Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATRA-2.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATPR-3.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/Vehicle-1.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATRA-1.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATPR-2.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/Vehicle-2.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATPR-1.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/Vehicle-3.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATRA-3.prot.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATPR-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATRA-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/Vehicle-2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATRA-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATPR-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/Vehicle-3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATPR-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/Vehicle-1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD005605/ATRA-2.rawprimaryOK200002940xiaquan2010@163.comXia QuanMass SpectrometryShotgun proteomicsGastric AdenocarcinomaNot availableAtpr,cell cycle arrest and differentiation,proteomics analysis,pi3k-akt-foxo-p27kip1 pathway,sgc-7901 cellshttp://www.ebi.ac.uk/pride/archive/projects/PXD005605Cell CultureGastric GlandProtein sample preparation Cells were lysed using a total protein extraction kit (Vazyme Biotech) containing protease inhibitor, and a phosphatase inhibitor cocktail (Pierce USA) was added according to the instructions. Samples were incubated for 15 min on ice with intervals of vigorous vortexing. Proteins were collected by centrifugation for 15 min at 14000×g at 4℃ to pellet the unbroken cells and debris. The supernatant was collected, and the protein concentrations were determined using a BCA Protein Assay Kit (Beyotime China) with BSA as the standard. Each 200μg aliquot of the SGC-7901 cell lysate was stored in 1.5 ml centrifuge tube at -80 ℃ prior to further purification. Protein digestion A total of 200μg of cell lysate from the different group was precipitated by adding 4 vol pre-iced acetone and incubating for 12 h at -20℃. The precipitated protein was then recovered by centrifugation at 10000 g for 5 min at 4 ℃, and the resulting pellet was washed three times with 100μL ice-cold acetone. The residual acetone was volatilized at room temperature and the protein pellet was then resuspended in 12.5 μL ULB solution (7 M urea, 2 M thiourea, 4 % CHAPS) with vigorous vortexing. To ensure good efficiency of trypsin digestion, 87.5 μL of 50 mM NH4HCO3 was added to ensure that the final concentration of urea was 1 M in the mixture. A sample containing 200 μg of protein was reduced using 4 μL of 100 mM DTT for 15 min at 50℃ and alkylated with 4 μL of 300 mM iodoacetamide for 15min at room temperature in darkness. Alkylated proteins were digested with 4 μg of mass spectrometry grade trypsin (Promega, USA) at a 1:50 enzyme/protein ratio at 37℃overnight (17 h). The resulting samples were dried using a Speed Vac concentrator (Labconco, USA). These experiments were repeated three times. Mass spectrometric analysis The vacuum concentrated peptides were reconstituted in 0.1% formic acid and were analyzed on a LTQ XL Orbitrap MS (ThermoFisher Science, USA) equipped with a nano-ESI and operated in data-dependent mode with the Xcalibur software (version 2.1.0.1139, Thermo Fisher Science). An ACCELA 600 liquid chromatography system (Thermo Fisher Science, USA) was used and 2μL of peptide mixtures were injected into a C18 reversed phase column (Zorbax 300SB, 3.5μm,150x0.075mm,300A, Agilent ) using solvent A (0.1% formic acid) and solvent B (100% acetonitrile). Separation of peptides was conducted using a continuous gradient consisting of the following: 5% solvent B was used for 10 min, solvent B was increased from 5% to 40% over 100min, solvent B was increased to 95% over 30 min, and finally solvent B was maintained at 95% for 25 min. To re-equilibrate the system, solvent B was decreased to 5% over 5 min and maintained at 5% for 10 min. A 120 min liner gradient blank was run between samples to prevent sample carryover. The flow rate was 300 nL/min, and the eluted peptides were directly electrosprayed into the mass spectrometer with a voltage of 1.8 KV in positive ion mode. The ion transfer tube temperature was set at 200 °C. Full scan mass spectra were acquired in the Orbitrap over a mass range of 300-2000 m/z with the resolution set to 60000. The top ten most intense parent ions were selected for CID in the liner ion trap at normalized collision energy of 35%. Dynamic exclusion was set at 60 s. 2.5 Identification and quantification of proteins using a label-free approach The raw data files were analyzed using the SEQUEST (v.1.13, ThermoFisher Science) search engine and the Proteome Discoverer (v.1.2, ThermoFisher Science) using the human nonredundant peptide database obtained from the Uniprot human database (Nov 3 2014, 88717 sequences). FDR for peptide identification of all of the searches were less than 1%. Carbamidomethyl / +57.021 Da (cysteine) was set as static modification and Oxidation / +15.995Da (methionine) was set as the dynamic modification. Trypsin (full) was specified as the proteolytic enzyme and one missed cleavage was allowed. The precursor mass tolerance was set at 10ppm, and the fragment mass tolerance was set at 0.8 Da. For differential analyses of proteins between the ATPR group and the Vehicle group, a label-free mass spectrometry-based protein quantification software, SIEVE (v 1.3, ThermoFisher Science), was used for comparing the relative abundance of peptides and proteins. The chromatograms were time-aligned before the intensities of all of the identified peptides were measured; then, the framing parameters were set at 2.5 min frame time widths and 0.02 frame m/z widths. The criteria used to identify differentially expressed proteins were: at least six peptide sequence matches, more than 10% sequence coverage and peptide scores greater than 16 scores, and more or less than a 1.2-fold change of the protein quantities between the ATPR treated samples and the Vehicle samples. Significant differences of P<0.05 were accepted for differentially expressed proteins.PrideLabel freeiodoacetamide derivatized residuemonohydroxylated residueExclusively expressed proteins from the protein profiles of the ATPR and Vehicle groups were subjected to DAVID bioinformatics resources to analyze their molecular functions, subcellular localizations and biological processes. Differentially expressed proteins from the SIEVE processing were analyzed using IPA and the KEGG Pathway Database to find concurrent patterns, functional interactions and stable interactomes. For DAVID analysis, the exclusively expressed proteins were compiled by reporting the UniProtKB accession number, which were then were uploaded into the DAVID database and mapped against the human dataset for Gene Ontology (GO) analysis using the default settings. For the IPA and KEGG investigations, the proteins derived from the SIEVE differential analysis and related to cell differentiation were imported and analyzed. The biological networks were generated to observe the potential direct and indirect relationship in which the differentially expressed proteins were involved.ProteomicsQuan XiaLTQ OrbitrapSchool of Pharmacy, Anhui Medical University, Hefei, ChinaPARTIALHomo Sapiens (human)28164444 Xia Q, Zhao Y, Wang J, Qiao W, Zhang D, Yin H, Xu D, Chen F. Proteomic analysis of cell cycle arrest and differentiation induction caused by ATPR, a derivative of all-trans retinoic acid, in human gastric cancer SGC-7901 cells. Proteomics Clin Appl. 2017 Feb 6 10.1002/prca.201600099xiaquan2010@163.comBiomedicalDepartment of Pharmacy, The First Affiliated Hospital of Anhui Medical University<h4>Purpose</h4>4-amino-2-trifluoromethyl-phenyl retinate (ATPR) was reported to potentially inhibit proliferation and induce differentiation activity in some tumor cells. In this study, a proteomics approach was used to investigate the possible mechanism by screening the differentially expressed protein profiles of SGC-7901 cells before and after ATPR-treatment in vitro.<h4>Experimental design</h4>Peptides digested from the total cellular proteins were analyzed by reverse phase LC-MS/MS followed by a label-free quantification analysis. The SEQUEST search engine was used to identify proteins and bioinformatics resources were used to investigate the involved pathways for the differentially expressed proteins.<h4>Results</h4>Thirteen down-regulated proteins were identified in the ATPR-treated group. Bioinformatics analysis showed that the effects of ATPR on 14-3-3ε might potentially involve the PI3K-AKT-FOXO pathway and P27Kip1 expression. Western blot and RT-PCR analysis showed that ATPR could inhibit AKT phosphorylation, up-regulate the expression of FOXO1A and P27Kip1 at both the protein and mRNA levels, and down-regulate the cytoplasmic expression of cyclin E and CDK2. ATPR-induced G0/G1 phase arrest and differentiation can be ablated if the P27kip1 gene is silenced with sequence-specific siRNA or in 14-3-3ε overexpression of SGC-7901 cells.<h4>Conclusion and clinical relevance</h4>ATPR might cause cell cycle arrest and differentiation in SGC-7901 cells by simultaneously inhibiting the phosphorylation of AKT and down-regulating 14-3-3ε. This change would then enhance the inhibition of cyclin E/CDK2 by up-regulating FOXO1A and P27Kip1. Our findings could be of value for finding new drug targets and for developing more effective differentiation inducer.Proteomic analysis of cell cycle arrest and differentiation induction caused by ATPR, a derivative of all-trans retinoic acid, in human gastric cancer SGC-7901 cells.Xia Quan Q, Zhao Yingli Y, Wang Jiali J, Qiao Wenhao W, Zhang Dongling D, Yin Hao H, Xu Dujuan D, Chen Feihu Fsodium salt, l(4)17, CPD photolyase activity, l(4)13, ammonium formate, Gli, 13C-labeled, IL1BC, cadmium salt, MeCN, PhrB photolyase activity, ion, Raw, Ass-1, Cid[Mel], Ci[D], CASP-1, AUTSX5, chronic obstructive pulmonary disease (COPD), Basodexan, magnesium formate, zinc salt, Solvent, CENP-A, Long Term, CENP-C, Bca, 5730420M11Rik, 2-Propanone, Polypeptides, protein polypeptide chains, KL receptor activity, Drug Tolerance, T22F8_160, 12-trihydroxy-24-oxocholan-24-yl)amino)propyl)-, cobalt(II) formate dihydrate, ATGPR7, CH3-C#N, B1, SCO5, Chronic irreversible airway obstruction, Urea, fold, GRP8, AGM4, 3, GRP7, SCO1, NUP96, Software Engineering, Analysis, outer pigmented layer of retina, 7, Gsfsow3, Il1bc, epithelium, WMS, Sinkiang, bca, SET, BcDNA:RE21270, Analyses, M, N, phosphatase 2A inhibitor I2PP2A, CAFL - Chronic airflow limitation, proteins, W, IL-1BC, SUPPRESSOR OF AUXIN RESISTANCE 3, AI047805, DmelCG4299, set, pigment epithelium of retina, decreased, CI, disease (COPD), anatomical tube, sample, D1, n, pigmented retina epithelium, Bs, Half Cystine, NOVh, phosphatase, 12-trihydroxy-24-oxocholan-24-yl)amino)-, drug tolerance, SGS, nickel salt, CiD, Ce, chronic obstructive lung disease [Ambiguous], Degradations, Ci, Caspase-1 subunit p10, Chp, cobalt (+2) salt, Zinc Cysteinate, immune system tolerance, Liquid Chromatography, Longterm Effect, Spectrum Analysis, not genetically inherited, collisionally activated dissociation, Software Tools, CID, ciD, Cid, DmelCG7788, ACMICD, CHRONIC OBSTRUCTIVE AIRWAY DIS, PBT, Computer Applications, sodium (4:1:1) salt, Dm1, magnesium salt, CHAPS, Computer Applications Software, dipyrimidine photolyase (photosensitive), ci-D, Methionin, methionine, Hmet, Airflow Obstruction, 5beta, GLYCINE-RICH PROTEIN 8, Chronic Obstructive Airways Disease, N-dimethyl-N-(3-sulfopropyl)-3-(((3alpha, pbt, Chronic obstructive lung disease, Plxn1, Software Applications, Mainland China, HLA-DR-associated protein II, DI-2, CENP-A/Cid, CENP-A/CID, LY57, Source Software, CENPA, I-2Dm, Protein Digestions, formate, Spectrometry, cromium (+3), SGC 7901 cell, inhibitor of granzyme A-activated DNase, lysed material, beta Trypsin, mKIAA4053, human, I-2PP1, 7alpha, Applications, TAF-IBETA, Self Tolerance, F2G1.4, OBSTRUCTIVE PULMONARY DISEASE (COPD), duct, Drice, ammonium (4:1) salt, TAF-Ibeta, methyl cyanide, DRICE, lead (+2) salt, Liquimeth, Ci-155, krk1, Computer Software Applications, 2-amino-4-(methylsulfanyl)butanoic acid, nickel formate dihydrate, lead formate, Effects, DrIce, DrICE, aluminum salt, CAO - 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Chronic obstructive lung disease, acetonitrile, L-Isomer, Digestions, Cell, chronic, Engine, Tool, polypeptide, Inner Mongolia, native protein, Temperatures, Immune Tolerance, Proteolyses, carbonyldiamide, I-2PP2A, ci[D], KIT ligand receptor activity, C18, cupric formate, chemical analysis, Dm I-2, Long Term Effects, MFS1, (COPD), chronic airway obstruction, chronic obstructive, aluminum formate, dJ142L7.2, CAL - Chronic airflow limitation, Mass Spectrum Analyses, Met, XKrk1, AU020952, RPE, lithium formate, DmelCG2125, Col4a-1, ci155, CenH3, underdeveloped, Protein., increased number, GR-RBP7, GR-RBP8, IL-1 beta-converting enzyme, ethanenitrile, Interleukin-1 beta-converting enzyme, CD117, retinal pigment epithelium, primary structure of sequence macromolecule, Longterm Effects, ME-IV, p. pigmentosa retinae, Computer Programs, Gene Proteins, Applications Softwares, C-Kit, Ssm, chronic obstructive lung disease (disorder), EG:95B7.8, xkl-1, 2600013D04Rik, deoxyribonucleate pyrimidine dimer lyase (photosensitive), CenpA/CID, chronic obstructive pulmonary disease, Immunological Tolerance, IPP2A2, Bru, T22F8.160, NCMe, determination, and rna binding 2, Chronic Airflow Obstructions, zinc formate, cleavage, CG7788, crice, lead salt, protein, Xkl-1, combined T cell and B cell immunodeficiency, Cahp, pigmented epithelium, CCN3, QM, Productivity, peptide, L-Isomer Methionine, hydroxide, Gsfsco1, ammonium tetraformate, Methionine, peptido, ClvPrd, uninterrupted, AA408052, chronic obstructive airways disease NOS (disorder), Min, Chronic Obstructive Pulmonary Disease (COPD), protein aggregate, Gsfsco5, present in fewer numbers in organism, Effect, Computer Program, fs(1)M104, DmelCG42273, SOW3, Mass Spectrum Analysis, CG13329, Svc, increased, COLD (chronic obstructive lung disease), peptides, NEC in ICD9CM_2006, TAF-I, E927b, Open, pigmented retina, hypoplasia, min, Computer Programs and Programming, mAPC, copper, Protein Degradation, free, DNA cyclobutane dipyrimidine photolyase activity, Chronic airflow limitation, IBP-9, ASS, IGAAD, lithium salt, DmelCG10574, ICE, GLYCINE RICH PROTEIN 7, Cenp-A, Lyw-57, glycine-rich RNA-binding protein 8, Sl, GPHYSD2, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, Racemethionine, ammonium (2:1) salt, Long-Term Effects, inner salt, CHRONIC, phapii, PRE, Tube, obstructive lung disease, ice, iCE, drice, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, 2-Amino-4-(methylthio)butyric acid, Dmel_CG7826, StF-IT-1, Tr-kit, Th, Search, pigmented retinal epithelium, Airflow Obstructions, ur, Source Softwares, Programs, Manchuria, Spectroscopy, pulmonary disease (COPD), SLP65, TUBE, Program, Ly-57, carbamide, retinal pigment, Ionen, drIce, drICE, Digestion, low temperature, CHRONIC OBSTRUCTIVE, chronic obstructive pulmonary disease and allied conditions, Computer Applications Softwares, kl1-A, Chronic airway disease, Immunologic Tolerance, NOS, p24, NOV, Softwares, KIT, nickel (+2) salt, PlexA1, retinal pigment layer, Dmel_CG7835, COPD NOS, SGC7901 cell, cenpA, Mnb, MNB, CHRONIC OBSTRUCTIVE LUNG DIS, parent ion, tyrosine-protein kinase Kit, Chronic airway obstruction, SLP-65, ammonium salt, Ci/Gli, Ci/GLI, CenH3/CID, BASH, cold, Xylella fastidiosa str. Temecula1, retinal pigmented epithelium, P45, cobaltous formate, nov, L-Cysteine, kit, MASS, CG4299, AW124434, Sid470p, fs(1)Y[b], organ system, congenital combined immunodeficiency, Chronic Airflow Obstruction, phr A photolyase activity, H2NC(O)NH2, DNA-photoreactivating enzyme, precursor ion, Tolerance, COPD - Chronic obstructive pulmonary disease, Acetamide, C130088N23Rik, copper salt, chronic obstructive airways disease, p45, Polypeptide, obstructive pulmonary disease (COPD), AI046351, DXS648E, i2pp2a, COLD, chronic obstructive lung disease, 1728, time, accessory, Gruppe, human being, Cysteine Hydrochloride, YB, DISEASE (COPD), Degradation, cesium salt, SCF receptor activity, L Isomer, FBN, Gene, circadian rhythm, Spectrum Analyses, Computer, photoreactivating enzyme activity, vac, aligned, supernumerary, PHAPII, formic acid, Karbamid, l(4)102ABc, Cold, potassium salt, Pulmonary Disease, polypeptide chain, scfr, reduced, template-activating factor I, Yb, subnumerary, ECTOL1, 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DXS648, inhibitor, cenH3, aligned to, Protein Digestion, strontium salt, People's Republic of China, PULM DIS CHRONIC OBSTRUCTIVE, Peptide, group, Chronic obstructive pulmonary disease finding (finding), stratum pigmentosum (retina), MODIFIER OF SNC1, Software Tool, CAD, natural protein, IGFBP-9, Ci155, Protein, 3-(3-cholamidopropyl)dimethylammoniumpropane sulfonate, AI551343, deoxyribonucleic photolyase activity, I2PP2A, sequence, Dyrk1, CES2A1, GLYCINE-RICH RNA-BINDING PROTEIN 7, Vacuums, connected anatomical system, Software, ACETONITRILE, WMS2, cyanomethane, Data Base, chronic obstructive airway disease, Temperature, Mass Spectrum, c-KIT, 10^[-9], photolyase activity, uree, Dops, urea, CC1, Engineering, Rest, Tripcellim, phosphoric monoester hydrolase activity, sample population, chromic formate, UREA, Interleukin-1 beta convertase, Protein Gene Products, Trypure, present in greater numbers in organism, dSET/TAF-Ibeta, c-kit, 2610030F17Rik, Ion, concentration, velocity, SSKS, 3.4.22.36, calcium salt, alpha-amino-gamma-methylmercaptobutyric acid, cold (chronic obstructive lung disease), Peptid, Chronic Obstructive Lung Disease, assay, AA407739, groupe, CID/CENP-Ahuman being, tumor suppressor, tretinoin, Tretin M, Refissa, trans-Retinoic Acid, Vitamin A, arrest of cell cycle progression, 8E-tetraenoic acid, beta all trans Retinoic Acid, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, Potassium Salt, Retinoic Acid, cell cycle regulator, termination of cell cycle, Cordes vas, 3, Cell., 4, 6, Retin-A, gastric neoplasm, Vesanoid, Stieva-A, 6-trimethylcyclohex-1-en-1-yl)nona-2, Retinoic acid, Retinoic, all-trans-beta-Retinoic acid, Renova, Salt, all trans Retinoic Acid, Atralin, Tretinoin Potassium Salt, Betarretin, 8E)-3, trans Retinoic Acid, man, Tretinoin Sodium Salt, 6-trimethyl-1-cyclohexenyl)nona-2, gastric cancer, beta-all-trans-Retinoic, Altreno, control of cell cycle progression, regulation of progression through cell cycle, regulation of cell cycle 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Salt, Sodium Salt, 7-dimethyl-9-(2, all-(E)-retinoic acid, Avita, regulation of cell cycle arrest, vitamin A acid, Retisol-A, (all-E)-3, 8-tetraenoic acid, tretinoine, cell cycle regulationprojections, Ito, anatomical protrusion, human being, Gene Ontology Projects, Data Set, hi syndrome, determination, hypomelanosis of Ito, protein complex, lamellae, anatomical process, Proteins, lamina, number, flanges, Incontinentia pigmenti type 1, Gene, protein, extra or missing physical or functional parts, protein-containing complex, process of organ, presence, Gene Ontology Project, Cell, Gene Ontology, protrusion, mereological quality, lamella, Incontinentia pigmenti type 1 (formerly), protein polypeptide chains, count in organism, native protein, natural protein, polypeptide chain, pigmentary mosaicism, type I, Protein, chemical analysis, shelf, Gene Products, Project, Ontology Projects, protein aggregate, Ito type, flange, organ process, Data Base, Differentiations, Ontology Project, Gene 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protein aggregate, MEN1B, DmQ95V5, D14-3-3e, l(2)07103, CG31196, 1C5, FOXO1A, Dp60, dFOXO, dFoxO, Gap Phase, peptides, CDKA1, K, Pi3K92D, CG4141, PI3K_59F, anon-WO02059370.52, FKH1, catalyst activity, par-5, Pi3k, PI3-kinase activity, dfoxo, proteins, experimental design, PI[[3]]K, Phase 1, PI3Kgamma, PKB|Akt, Q95V55, INSDC_feature:ncRNA, RacPK, INSDC_qualifier:siRNA, 5.11, MCAP, First Gap, p55alpha, regulation of cell cycle progression, medicine, dCdk2, PI3K 68D, Pi3K, PI3k, FoxO1A, Cyclin-dependent kinase inhibitor p27, G1b Phase, MCMTC, 2G1, ATP - 1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, PKB alpha, screening, dVps34, PI3K68D, HS1, dakt, 14-3-3e, small interfering RNA, P110DELTA, PtdIns-3-kinase activity, Fkhr, rea, p50alpha, Search, RAC-PK-alpha, l(3)89Bq, First, anon-WO0172774.141, CG2699, results, vacuolar protein sorting 34, DmelCG5373, dPIK, 1-phosphatidylinositol 3-kinase activity, AKT1 kinase, d14-3-3zeta, PKB/Akt, PKB/AKT, AKT/PKB, protein kinase B alpha, C530050K14, dAkt, dAKT, arrest of mitotic cell cycle progression, DmelCG31196, type-1 PI3K, FKHR, DmCdc2, modulation of cell cycle progression, 4-3-3 zeta, p-Akt, p27, Gap, DAkt, l(3)04226, cell division control 2, CG11621, p27Kip1, DPKB, First Gap Phase, d14-3-3epsilon, protein_coding_transcript, G1 Phases, pAkt, p85alpha, G1, cessation of cell cycle, Afx, signs, p33(CDK2), DmelCG10498, G1a, INSDC_feature:gene, SR3-9, proto-oncogene c-Akt, PI3K 68_D, G1b, dAKT/dPKB, PKB/dAKT, 14-3-3EPSILON, DmelCG4141, F8A5_4, protein kinase B, 14-3-3, APDS, CDKN4, p110D, Dakt, PI3KBETA, dPKB, 1433epsilon, Cyclin-dependent kinase inhibitor 1B, regulation of cell cycle arrest, Polypeptide, p120-PI3K, droPIK57, cell cycle regulation, Gruppe, RAC-ALPHA, CDKN2, DRAC-PK85, AA408329, DmelCG4006, Gap Phase 1, PI3K92E, l(2)46Ee, D14-3-3epsilon, Gene, Pi3K_59F, arrest of cell cycle progression, type I phosphatidylinositol kinase activity, MEN4, protein-containing complex, G1a Phases, phosphatidylinositol 3-kinase, Gap Phases, Dpkb, DmelCG3143, PIK3, Pi3Kp60, dVps34/PI3K59F, eps, polypeptide chain, First Gap Phases, p60, termination of cell cycle, PI3K-dp110, Gene Products, dPI3K, PHOSPATIDYLINOSITOL 3-KINASE, anon-92Ed, anon-WO0118547.374, drug., Dp110/PI3K, BEST:GH05075, PI3K-68D/E, class I, Search Engines, l(3)j2B10, 3143, foxO, messenger RNA, P34CDC2, G1a Phase, PI3'K, Pi3Kp110, EK3-5, P110BETA, PI3K-68D, template RNA, drugs, cdk2, PI3K21B, control of cell cycle progression, CDKA, regulation of progression through cell cycle, grupos, AKT, Akt, Fkhr1, PAR-5, P27 kip1, DRAC-PK, CG17870, cg3143, peptidos, MCM, CDK2, Cdk2, 14-3-3-epsilon, 549, Par-5, negative regulation of cell cycle arrest, Cpk, Foxo, dP110, cell cycle modulation, CT24092, findings, grupo, AI876417, AA414921, akt, p120, class II, protein complex, cell cycle arrest, type III phosphoinositide 3-kinase activity, Proteins, Phosphorylations, p110, CG3143, Vps34p, DAkt1, DAKT1, KIP1, Kip1, Peptide, PI(3)K, Cell, Engine, group, cpk, PI3K-92E/Dp110, FoxO, FOXO, polypeptide, PIK3C1, positive regulation of cell cycle arrest, 14-3-3omicron, ATP:1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, PKB, dFoxo, A630093N05Rik, CWS6, native protein, CWS5, vps34, natural protein, Protein, chemical analysis, Cyclin kinase inhibitor, 14-3-3leo, PKB-ALPHA, dp110, 14-3-30epsilon, 14-3-3-zeta, INSDC_feature:mRNA, sequence, D-Akt, CG4006, PI3CG, DmCdk2, Protein Cdkn1b, P27KIP1, 14-3-3 epsilon, PI-3-K, Dakt1, serine-threonine kinase Akt, CG10498, Dmcdc2c, Phase, PI3K-59F, CYCLIN-DEPENDENT KINASE A, PI3K-Dp110, akt1, P27kip1, mRNA, dAkt1, eg1, DRAC-PK66, AI843786, Rest, class III, CDK2/CDC2c, CDC2AAT, DmelCG11621, p110gamma, primary structure of sequence macromolecule, mitotic cell cycle arrest, Protein Gene Products, Su(Raf)3B, Gene Proteins, dAkt/PKB, Dcdc2c, dakt1, CLOVE, DmVps34, Afxh, S(Sev-CycE)3A, IMD14, PI3K_68D, 14-3-3ZETA, PI3K-92D, PKBalpha, PAR5, D14-3-3zeta, Peptid, Dmp110, dAKT1, assay, Rac, RAC, LEO, Leo, reverse transcription polymerase chain reaction, 14-3-3 zeta, groupe, l(2)46CFe, thymoma viral proto-oncogeneliquid chromatography tandem mass spectroscopy, CDC2A, CDC2C, PRKBA, Akt/PKB, dP60, CG5373, fd88A, Activity, tumor suppressor, label-free protein quantification, determination, ATVPS34, Vps34, DAKT1/PKB, Phases, PI3K, Dp110, BcDNA:LD15217, LFQ, RT-PCR, protein, Tumor, AKT1, VPS34, 11621, phosphorylation, G1b Phases, PI-3 kinase, peptide, p110-alpha, Polypeptides, CDC2c, protein polypeptide chains, cell cycle regulator, PHOSPHATIDYLINOSITOL 3-KINASE, peptido, DmelCG2699, F8A5.4, Dfoxo, Cdc2c, symptoms, 1, phosphatidylinositol 3-kinase activity, Foxo1a, protein aggregate, Cdki1b, MEN1B, DmQ95V5, FOXO1A, Dp60, dFOXO, dFoxO, LCMSMS, Gap Phase, peptides, CDKA1, Pi3K92D, CG4141, PI3K_59F, FKH1, catalyst activity, Clinical Importance, Pi3k, PI3-kinase activity, dfoxo, proteins, experimental design, PI[[3]]K, Phase 1, PI3Kgamma, PKB|Akt, Q95V55, INSDC_feature:ncRNA, RacPK, INSDC_qualifier:siRNA, MCAP, First Gap, p55alpha, regulation of cell cycle progression, medicine, dCdk2, PI3K 68D, Pi3K, PI3k, FoxO1A, Cyclin-dependent kinase inhibitor p27, G1b Phase, MCMTC, ATP - 1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, PKB alpha, LC-MS2, screening, dVps34, PI3K68D, dakt, small interfering RNA, P110DELTA, PtdIns-3-kinase activity, Fkhr, rea, LC-MS/MS, p50alpha, ATPR compound, Search, RAC-PK-alpha, l(3)89Bq, First, CG2699, results, vacuolar protein sorting 34, DmelCG5373, Significance, dPIK, 1-phosphatidylinositol 3-kinase activity, AKT1 kinase, PKB/Akt, PKB/AKT, AKT/PKB, protein kinase B alpha, C530050K14, dAkt, dAKT, arrest of mitotic cell cycle progression, type-1 PI3K, FKHR, DmCdc2, modulation of cell cycle progression, p-Akt, p27, Gap, DAkt, l(3)04226, cell division control 2, CG11621, p27Kip1, DPKB, First Gap Phase, protein_coding_transcript, G1 Phases, pAkt, p85alpha, G1, cessation of cell cycle, Relevance, Afx, signs, p33(CDK2), DmelCG10498, G1a, INSDC_feature:gene, proto-oncogene c-Akt, PI3K 68_D, G1b, dAKT/dPKB, PKB/dAKT, DmelCG4141, F8A5_4, protein kinase B, APDS, CDKN4, p110D, Dakt, liquid chromatography-tandem mass spectroscopy, PI3KBETA, dPKB, Cyclin-dependent kinase inhibitor 1B, regulation of cell cycle arrest, Polypeptide, p120-PI3K, droPIK57, cell cycle regulation, Gruppe, RAC-ALPHA, CDKN2, DRAC-PK85, AA408329, DmelCG4006, Peptidomics, Gap Phase 1, PI3K92E, Importance, Gene, Pi3K_59F, arrest of cell cycle progression, protein-containing complex, type I phosphatidylinositol kinase activity, MEN4, G1a Phases, LC-MS-MS, phosphatidylinositol 3-kinase, Gap Phases, Dpkb, DmelCG3143, PIK3, Pi3Kp60, dVps34/PI3K59F, polypeptide chain, First Gap Phases, p60, termination of cell cycle, PI3K-dp110, LC-MSMS, Gene Products, dPI3K, PHOSPATIDYLINOSITOL 3-KINASE, anon-92Ed, anon-WO0118547.374, Clinical Significance, drug., Dp110/PI3K, PI3K-68D/E, class I, study, Search Engines, Clinical, 3143, foxO, messenger RNA, P34CDC2, G1a Phase, PI3'K, Pi3Kp110, P110BETA, PI3K-68D, template RNA, drugs, cdk2, PI3K21B, control of cell cycle progression, CDKA, regulation of progression through cell cycle, grupos, AKT, Akt, Fkhr1, P27 kip1, DRAC-PK, cg3143, peptidos, MCM, CDK2, Cdk2, negative regulation of cell cycle arrest, Cpk, Foxo, dP110, cell cycle modulation, findings, grupo, AI876417, AA414921, akt, protein complex, p120, class II, cell cycle arrest, type III phosphoinositide 3-kinase activity, Proteins, Phosphorylations, p110, CG3143, Vps34p, DAkt1, DAKT1, KIP1, Kip1, Cell, Peptide, PI(3)K, Engine, group, cpk, PI3K-92E/Dp110, FoxO, FOXO, polypeptide, PIK3C1, positive regulation of cell cycle arrest, LC/MS/MS, ATP:1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, PKB, dFoxo, A630093N05Rik, native protein, CWS6, natural protein, CWS5, vps34, Protein, chemical analysis, Cyclin kinase inhibitor, PKB-ALPHA, dp110, INSDC_feature:mRNA, sequence, D-Akt, CG4006, PI3CG, DmCdk2, Protein Cdkn1b, P27KIP1, PI-3-K, Dakt1, serine-threonine kinase Akt, CG10498, Dmcdc2c, Phase, PI3K-59F, CYCLIN-DEPENDENT KINASE A, PI3K-Dp110, akt1, P27kip1, mRNA, dAkt1, eg1, DRAC-PK66, AI843786, Rest, class III, CDK2/CDC2c, CDC2AAT, DmelCG11621, p110gamma, primary structure of sequence macromolecule, mitotic cell cycle arrest, Protein Gene Products, Gene Proteins, dAkt/PKB, Dcdc2c, dakt1, CLOVE, DmVps34, Afxh, S(Sev-CycE)3A, IMD14, PI3K_68D, PI3K-92D, PKBalpha, liquid chromatography tandem mass spectrometry, Peptid, Dmp110, dAKT1, assay, Rac, RAC, reverse transcription polymerase chain reaction, General activity, groupe, thymoma viral proto-oncogenehuman being, tumor suppressor, tretinoin, Tretin M, Refissa, trans-Retinoic Acid, Vitamin A, arrest of cell cycle progression, 8E-tetraenoic acid, beta all trans Retinoic Acid, 6-trimethyl-1-cyclohexen-1-yl)-2, AGN 100335, Potassium Salt, Retinoic Acid, cell cycle regulator, termination of cell cycle, Cordes vas, 3, Cell., 4, 6, Retin-A, gastric neoplasm, Vesanoid, Stieva-A, 6-trimethylcyclohex-1-en-1-yl)nona-2, Retinoic acid, Retinoic, all-trans-beta-Retinoic acid, Renova, Salt, all trans Retinoic Acid, Atralin, Tretinoin Potassium Salt, Betarretin, 8E)-3, trans Retinoic Acid, man, Tretinoin Sodium Salt, 6-trimethyl-1-cyclohexenyl)nona-2, gastric cancer, beta-all-trans-Retinoic, Altreno, control of cell cycle progression, regulation of progression through cell cycle, regulation of cell cycle progression, Vitamin A Acid, (2E, negative regulation of cell cycle arrest, trans-Retinoic, Veltin, all-trans-vitamin A1 acid, cell cycle modulation, GASC, cell cycle arrest, Tretinoin Zinc Salt, 8-all-trans-tetraenoic acid, 4E, Dermairol, Tretinoin Potassium, Ro 1-5488, Tri-luma, Gastric cancer, Tretinoin, trans-retinoic acid, all-trans retinoic acid, all-trans-Retinoic Acid, positive regulation of cell cycle arrest, 8-nonatetraenoic acid, Tretinoin Sodium, all-trans-vitamin A acid, Biacna, 6-trimethylcyclohex-1-enyl)nona-2, arrest of mitotic cell cycle progression, Retin A, proteomic analysis, modulation of cell cycle progression, retinoic acid, all-trans-tretinoin, all-trans-Retinoic, 6-trimethyl-1-cyclohexene-1-yl)-2, Acide retinoique (French), Stomach Cancer, beta-Retinoic acid, Acid, tretinoina, cessation of cell cycle, 6E, Tretinoin Zinc, all-trans-retinoic acid, beta-all-trans-Retinoic Acid, tretinoinum, 6-trimethylcyclohexen-1-yl)nona-2E, human, mitotic cell cycle arrest, Zinc Salt, Sodium Salt, 7-dimethyl-9-(2, all-(E)-retinoic acid, Avita, regulation of cell cycle arrest, vitamin A acid, Retisol-A, (all-E)-3, 8-tetraenoic acid, tretinoine, cell cycle regulation294trueProteomic analysis of cell cycle arrest and differentiation induction caused by ATPR, a derivative of all-trans retinoic acid, in human gastric cancer SGC-7901 cellsExperimental design: Peptides digested from the total cellular proteins were analyzed by reverse phase LC–MS/MS followed by a label-free quantification analysis. The SEQUEST search engine was used to identify proteins and bioinformatics resources were used to investigate the involved pathways for the differentially expressed proteins. Results: 13 down-regulated proteins were identified in the ATPR-treated group. Bioinformatics analysis showed that the effects of ATPR on 14-3-3 might potentially involve the PI3K-AKT-FOXO pathway and P27Kip1 expression. Western blot and RT-PCR analysis showed that ATPR could inhibit AKT phosphorylation, up-regulate the expression of FOXO1A and P27Kip1 at both the protein and mRNA levels, and down-regulate the cytoplasmic expression of cyclin E and CDK2. ATPR-induced G0/G1 phase arrest and differentiation can be ablated if the P27kip1 gene is silenced with sequence-specific siRNA. Conclusions and clinical relevance: ATPR might cause cell cycle arrest and differentiation in SGC-7901 cells by simultaneously inhibiting the phosphorylation of AKT and down-regulating 14-3-3. This change would then enhance the inhibition of cyclin E/CDK2 by up-regulating FOXO1A and P27Kip1. Our findings could be of value for finding new drug targets and for developing more effective differentiation 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