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Methods for Systematic Identification of Membrane Proteins for Specific Capture of Cancer-Derived Extracellular Vesicles

Zaborowski MP 1 , Lee K 2 , Na YJ 3 , Sammarco A 4 , Zhang X 5 , Iwanicki M 6 Show all authors , Cheah PS 7 , Lin HY 2 , Zinter M 8 , Chou CY 9 , Fulci G 3 , Tannous BA 10 , Lai CP 5 , Birrer MJ 3 , Weissleder R 11 , Lee H 2 , Breakefield XO 12

Affiliations 

  • 1 Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Department of Gynecology, Obstetrics and Gynecologic Oncology, Division of Gynecologic Oncology, Poznań University of Medical Sciences, 60-535 Poznań, Poland. Electronic address: mikolaj.zaborowski@gmail.com
  • 2 Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
  • 3 Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
  • 4 Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Padua, Italy
  • 5 Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
  • 6 Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
  • 7 Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Seri Kembangan, Malaysia
  • 8 Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
  • 9 Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City 320, Taiwan
  • 10 Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA
  • 11 Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
  • 12 Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address: breakefield@hms.harvard.edu
Cell Rep, 2019 Apr 02;27(1):255-268.e6.
PMID: 30943406 DOI: 10.1016/j.celrep.2019.03.003

Abstract

Analysis of cancer-derived extracellular vesicles (EVs) in biofluids potentially provides a source of disease biomarkers. At present there is no procedure to systematically identify which antigens should be targeted to differentiate cancer-derived from normal host cell-derived EVs. Here, we propose a computational framework that integrates information about membrane proteins in tumors and normal tissues from databases: UniProt, The Cancer Genome Atlas, the Genotype-Tissue Expression Project, and the Human Protein Atlas. We developed two methods to assess capture of EVs from specific cell types. (1) We used palmitoylated fluorescent protein (palmtdTomato) to label tumor-derived EVs. Beads displaying antibodies of interest were incubated with conditioned medium from palmtdTomato-expressing cells. Bound EVs were quantified using flow cytometry. (2) We also showed that membrane-bound Gaussia luciferase allows the detection of cancer-derived EVs in blood of tumor-bearing animals. Our analytical and validation platform should be applicable to identify antigens on EVs from any tumor type.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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