GPMDB00185OtherHoover H, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Humanheather.hoover@novartis.com26151158Novartis Institutes for Biomedical Research, Cambridge, Massachusettshttp://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017553http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017542http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017531http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017564http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017512http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017501http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017633http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017521http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017587http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017576http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017621http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017599http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017500Not availableGPMDBTumor types can be defined cytologically by their regions of chromosomal amplification, which often results in the high expression of both mRNA and proteins of certain genes contained within the amplicon. An important strategy for defining therapeutically relevant targets in these situations is to ascertain which genes are amplified at the protein level and, concomitantly, are key drivers for tumor growth or maintenance. Furthermore, so-called passenger genes that are amplified with driver genes and a manifest on the cell surface can be attractive targets for an antibody-drug conjugate approach (ADC). We employed a tandem mass spectrometry proteomics approach using tumor cell lines to identify the cell surface proteins whose expression correlates with the 11q13 amplicon. The 11q13 amplicon is one of the most frequently amplified chromosomal regions in human cancer, being present in 45% of head and neck and oral squamous cell carcinoma (OSCC) and 13-21% of breast and liver carcinomas. Using a panel of tumor cell lines with defined 11q13 genomic amplification, we identified the membrane proteins that are differentially expressed in an 11q13 amplified cell line panel using membrane-enriched proteomic profiling. We found that DSG3, CD109, and CD14 were differentially overexpressed in head and neck and breast tumor cells with 11q13 amplification. The level of protein expression of each gene was confirmed by Western blot and FACS analysis. Because proteins with high cell surface expression on selected tumor cells could be potential antibody drug conjugate targets, we tested DSG3 and CD109 in antibody piggyback assays and validated that DSG3 and CD109 expression was sufficient to induce antibody internalization and cell killing in 11q13-amplified cell lines. Our results suggest that proteomic profiling using genetically stratified tumors can identify candidate antibody drug conjugate targets. Data are available via ProteomeXchange with the identifier PXD002486.Quantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers.Hoover Heather H,Li Jun J,Marchese Jason J,Rothwell Christopher C,Borawoski Jason J,Jeffery Douglas A DA,Gaither L Alex LA,Finkel Nancy N,Hoover Heather H, Li Jun J, Marchese Jason J, Rothwell Christopher C, Borawoski Jason J, Jeffery Douglas A DA, Gaither L Alex LA, Finkel Nancy NIntegral Membrane Proteins, Cell Membrane, Surface, Proteins, Membrane-Associated, Surface Proteins, number, Cell Surface, Cell Membrane Proteins, Membrane-Associated Proteins, Integral, Membrane, presence, count in organism, Integral Membrane Protein, count, Protein, Membrane Proteins, Membrane Associated Proteins, Integral., quantitative, Membrane Protein, Cell Surface Proteins, Integral Membrane, presence or absence in organismmamma, mammary region, data, Squamous Cell Carcinoma of the Mouth, Breasts, human being, Malignant Neoplasm, Tandem, Oral Cavity SCC, SCC of Mouth, Proteins, oral squamous carcinoma, Gene, Squamous Cell Carcinoma of Oral Cavity, cephalic part of animal, Homo sapiense, OSCC cell, Mass Spectrometry Mass Spectrometry, cell associated, jecur, polypeptide, SCC of Oral Cavity, Homo spaiens, Experiment, Homo sapien, Homo sapian, Homo sapians, Protein, Gene Products, Homo sapeins, malignant tumour, SCC of the Oral Cavity, Squamous Cell Carcinoma of the Oral Cavity, Homo sapients, tumor cell, cephalic area, head or neck, mammary part of chest, Humo sapiens, malignant neoplasia, iecur, Mass Spectrometry, proteins, present in organism, Mouth SCC, Mass Spectrometry-Mass Spectrometry, Cancers, head and neck, man, Homo sapines, malignant tumor, human, Protein Gene Products, OSCC, Gene Proteins, Livers, cephalic region, Homo spiens, "human" EXACT genbank_common_name [], Oral Cavity Squamous Cell Carcinoma, tumour cell, Homo sapience, SCC of the Mouth, Squamous Cell Carcinoma of Mouth, Homo sampiens, Mouth Squamous Cell Carcinoma, Entire liver., cell bound, Home sapiens, Proteomes, CancerIntegral Membrane Proteins, Cell Membrane, Surface, Proteins, Membrane-Associated, Surface Proteins, number, Cell Surface, Cell Membrane Proteins, Membrane-Associated Proteins, Integral, Membrane, presence, count in organism, Integral Membrane Protein, count, Protein, Membrane Proteins, Membrane Associated Proteins, Integral., quantitative, Membrane Protein, Cell Surface Proteins, Integral Membrane, presence or absence in organismIntegral Membrane Proteins, Breasts, Materials, Tandem, Oral Cavity SCC, determination, Breast Neoplasms, Surface Proteins, Human Mammary Neoplasms, LACS 1, B-cell receptor complex, Membrane-Associated Proteins, Tumor, Homo sapiense, Integral, Mass Spectrometry Mass Spectrometry, cell associated, HuADC, Facl2, Homo sapien, Homo sapians, Line, monocyte differentiation antigen CD14, B8, Mammary Neoplasms, Homo sapients, tumor cell, FACS, membrane bound, Surface, Human Mammary Carcinomas, iecur, cell line cell, proteins, Mass Spectrometry, present in organism, myeloid cell-specific leucine-rich glycoprotein, CD14, cell line, LACS1, CA - Carcinoma of breast, cephalic region, Homo sapience, medicine, data., Acs, Carcinoma of breast (disorder), Membrane Associated Proteins, necrosis, B-lymphocyte receptor complex, Home sapiens, Membrane Protein, Tumors, ADC, mamma, Carcinoma, membranous organ component, antibodies, tumours, results, Homo sapian, Genetic Materials, Mammary carcinoma, Genetic Material, Lines, Carcinomas, membrane of organ, protein_coding_transcript, growth pattern, 4.1.1.11, NEOPL BREAST, non-developmental growth, Membrane-Associated, carcinoma OF breast, Mouth SCC, Cell Membrane Proteins, Homo sapines, FAC sorting, human, 4.1.1.29, immunoglobulin, B cell receptor accessory molecule complex, Material, SCC of the Mouth, Squamous Cell Carcinoma of Mouth, 1110027M19Rik, Breast Tumors, B lymphocyte receptor complex, Mouth Squamous Cell Carcinoma, Cistron, cell bound, Integral Membrane, mammary region, CIB8, Carcinoma of breast NOS, human being, Neoplasms, SCC of Mouth, Gene, Squamous Cell Carcinoma of Oral Cavity, OSCC cell, Monocyte differentiation antigen CD14, NEOPL, jecur, Human, SCC of Oral Cavity, antibody, Homo spaiens, BCR complex, urinary form, Breast Tumor, BREAST NEOPL, Gene Products, Carcinoma of the Breast, immunoglobulin complex, malignant tumour, SCC of the Oral Cavity, HuCSADC, Cell Membrane, Human Mammary, Genetic, Mammary Neoplasm, Carcinoma of breast NOS (disorder), cephalic area, Mammary Carcinoma, head or neck, mammary part of chest, Cysteine sulfinic acid decarboxylase, malignant neoplasia, messenger RNA, tumour, head and neck, Maintenances, man, Cancer of the Breast, OSCC, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS), template RNA, drugs, neoplasm of the breast, tumour cell, Homo sampiens, Breast, Neoplastic Growth, Cancer, Acas1, membrane, Human Mammary Neoplasm, adequate, Squamous Cell Carcinoma of the Mouth, Malignant Neoplasm, Entire liver, drug, Proteins, oral squamous carcinoma, Cell Lines, Cell Surface, cell_line, cephalic part of animal, Cistrons, Cell, polypeptide, Mammary Carcinomas, Myeloid cell-specific leucine-rich glycoprotein, Protein, chemical analysis, Membrane Proteins, Neoplasm, INSDC_feature:mRNA, membrane-bound form, Human Mammary Carcinoma, Homo sapeins, Glutamate decarboxylase-like protein 1, Cell Surface Proteins, opsonin activity, Squamous Cell Carcinoma of the Oral Cavity, Breast Neoplasm, CSADC, mRNA, Humo sapiens, Mass Spectrometry-Mass Spectrometry, Cancers, Membrane, malignant tumor, Protein Gene Products, Aspartate 1-decarboxylase, Gene Proteins, Livers, Homo spiens, "human" EXACT genbank_common_name [], Oral Cavity Squamous Cell Carcinoma, Integral Membrane Protein, Acas, Breast Cancer, B cell receptor activity, Cancer of Breast, assay, NEOPLASMS BENIGN, Neoplasia1805http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320017500dbgap_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 Reanalysis0.00.00.0055521283158544110.01.0falseQuantitative Proteomic Verification of Membrane Proteins as Potential Therapeutic Targets Located in the 11q13 Amplicon in Cancers.Data from ProteomeXchange, PXD ID: PXD002486. Experiment: 11q13_group3_HHn1, file: folder summary. Published as part of J Proteome Res. 2015 Jul 29 . From the Abstract: {{i}} ... We employed a tandem mass spectrometry proteomics approach using tumor cell lines to identify the cell surface proteins whose expression correlates with the 11q13 amplicon. The 11q13 amplicon is one of the most frequently amplified chromosomal regions in human cancer, being present in 45% of head and neck and oral squamous cell carcinoma (OSCC) and 13-21% of breast and liver carcinomas ... {{/i}}2015-08-05GPM3232001750026151158PXD002486PXD002486