{"database":"JPOST Repository","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["https://storage.jpostdb.org/JPST003403/files/report.pg_matrix.tsv"],"Wiff":["https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS_1_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-TN2_3_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-TN2_3_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS_2_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS_3_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-TN2_1_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-Tx30a_1_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-Tx30a_1_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS_1_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-TN2_2_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-Tx30a_3_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-TN2_2_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-Tx30a_2_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS_2_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-Tx30a_3_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-Tx30a_2_SWATH.wiff","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS_3_SWATH.wiff.scan","https://storage.jpostdb.org/JPST003403/files/230919_Phawinee_AGS-TN2_1_SWATH.wiff"],"Other":["https://storage.jpostdb.org/JPST003403/files/DIA-NN.human.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Krisana Asano"],"species":["Homo Sapiens (human)"],"full_dataset_link":["https://repository.jpostdb.org/entry/JPST003403"],"submitter_affiliation":["Hirosaki University"],"sample_protocol":[""],"repository":["jPOST"],"data_protocol":[""],"pubmed_abstract":["<h4>Background</h4>Helicobacter pylori (H. pylori) has been identified as a type I carcinogen and contributes to a high rate of gastric cancer (GC), especially in Eastern Asia. Extracellular vesicles (EVs) have the potential to be used to detect various cancer types and diseases. However, the protein markers in EVs for the prognosis of H. pylori infection and GC are unknown. We aim to identify the proteins within EVs derived from a gastric epithelial cell line (AGS) infected with H. pylori by using LC-MS/MS.<h4>Materials and methods</h4>EVs were isolated from AGS cells infected with high- and low-virulence H. pylori (strains TN2wt and Tx30a) by ultracentrifugation. Proteins within these EVs were identified and analyzed for potential marker candidates through bioinformatics. Proteins in H. pylori-derived EVs (HpEVs) from bacterial culture supernatant and HpEVs derived from H. pylori-infected AGS cells were elucidated.<h4>Results</h4>Differentially expressed proteins by proteomic analysis in AGSEVs-Tx30a vs. AGSEVs-noninfected (NI) and AGSEVs-TN2wt vs. AGSEVs-NI were 107 and 55 proteins, respectively. Bioinformatics of these proteomes revealed that essential proteins for H. pylori survival and pathogenicity including outer membrane proteins, metabolism-related, host cell infection-related, and virulence-related proteins were observed in HpEVs. Interestingly, EVs derived from AGS cells infected with H. pylori TN2wt significantly contained multiple proteins related to GC (ATP6V0A1, GAPDH, HINT1, LYZ, and RBX1).<h4>Conclusion</h4>This study provides a comprehensive protein profile of EVs from H. pylori-infected AGS cells and HpEVs, which could serve as liquid-based biomarkers in the future for screening H. pylori infection, especially GC-related."],"pubmed_title":["Proteomic Profiling of Extracellular Vesicles Reveals Potential Biomarkers for Helicobacter pylori Infection and Gastric Cancer."],"pubmed_authors":["Subsomwong Phawinee P, Asano Krisana K, Akada Junko J, Matsumoto Takashi T, Nakane Akio A, Yamaoka Yoshio Y"],"name_synonyms":["Exovesicles, Campylobacter pyloridis, Helicobacter nemestrinae, Apoptotic Body, Bodies, Apoptotic Bodies, Sprain, number, Vesicles, Infestations and Infections, Infection and Infestation, Extracellular Vesicle, presence, Body, Vesicle, Infestation and Infection, count in organism, Campylobacter pylori subsp. pylori, Extracellular, Apoptotic, proteomic analysis, Strain, Infection, Campylobacter pylori, Strains, Infections and Infestations, clinical infection., Sprains, Strains and Sprains, Exovesicle"],"pubmed_abstract_synonyms":["Dehydrogenases, dRoc1, Surrogate Endpoints, Vpp-1, Laboratory, ATRBX1, Metabolic Concepts, A4, Tumor, Integral, anon-EST:Posey65, MFGM, Stomach Neoplasms, infectivity, malignant fundus of stomach neoplasm, HEL-S-162eP, D-Glyceraldehyde-3-phosphate:NADP+ oxidoreductase, RING-box protein 1, Bio Informatics, Method, Biological, 38 kDa BFA-dependent ADP-ribosylation substrate, symptoms, Prkci, Metabolism Concept, gastric neoplasm, gamma sarcoglycan, pseudotoxoplasmosis syndrome, catabolism, Surface, Gapd, Promoter, Helicobacter pylori infection, metabolic process resulting in cell growth, procedures, D17Mit170, Computational, malignant neoplasm of body of stomach, Lyz, GAPD, Surface Protein, Homo sapiens disease, Phosphoglyceraldehyde, Infections and Infestations, CXXC finger protein 9, DmelCG8893, Computational Molecular Biologies, LZM, Tumors, LC-MS2, screening, E3 ubiquitin-protein ligase RBX1, Viral, BA554C12.1, GASC, with intracranial calcification and chronic cerebrospinal fluid lymphocytosis, 6.3.2.-, metabolism resulting in cell growth, Ipk1, Biologies, Procedure, Tl3, CDABP0047, Tl2, Stv1, Far East, Computational Molecular, Peptidyl-cysteine S-nitrosylase GAPDH, STOMACH NEOPL, ATP6a1, OK/SW-cl.12, Benign, Marker, Oncogen, Computational Molecular Biology, Pathogenicity, sarcoglycan, secretion, PRKCNH1, Stomach Cancer, Cell Membrane Protein, HRT1, gastric tumour, fast rate, death rate, HRT2, End Points, Membrane-Associated, signs, Benign Neoplasms, Infection and Infestation, Cell Membrane Proteins, MFGMP-E8, Methodological, Immunologic, Laboratory Marker, Malignant Neoplasms, Oncogens, 35kD dystrophin-associated glycoprotein, liquid chromatography-tandem mass spectroscopy, Ags, AGS, tumor of stomach, with calcification of basal ganglia and chronic cerebrospinal fluid lymphocytosis, AGS1, AHD, East Asia, Apoptotic Body, Vph1, Processes, Dehydrogenase, encephalopathy, Clinical Marker, Neoplasms, Gapdh13F, Prognostic Factors, Metabolic Processes, protein-containing complex, Atp6n1, Atpv0a1, Aim, culture filtrate, AIM, Membrane-Associated Protein, F7C8_160, LC-MSMS, Rbx1, RBX1, Gene Products, disease or disorder, Screening, Projections and Predictions, malignant tumor of fundus of stomach, MAM, gamma-SG, Technique, RNF75, Cell Membrane, DNMT1, ATP6N1A, Clinical, DNMT1_HUMAN, RING finger protein 75, pip1, Metabolic Concept, Gastric Cancer, GAPDH2, clinical infection, Neoplasias, Study, API6, Glyceraldehyde-3-Phosphate Dehydrogenase, Extracellular, Aicardi-Goutieres syndrome 1, Biologic, Cancer, DNA (cytosine-5)-methyltransferase 1, Lzp-s, tumour of stomach, Helicobacter, Stomach Neoplasm, findings, Malignant Neoplasm, cou, 35 kDa dystrophin-associated glycoprotein, degradation, Triosephosphate Dehydrogenase, Proteins, Serum Markers, disorders, Cell Surface, Cell Surface Protein, Factor, MCMT, cancer of fundus of stomach, Cell, SGCG, Immune Marker, Vesicle, Concept, Stomach Cancers, Lr, MT, native protein, Surrogate End Point, Gapdh, Strain, proteomic analysis, Neoplasm, Phosphoglyceraldehyde Dehydrogenase, condition, Gastric, metabolism, Cell Surface Proteins, GAPDH, Membrane Associated Protein, Metabolic Phenomenon, Biologic Markers, CXXC9, PKCI-1, multicellular organism metabolic process, primary cancer, DMDA1, CT-2, Surrogate, culture supernatant, Endpoints, Cancers, malignant tumor, CXXC-type zinc finger protein 9, Body, Gene Proteins, gastric epithelial cell line, Atp6n1a, Bra, liquid chromatography tandem mass spectrometry, virulence, AA959968, tumour of the stomach, Neoplasia, CLEC2C, Helicobacter infection., Anabolism, Immune Markers, liquid chromatography tandem mass spectroscopy, biochemical pathways, Integral Membrane Proteins, MGC130048, Metabolic Process, Biological Markers, Viral Marker, NMAN, HSN1E, Surface Proteins, Biochemical, Infestations and Infections, Endpoint, Extracellular Vesicle, protein, CD339, Membrane-Associated Proteins, SED1, Serum, Eastern Asia, Molecular Biologies, NEOPL STOMACH, AA517855, Techniques, Laboratory Markers, GADPH, diseases, CG8893, malignant neoplasm of fundus of stomach, Familial Diffuse, Promoters, Concepts, Tumor Initiator, diseases and disorders, Vpp1, VPP1, Glyceraldehydephosphate, tumor of the stomach, protein aggregate, gastric fundus cancer, Phenomenon, viral infection, human disease, me75, Prognoses, Aicardi-Goutières syndrome, LCMSMS, Biology, Roc1alpha, Futurology, Bio-Informatic, T1, BARS-38, Immune, Markers, Methodological Studies, malignant neoplasm, malignant tumour of fundus of stomach, Bio-Informatics, Viral Markers, gamma-sarcoglycan, Rbx1/Roc, Membrane Associated Proteins, biotransformation, MFGME8, Malignancies, Strains, Cancer of the Stomach, Membrane Protein, Catabolism, Triosephosphate, Ca body - stomach, Predictions and Projections, HIS triad family protein 3, AA673479, Initiators, Hint, Surrogate Endpoint, Process, SG-gamma, LC-MS/MS, HINT1, Initiator, Biochemical Markers, neoplasm of the stomach, infections, Pseudotoxoplasmosis syndrome, Biologic Marker, HINT, Screenings, Regulator of cullins 1, Apoptotic, Diseases, Gastric Neoplasms, Protein ZYP, GAP, carcinogenic agent, BEST:CK01110, ADCADN, Factors, Bioinformatic, Helicobacter nemestrinae, UNQ203/PRO229, stomach neoplasm (disease), dRbx1, Prognostic, DNA (cytosine-5-)-methyltransferase 1, susceptibility to, Tumor Promoters, Glyceraldehydephosphate Dehydrogenase, 1500002P15Rik, gamma (35kDa dystrophin-associated glycoprotein), Methodological Study, RING-box 1, AWS, Stomach, disease, EG:115C2.11, DMDA, Milk fat globule-EGF factor 8, Biochemical Marker, neoplasm of stomach, Carcinogen, 2.6.99.-, Strains and Sprains, Proteomes, ca greater curvature of stomach, Integral Membrane, 1.2.1.12, Prognostic Factor, CG16982, other disease, Campylobacter pyloridis, SGCG_HUMAN, Exovesicles, Procedures, Bodies, F7C8.160, Clinical Markers, GAPDH II, RING-BOX 1, Benign Neoplasm, Vesicles, ATP6N1, Gene, Glyceraldehyde 3 Phosphate Dehydrogenase, Malignant, autosomal dominant, TYPE, LC-MS-MS, Surrogate End Points, DAGA4, familial infantile, Surrogate Markers, Ca fundus - stomach, stomach neoplasm, Metabolism, 35DAG, Studies, Mass, Low, SCG3, Tumor Promoter, Sprains, Metabolism Phenomena, stomach tumor, infection, study, Biomarker, Cree encephalitis, Malignancy, GA3PDH, Biological Marker, stomach tumour, Glyceraldehyde-3-Phosphate, non-neoplastic, Infestation and Infection, gastric cancer, JAGL1, Immunologic Markers, Gapdh-2, time of survival, Cancer of Stomach, ROC1, HJ1, disorder, liquid, Immunologic Marker, DNA MTase HsaI, DmelCG16982, Molecular Biology, culture medium, protein complex, Apoptotic Bodies, Sprain, DNMT, MFG-E8, End Point, medical condition, HISTIDINE TRIAD NUCLEOTIDE-BINDING 1, fundus of stomach cancer, Gastric cancer, gastric tumor, Bioinformatics, LGMD2C, Metabolic Phenomena, Metabolism Concepts, high rate, LC/MS/MS, survival, Mass Screenings, Helicobacter infection, DNA methyltransferase HsaI, Protein, Phenomena, Membrane Proteins, Infection, techniques, Exovesicle, Serum Marker, biodegradation, Metabolic, REGULATOR OF CULLINS-1, N-terminally processed, dRoc1a, Gastric Cancers, Membrane, Gastric Neoplasm, Surrogate Marker, Protein Gene Products, G3PD, Tumor Initiators, O-acetyl GD3 ganglioside synthase, Pkci, OAcGD3S, Integral Membrane Protein, Campylobacter pylori subsp. pylori, NEOPL GASTRIC, SCARMD2, a1, Campylobacter pylori, Future, m.HsaI, methodology, GASTRIC NEOPL, CK01110"],"pubmed_title_synonyms":["Biological Markers, Viral Marker, Exovesicles, Surrogate Endpoints, Apoptotic Body, Bodies, Clinical Markers, Laboratory, Clinical Marker, Neoplasms, Vesicles, Biochemical, Endpoint, Extracellular Vesicle, Serum, Stomach Neoplasms, malignant fundus of stomach neoplasm, NEOPL STOMACH, Surrogate End Points, Surrogate Markers, Laboratory Markers, Ca fundus - stomach, stomach neoplasm, malignant neoplasm of fundus of stomach, Familial Diffuse, Biological, malignant tumor of fundus of stomach, tumor of the stomach, gastric fundus cancer, gastric neoplasm, stomach tumor, Biomarker, infection, Clinical, Biological Marker, stomach tumour, Helicobacter pylori infection, Gastric Cancer, malignant neoplasm of body of stomach, gastric cancer, Immunologic Markers, Immune, Markers, malignant tumour of fundus of stomach, Viral Markers, Cancer of Stomach, Extracellular, Cancer of the Stomach, Immunologic Marker, Ca body - stomach, Biologic, Cancer, tumour of stomach, Helicobacter, Viral, Stomach Neoplasm, Surrogate Endpoint, GASC, Apoptotic Bodies, Serum Markers, End Point, Biochemical Markers, infections, neoplasm of the stomach, Biologic Marker, fundus of stomach cancer, cancer of fundus of stomach, Gastric cancer, gastric tumor, STOMACH NEOPL, Immune Marker, Vesicle, Stomach Cancers, Marker, Surrogate End Point, Helicobacter infection, Apoptotic, Neoplasm, Gastric Neoplasms, Gastric, Exovesicle, Biologic Markers, Stomach Cancer, Serum Marker, gastric tumour, End Points, stomach neoplasm (disease), Surrogate, susceptibility to, Endpoints, Gastric Cancers, Immunologic, Cancers, Laboratory Marker, Gastric Neoplasm, Body, Surrogate Marker, GASTRIC NEOPL., Stomach, Biochemical Marker, neoplasm of stomach, NEOPL GASTRIC, tumor of stomach, tumour of the stomach, ca greater curvature of stomach, Immune Markers"],"description_synonyms":["Protein Structure Database, Sodium Dodecyl, E 920, Dodecyl Sulfate, Infestations and Infections, Protein Sequence Database, CD339, Basodexan, protein, Trifluoroethyl Alcohol, SED1, MFGM, Alkylations, 2-Propanone, Protein Databases, Polypeptides, Ethanol, peptido, 1, 2, Min, protein aggregate, methyl ketone, DmelCG42273, (R*, C, pseudotoxoplasmosis syndrome, E290, Divorced, Aicardi-Goutières syndrome, Man (Taxonomy), peptides, E927b, hypoplasia, min, mAPC, Lauryl Sulfate, IBP, Divorces, AI047805, STAD, R-744, Propanon, Sputolysin, sample, MFGME8, Infections and Infestations, Sequence Databases, Bladder pain syndrome, stomach adenocarcinoma, 2-Trifluoroethanol, Bonin Islands, BZRP, Alcohol, with intracranial calcification and chronic cerebrospinal fluid lymphocytosis, 2-trifluoro-, Protein Structure Databases., dimethylketone, Modern, Liquid Chromatography, Dmel_CG7826, 4-dimercapto-2, Pseudotoxoplasmosis syndrome, Cys, not genetically inherited, ur, Aceton, E-290, PBS, PBR, Sequence Database, carbamide, Pyroacetic ether, Dm1, Cleland, Trifluoroethyl, (2R)-2-amino-3-sulfanylpropanoic acid, Dmel_CG7835, Mnb, MNB, absence of, Painful Bladder Syndrome, Infection and Infestation, 3-Butanediol, MFGMP-E8, AW124434, beta-Ketopropane, human, AWS, L-Cystein, Protein Sequence, Irium, R*)-1, H2NC(O)NH2, Painful bladder syndrome, Milk fat globule-EGF factor 8, Ags, AGS, Protein Database, Polypeptide, with calcification of basal ganglia and chronic cerebrospinal fluid lymphocytosis, AGS1, 4-Dimercapto-2, 1728, AHD, Bladder Pain Syndrome, BPBS, Cleland Reagent, rac-Dithiothreitol, human being, threo-1, encephalopathy, Reagent, Cleland's reagent, Sodium Lauryl, L-Zystein, Gene, 4-dimercapto-, Carbamide, Database, R*)-, abdominal muscles, Protein Structure Databases, protein-containing complex, autosomal dominant, CG7826, Human, Protein Sequence Databases, Karbamid, familial infantile, propanone, Homo sapiens, reduced, Harnstoff, dimethylcetone, CG7835, Gene Products, CG42273, tiny, Carmol, Separated, Man, Cree encephalitis, adenocarcinoma of stomach, CO2, E-920, SWISS PROT, pk18, clinical infection, MBR, Infestation and Infection, JAGL1, CYSTEINE, Protein Structure, HJ1, Structure Database, PTBR, FREE CYSTEINE, peptidos, Azeton, (2R)-2-amino-3-mercaptopropanoic acid, Dimethyl ketone, Aicardi-Goutieres syndrome 1, small, 3-butanediol, SWISS-PROT, Sulfuric acid monododecyl ester sodium salt, DYRK1, Dimethylketon, DBI, protein complex, SwissProt, Proteins, MFG-E8, carbonic anhydride, [CO2], Clelands Reagent, Cell, Dithiothreitol, Peptide, Dithiotreitol, Amino Acid Sequence, Sodium Lauryl Sulfate, native protein, PKBS, carbonyldiamide, Protein, DL-threo-1, Infection, Sodium, E 290, Dyrk1, Amino Acid Sequence Databases, eagle-Barrett syndrome, DTL, Cleland's, AU020952, Separation, DTT, with urinary tract Abnormality and cryptorchidism, underdeveloped, uree, culture supernatant, Separations, CC1, Databases, L-2-Amino-3-mercaptopropionic acid, (R)-2-amino-3-mercaptopropanoic acid, mDRC, sample population, ME-IV, Protein Gene Products, Cleland's Reagent, Gene Proteins, O-acetyl GD3 ganglioside synthase, OAcGD3S, Modern Man, E920, Peptid, Structure Databases, Sulfate"],"additional_accession":[]},"is_claimable":false,"name":"The quantitative proteomic analysis of extracellular vesicles derived from gastric cell line infected with Helicobacter pylori Tx30a, TN2wt strains, and non-infection","description":"Human gastric adenocarcinoma AGS cells were infected with H. pylori Tx30a or TN2wt at a multiplicity of infection = 100 and incubated at 5% CO2,37oC for 48 h. The cells/debris were removed from the cell culture supernatant by centrifugation at 2,000 x g for 30 min at 4oC and filtered through a 0.45 m filter.  The EVs were collected by ultracentrifugation at 110,000 x g for 70 min using Himac CP80NX Preparative Ultracentrifuge (HITACHI, Tokyo, Japan). After removing the supernatant, the EVs were washed with PBS and then collected by ultracentrifugation at 100,000 x g for 70 min at 4oC. Finally, the EVs were resuspended in PBS, and stored at -80oC. The AGS-derived EVs were lysed with 2% sodium dodecyl sulfate/ 7M urea, and equal amounts of proteins from each sample were precipitated with acetone. The proteins were then denatured and reduced with 50% trifluoroethanol and 4 mM dithiothreitol followed by alkylation of the free cysteine residues and trypsinization. The desalted peptides were then separated using liquid chromatography. The mass spectrometer was operated in information-dependent acquisition mode, and acquired spectra were searched against the AGS cell protein database. Differential protein expression was analyzed to determine the relative abundances of proteins in EVs derived from AGS cells infected with H. pylori Tx30a or TN2wt, compared to non-infected cells. H. pylori proteins in AGS-derived EV, the spectra were searched against the H. pylori ATCC 51932 (Tx30a) and TN2wt protein database.","dates":{"publication":"Mon Mar 17 00:00:00 GMT 2025"},"accession":"PXD056529","cross_references":{"TAXONOMY":["9606"],"pubmed":["40033163"]}}