen, USA). The nuclei were counterstained with DAPI. The cells were photographed under an inverted fluorescence microscope. For quantitative analysis, ImageJ was used to calculate the fluorescent intensity; the relative ratio to DAPI staining was determined [98 (link)].
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8

Protein Expression Analysis of Cellular Samples

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Cell lysates were subjected to polyacrylamide gel electrophoresis, and then blotted onto Immobilin-P polyvinylidene difluoride membranes (Millipore, Bedford, MA). Antibodies for cyclin D1 (catalog # 2978), CDK2 (catalog # 2546), phospho-Rb (catalog # 8516), Rb (catalog # 9309), PARP(catalog No # 9532), Caspase 3 (catalog # 9662), Bcl2 (catalog # 2876), BclXL (catalog # 2764), Bax (catalog No # 5023), CD44 (catalog # 3570), CD133 (catalog # 64326), phospho-STAT5 (catalog #s 4332, 9359), STAT5 (catalog # 25656), phospho-STAT3 (catalog # 9131), STAT3 (catalog # 4904), phospho-ERK (catalog # 4370) and ERK (catalog # 9102), ABCG2 (catalog #42078), DCLK1 (catalog # 62257) were purchased from Cell Signaling Technology (Danvers, MA, USA), for DCLK1 (catalog # ab37994), Oct-4 (catalog # ab189857) from Abcam Inc. (Cambridge, MA, USA), CDK4 (catalog # MA5–13498), CDK6 (catalog # MA5–13338) from Thermofisher (Waltham, MA, USA) and DCLK1 (catalog # SAB2420186) and Actin (catalog # A1978) from Sigma Aldrich and GAPDH (catalog # sc-365062) Santacruz Biotechnology Inc (Santa Cruz, CA, USA). Specific proteins were detected by chemiluminescence system.
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9

Protein Expression Profiling of HCC Cells

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Total lysates of HCC cells were prepared, and proteins were extracted after centrifugation. 30 µg proteins of each sample were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotted with indicated antibodies. The visualization of protein signals was performed using a chemiluminescence reaction system following the manufacturer's recommenddations. Antibody for cleaved PARP, cleaved Caspase-3, CD133, Sox-2, Oct-4, Vimentin, SHP-1, JAK2, STAT3, p-STAT3, and β-Actin were purchased from Cell Signaling Technology (Danvers, MA). Slug, Snail, p-JAK2, and the second antibodies were acquired from Abcam (Cambridge, UK).
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10

Immunohistochemical Staining Protocol

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IHC staining was performed according to the standard procedure. Details could be found in Supplementary Materials and Methods. The antibodies used for IHC included PITX2 from Sigma-Aldrich (St. Louis, MO), proliferating cell nuclear antigen (PCNA) from Immunoway Biotechnology Company (Plano, TX, USA), and c-Myc, NANOG, CD133 and EPCAM from Cell signaling Technology (Danvers, MA, USA).
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