Gene description for HMGB1
Gene name high mobility group box 1
Gene symbol HMGB1
Other names/aliases HMG1
HMG3
SBP-1
Species Homo sapiens
 Database cross references - HMGB1
ExoCarta ExoCarta_3146
Vesiclepedia VP_3146
Entrez Gene 3146
HGNC 4983
MIM 163905
UniProt P09429  
 HMGB1 identified in sEVs derived from the following tissue/cell type
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Breast cancer cells 34108659    
Breast cancer cells 34108659    
Breast cancer cells 34108659    
Breast cancer cells 34108659    
Chondrocytes 35931686    
Chondrocytes 35931686    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 34887515    
Embryonic kidney cells 34108659    
Embryonic kidney cells 34108659    
Embryonic kidney cells 34108659    
Foreskin fibroblasts 34108659    
Gastric cancer cells 33991177    
Gastric cancer cells 33991177    
Gastric cancer cells 33991177    
Lymphoma cells 34108659    
Mammary cancer-associated fibroblasts 34108659    
Mesenchymal stem cells 36408942    
Monocytic leukemia cells 34108659    
Neuroblastoma cells 25944692    
Normal mammary epithelial cells 34108659    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
Pancreatic cancer cells 34108659    
Pancreatic cancer cells 34108659    
Pancreatic cancer cells 34108659    
Pancreatic cancer cells 34108659    
Pancreatic duct epithalial cells 34108659    
Pancreatic duct epithalial cells 34108659    
Pluripotent stem cells 34108659    
Squamous carcinoma cells 20124223    
T lymphocytes 34108659    
 Gene ontology annotations for HMGB1
Molecular Function
    four-way junction DNA binding GO:0000400 ISS
    bubble DNA binding GO:0000405 ISS
    transcription cis-regulatory region binding GO:0000976 IDA
    lipopolysaccharide binding GO:0001530 IDA
    phosphatidylserine binding GO:0001786 IDA
    damaged DNA binding GO:0003684 IDA
    damaged DNA binding GO:0003684 ISS
    double-stranded DNA binding GO:0003690 ISS
    single-stranded DNA binding GO:0003697 ISS
    transcription coactivator activity GO:0003713 IDA
    transcription corepressor activity GO:0003714 IDA
    RNA binding GO:0003723 HDA
    cytokine activity GO:0005125 ISS
    integrin binding GO:0005178 IDA
    protein binding GO:0005515 IPI
    DNA binding, bending GO:0008301 IBA
    DNA binding, bending GO:0008301 IMP
    DNA binding, bending GO:0008301 ISS
    lyase activity GO:0016829 IDA
    C-X-C chemokine binding GO:0019958 IDA
    chemoattractant activity GO:0042056 ISS
    receptor ligand activity GO:0048018 IDA
    RAGE receptor binding GO:0050786 ISS
    RNA polymerase II-specific DNA-binding transcription factor binding GO:0061629 IPI
    DNA polymerase binding GO:0070182 IDA
    supercoiled DNA binding GO:0097100 ISS
    DNA-binding transcription factor binding GO:0140297 IPI
Biological Process
    negative regulation of transcription by RNA polymerase II GO:0000122 IDA
    negative regulation of transcription by RNA polymerase II GO:0000122 IGI
    negative regulation of transcription by RNA polymerase II GO:0000122 IMP
    myeloid dendritic cell activation GO:0001773 ISS
    activation of innate immune response GO:0002218 IDA
    dendritic cell chemotaxis GO:0002407 ISS
    inflammatory response to antigenic stimulus GO:0002437 IEP
    regulation of tolerance induction GO:0002643 IDA
    regulation of T cell mediated immune response to tumor cell GO:0002840 ISS
    DNA topological change GO:0006265 ISS
    double-strand break repair via nonhomologous end joining GO:0006303 ISS
    DNA recombination GO:0006310 ISS
    regulation of transcription by RNA polymerase II GO:0006357 IBA
    autophagy GO:0006914 IEA
    inflammatory response GO:0006954 IDA
    signal transduction GO:0007165 IEA
    positive regulation of cytosolic calcium ion concentration GO:0007204 IDA
    positive regulation of autophagy GO:0010508 IMP
    negative regulation of RNA polymerase II transcription preinitiation complex assembly GO:0017055 IDA
    neuron projection development GO:0031175 ISS
    heterochromatin formation GO:0031507 IGI
    regulation of restriction endodeoxyribonuclease activity GO:0032072 IDA
    DNA geometric change GO:0032392 ISS
    positive regulation of mismatch repair GO:0032425 IDA
    negative regulation of type II interferon production GO:0032689 IDA
    positive regulation of interleukin-1 production GO:0032732 IDA
    positive regulation of interleukin-10 production GO:0032733 IDA
    positive regulation of interleukin-12 production GO:0032735 IMP
    positive regulation of interleukin-6 production GO:0032755 IDA
    positive regulation of interleukin-8 production GO:0032757 IDA
    positive regulation of tumor necrosis factor production GO:0032760 IDA
    V(D)J recombination GO:0033151 IDA
    positive regulation of toll-like receptor 9 signaling pathway GO:0034165 ISS
    T-helper 1 cell activation GO:0035711 IDA
    positive regulation of activated T cell proliferation GO:0042104 IMP
    positive regulation of apoptotic process GO:0043065 IDA
    apoptotic cell clearance GO:0043277 IDA
    negative regulation of CD4-positive, alpha-beta T cell differentiation GO:0043371 IDA
    positive regulation of DNA binding GO:0043388 IDA
    positive regulation of MAPK cascade GO:0043410 IDA
    positive regulation of blood vessel endothelial cell migration GO:0043536 IMP
    negative regulation of blood vessel endothelial cell migration GO:0043537 IDA
    T-helper 1 cell differentiation GO:0045063 IMP
    innate immune response GO:0045087 IEA
    positive regulation of transcription by RNA polymerase II GO:0045944 IDA
    positive regulation of JNK cascade GO:0046330 IDA
    positive regulation of viral entry into host cell GO:0046598 IMP
    positive chemotaxis GO:0050918 IEA
    positive regulation of DNA ligation GO:0051106 ISS
    positive regulation of ERK1 and ERK2 cascade GO:0070374 IDA
    cellular response to lipopolysaccharide GO:0071222 ISS
    positive regulation of monocyte chemotaxis GO:0090026 IDA
    neutrophil clearance GO:0097350 IDA
    positive regulation of vascular endothelial cell proliferation GO:1905564 IMP
    positive regulation of chemokine (C-X-C motif) ligand 2 production GO:2000343 IDA
    negative regulation of apoptotic cell clearance GO:2000426 IDA
    positive regulation of cysteine-type endopeptidase activity GO:2001056 IDA
    positive regulation of dendritic cell differentiation GO:2001200 IMP
Subcellular Localization
    condensed chromosome GO:0000793 IDA
    extracellular region GO:0005576 TAS
    extracellular space GO:0005615 IDA
    extracellular space GO:0005615 IDA
    extracellular space GO:0005615 ISS
    nucleus GO:0005634 IDA
    nucleus GO:0005634 ISS
    nucleoplasm GO:0005654 TAS
    endosome GO:0005768 IEA
    endoplasmic reticulum GO:0005783 IDA
    endoplasmic reticulum-Golgi intermediate compartment GO:0005793 IEA
    cell surface GO:0009986 IDA
    transcription repressor complex GO:0017053 IDA
    secretory granule lumen GO:0034774 TAS
    alphav-beta3 integrin-HMGB1 complex GO:0035868 IDA
    ficolin-1-rich granule lumen GO:1904813 TAS
 Experiment description of studies that identified HMGB1 in sEVs
1
Experiment ID 489
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 6
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
2
Experiment ID 490
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 7
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
3
Experiment ID 491
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 8
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
4
Experiment ID 492
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 9
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
5
Experiment ID 412
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX|ACTB
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Breast cancer cells
Sample name MCF7
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
6
Experiment ID 414
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Breast cancer cells
Sample name MDA-MB-231
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
7
Experiment ID 426
MISEV standards
✘ Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Breast cancer cells
Sample name MDA-MB-231 - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
8
Experiment ID 427
MISEV standards
✘ Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Breast cancer cells
Sample name MDA-MB-231 - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
9
Experiment ID 497
MISEV standards
✘ Biophysical techniques
✔
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
10
Experiment ID 498
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
11
Experiment ID 282
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
12
Experiment ID 283
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
13
Experiment ID 285
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
14
Experiment ID 286
MISEV standards
✔
CEM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81|EpCAM
Enriched markers
✘ Negative markers
✔
DLS
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors "Xu R, Greening DW, Rai A, Ji H, Simpson RJ."
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
15
Experiment ID 1203
MISEV standards
✔
EM
Biophysical techniques
✔
SDCBP|FLOT1|CD9|CD81|CD63|EPCAM|GAPDH|LAMP1|TFRC|CD151|CD82|LAMP2|RAB35|TSG101|FLOT2|RAB5B|ICAM1|RAB5A
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 34887515    
Organism Homo sapiens
Experiment description Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets
Authors "Zhang Q, Jeppesen DK, Higginbotham JN, Graves-Deal R, Trinh VQ, Ramirez MA, Sohn Y, Neininger AC, Taneja N, McKinley ET, Niitsu H, Cao Z, Evans R, Glass SE, Ray KC, Fissell WH, Hill S, Rose KL, Huh WJ, Washington MK, Ayers GD, Burnette DT, Sharma S, Rome LH, Franklin JL, Lee YA, Liu Q, Coffey RJ."
Journal name Nat Cell Biol
Publication year 2021
Sample Colorectal cancer cells
Sample name DiFi
Isolation/purification methods Differential centrifugation
Filtration
Centrifugal ultrafiltration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
miRNA
Methods used in the study Western blotting
Mass spectrometry
RNA sequencing
16
Experiment ID 407
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD63|CD81|SDCBP|TSG101|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
17
Experiment ID 419
MISEV standards
✘ Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
18
Experiment ID 419
MISEV standards
✘ Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
19
Experiment ID 420
MISEV standards
✘ Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
20
Experiment ID 420
MISEV standards
✘ Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Embryonic kidney cells
Sample name HEK293T - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
21
Experiment ID 405
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD63|CD81|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Foreskin fibroblasts
Sample name BJ
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
22
Experiment ID 363
MISEV standards
✘ Biophysical techniques
✔
TSG101|GAPDH|AQP1|CD151|CD81|CD82|CD9|EPCAM|FLOT1|FLOT2|ICAM1|ITGA2B|LAMP2|RAB35|RAB5A|RAB5B|SDCBP|TFRC|UCHL1
Enriched markers
✔
DCLK1
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 33991177    
Organism Homo sapiens
Experiment description Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells
Authors "Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M."
Journal name Proteomics
Publication year 2021
Sample Gastric cancer cells
Sample name MKN1 - 100K pellet
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
23
Experiment ID 364
MISEV standards
✘ Biophysical techniques
✔
TSG101|GAPDH|AQP1|CD151|CD81|CD82|CD9|EPCAM|FLOT1|FLOT2|ICAM1|ITGA2B|LAMP2|RAB35|RAB5A|RAB5B|SDCBP|TFRC|UCHL1
Enriched markers
✔
DCLK1
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 33991177    
Organism Homo sapiens
Experiment description Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells
Authors "Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M."
Journal name Proteomics
Publication year 2021
Sample Gastric cancer cells
Sample name MKN1 - 100K pellet
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
24
Experiment ID 365
MISEV standards
✘ Biophysical techniques
✔
TSG101|GAPDH|AQP1|CD151|CD81|CD82|CD9|EPCAM|FLOT1|FLOT2|ICAM1|ITGA2B|LAMP2|RAB35|RAB5A|RAB5B|SDCBP|TFRC|UCHL1
Enriched markers
✔
DCLK1
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 33991177    
Organism Homo sapiens
Experiment description Cancer stem cell marker DCLK1 reprograms small extracellular vesicles toward migratory phenotype in gastric cancer cells
Authors "Carli ALE, Afshar-Sterle S, Rai A, Fang H, O'Keefe R, Tse J, Ferguson FM, Gray NS, Ernst M, Greening DW, Buchert M."
Journal name Proteomics
Publication year 2021
Sample Gastric cancer cells
Sample name MKN1 - 100K pellet
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
25
Experiment ID 417
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD63|SDCBP|LAMP1|CD9|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX|ACTB
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Lymphoma cells
Sample name Raji
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
26
Experiment ID 411
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Mammary cancer-associated fibroblasts
Sample name mCAF
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
27
Experiment ID 488
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD81|CD63|GAPDH|SDCBP|LAMP1|TFRC|UCHL1|FLOT2|LAMP2|FLOT1|ICAM1|RAB5B|CD151|RAB35|TSG101|RAB5A|CD82
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Homo sapiens
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Mesenchymal stem cells
Sample name UCMSC
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
28
Experiment ID 418
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Monocytic leukemia cells
Sample name THP-1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
29
Experiment ID 418
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Monocytic leukemia cells
Sample name THP-1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
30
Experiment ID 224
MISEV standards
✔
EM|AFM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81
Enriched markers
✔
GOLGA2
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25944692    
Organism Homo sapiens
Experiment description Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes
Authors "Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Mechler A, Adda CG, Ang CS, Mathivanan S"
Journal name Oncotarget
Publication year 2015
Sample Neuroblastoma cells
Sample name SH-SY5Y
Isolation/purification methods Differential centrifugation
Ultracentrifugation
OptiPrep density gradient
Flotation density 1.10 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
31
Experiment ID 413
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Normal mammary epithelial cells
Sample name MCF10A
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
32
Experiment ID 211
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|Alix|EpCAM|TFRC
Enriched markers
✔
cytochrome c|GOLGA2
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors "Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K."
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name IGROV1
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
33
Experiment ID 212
MISEV standards
✔
CEM
Biophysical techniques
✔
TSG101|Alix|EpCAM|TFRC
Enriched markers
✔
Cytochrome C|GOLGA2
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors "Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K."
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name OVCAR-3
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
34
Experiment ID 406
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35|CD81
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic cancer cells
Sample name BxPC3
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
35
Experiment ID 415
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic cancer cells
Sample name PANC-1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
36
Experiment ID 434
MISEV standards
✘ Biophysical techniques
✔
SDCBP|FLOT1|CD81|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic cancer cells
Sample name PANC-1 - Exo-rich fractions 7-10 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Size exclusion chromatography
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
37
Experiment ID 435
MISEV standards
✘ Biophysical techniques
✔
CD81|SDCBP|FLOT1|CD9|CD151|FLOT2|TSG101|LAMP1|TFRC|RAB5A|RAB35|GAPDH|UCHL1|ICAM1
Enriched markers
✔
CANX
Negative markers
✘ Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic cancer cells
Sample name PANC-1 - Exo-rich fractions 1-6 pooled
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
38
Experiment ID 408
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD63|CD81|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX|ACTB
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic duct epithalial cells
Sample name HPDE
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
39
Experiment ID 409
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD63|SDCBP|LAMP1|CD9|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Pancreatic duct epithalial cells
Sample name HPNE
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
40
Experiment ID 416
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD9|CD63|SDCBP|LAMP1|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample Pluripotent stem cells
Sample name PSC
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
41
Experiment ID 191
MISEV standards
✘ Biophysical techniques
✔
Alix|CD81|CD9
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 20124223    
Organism Homo sapiens
Experiment description Hypoxic tumor cell modulates its microenvironment to enhance angiogenic and metastatic potential by secretion of proteins and exosomes.
Authors "Park JE, Tan HS, Datta A, Lai RC, Zhang H, Meng W, Lim SK, Sze SK."
Journal name Mol Cell Proteomics
Publication year 2010
Sample Squamous carcinoma cells
Sample name Squamous carcinoma cell (A431)
Isolation/purification methods Differential centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
42
Experiment ID 410
MISEV standards
✔
EM
Biophysical techniques
✔
CD81|CD63|SDCBP|LAMP1|CD9|GAPDH|FLOT1|TFRC|FLOT2|TSG101|RAB35
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 34108659    
Organism Homo sapiens
Experiment description Quantitative Proteomics Identifies the Core Proteome of Exosomes with Syntenin-1 as the highest abundant protein and a Putative Universal Biomarker
Authors "Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R."
Journal name Nat Cell Biol
Publication year 2021
Sample T lymphocytes
Sample name Jurkat
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
mRNA
Methods used in the study RT-qPCR
Western blotting
Mass spectrometry
Flow cytometry
 Protein-protein interactions for HMGB1
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 UBE2H 7328
Affinity Capture-MS Homo sapiens
2 CDC14B 8555
Proximity Label-MS Homo sapiens
3 KPNA6 23633
Co-fractionation Homo sapiens
4 XPC  
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
5 ATF7IP 55729
Two-hybrid Homo sapiens
6 HDAC4  
Affinity Capture-MS Homo sapiens
7 Mdm2  
Affinity Capture-MS Mus musculus
8 ATPIF1 93974
Affinity Capture-MS Homo sapiens
9 HOXD11  
Reconstituted Complex Homo sapiens
10 COIL  
Proximity Label-MS Homo sapiens
11 PRPF8 10594
Cross-Linking-MS (XL-MS) Homo sapiens
12 DAG1 1605
Two-hybrid Homo sapiens
13 NOP14 8602
Co-fractionation Homo sapiens
14 AES 166
Reconstituted Complex Homo sapiens
15 TPM2 7169
Co-fractionation Homo sapiens
16 CSNK1A1 1452
Co-purification Homo sapiens
17 ACTC1 70
Affinity Capture-MS Homo sapiens
18 GFAP 2670
Co-localization Homo sapiens
Affinity Capture-MS Homo sapiens
19 XPA  
Affinity Capture-Western Homo sapiens
20 CSNK2A1 1457
Co-fractionation Homo sapiens
21 PGR  
Reconstituted Complex Homo sapiens
22 TERF2IP 54386
Two-hybrid Homo sapiens
23 HOXC6  
Reconstituted Complex Homo sapiens
24 PLG 5340
Reconstituted Complex Homo sapiens
25 Pik3r2  
Affinity Capture-MS Mus musculus
26 CENPA  
Proximity Label-MS Homo sapiens
27 HDAC1 3065
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
28 KIAA1429 25962
Affinity Capture-MS Homo sapiens
29 POTEE 445582
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
30 PPTC7 160760
Affinity Capture-MS Homo sapiens
31 DDX23 9416
Proximity Label-MS Homo sapiens
32 WDR76  
Affinity Capture-MS Homo sapiens
33 ZNF24  
Reconstituted Complex Homo sapiens
34 TFAM 7019
Proximity Label-MS Homo sapiens
35 KLF8  
Affinity Capture-MS Homo sapiens
36 PTPRZ1  
Reconstituted Complex Homo sapiens
37 EIF3B 8662
Co-fractionation Homo sapiens
38 C4orf27  
Reconstituted Complex Homo sapiens
39 POU5F1  
Affinity Capture-Western Homo sapiens
Affinity Capture-RNA Homo sapiens
40 EIF5B 9669
Cross-Linking-MS (XL-MS) Homo sapiens
41 RBFOX3  
Co-localization Homo sapiens
42 SF3A2 8175
Cross-Linking-MS (XL-MS) Homo sapiens
43 SRP14 6727
Co-fractionation Homo sapiens
44 HIST1H1E 3008
Cross-Linking-MS (XL-MS) Homo sapiens
45 ITGA4 3676
Affinity Capture-MS Homo sapiens
46 CRMP1 1400
Two-hybrid Homo sapiens
47 RPL29 6159
Two-hybrid Homo sapiens
48 DDX18 8886
Cross-Linking-MS (XL-MS) Homo sapiens
49 HNRNPK 3190
Reconstituted Complex Homo sapiens
50 Ccdc15  
Affinity Capture-MS Mus musculus
51 LHX4  
Proximity Label-MS Homo sapiens
52 MECP2 4204
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
53 CCNDBP1 23582
Two-hybrid Homo sapiens
54 MYCN  
Affinity Capture-MS Homo sapiens
55 USP7 7874
Co-fractionation Homo sapiens
56 SMARCA2 6595
Co-fractionation Homo sapiens
57 YAF2  
Affinity Capture-MS Homo sapiens
58 SOD1 6647
Affinity Capture-MS Homo sapiens
59 RPL19 6143
Cross-Linking-MS (XL-MS) Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
60 WDR60 55112
Two-hybrid Homo sapiens
61 HOXB3 3213
Reconstituted Complex Homo sapiens
62 PRNP 5621
Affinity Capture-MS Homo sapiens
63 Arhgap1 228359
Affinity Capture-MS Mus musculus
64 MAPK1 5594
Affinity Capture-MS Homo sapiens
65 RB1 5925
Reconstituted Complex Homo sapiens
66 CHMP4C 92421
Affinity Capture-MS Homo sapiens
67 PRDX2 7001
Cross-Linking-MS (XL-MS) Homo sapiens
68 HNF1A  
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
69 FOXC1  
Affinity Capture-MS Homo sapiens
70 USP12 219333
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
71 HIST1H4A 8359
Affinity Capture-MS Homo sapiens
72 TGM2 7052
Two-hybrid Homo sapiens
73 WHSC1 7468
Proximity Label-MS Homo sapiens
74 MSX2  
Affinity Capture-MS Homo sapiens
75 IKZF3  
Affinity Capture-MS Homo sapiens
76 CCT5 22948
Cross-Linking-MS (XL-MS) Homo sapiens
77 LRIF1  
Two-hybrid Homo sapiens
78 AGTRAP 57085
Two-hybrid Homo sapiens
79 CBX3 11335
Proximity Label-MS Homo sapiens
80 NCAN  
Reconstituted Complex Homo sapiens
81 SMARCA4 6597
Co-fractionation Homo sapiens
82 RAG1  
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
83 NELFE 7936
Affinity Capture-MS Homo sapiens
84 LHX2  
Proximity Label-MS Homo sapiens
85 VCP 7415
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
86 ACTN4 81
Co-fractionation Homo sapiens
87 Inpp5b  
Affinity Capture-MS Mus musculus
88 RPL31 6160
Cross-Linking-MS (XL-MS) Homo sapiens
89 YWHAH 7533
Co-fractionation Homo sapiens
90 U2AF2 11338
Affinity Capture-MS Homo sapiens
91 ARNT 405
Affinity Capture-MS Homo sapiens
92 HOXD9  
Reconstituted Complex Homo sapiens
93 XPOT 11260
Co-fractionation Homo sapiens
94 TRIM11  
Affinity Capture-MS Homo sapiens
95 MB21D1  
Proximity Label-MS Homo sapiens
96 ENO1 2023
Cross-Linking-MS (XL-MS) Homo sapiens
97 DNM2 1785
Two-hybrid Homo sapiens
98 MARCKSL1 65108
Cross-Linking-MS (XL-MS) Homo sapiens
99 Ube2i  
Two-hybrid Mus musculus
100 UTP14C  
Cross-Linking-MS (XL-MS) Homo sapiens
101 PSMD2 5708
Co-fractionation Homo sapiens
102 CYLC2  
Cross-Linking-MS (XL-MS) Homo sapiens
103 HMGB2 3148
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Co-fractionation Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
104 SP100 6672
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
105 CD3EAP  
Proximity Label-MS Homo sapiens
106 TUBA3C 7278
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
107 GTF2A1 2957
Reconstituted Complex Homo sapiens
108 PBK  
Co-fractionation Homo sapiens
109 UBE2N 7334
Affinity Capture-MS Homo sapiens
110 UFD1L 7353
Affinity Capture-MS Homo sapiens
111 PLAT 5327
Co-purification Homo sapiens
112 PSEN1 5663
Two-hybrid Homo sapiens
113 SMARCE1 6605
Co-fractionation Homo sapiens
114 C14orf1 11161
Two-hybrid Homo sapiens
115 SMARCD1 6602
Co-fractionation Homo sapiens
116 NTRK1 4914
Affinity Capture-MS Homo sapiens
117 OCRL 4952
Affinity Capture-MS Homo sapiens
118 NELFCD 51497
Co-fractionation Homo sapiens
119 RPL35 11224
Cross-Linking-MS (XL-MS) Homo sapiens
120 C1QA 712
Two-hybrid Homo sapiens
121 CTNNB1 1499
Affinity Capture-MS Homo sapiens
122 Nrip3  
Affinity Capture-MS Mus musculus
123 CD274 29126
Affinity Capture-MS Homo sapiens
124 UHRF2  
Two-hybrid Homo sapiens
125 TFAP4 7023
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
126 NR3C1 2908
Reconstituted Complex Homo sapiens
127 PDIA3 2923
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Co-fractionation Homo sapiens
128 EGFR 1956
Affinity Capture-MS Homo sapiens
Negative Genetic Homo sapiens
129 PPP2R2A 5520
Co-fractionation Homo sapiens
130 BAP1 8314
Co-localization Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
131 RSF1  
Two-hybrid Homo sapiens
132 IKZF1  
Affinity Capture-MS Homo sapiens
133 TP73  
Reconstituted Complex Homo sapiens
134 FN1 2335
Affinity Capture-MS Homo sapiens
135 HOXD8  
Reconstituted Complex Homo sapiens
136 CDC42 998
Cross-Linking-MS (XL-MS) Homo sapiens
137 TBP  
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
138 CDK2 1017
Affinity Capture-MS Homo sapiens
139 TPM1 7168
Co-fractionation Homo sapiens
140 MYC  
Affinity Capture-MS Homo sapiens
141 RPA3 6119
Proximity Label-MS Homo sapiens
142 VIM 7431
Co-fractionation Homo sapiens
143 CSNK2A2 1459
Co-fractionation Homo sapiens
144 TPM4 7171
Co-fractionation Homo sapiens
145 TXNL1 9352
Co-fractionation Homo sapiens
146 HOXD3  
Reconstituted Complex Homo sapiens
147 UNC119 9094
Two-hybrid Homo sapiens
148 NFKB1 4790
Reconstituted Complex Homo sapiens
149 ETV3  
Proximity Label-MS Homo sapiens
150 DDRGK1 65992
Affinity Capture-MS Homo sapiens
151 VDAC1 7416
Cross-Linking-MS (XL-MS) Homo sapiens
152 CLTC 1213
Co-fractionation Homo sapiens
153 HSPA9 3313
Cross-Linking-MS (XL-MS) Homo sapiens
154 ARHGAP31 57514
Affinity Capture-MS Homo sapiens
155 AKIP1  
Two-hybrid Homo sapiens
156 SUPT16H 11198
Co-fractionation Homo sapiens
157 HMGB1P1 10357
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
158 RRAGC 64121
Co-fractionation Homo sapiens
159 HUWE1 10075
Affinity Capture-MS Homo sapiens
160 NASP 4678
Co-fractionation Homo sapiens
161 RELA 5970
Affinity Capture-Western Homo sapiens
162 LRP1 4035
Cross-Linking-MS (XL-MS) Homo sapiens
163 SEC23IP 11196
Cross-Linking-MS (XL-MS) Homo sapiens
164 TERF2  
Two-hybrid Homo sapiens
165 SOD2 6648
Affinity Capture-MS Homo sapiens
166 PARP1 142
Biochemical Activity Homo sapiens
Proximity Label-MS Homo sapiens
Proximity Label-MS Homo sapiens
167 H3F3A 3020
Affinity Capture-MS Homo sapiens
168 TP53 7157
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
169 HSPA8 3312
Affinity Capture-Western Homo sapiens
Co-fractionation Homo sapiens
170 DNAJA2 10294
Co-fractionation Homo sapiens
171 Aifm1  
Affinity Capture-MS Mus musculus
172 ASB1 51665
Affinity Capture-MS Homo sapiens
173 TLE1 7088
Reconstituted Complex Homo sapiens
174 EIF3I 8668
Co-fractionation Homo sapiens
175 Arhgap30  
Affinity Capture-MS Mus musculus
176 THRAP3 9967
Cross-Linking-MS (XL-MS) Homo sapiens
177 CLUH 23277
Co-fractionation Homo sapiens
178 CREBBP  
Biochemical Activity Homo sapiens
179 MAP2K1 5604
Affinity Capture-MS Homo sapiens
180 CDK1 983
Biochemical Activity Homo sapiens
Reconstituted Complex Homo sapiens
181 HOXD10  
Reconstituted Complex Homo sapiens
182 PSMA1 5682
Co-fractionation Homo sapiens
183 UFL1 23376
Affinity Capture-MS Homo sapiens
184 MALAT1 378938
Two-hybrid Homo sapiens
185 HOXB1  
Reconstituted Complex Homo sapiens
186 CEBPA  
Protein-peptide Homo sapiens
187 GAPDH 2597
Co-fractionation Homo sapiens
188 RPL7A 6130
Cross-Linking-MS (XL-MS) Homo sapiens
189 RAD23B 5887
Reconstituted Complex Homo sapiens
190 RPS6 6194
Proximity Label-MS Homo sapiens
191 PHF23 79142
Co-fractionation Homo sapiens
192 TTN 7273
Cross-Linking-MS (XL-MS) Homo sapiens
193 EP300 2033
Affinity Capture-MS Homo sapiens
194 INTS3 65123
Co-fractionation Homo sapiens
195 ARHGAP23 57636
Affinity Capture-MS Homo sapiens
196 AR 367
Reconstituted Complex Homo sapiens
197 SMARCD3  
Co-fractionation Homo sapiens
198 PTRF 284119
Co-fractionation Homo sapiens
199 SSRP1 6749
Co-fractionation Homo sapiens
Co-fractionation Homo sapiens
200 RPA2 6118
Proximity Label-MS Homo sapiens
201 HMGB3 3149
Cross-Linking-MS (XL-MS) Homo sapiens
Cross-Linking-MS (XL-MS) Homo sapiens
202 KRT7 3855
Two-hybrid Homo sapiens
203 ASB2  
Affinity Capture-MS Homo sapiens
204 ATP2A1 487
Affinity Capture-MS Homo sapiens
View the network image/svg+xml
 Pathways in which HMGB1 is involved
PathwayEvidenceSource
Adaptive Immune System TAS Reactome
Advanced glycosylation endproduct receptor signaling TAS Reactome
Advanced glycosylation endproduct receptor signaling IEA Reactome
Antigen processing-Cross presentation TAS Reactome
Apoptosis TAS Reactome
Apoptosis induced DNA fragmentation TAS Reactome
Apoptotic execution phase TAS Reactome
Class I MHC mediated antigen processing & presentation TAS Reactome
Cytokine Signaling in Immune system TAS Reactome
DDX58/IFIH1-mediated induction of interferon-alpha/beta TAS Reactome
Disease TAS Reactome
Diseases associated with the TLR signaling cascade TAS Reactome
Diseases of Immune System TAS Reactome
ER-Phagosome pathway TAS Reactome
Immune System TAS Reactome
Immune System IEA Reactome
Innate Immune System TAS Reactome
Innate Immune System IEA Reactome
Interleukin-1 family signaling TAS Reactome
Interleukin-1 signaling TAS Reactome
IRAK4 deficiency (TLR2/4) TAS Reactome
MyD88 cascade initiated on plasma membrane TAS Reactome
MyD88 deficiency (TLR2/4) TAS Reactome
MyD88 dependent cascade initiated on endosome TAS Reactome
MyD88-independent TLR4 cascade TAS Reactome
MyD88:MAL(TIRAP) cascade initiated on plasma membrane TAS Reactome
Neutrophil degranulation TAS Reactome
Programmed Cell Death TAS Reactome
Pyroptosis TAS Reactome
Regulated Necrosis TAS Reactome
Regulation of TLR by endogenous ligand TAS Reactome
Signaling by Interleukins TAS Reactome
TAK1-dependent IKK and NF-kappa-B activation TAS Reactome
Toll Like Receptor 10 (TLR10) Cascade TAS Reactome
Toll Like Receptor 2 (TLR2) Cascade TAS Reactome
Toll Like Receptor 3 (TLR3) Cascade TAS Reactome
Toll Like Receptor 4 (TLR4) Cascade TAS Reactome
Toll Like Receptor 5 (TLR5) Cascade TAS Reactome
Toll Like Receptor 7/8 (TLR7/8) Cascade TAS Reactome
Toll Like Receptor 9 (TLR9) Cascade TAS Reactome
Toll Like Receptor TLR1:TLR2 Cascade TAS Reactome
Toll Like Receptor TLR6:TLR2 Cascade TAS Reactome
Toll-like Receptor Cascades TAS Reactome
TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation TAS Reactome
TRAF6 mediated NF-kB activation TAS Reactome
TRIF (TICAM1)-mediated TLR4 signaling TAS Reactome





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