GPMDB00145OtherKume H, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Humanhkume@nibio.go.jp24687888http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210027053http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210027052http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210027051http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210027050http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210027049National Institute of Biomedical Innovation, JapanNot availableGPMDBRecent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851.Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis.Kume Hideaki H,Muraoka Satoshi S,Kuga Takahisa T,Adachi Jun J,Narumi Ryohei R,Watanabe Shio S,Kuwano Masayoshi M,Kodera Yoshio Y,Matsushita Kazuyuki K,Fukuoka Junya J,Masuda Takeshi T,Ishihama Yasushi Y,Matsubara Hisahiro H,Nomura Fumio F,Tomonaga Takeshi T,Kume Hideaki H, Muraoka Satoshi S, Kuga Takahisa T, Adachi Jun J, Narumi Ryohei R, Watanabe Shio S, Kuwano Masayoshi M, Kodera Yoshio Y, Matsushita Kazuyuki K, Fukuoka Junya J, Masuda Takeshi T, Ishihama Yasushi Y, Matsubara Hisahiro H, Nomura Fumio F, Tomonaga Takeshi Tportion of tissue, membrane, Cancer of Large Bowel, Large Bowel Carcinoma, membrane of organ, simple tissue., Colorectal Cancer, Large Intestine Cancer, MRM, SRM, Tissue, Cancer of Large Intestine, Cancers, membranous organ component, Large Intestine Carcinoma, Multiple Reaction Monitoring, Colorectal, tissue portion, Carcinoma of Large Intestine, biological marker, CRC, Colorectal Cancers, Malignant Colorectal Neoplasm, Large Bowel Cancer, Cancer, Carcinoma of Large BowelGene., IGF-I, membrane, data, SeptD1, steel factor, Large Bowel Carcinoma, Colorectal Cancer, JCAP, IRF-1, mol, Slf, Slpa, hematopoietic growth factor KL, Eseptin, Proteins, Somatomedin-C, number, FNZ, somatomedin, Cancer of Large Intestine, FPH2, FINC, HAPO, membranous organ component, LETS, Large Intestine Carcinoma, presence, Cell, sKITLG, CIG, polypeptide, Colorectal, count in organism, SINT1, count, mechano growth factor, Protein, proteomic analysis, Gene Products, tissue portion, Carcinoma of Large Intestine, PNUTL4, ED-B, simple tissue, CRC, Sint1, Colorectal Cancers, Igf-1, AF17q25, Large Bowel Cancer, MAR, Carcinoma of Large Bowel, NAPB, portion of tissue, SHEP7, Cancer of Large Bowel, membrane of organ, SZP, FN, Large Intestine Cancer, mast cell growth factor, cell, Stem cell factor, Tissue, somatomedin-C, SF, CACP, Kitl, proteins, Cancers, STAT5, Mast cell growth factor, Protein Gene Products, MSF, Msf, Gene Proteins, stem cell factor, KL-1, IGF1, MGF, c-Kit ligand, Mechano growth factor, KITLG, GFND2, GFND, biological marker, MSF1, Soluble KIT ligand, quantitative, SCF, Sl, Malignant Colorectal Neoplasm, presence or absence in organism, Cancerportion of tissue, membrane, Cancer of Large Bowel, Large Bowel Carcinoma, membrane of organ, Colorectal Cancer, Large Intestine Cancer, MRM, determination, SRML1, SRM, PAPT, Tissue, Cancer of Large Intestine, chemical analysis., Cancers, membranous organ component, SPDSY, Large Intestine Carcinoma, Multiple Reaction Monitoring, Colorectal, proteomic analysis, tissue portion, Carcinoma of Large Intestine, microarray, biological marker, simple tissue, CRC, assay, Colorectal Cancers, Malignant Colorectal Neoplasm, Large Bowel Cancer, SPS1, Cancer, Carcinoma of Large BowelIntegral Membrane Proteins, TfR, AI426448, scale tissue, IPP2A2, TFRC, Viral Marker, Biological Markers, Large Bowel Carcinoma, artificial sequence, Surrogate Endpoints, determination, Laboratory, Metastasis, Surface Proteins, Biochemical, Endpoint, Neoplasm Metastases, TfR1, Membrane-Associated Proteins, JTK12, Serum, Integral, Large Intestine Carcinoma, 5730420M11Rik, TFR, Polypeptides, Laboratory Markers, AU015758, Biological, Method, TFR1, Large Bowel Cancer, portion of tissue, Set, SET, Large Intestine Cancer, reference sample, Pdgfr, Identification, TAF-I, Sets (Psychology), plant peltate hair, Surface, phosphatase 2A inhibitor I2PP2A, Tissue, AI528809, proteins, procedures, PDGFR, Mtvr-1, reaction, IGAAD, polyp (morphologic abnormality), T9, Immune, Markers, fully spanning plasma membrane, Methodological Studies, GPCR5A, data., Viral Markers, Membrane Associated Proteins, Membrane Protein, TR, Viral, Surrogate Endpoint, Arts, Cancer of Large Intestine, integral to membrane, StF-IT-1, Raig1, Biochemical Markers, sTfR, membranous organ component, Procedure, SPDSY, Biologic Marker, results, predicted, Polyp, Multiple Reaction Monitoring, AI195355, count, Marker, Algorithm, tissue portion, cellular component unknown, simple tissue, DSCD75, Colorectal Cancers, Carcinoma of Large Bowel, Industrial, PEIG-1, membrane of organ, PDGFR-1, Industrial Arts, HLA-DR-associated protein II, End Points, Membrane-Associated, expanded, Identifications (Psychology), cellular component, Cell Membrane Proteins, FNRA, Immunologic, Methodological, inhibitor of granzyme A-activated DNase, Laboratory Marker, Methodological Study, SYNTHETIC CONSTRUCT sequences, CD71, RAIG1, TAF-IBETA, VLA5A, enlarged, Biochemical Marker, IMF1, artificial, microarray, cell or subcellular entity, Integral Membrane, big, Colorectal Cancer, Procedures, Clinical Markers, SRML1, Clinical Marker, peltate hair, number, Gene, presence, PHAPII, Surrogate End Points, Surrogate Markers, Colorectal, large, template-activating factor I, E430033M20Rik, Gene Products, Studies, Carcinoma of Large Intestine, 2610028K12Rik, Fnra, synthetic genetic interaction (sensu inequality), malignant tumour, IBGC4, Cell Membrane, study, Cancer of Large Bowel, Clinical, MRM, cellular_component, Biological Marker, PDGFR1, malignant neoplasia, synthetic genetic interaction defined by inequality, Rai3, RAI3, CD140b, Study, VLA5, Immunologic Markers, 2PP2A, great, biological marker, Transferrin receptor protein 1, Immunologic Marker, Biologic, SPS1, Controlled, Cancer, CD140B, Cd49e, membrane, serum form, Controlling, p90, Malignant Neoplasm, Metastases, Serum Markers, Proteins, PAPT, End Point, Cell Surface, artificial gene, function, synthetic DNA, Immune Marker, polypeptide, polyps, count in organism, I-2PP2A, Surrogate End Point, C8orf55, Protein, chemical analysis, proteomic analysis, I2PP2A, Neoplasm, Membrane Proteins, CD49e, synthetic, CRC, subcellular entity, techniques, scales, Cell Surface Proteins, Mtvr1, Biologic Markers, Serum Marker, transmembrane, scale, Surrogate, Trfr, SRM, Endpoints, patient, Cancers, TIG1, Membrane, synthetic constructs, malignant tumor, Surrogate Marker, Protein Gene Products, Gene Proteins, extracellular, 2610030F17Rik, Integral Membrane Protein, VLA-5, TRFR, assay, quantitative, AA407739, Malignant Colorectal Neoplasm, methodology, presence or absence in organism, Immune Markers1405http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210027051dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.004318322023442320.01.0falseDiscovery of colorectal cancer biomarker candidates by membrane proteomic analysisand subsequent verification using selected reaction monitoring and tissue microarrayanalysisData from ProteomeXchange, PXD ID: PXD000851. File: iTRAQ3.msf.mgf. Published as part of Mol Cell Proteomics. 2014 Mar 31 . From the Abstract: {{i}} We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. {{/i}}2014-05-07GPM1121002705124687888PXD000851PXD000851