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Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis

Banijamali, Mahsan (author)
KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
Höjer, Pontus (author)
KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
Nagy, Abel (author)
KTH,Proteinvetenskap,Albanova VinnExcellence Center for Protein Technology, ProNova
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Haag, Petra (author)
Karolinska Institutet
Paz Gomero, Elizabeth (author)
KTH,Proteinvetenskap,Albanova VinnExcellence Center for Protein Technology, ProNova
Stiller, Christiane (author)
KTH,Proteinvetenskap,Albanova VinnExcellence Center for Protein Technology, ProNova
Kaminskyy, Vitaliy O. (author)
Karolinska Institutet
Ekman, Simon (author)
Karolinska Institutet
Lewensohn, Rolf (author)
Karolinska Inst, Dept Oncol Pathol, Solna, Sweden.;Karolinska Univ Hosp, Theme Canc, Med Unit Head & Neck Lung & Skin Tumors, Thorac Oncol Ctr, Solna, Sweden.
Eriksson Karlström, Amelie (author)
KTH,Albanova VinnExcellence Center for Protein Technology, ProNova,Proteinvetenskap
Viktorsson, Kristina (author)
Karolinska Institutet
Ahmadian, Afshin (author)
KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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 (creator_code:org_t)
2022-11-03
2022
English.
In: Journal of Extracellular Vesicles. - : Wiley. - 2001-3078. ; 11:11
  • Journal article (peer-reviewed)
Abstract Subject headings
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  • Small extracellular vesicles (sEVs) have in recent years evolved as a source of biomarkers for disease diagnosis and therapeutic follow up. sEV samples derived from multicellular organisms exhibit a high heterogeneous repertoire of vesicles which current methods based on ensemble measurements cannot capture. In this work we present droplet barcode sequencing for protein analysis (DBS-Pro) to profile surface proteins on individual sEVs, facilitating identification of sEV-subtypes within and between samples. The method allows for analysis of multiple proteins through use of DNA barcoded affinity reagents and sequencing as readout. High throughput single vesicle profiling is enabled through compartmentalization of individual sEVs in emulsion droplets followed by droplet barcoding through PCR. In this proof-of-concept study we demonstrate that DBS-Pro allows for analysis of single sEVs, with a mixing rate below 2%. A total of over 120,000 individual sEVs obtained from a NSCLC cell line and from malignant pleural effusion (MPE) fluid of NSCLC patients have been analyzed based on their surface proteins. We also show that the method enables single vesicle surface protein profiling and by extension characterization of sEV-subtypes, which is essential to identify the cellular origin of vesicles in heterogenous samples.

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)

Keyword

droplet barcode sequencing (DBS)
droplet barcode sequencing for protein analysis (DBS-Pro)
protein profiling
sEV subtypes
single vesicle
small extracellular vesicles (sEVs)
surface protein

Publication and Content Type

ref (subject category)
art (subject category)

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