Journal: Science (New York, N.Y.)

Article Title: A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity

doi: 10.1126/science.abf2911

Figure Lengend Snippet: Key Resources

Article Snippet: Gαi-DREADD (pcDNA3.1) Antibodies RSK1/2/3 antibody Cell Signaling Technology 9355 ERK1/2 Cell Signaling Technology 4695 phospho-PAK1(S199/204)/PAK2(S192/197) Cell Signaling Technology 2605 PAK1 Cell Signaling Technology 2602 PAK2 Cell Signaling Technology 2608 pERK Cell Signaling Technology 9106 FGFR3 OriGene TA801078 Daple Millipore EMD ABS515 GAPDH Cell Signaling Technology 2118 secondary goat anti-rabbit HRP Southern Biotech 4010-05 P-HER3-Y1197 Cell Signaling Technology 4561 HER3 Cell Signaling Technology 12708 goat anti-mouse HRP Southern Biotech 1010-05 anti-B-tubulin Abcam ab6276 ERK Cell Signaling Technology 9102 Deposited data Unprocessed peptide files This paper PRIDE ProteomeXchange: PXD019469 Raw data This paper PRIDE ProteomeXchange: PXD019469 Chemicals, Peptides, and Recombinant Proteins Tris G-Biosciences RC108 Acetonitrile, HPLC grade (ACN) Thermo Fisher Scientific A955-4 cOmplete protease inhibitor cocktail tablets mini, EDTA-free Roche 11846 170 001 Dithiothreitol (DTT) Sigma-Aldrich 43819 Formic acid (FA) Thermo Fisher Scientific 28905 Iodoacetamide (IAA) Acros Organic 122270250 Sequencing-grade modified trypsin Promega V5111 Benzonase Sigma E1014-25KU Trifluoroacetic acid (TFA) Thermo Fisher Scientific 28904 Urea Sigma-Aldrich U5378-1kg Fetal bovine serum (FBS) Gibco A3160502 DMEM Corning MT10013CV DMEM/F12 Corning MT10092CV Water, HPLC grade Sigma-Aldrich 270733-4 L Igepal (NP-40) Sigma-Aldrich I3021 Minimal Essential Media Corning 10-009-CV Opti-MEM Thermo Fisher Scientific 31985062 BEGM™ (Lonza) Lonza CC-3170 1% Penicillin-Streptomycin Corning MT30002Cl Paraformaldehyde, 4% solution in PBS Thermo Scientific MFCD00133991 PolyJet SignaGen SL100688 Lipofectamine 3000 ThermoFisher Scientific L3000008 hydrocortisone Sigma H6909-10ML Rapigest Waters 186001861 3x Flag Peptide Sigma F4799-4MG Anti-Flag M2 Magnetic Beads Sigma M8823-5ML Lipofectamine RNAiMAX Thermo Fisher Scientific 100014472 siFGFR3 Sigma Aldrich SIHK0780, SIHK0781, SIHK0782 native coelenterazine Biotium 10110-1 pooled siControl Dharmacon D-001810-10-20 siDaple Dharmacon L-033364-01-0005 10μM clozapine-N-oxide Cayman Chemical NC1044836 5μM native coelenterazine Biotium 10110-1 RPS6KA1 siRNA pool OriGene SR304161 non-targeting control siRNA Dharmacon D-001810-10 Triton X-100 Thermo Scientific 9002-93-1 Software and Algorithms artMS Bioconductor https://www.bioconductor.org/packages/release/bioc/html/artMS.html MSstats Bioconductor https://bioconductor.org/packages/release/bioc/html/MSstats.html Skyline MacCoss Lab https://skyline.ms/project/home/begin.view?

Techniques: Mutagenesis, Recombinant, Protease Inhibitor, Sequencing, Modification, Magnetic Beads, Software, Mass Spectrometry

Journal: Cell Death and Differentiation

Article Title: Reducing FASN expression sensitizes acute myeloid leukemia cells to differentiation therapy

doi: 10.1038/s41418-021-00768-1

Figure Lengend Snippet: A FASN mRNA levels in AML blasts, CD34 + progenitor cells and granulocytes from healthy donors were quantified by qPCR. All the samples were obtained from the Inselspital, Bern, Switzerland. AML patient cells and granulocytes were isolated using Ficoll gradient density centrifugation. Values are the differences in Ct-values between FASN and the housekeeping genes HMBS and ABL1. MNW * p < 0.05, ** p < 0.0. B Blood spot data bank analysis of FASN expression in AML blasts compared to granulocytes from healthy donors. MNW * p < 0.05, ** p < 0.01. C Western blot analysis of FASN regulation in NB4 and HT93 APL cells upon ATRA treatment at different time points (1, 2 and 3 days). Total protein was extracted and submitted to immunoblotting using anti-FASN antibody. Total protein is shown as loading control. The relative protein expressions were normalized to total protein and quantified using ImageJ software (NIH, Bethesda, MD, USA). Data are represented as a mean ( n = 3), Error bars: SD. D Evaluation of FASN transcript levels upon ATRA treatment was done by qPCR. Values were normalized to the HMBS housekeeping gene. Results of at least three independent experiments are shown as n-fold regulation compared with non-treated cells.

Article Snippet: The human AML cell lines HT93, OCI/AML2, MOLM-13 and NB4 were obtained from the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ, Braunschweig, Germany).

Techniques: Isolation, Centrifugation, Clinical Proteomics, Expressing, Western Blot, Control, Software

Journal: World Journal of Gastroenterology

Article Title: Attenuation of MET-mediated migration and invasion in hepatocellular carcinoma cells by SOCS1

doi: 10.3748/wjg.v23.i36.6639

Figure Lengend Snippet: Suppressor of cytokine signaling 1 attenuates invasive growth of orthotopic Hepa cell tumors. A: Hepa-V and Hepa-SOCS1 cells were injected via intravenous route into NOD. scid.gamma (NSG) mice and the livers were examined macroscopically after 20 d. Representative images (left) and quantification of the liver tumor nodules (right) from four mice per group are shown; B-D: Hepa-vector and Hepa-SOCS1 were injected via intrasplenic route into NSG mice (1 × 10 6 cells per mouse; n = 6 per group from two separate experiments) and the mice were splenectomized. After 20 d, the liver tissues were examined macroscopically for tumor nodules. The dorsal and ventral views of representative livers (B, left) and H and E-stained sections of a representative liver for each group (B, right) are shown; C: For each group, the areas of thirty random tumor nodules from three different mice were measured digitally using the NDP software and compared by Student’s paired t test; D: Western blot evaluation of STAT3 and ERK phosphorylation in the tumors from 2 mice per group; E: Western blot evaluation of MET expression and its quantification in the tumors from 3 mice per group. SOCS1: Suppressor of cytokine signaling 1.

Article Snippet: Antibodies (Ab) against total ERK (sc-93, sc-153), STAT3 (sc-483) and MET (sc-161) were from Santa Cruz Biotechnology (Santa Cruz, CA).

Techniques: Injection, Plasmid Preparation, Staining, Software, Western Blot, Phospho-proteomics, Expressing

Journal: The Journal of Biological Chemistry

Article Title: Acquisition of Chemoresistance and Other Malignancy-related Features of Colorectal Cancer Cells Are Incremented by Ribosome-inactivating Stress *

doi: 10.1074/jbc.M115.696609

Figure Lengend Snippet: RIS exposure attenuates proapoptotic signaling molecules in vivo. A, allograft assay with CMT-93 cells pre-exposed to DON. CMT-93 C57BL/6 mouse colon cancer cells pre-exposed to 500 ng/ml DON for 24 h were dissociated into single cells with trypsin, and 5 × 106 cells resuspended with 200 μl of PBS were injected subcutaneously into 14-week-old male C57BL/6 mice. Seven days later, 100 mg/ml 5-FU was intraperitoneally injected, and tumors were excised surgically 24 h later. The tumor volume was calculated as tumor volume = π/6 × major diameter (W) × minor diameter (L)2, presented by vertical scatter plot, and statistically analyzed by unpaired two-tailed t test (bottom panel). The difference in tumor volume was statistically significant (**, p = 0.0022). Con, control. B, a histological section of allograft tumors was analyzed by immunohistochemistry with MIC-1, EGR-1, and ATF3. 3,3′-diaminobenzidine intensity versus hematoxylin was quantitatively assessed by HistoQuest software and statistically analyzed by unpaired two-tailed t test (bottom panel). **, p < 0.01; ***, p < 0.001.

Article Snippet: Allograft of CMT-93 CMT-93, a C57BL/6 mouse colon cancer cell line, was purchased from the ATCC and maintained in DMEM (Welgene) supplemented with 10% (v/v) heat-inactivated FBS (Welgene), 50 units/ml penicillin, and 50 μg/ml streptomycin (Welgene) in a 5% CO 2 humidified incubator at 37 °C.

Techniques: In Vivo, Injection, Two Tailed Test, Immunohistochemistry, Software