| Literature DB >> 27805059 |
Siri Hildonen1, Ellen Skarpen2, Trine Grønhaug Halvorsen1, Léon Reubsaet1.
Abstract
The aim of the present study was to develop a LC-MS/MS-based proteomic analysis method of urinary exosomal proteins that has the potential to discover disease biomarkers. In short, urinary exosomes from healthy subjects were isolated by immunocapture on magnetic beads, detected by immunofluorescence and TEM, trypsin digested directly on the beads for an accelerated time with no addition of detergents before performing an LC-MS analysis of the trypsinate. To our knowledge, this is the first proteomic analysis of proteins displayed on the outer surface of exosomes. The outer exosome proteome may contain proteins that are of higher biomarker value compared to soluble cargo protein as the proteins projecting into the extracellular milieu might be more directly involved in physiological functions of exosomes. The proteomic analysis identified 49 proteins that were considered significant; the majority is involved in carbohydrate and lipid metabolism or in immune responses. Thirty of the proteins are linked to diseases. The developed proteomic method exploiting urinary exosomes might be of great value in search for diagnostic or prognostic biomarkers of especially metabolic and immune-related diseases.Entities:
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Year: 2016 PMID: 27805059 PMCID: PMC5090863 DOI: 10.1038/srep36331
Source DB: PubMed Journal: Sci Rep ISSN: 2045-2322 Impact factor: 4.379
Schematic overview of the exosome immunoisolation and immunodetection protocol.
| 1. Isolation step | 2. IF CM detection step | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| theoretical result | experimental result | ||||||||
| Dynabeads® | + | anti-CD9 Ab (rabbit) | + | urine sample | anti-CD63 Ab (mouse) | + | Alexa Fluor® 594 anti-mouse Ab | + | + |
| anti-CD81 Ab (goat) | + | Alexa Fluor® 647 anti-goat Ab | + | + | |||||
| − | + | Alexa Fluor® 488 anti-rabbit Ab | + | + | |||||
| Dynabeads® | + | anti-CD63 Ab (mouse) | + | urine sample | anti-CD9 Ab (rabbit) | + | Alexa Fluor® 488 anti-rabbit Ab | + | + |
| anti-CD81 Ab (goat) | + | Alexa Fluor® 647 anti-goat Ab | + | + | |||||
| − | + | Alexa Fluor® 594 anti-mouse Ab | + | + | |||||
| Dynabeads® | + | anti-CD81 Ab (goat) | + | urine sample | anti-CD9 Ab (rabbit) | + | Alexa Fluor® 488 anti-rabbit Ab | + | + |
| anti-CD63 Ab (mouse) | + | Alexa Fluor® 594 anti-mouse Ab | + | + | |||||
| − | + | Alexa Fluor® 647 anti-goat Ab | + | + | |||||
| Dynabeads® | + | no Ab | + | urine sample | − | + | Alexa Fluor® 594 anti-mouse Ab | − | − |
| − | + | Alexa Fluor® 647 anti-goat Ab | − | − | |||||
| − | + | Alexa Fluor® 488 anti-rabbit Ab | − | − | |||||
Figure 1Illustrative overview of the exosome immunoisolation and immunodetection protocol.
Figure 2IF CM of the three antibody-secondary antibody combination that was used after immunocapturing exosomes on 2.8 μM magnetic beads.
Figure 3Transmission electron microscopy of clean and 2.8 μM magnetic beads.
Arrows points to single vesicle when there are only few visible on the beads. Size bar displayed in the right lower corner of each image; (a) Clean Dynabeads M-280 Tosylactivated magnetic beads ; (b) Eluate solution from Dynabeads M-280 Tosylactivated magnetic beads used for CD63 immunocapturing in urine; (c) Eluate solution from Dynabeads M-280 Tosylactivated magnetic beads used for CD81 immunocapturing in urine; (d) Clean Dynabeads Protein G magnetic beads; (e) Dynabeads Protein G magnetic beads after CD9 immunocapturing in urine; (f) Dynabeads Protein G magnetic beads after CD63 immunocapturing in urine; (g) Dynabeads Protein G magnetic beads after CD81 immunocapturing in urine; (h) Dynabeads Protein G magnetic beads after CD63 immunocapturing. Arrow pointing to aggregates; (i) Dynabeads Protein G magnetic beads after CD63 immunocapturing. Arrow pointing to structure similar in morphology to MVBs.
Table of proteins considered significant hits.
| Gene name | Accession | Name | Coverage range % | PTMs | Location | Peptide hits domains | Molecular function | Biological Function | Disease associated | Vesiclepedia/urine | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| GLUCOSE METABOLISM16 proteinswhen no gene symbol is found, gene number it is similar to is denoted by* | GAA | P10253 | Lysosomal alpha-glucosidase | 23–39 | S, N-linked G | lysosome (lumen and membrane associated) | na | glucosidase | degradation of glygogen to glucose in lysosomes | Pompe disease, Glycogen storage disease type II (lysosomal storage disease) | Y/Y |
| GAA* | B7Z5V6 | cDNA FLJ57046, highly similar to Lysosomal alpha-glucosidase | 17–30 | S, N-linked G | lysosome (lumen and membrane associated) | na | glucosidase | carbohydrate metabolisme | Pompe disease, Glycogen storage disease type II (lysosomal storage disease) | Y/Y | |
| CTSA | P10619-2 | Lysosomal protective protein | 5–10 | S, N-linked G | lysosome (lumen) | na | carboxypeptidase | carbohydrate metabolisme | Galactosialidosis (lysosomal storage disease) | Y/Y | |
| HYAL1 | Q12794-2 | Isoform 2 of Hyaluronidase-1 | 6–16 | S, N-linked G | lysosome (lumen) | na | glycosidase | carbohydrate metabolisme | Mucopolysaccharidosis 9 (lysosomal storage disease) | Y/Y | |
| GLB1 | P16278 | Beta-galactosidase | 6–17 | N-linked G | cytoplasma, lysosome (lumen) | na | hydrolase | carbohydrate metabolisme | GM1-gangliosidosis 1,2 and 3, Mucopolysaccharidosis 4B (lysosomal storage diseases) | Y/Y | |
| NAGLU | P54802 | Alpha-N-acetylglucosaminidase | 10–23 | N-linked G | lysosome (lumen) | na | glycosidase | carbohydrate metabolisme | Mucopolysaccharidosis 3B (lysosomal storage disease) | Y/Y | |
| NEU1 | Q99519 | Sialidase-1 | 3–16 | N-linked G | cell membrane, cytoplasmic vesicle, lysosome (lumen and membrane associated) | na | glycosidase | carbohydrate and lipid metabolisme | Sialidosis (lysosomal storage disease) | Y/Y | |
| PGAM2 | P15259 | Phosphoglycerate mutase 2 | 4–26 | cytosol, exosome (extracellular) | na | hydrolase | glucose metabolisme | Glycogen storage disease 10 (lysosomal storage disease) | Y/Y | ||
| PGLS | O95336 | 6-phosphogluconolactonase | 11–33 | P | cytoplasma | na | hydrolase | carbohydrate metabolisme | Diabetic nephropathy | Y/Y | |
| ALDOB | P05062 | Fructose-bisphosphate aldolase B | 13–27 | P | cytoplasma | na | lyase | glycolysis | Hereditary fructose intolerance | Y/Y | |
| DCXR | Q7Z4W1 | L-xylulose reductase | 5–21 | P | peripherial membrane | na | reductase | carbohydrate metabolisme | Pentosuria | Y/Y | |
| B4GALT1 | P15291-2 | Isoform short of Beta-1,4-galactosyltransferase 1 | 5–18 | S, N-linked G | SP TM: Golgi, plasma membrane. | Luminal | transferase | glycolysis | Congenital disorder of glycosylation 2D | Y/Y | |
| GAPDH | P04406 | Glyceraldehyde-3-phosphate dehydrogenase | 10–25 | P | cytoplasma, cytoskeleton, membrane | na | oxidoreductase, transferase | glycolysis, apoptosis | Y/Y | ||
| MAN1A1 | P33908 | Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA | 19 -46 | S, N-linked G | SP TM: membrane (exosome, ER, Golgi) | Luminal | glycosidase | carbohydrate metabolisme | Y/Y | ||
| CPN2 | P22792 | Carboxypeptidase N subunit 2 | 12–32 | N-linked G | secreted extracellulr space (exosomes) | na | enzyme regulator | carbohydrate metabolisme. Immune | Y/Y | ||
| GSTA1 | P08263 | Glutathione S-transferase A1 | 6–18 | cytoplasma, exosomes | na | transferase | metabolisme | Y/Y | |||
| ASAH1 | B1B5Q3 | N-acylsphingosine amidohydrolase 1 | 11–36 | N-linked G | lysosome (lumen), exosomes | na | sphingosine hydrolase | lipid metabolisme | Farber lipogranulomatosis (lysosomal storage disease) | Y/Y | |
| ASAH1* | B3KUZ6 | cDNA FLJ40980 fis, clone UTERU2014464, highly similar to ACID CERAMIDASE | 19–41 | N-linked G | lysosome (lumen), exosomes | na | sphingosine hydrolase | lipid metabolisme | Farber lipogranulomatosis (lysosomal storage disease) | Y/Y | |
| GM2A | P17900 | Ganglioside GM2 activator | 6–10 | S, N-linked G | lysosome (lumen), exosome (extracellular), plasma membrane (cytoplasmic) | na | hydrolase | lipid metabolisme | GM2-gangliosidosis AB (lysosomal storage disease) | Y/Y | |
| APOE | P02649 | Apolipoprotein E | 4–18 | P, O-linked G | ubiquitous (membrane associated) | na | binding | lipid, sterol and cholesterol metabolisme and transport | Lipoprotein glomerulopathy; Alzheimer disease, Amyloidosis, Hyperlipidemia | Y/Y | |
| CEL | P19835 | Bile salt-activated lipase | 11–33 | S, N- and O-linked G | secreted extracellular space | na | hydrolase | lipid metabolisme | Maturity-onset diabetes of the young 8 with exocrine dysfunction | Y/Y | |
| LCAT | P04180 | Phosphatidylcholine-sterol acyltransferase | 12–23 | S, N- and O -linked G | secreted extracelluar space | na | acyl transferase | cholesterol, lipid, sterol, steroid metabolisme | Lecithin-cholesterol acyltransferase deficiency, Fish-eye disease | Y/Y | |
| CTSD | P07339 | Cathepsin D | 11–3 0 | S, N- and O-linked G | lysosome (lumen), secreted extraqcellular space | na | lysosomale endoprotease | autophagy, metabolic degradation, immune | Ceroid lipofuscinosis, neuronal, 10 (lysosomal storage disease), Alzheimer disease | Y/Y | |
| C3 | P01024 | Complement C3 | 3–16 | S, N-Linked G | extracellular space, exosomes | na | promotes binding | immune | Hemolytic uremic syndrome atypical 5, Complement component 3 deficiency, Macular degeneration age-related 9; | Y/Y | |
| C4B | P0C0L5 | Complement C4-B | 5–12 | S, N-linked G | secreted extracellular space, exosomes | na | binding | immune | Systemic lupus erythematosus | Y/Y | |
| KNG1 | P01042-2 | Kininogen-1 | 13–29 | P, S, N-linked G | secreted extracellular space, exosomes | na | protease inhibitor | immune, blood coagulation | High molecular weight kininogen deficiency | Y/Y | |
| SERPING1 | P05155 | Plasma protease C1 inhibitor | 27–41 | S, N- and O-linked G | secreted extracellular space | na | protease inhibitor | immune; blood coagulation | Hereditary angioedema | Y/Y | |
| TPP1 | O14773 | Tripeptidyl-peptidase 1 | 9–33 | S, N-linked G | lysosome (lumen), exosomes | na | endopeptidase | many, immune | Ceroid lipofuscinosis, neuronal 2, Spinocerebellar ataxia autosomal recessive 7 | Y/Y | |
| OLFM4 | Q6UX06 | Olfactomedin-4 | 13–29 | S, N-linked G | secreted extracellular space | na | binding | cell adhesion, immiune | Pancreatic cancer? | Y/Y | |
| PGLYRP2 | Q96PD5 | N-acetylmuramoyl-L-alanine amidase | 12–27 | P, N-linked G | secreted (membrane associated) | na | hydrolase | immune | Y/Y | ||
| CLU | E7ERK6 | Clusterin | 25–36 | S, N-linked G, P | ubiquitous including vesicles | na | chaperone | many (Immune, apoptosis) | Y/Y | ||
| CLU | P10909-2 | Isoform 2 of Clusterin | 29–32 | P, S, N-linked G | ubiquitous including vesicles | na | chaperone | many (Immune, apoptosis) | Y/Y | ||
| SERPINA1 | P01009 | Alpha-1-antitrypsin | 9–46 | P, N-linked G | extracellular (ER, exosomes) | na | peptidase inhibitor | acute phase, blood coagulation | Alpha-1-antitrypsin deficiency | Y/Y | |
| ALB | P02768 | Serum albumin | 3–12 | P, S, N-linked G | ubiquitous (exosomes) | na | binding | transport | Hyperthyroxinemia, Analbuminemia | Y/Y | |
| NID1 | P14543-2 | Isoform 2 of Nidogen-1 | 10–23 | N-linked G | secreted extracellular space | na | binding | cell adhesion | Bethlem myopathy, Ullrich congenital muscular dystrophy | Y/Y | |
| ACTB | P60709 | Actin, cytoplasmic 1 | 25–51 | cytoplasma | na | binding | ubiquitous | Dystonia juvenile-onset, Baraitser-Winter syndrome 1 | Y/Y | ||
| EFEMP1 | Q12805-4 | EGF-containing fibulin-like extracellular matrix protein 1 | 10–35 | S, N-linked G | secreted extracellular space | na | growth factor | ubiquitous | Doyne honeycomb retinal dystrophy | Y/Y | |
| EGF | P01133-3 | Isoform 3 of Pro-epidermal growth factor | 21–37 | S, N-linked G | SP TM (PM and vesicles) | extracellular | growth factor | ubiquitous | Y/Y | ||
| LMAN2* | A8K7T4 | cDNA FLJ75774, highly similar to Homo sapiens Vesicular integral-membrane protein VIP36 (LMAN2), mRNA | 20–41 | na | membrane | na | carbohydrate binding | carbohydrate binding | Y/Y | ||
| QSOX1 | O00391 | Sulphydryl oxidase 1 | 9–19 | S, N-linked G | SP TM membrane | extracellular | sulhydryl oxidase | redox homeostasis, regulator macroautophagy | Y/Y | ||
| PIGR | P01833 | Polymeric immunoglobulin receptor | 5–14 | P, S, N-linked G | SP TM, membrane (exosome) | extracellular | receptor | transcytose in epithelial cells | Y/Y | ||
| AHSG | P02765 | Alpha-2-HS-glycoprotein | 3–17 | P, S, N- and O-linked G | secreted extracellular space | na | inhibitor | promotes endocytosis | Y/Y | ||
| SERPINA5 | P05154 | Plasma serine protease inhibitor | 44–72 | N-and O-linked G | ubiquitous | na | protease inhibitor | lipid transport | Y/Y | ||
| PROZ | P22891 | Vitamin K-dependent protein Z | 9–23 | S, N and O-linked G | secreted extracellular space | na | protease | blood coagulation | Y/Y | ||
| ITIH4 | Q14624-2 | Inter-alpha-trypsin inhibitor heavy chain H4 | 10–29 | N- and O-linked G | secreted extracellular space | na | protease inhibitor | acute phase | Y/Y | ||
| VASN | Q6EMK4 | Vasorin | 15–24 | S, N-linked G | SP TM (lysosomal, exosome, PM) | extracellular | TGF-beta binding | hypoxia, redox | Y/Y | ||
| LRRC15 | Q8TF66 | Leucine-rich repeat-containing protein 15 | 9–21 | N -linked G | membrane | extracellular | binding | cell migration | Y/Y | ||
| ZG16B | Q96DA0 | Zymogen granule protein 16 homolog B | 12–49 | N -linked G | secretetd extracellular space | na | carbohydrate binding | retina homeostasis | Y/Y | ||
| PCDHGC3 | Q9UN70-2 | Isoform 2 of protocadherin gamma-C3 | 5–17 | N-linked G | SP TM membrane (exosomes, PM) | extracellular | binding | cell adhesion | Y/Y |
Information retrieved from own data, uniprot.org and microvesicles.org. Table displays gene name, accession number, name, coverage range in three parallel MS-runs, known PTMs, known location, peptide hit domain in identified protein, known molecular function, known biological function, disease association and if previously identified in exosome samples and in urine denoted with Y (yes).
Figure 4Molecular function based on gene ontology annotation of 49 proteins considered significant protein hits.
The Software Tool for Researching Annotations of Proteins (STRAP) was used for generating GO ontology information and MS Excel was used for generating the chart. Each protein might be annotated to more than one category.
Figure 5Biological function based on gene ontology annotation of 49 proteins considered significant protein hits.
The Software Tool for Researching Annotations of Proteins (STRAP) was used for generating GO ontology information and MS Excel was used for generating the chart. Each protein might be annotated to more than one category.