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8 protocols using c myc y69

1

Peripheral Blood and Tissue Analysis

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Peripheral blood was collected from tail veins and analyzed on an automated blood
counter, HEMAVET HV950FS (Drew Scientific). Tissue samples were fixed
immediately after isolation and processed into paraffin, sectioned and examined
histologically using hematoxylin and eosin, Congo red, or immunohistochemical
techniques. Immunohistochemical staining was performed using the following
anti-mouse antibodies: CD138 (281-2, BD Pharmingen), λ
(SouthernBiotech), κ (SouthernBiotech), and c-Myc (Y-69, Abcam).
Samples were reviewed by pathologists and diagnosed using uniform criteria.
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2

Antibody Characterization for Immunostaining

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Antibodies for immunostaining and western blotting were used as per the manufacturer’s recommendations. The following antibodies were used within this study: β-tubulin (Cell Signalling Technology, Cat # 2146 (1:1000)), Cleaved Caspase-3 [Asp175] (Abcam, Cat # ab49899 (WB 1:500, IHC 1:1500)), CDKN2A/p19ARF (Abcam, Cat # ab80 (1:1000)), cMYC [Y69] (Abcam, Cat # ab32072 (WB 1:1000, IHC 1:500)), Cyclophilin B (Cell Signalling Technology, Cat # 43603 (1:1000)), GFAP [GA5] (Millipore, Cat # MAB3402 (1:1000)), GFP (Abcam, Cat # ab13970 (1:1000)), HSF1 (Abcam, Cat # ab61382 (1:1000)), HSP70 (Abcam, Cat # ab2787 (1:1000)), HSP90 [EPR16621] (Abcam, Cat # ab203085 (1:1000)), Ki67 [SP6] (Abcam, Cat # ab16667 (1:2000)), n-MYC [NCM II 100] (Abcam, Cat # ab16898 (1:250)), NPR3 (Abcam, Cat # ab97389 (1:250)), Olig-2 (Millipore, Cat # AB9610 (1:1000)), OTX2 (R&D Systems, Cat # AF1979 (1:500)), p21 (Abcam, Cat # ab109199 (1:1000)), Synaptophysin [SY38] (Millipore, Cat # MAB5258 (1:500)), TUJ1 (Covance, Cat # MMS-435P (1:500)), β-actin (Santa Cruz Biotechnology, Cat # sc-47778 (1:1000)), CDKN2A/p16INK4A (Abcam, Cat # ab211542 (1:1000)), anti-mouse IgG secondary HRP (VWR, Cat # NXA931 (1:1000)), anti-rabbit IgG secondary HRP (GE Healthcare, Cat # NA934 (1:1000)), and Lamin B1 (Abcam, Cat # ab16048 (1:1000)).
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3

Phospho-Aurora Kinase Signaling Assay

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Cells were treated with 100nM MLN8237 and 1mM cyclophosphamide for 24-48h. To detect Phospho-Aurora Kinases, cells were treated with 60nM nocodazole for 16h, followed by 100nM MLN8237 and/or 1mM cyclophosphamide for 2h. Lysate was obtained, and equivalent amounts of protein were loaded onto 10% SDS-PAGE gels. The gels were transferred to nitrocellulose and incubated with primary and secondary antibodies purchased from Cell Signaling Technology, as previously described. Primary antibodies used: Mdm2 (D12), p53 (DO-7), actin (2Q1055; Santa Cruz Biotechnology, Inc.; Dallas, TX, USA), c-Myc (Y69; Abcam, Cambridge, UK), P-Rb (D20B12), Mdr1 (E1Y7B), AurkA (D3V7T), AurkB (3094), P-AurkA/B/C (D13A11), P-Histone H3 (Ser10; D7N8E), P-Src Family Y416 (D49G4), LC3B (E5Q2K), Bcl2 (124), Bax (D2E11), GAPDH (D16H11), AIF (D39D2), TBP (D5C9H), Caspase 3 (9662), Caspase 7 (C7), tubulin (2148; Cell Signaling Technology, Danvers, MA, USA).
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4

Western Blot Analysis of Signaling Proteins

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This was performed as described56 (link),57 (link). The following primary antibodies were used: EPHB4 (D1C7N) (1: 1000, Cell Signaling #14960), EPHB4 (1:500, Abcam #ab73259), phospho-eiF2α S51 (1:1000, Cell Signaling #9721 S), eiF2α (1:000, Cell Signaling #9722), phospho-IRE1(S724) (1:1000, Abcam #ab48187), c-Myc (Y69) (1:5000, Abcam #ab32072), GLUT3 (1:5000, Abcam #ab191071), Calreticulin (1:400, Abcam #ab2907), HMGB1 (Abcam #ab18256), Actin (1:10000, Cell Signaling #5125), GAPDH (1:5000, Cell Signaling #3683), Phospho-Src Family Tyr416 (1:1000, Cell Signaling #2101), Phospho-p38 MAPK Thr180/Tyr182 (1:1000, Cell Signaling #9211), and Phospho-4EBP1 Thr37/46 (236B4) (1:1000, Cell Signaling #2855). Following incubation with horseradish peroxidase-conjugated goat anti-rabbit/mouse (1:5000, Biorad) or goat anti-rat (1:5000, Santa Cruz) for 1 h, the binding of secondary antibodies were detected with the Supersignal West Femto Maximum Sensitivity Substrate detection system (Pierce) followed by visualization. Quantification analyses were performed by Biorad ChemiDoc Imager and Bio-Rad Image Lab software.
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5

Western Blot Analysis of Protein Signaling

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Cells and xenograft tumor samples were resuspended in high SDS-RIPA Buffer (50 mM Tris-HCl, pH 7.5, 150 mM Sodium Chloride, 1 % Triton X-100, 1 % sodium deoxycholate, 1 % SDS, 2 mM EDTA; Sigma Aldrich). Tissues were disrupted and homogenized with a TissueLyser II (Qiagen) for 2 × 2 min intervals at 30Hz. Protein concentration was determined using the Pierce™ BCA Protein Assay Kit (Pierce). A total of 15–50 μg of protein extracts were loaded onto NuPAGE® Novex® 4–12 % Bis-Tris Protein Gels (Life Technologies) and subsequently transferred onto nitrocellulose membranes using the iBlot® Dry Blotting System (Life Technologies). The blots were developed using SuperSignal™ West Pico Chemiluminescent Substrate (Thermo Scientific). Antibodies: S6-Ribosomal protein (5G10), Phospho-S6 Ribosomal protein (Ser240/244) (D68F8), Phospho-4E-BP1 (Thr37/46) (236B4), p44/42 MAPK (Erk1/2) (137 F5), and Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) were purchased from Cell Signaling Technology. C-MYC (Y69) and N-MYC (NCM II 100) were purchased from Abcam. FLAG (M2) and β-actin (A2066) antibodies were purchased from Sigma Aldrich.
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6

Chemotherapeutic Agents and Antibody Procurement

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TA3 (Figure 1A) was purchased from Chemfaces (Wuhan Chemfaces Biochemical Co., Ltd., China). DOX was purchased from Selleckchem (Munich, Germany), while 5-FU was purchased from Sigma-Aldrich (St. Louis, MO, USA). Primary antibodies for CNOT2 (Cat No. 34214) and PARP (Cat No. 9542) were purchased from Cell Signaling Technology (Beverly, MA, USA), MID1IP1 (Cat No.15764-1) was purchased from Proteintech (Rosemont, IL, USA), and c-Myc(Y69) (Cat No. 32072) was purchased from Abcam (Cambridge, UK). Caspase 3 (Cat No. sc-7272), β-actin (Cat No. sc-47778), and secondary antibodies (Cat No. sc-516102; sc-2004) were purchased from Santa Cruz Biotechnology (Dallas, TX, USA).
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7

Comprehensive Immune Cell Phenotyping

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The following antibodies were used: APC labeled PBS57 loaded CD1d-tetramers from the NIH tetramer facility, TCRβ APC-e780 (H57-597, eBiosciences) or Pacific Blue (H57-597, Biolegend), CD44 AlexaFluor(AF)700 (IM7, Biolegend), CD45.2 Pacific Blue (104, Biolegend), Thy1.1 phycoerythrin (PE) (A85-1, BD Pharmingen), Thy1.2 FITC (53-2.1, BD Pharmingen), NK1.1 PE-Cy7 or PE (PK136, BD Pharmingen), or Pacific Blue (PK136, Biolegend), or NK1.1-biotin (PK136, eBiosciences) followed by streptavidin-PE Texas Red, CD24 PerCPCy5.5 (M1/69, eBiosciences) or FITC or PE (M1/69, BD Pharmingen), IL-17A PE (17B7, eBiosciences), IL-4 PE-Cy7 (BVD6-24G2, eBiosciences), IFN-γ PerCPCy5.5 (XMG1.2, Biolegend), cMyc (Y69, abcam) or p27kip1 (D69C12; Cell Signaling Technology) followed by anti-rabbit IgG PE (Life Sciences), Ki67-PeCy7 (B56, BD Pharmingen), rabbit IgG isotype (Life Technologies) and BrdU (BrdU flow kit; BD Pharmingen). For transcription factor staining, cells were incubated with antibody to PLZF (D-9, Santa Cruz), followed by anti-mouse IgG1 PE (A85-1, eBiosciences), and then T-bet PE-Cy7 (4B10, eBiosciences), GATA3 PerCpCy5.5 (TWAJ, eBiosciences), and RORγt-BV421 (Q31-378, BD Biosciences).
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8

Western Blot Analysis of Uhrf1, c-Myc, and AP4

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Western blot analysis was performed as previously described (Muppidi et al., 2014 (link)). In brief, cell lysates were separated by SDS-PAGE. Proteins were detected with antibodies against Uhrf1 (M-132; Santa Cruz Biotechnology), c-Myc (Y69; Abcam), AP4 (A-8; Santa Cruz Biotechnology), and β-actin (Cell Signaling Technology).
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