{"database":"iProX","file_versions":[],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Chu Wang"],"species":["Homo Sapiens"],"full_dataset_link":["http://www.iprox.org/page/project.html?id=IPX0009239000"],"submitter_email":["chuwang@pku.edu.cn"],"submitter_affiliation":["Peking University"],"sample_protocol":[""],"repository":["iProX"],"data_protocol":[""],"pubmed_abstract":["Colorectal cancer (CRC) is a major cause of cancer-related death worldwide and an effective screening strategy for diagnosis of early-stage CRC is highly desired. Although extracellular vesicles (EVs) are expected to become some of the most promising tools for liquid biopsy of early disease diagnosis, the existing EV-based proteomics methods for practical application in clinical samples are limited by technical challenges in high-throughput isolation and detection of EVs. In the current study, we have developed a simplified and efficient EV-based proteomics strategy for early diagnosis of CRC. DSPE-functionalized beads were specifically designed that enabled direct capture of EVs from plasma samples in 10 minutes with good reproducibility and comprehensive proteome coverage. The single-pot, solid-phase-enhanced sample-preparation (SP3) technology was then combined with data-independent acquisition mass spectrometry (DIA-MS) for in-depth analysis and quantification of EV proteomes. From a cohort with 30 individuals including 11 healthy controls, 8 patients with adenomatous polyp and 11 patients with early-stage CRC, our streamlined workflow reproducibly quantified over 800 proteins from their plasma-derived EV samples, from which dysregulated protein signatures for molecular diagnosis of CRC were revealed. We selected a panel of 10 protein markers to train a machine learning (ML) model, which resulted in accurate prediction of polyp and early-stage CRC in an independent and single-blind validation cohort with excellent diagnostic ability of 89.3% accuracy. Our simplified and efficient clinical proteomic strategy will serve as a valuable tool for fast, accurate, and cost-effective diagnosis of CRC that can be easily extended to other disease samples for discovery of unique EV-based biomarkers."],"pubmed_title":["A simplified and efficient extracellular vesicle-based proteomics strategy for early diagnosis of colorectal cancer."],"pubmed_authors":["Zhang Jin J, Gao Zhaoya Z, Xiao Weidi W, Jin Ningxin N, Zeng Jiaming J, Wang Fengzhang F, Jin Xiaowei X, Dong Liguang L, Lin Jian J, Gu Jin J, Wang Chu C"],"name_synonyms":["Colorectal Tumors, Carcinomas, large bowel cancer, Disease Early Detection, Colorectal Neoplasm, Carcinoma, Exovesicles, Colorectal Cancer, Apoptotic Body, Bodies, Peptidomics, Neoplasms, susceptibility to, Apoptotic Bodies, Colorectal Carcinoma, Vesicles, Colorectal Carcinomas, Extracellular Vesicle, Cancers, Tumor, Colorectal Tumor, Diagnosis, cancer of large bowel, autosomal dominant, Body, large intestine cancer, Vesicle, cancer of the large intestine, Early Detection of Disease, Colorectal, colorectal cancer, colon cancer, Extracellular, Apoptotic, Neoplasm, cancer of the large bowel, CRC, Colorectal Cancers, cancer of large intestine, colorectal (colon or rectal) cancer., Early, Exovesicle, somatic mutation, Tumors, Cancer"],"pubmed_abstract_synonyms":["Colorectal Neoplasm, deceased, CDF, Biological Markers, Viral Marker, Antemortem Diagnosis, Surrogate Endpoints, determination, Laboratory, Blood, Biochemical, Endpoint, Extracellular Vesicle, protein, Cardiac Death, Measure, Tumor, Serum, F20O9_210, End-Of-Life, Diagnosis, Cost-Minimization, (R)-isomer, Liquid Biopsies, Techniques, Weed, Laboratory Markers, POF, diseases, Method, Biological, symptoms, 1, diseases and disorders, Pot, AGAMOUS-like 61, Analysis, Work Flow, protein aggregate, Transfer, Fs(3)Hor, Cost Comparison, DiA, Polyps, Atf4, Colorectal Tumors, 929, Mass Spectrum Analysis, DmelCG8669, Fresh Frozen Plasmas, Fresh Frozen, DmelCG2684, human disease, l(2)k07135, Biopsies, Analyses, Machine, Cost-Minimization Analyses, F20O9.210, distearoyl-L-phosphatidylethanolamine, Colorectal Carcinomas, End Of Life, Comparison, CRUCIFERIN C, purification, procedures, Colorectal Tumor, NTef2, DIASP, DIA, Dia, Fast, large intestine cancer, isolation and purification, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Cost Analysis, polyp (morphologic abnormality), Immune, Markers, Methodological Studies, malignant neoplasm, Viral Markers, sample, 38E.16, Homo sapiens disease, Malignancies, stage, Biopsy, Comparisons, Affordabilities, polyp, somatic mutation, plasma, FAST, Diagnose, colorectal (colon or rectal) cancer, Tumors, screening, Carcinoma, c-SP3, Frozen Plasma, Viral, Surrogate Endpoint, DC18PE, potp, Arts, Learning, Aptitudes, Adenomatous, FASTK, Biochemical Markers, Procedure, Plasmas, Biologic Marker, Spectrum Analysis, Diagnoses, Fs(3)Sz11, Polyp, Ability, Spectroscopy, ms(2)04138, Desmoplastic infantile astrocytoma, Workflows, Benign, Screenings, Postmortem, Marker, Examinations and Diagnoses, Apoptotic, Diseases, Near-Death Experience, Colorectal Cancers, l(2)crc, Postmortem Diagnosis, Early, anon-EST:fe3D7, finances, Carcinomas, Diagnoses and Examination, Postmortem Diagnoses, cruciferin 3, Industrial, Industrial Arts, End Points, Determination of Death, POF2, susceptibility to, F27C12_24, F27C12.24, Spectrometry, signs, salaries, Benign Neoplasms, Methodological, Immunologic, Laboratory Marker, Methodological Study, cancer of large bowel, early, Malignant Neoplasms, ATF-4, disease, DSPE, Spn3, Patient, Biochemical Marker, Horka, DIANA, CG2684, cancer of the large bowel, Fs(3)Horka, Liquid, CG8669, cancer of large intestine, financial management, mKIAA0147, ATF4/crc, Proteomes, Work Flows, AI118201, Cost Analyses, Fresh, Disease Early Detection, other disease, Colorectal Cancer, Clr, Exovesicles, CG9334, Procedures, Fresh Frozen Plasma, Apoptotic Body, Bodies, Peptidomics, Clinical Markers, Hash, Clinical Marker, Neoplasms, developmental stage, Benign Neoplasm, 2-dioctadecanoyl-sn-glycero-3-phosphoethanolamine, STK10, Vesicles, Gene, Cost Comparisons, Spectrum Analyses, protein-containing complex, Malignant, SPR2, autosomal dominant, Surrogate End Points, Colorectal, colorectal cancer, Surrogate Markers, Cardiac, dATF-4, Cost Minimization Analysis, isolation, DmelCG1768, Mass, Studies, HILDA, Gene Products, Screening, disease or disorder, anon-EST:Liang-2.17, anon-EST:Liang-2.11, DmF2, clone 2.11, Antemortem, Technique, Mass Spectroscopy, lod, study, DmelCG2045, Biomarker, Transfer Learning, Blood Plasma, Clinical, Malignancy, clone 2.17, Cost Measures, Affordability, Biological Marker, Scrb1, CG9429, Measures, Ire1, Sp3, Diagnoses and Examinations, financing, cancer of the large intestine, non-neoplastic, Neoplasias, Study, funding, (S)-isomer, Abilities, Immunologic Markers, ATP:Fas-activated serine/threonine protein phosphotransferase activity, vartul, Clients, Extracellular, Blood Plasmas, disorder, SP2, DIA2, SP3, sp3, Immunologic Marker, 2-distearoylphosphatidylethanolamine, Biologic, Cancer, Antemortem Diagnoses, fees, findings, Malignant Neoplasm, Immune Markers., protein complex, SCRIB1, Desmoplastic astrocytoma of infancy, Apoptotic Bodies, Proteins, Serum Markers, disorders, total expressed protein, End Point, medical condition, eth, CG1768, DRF2, DmelCG9334, Client, Examination and Diagnoses, Immune Marker, Vesicle, Early Detection of Disease, Frozen Plasmas, polyps, MS, MT, native protein, SP#2, Mass Screenings, Surrogate End Point, MLPLI, chemical analysis, Protein, post-mortem, Neoplasm, condition, (+-)-isomer, CRC, Crc, techniques, Dias, Death, Exovesicle, Mass Spectrum Analyses, Costs and Cost Analyses, Biologic Markers, Adenomatous Polyp, large bowel cancer, Plasma, Mass Spectrum, Costs, death, primary cancer, Serum Marker, Surrogate, Cost, Colorectal Carcinoma, Endpoints, Cannabis, Cost-Minimization Analysis, portion of plasma, Talents, crc, Cancers, CRIB, Pricing, D130027J01Rik, Lds, malignant tumor, Body, sample population, Surrogate Marker, Protein Gene Products, DmelCG9429, Gene Proteins, cost, crt, colon cancer, Talent, assay, CG2045, Cost Measure, Neoplasia, methodology"],"pubmed_title_synonyms":["Colorectal Tumors, Carcinomas, large bowel cancer, Disease Early Detection, Colorectal Neoplasm, Carcinoma, Exovesicles, Colorectal Cancer, Apoptotic Body, Bodies, Peptidomics, Neoplasms, susceptibility to, Apoptotic Bodies, Colorectal Carcinoma, Vesicles, Colorectal Carcinomas, Extracellular Vesicle, Cancers, Tumor, Colorectal Tumor, Diagnosis, cancer of large bowel, autosomal dominant, Body, microparticle, large intestine cancer, Vesicle, cancer of the large intestine, Early Detection of Disease, Colorectal, colorectal cancer, colon cancer, Extracellular, Apoptotic, Neoplasm, cancer of the large bowel, CRC, Colorectal Cancers, cancer of large intestine, colorectal (colon or rectal) cancer., Early, Exovesicle, somatic mutation, Tumors, Cancer"],"description_synonyms":["Fresh, Disease Early Detection, Biological Markers, Viral Marker, apparatus, Surrogate Endpoints, Clr, GRP1/cytohesin 1, Fresh Frozen Plasma, Peptidomics, Clinical Markers, Laboratory, Medical Devices, Clinical Marker, Reagent, Sepharose C1 4B, Blood, STK10, 2-dioctadecanoyl-sn-glycero-3-phosphoethanolamine, Biochemical, instruments, Endpoint, Serum, F20O9_210, Diagnosis, autosomal dominant, Surrogate End Points, (R)-isomer, CG11633, cytohesin/GRP1, Surrogate Markers, colorectal cancer, Laboratory Markers, devices, Indicator., dATF-4, Biological, GRP1, Grp1, 1, anon-EST:Liang-2.17, anon-EST:Liang-2.11, clone 2.11, Medical, Reagents and Indicators, Atf4, Inventory, 929, DmelCG8669, Biomarker, Sepharose, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, appliances, Clinical, clone 2.17, Biological Marker, PTPSTEP, Scrb1, CG9429, F20O9.210, l(2)SH2 0323, distearoyl-L-phosphatidylethanolamine, CRUCIFERIN C, Ire1, Supplies, Fast, Indicators, large intestine cancer, cancer of the large intestine, (S)-isomer, Immunologic Markers, Immune, C1 4B, Markers, Neural-specific protein-tyrosine phosphatase, ATP:Fas-activated serine/threonine protein phosphotransferase activity, Viral Markers, vartul, l(2)k08110, Blood Plasmas, Agarose, Reagents, Immunologic Marker, 6-An-alpha-L-Galp-(1->3)-beta-D-Galp-(1->]n, FAST, somatic mutation, plasma, Biologic, 2-distearoylphosphatidylethanolamine, colorectal (colon or rectal) cancer, GPH, Medical Device, Apparatus and Instruments, Inventories, Frozen Plasma, Viral, Surrogate Endpoint, DC18PE, Devices, SCRIB1, 4B, potp, Serum Markers, End Point, stepk, FASTK, Biochemical Markers, eth, Biologic Marker, Plasmas, Immune Marker, Early Detection of Disease, Frozen Plasmas, Device, equipment, Marker, Surrogate End Point, [4)-3, Sepharose C1, 3.1.3.48, Supplies and Equipment, (+-)-isomer, Crc, CRC, l(2)crc, Early, l(2)SH0323, anon-EST:fe3D7, Biologic Markers, CYH1, large bowel cancer, Plasma, Serum Marker, cruciferin 3, End Points, Step, CG11628, Surrogate, susceptibility to, Endpoints, Instruments and Apparatus, portion of plasma, crc, Striatum-enriched protein-tyrosine phosphatase, Immunologic, CRIB, Laboratory Marker, cancer of large bowel, Surrogate Marker, DmelCG11628, ATF-4, DmelCG9429, crt, DSPE, colon cancer, Biochemical Marker, STEP, Sepharose 4B, cancer of the large bowel, CG8669, Equipment, cancer of large intestine, mKIAA0147, ATF4/crc, AI118201, Immune Markers"],"additional_accession":[]},"is_claimable":false,"name":"A simplified and efficient extracellular vesicles-based proteomics strategy for early diagnosis of colorectal cancer","description":"In this work, we have developed a simplified, fast and efficient EVs-based proteomics strategy to enable biomarker discovery for early diagnosis of CRC. By covalent conjugation of an EV-targeting probe, DSPE, to agarose beads, we achieved one-step enrichment of EVs from plasma fluids in 10 minutes without requirement of expensive equipment and reagents, demonstrating its potential and compatibility in clinical applications.","dates":{"publication":"Thu Jul 25 00:00:00 GMT+01:00 2024"},"accession":"PXD054231","cross_references":{"TAXONOMY":["9606"],"pubmed":["39421202"]}}